Citrobacter rodentium (DSM 16636, ATCC 51116, CDC 1843-73)

Name: Citrobacter rodentium (DSM 16636, ATCC 51116, CDC 1843-73)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 4340

Type strain

Strain Designation DO 14784

Culture col. no. DSM 16636 ATCC 51116 CDC 1843-73 CIP 104675 CCUG 30795 4 more

NCBI tax ID(s) 1218085 67825

Special Collections DSMZ CCUG JCM CIP

History <- ATCC; ATCC 51116 <- C. F. Riddle; <- Connecticut State Health Dept.; CCUG 30795 <-- R. E. Weaver CDC 1843-73 <-- Connecticut State Health Dept., USA, DO 14784. CIP <- 1996, ATCC <- CDC: strain 1843-73, Citrobacter sp. <- CT. Hlth. Dept.: strain DO 14784

Links

Citrobacter rodentium DO 14784 is a mesophilic, Gram-negative, rod-shaped animal pathogen that was isolated from hamster.

Gram-negative rod-shaped mesophilic animal pathogen genome sequence 16S sequence

Name and taxonomic classification

SI-ID 46897

NBRC 105723,ATCC 51116,CCUG 30795,CIP 104675,DSM 16636,JCM 14073,CCM 7398,CNCTC 5064

@ref 20215

Last LPSN update 2026-02-09 11:18:42

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Enterobacterales

Family Enterobacteriaceae

Genus Citrobacter

Species Citrobacter rodentium

Full scientific name Citrobacter rodentium Schauer et al. 1996

BacDive ID	Other strains from **Citrobacter rodentium** (2)	Type strain
136362	C. rodentium 3311-75, CIP 104934
138454	C. rodentium 2643-76, CIP 105015

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
122246	negative	rod-shaped
125438	negative		100
125439	negative		97.3

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
38514	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122246	CIP Medium 72	Medium recipe at CIP
122246	CIP Medium 3	Medium recipe at CIP
6539	TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)	Medium recipe at MediaDive	Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
6539	COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)	Medium recipe at MediaDive	Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
6539	positive	growth	37	mesophilic
38514	positive	growth	30	mesophilic
50275	positive	growth	37	mesophilic
67770	positive	growth	37	mesophilic

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125438		90.604
125439		95.2

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68368	27613 ChEBI	amygdalin	+	fermentation	from API 20E
68368	29016 ChEBI	arginine	-	hydrolysis	from API 20E
68368	16947 ChEBI	citrate	-	assimilation	from API 20E
68368	17634 ChEBI	D-glucose	+	fermentation	from API 20E
68368	16899 ChEBI	D-mannitol	+	fermentation	from API 20E
68368	5291 ChEBI	gelatin	-	hydrolysis	from API 20E
68368	30849 ChEBI	L-arabinose	+	fermentation	from API 20E
68368	62345 ChEBI	L-rhamnose	+	fermentation	from API 20E
68368	25094 ChEBI	lysine	-	degradation	from API 20E
68368	28053 ChEBI	melibiose	-	fermentation	from API 20E
68368	17268 ChEBI	myo-inositol	-	fermentation	from API 20E
68368	18257 ChEBI	ornithine	+	degradation	from API 20E
68368	30911 ChEBI	sorbitol	+	fermentation	from API 20E
68368	17992 ChEBI	sucrose	-	fermentation	from API 20E
68368	27897 ChEBI	tryptophan	-	energy source	from API 20E
68368	16199 ChEBI	urea	-	hydrolysis	from API 20E

Metabolite production

@ref	Chebi-ID	Metabolite
68368	15688 ChEBI	acetoin	from API 20E
68368	16136 ChEBI	hydrogen sulfide	from API 20E
68368	35581 ChEBI	indole	from API 20E

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Indole test
68368	15688 ChEBI	acetoin	+		from API 20E
68368	35581 ChEBI	indole		-	from API 20E

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68368	arginine dihydrolase	-	3.5.3.6	from API 20E
68382	beta-galactosidase	+	3.2.1.23	from API zym
68368	beta-galactosidase	+	3.2.1.23	from API 20E
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68382	cystine arylamidase	-	3.4.11.3	from API zym
68368	cytochrome oxidase	-	1.9.3.1	from API 20E
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68368	gelatinase	-		from API 20E
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68368	lysine decarboxylase	-	4.1.1.18	from API 20E
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
68368	ornithine decarboxylase	+	4.1.1.17	from API 20E
68382	trypsin	+	3.4.21.4	from API zym
68368	tryptophan deaminase	-	4.1.99.1	from API 20E
68368	urease	-	3.5.1.5	from API 20E
68382	valine arylamidase	+		from API zym

API 20E

@ref	ONPG	ADH (Arg)	LDC (Lys)	ODC	CIT	H2S productionH2S	URE	TDA (Trp)	IND	Acetoin production (Voges Proskauer test)VP	GEL	GLU	MAN	INO	Sor	RHA	SAC	MEL	AMY	ARA	OX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	OF-O	OF-F
6539	+	-	-	+	-	-	-	-	-	+	-	+	+	-	+	+	-	-	+	+	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
122246	-	+	+	+	-	+	+	-	+	-	+	+	-	+	-	+	-	-	-	-

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
122246	not determinedn.d.	+	+	+	+	+	-	-	-	-	+	+	+	-	+	-	+	-	-	-	+	+	+	-	+	-	-	-	-	-	-	-	+	-	+	-	-	+	-	-	-	-	-	-	+	+	-	-	+	+	+	-	-	+	+	+	+	+	-	-	+	+	-	-	-	-	+	+	-	-	-	-	-	+	-	-	-	-	-	-	+	+	-	+	-	-	-	+	-	-	+	-	+	+	+	+	+	+	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Mammals	#Rodentia (Other)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
6539	hamster	Connecticut	USA	USA	North America
50275	Mouse
67770	Hamster	CT	USA	USA	North America
122246	Animal, Hamster	Connecticut	United States of America	USA	North America

Interaction and safety

Risk assessment

@ref	Pathogenicity animal	Biosafety level	Biosafety level comment
6539		2	Risk group (German classification) According to TRBA 466
122246		1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM2127898v1 assembly for Citrobacter rodentium NBRC 105723 = DSM 16636	complete	GCA_021278985	67825.30	8113807353	1218085	98.8
67770	ASM75981v1 assembly for Citrobacter rodentium NBRC 105723 = DSM 16636	contig	GCA_000759815	1218085.3	2600255055	1218085	50.45
66792	PDT000619787.1 assembly for Citrobacter rodentium ATCC 51116	contig	GCA_015965415	67825.26	8118053978	67825	40.44
66792	PDT000619840.1 assembly for Citrobacter rodentium NBRC 105723 = DSM 16636	contig	GCA_015965555	67825.27	8119372218	1218085	38.7

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Citrobacter rodentium 16S ribosomal RNA gene, partial sequence	AF025363	1496	67825
67770	Citrobacter rodentium gene for 16S rRNA, partial sequence, strain: NBRC 105723	AB682287	1467	67825
67770	Citrobacter rodentium strain CIP 104675 16S ribosomal RNA gene, partial sequence	KM515972	1467	67825

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Citrobacter rodentium NBRC 105723 = DSM 16636
NCBI: GCA_000759815

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	76.60	no
125439	gram_stain	BacteriaNetⓘ	negative	97.30	no
125439	motility	BacteriaNetⓘ	yes	73.00	no
125439	spore_formation	BacteriaNetⓘ	no	95.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Citrobacter rodentium NBRC 105723 = DSM 16636 DSM 16636
NCBI: GCA_021278985.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	100.00	no
125438	anaerobic	anaerobicⓘ	no	94.63	no
125438	aerobic	aerobicⓘ	no	69.48	no
125438	spore-forming	spore-formingⓘ	no	90.60	no
125438	thermophilic	thermophileⓘ	no	99.50	yes
125438	flagellated	motile2+ⓘ	yes	77.84	no

Literature

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	Peracetic Acid Treatment Generates Potent Inactivated Oral Vaccines from a Broad Range of Culturable Bacterial Species.	Moor K, Wotzka SY, Toska A, Diard M, Hapfelmeier S, Slack E.	Front Immunol	10.3389/fimmu.2016.00034	2016
	A qPCR assay to detect and quantify Shiga toxin-producing E. coli (STEC) in cattle and on farms: a potential predictive tool for STEC culture-positive farms.	Verstraete K, Van Coillie E, Werbrouck H, Van Weyenberg S, Herman L, Del-Favero J, De Rijk P, De Zutter L, Joris MA, Heyndrickx M, De Reu K.	Toxins (Basel)	10.3390/toxins6041201	2014
	Caspase-11 auto-proteolysis is crucial for noncanonical inflammasome activation.	Lee BL, Stowe IB, Gupta A, Kornfeld OS, Roose-Girma M, Anderson K, Warming S, Zhang J, Lee WP, Kayagaki N.	J Exp Med	10.1084/jem.20180589	2018
Metabolism	Intestinal epithelial CD98 directly modulates the innate host response to enteric bacterial pathogens.	Charania MA, Laroui H, Liu H, Viennois E, Ayyadurai S, Xiao B, Ingersoll SA, Kalman D, Merlin D.	Infect Immun	10.1128/iai.01388-12	2013
	Mast cells limit systemic bacterial dissemination but not colitis in response to Citrobacter rodentium.	Wei OL, Hilliard A, Kalman D, Sherman M.	Infect Immun	10.1128/iai.73.4.1978-1985.2005	2005
	Citrobacter rodentium, the causative agent of transmissible murine colonic hyperplasia, exhibits clonality: synonymy of C. rodentium and mouse-pathogenic Escherichia coli.	Luperchio SA, Newman JV, Dangler CA, Schrenzel MD, Brenner DJ, Steigerwalt AG, Schauer DB.	J Clin Microbiol	10.1128/jcm.38.12.4343-4350.2000	2000
	Synthesis and Evaluation of the Antibacterial Activities of 13-Substituted Berberine Derivatives.	Olleik H, Yacoub T, Hoffer L, Gnansounou SM, Benhaiem-Henry K, Nicoletti C, Mekhalfi M, Pique V, Perrier J, Hijazi A, Baydoun E, Raymond J, Piccerelle P, Maresca M, Robin M.	Antibiotics (Basel)	10.3390/antibiotics9070381	2020
Enzymology	Novel class A beta-lactamase Sed-1 from Citrobacter sedlakii: genetic diversity of beta-lactamases within the Citrobacter genus.	Petrella S, Clermont D, Casin I, Jarlier V, Sougakoff W.	Antimicrob Agents Chemother	10.1128/aac.45.8.2287-2298.2001	2001
	Resveratrol attenuates Citrobacter rodentium-infected colitis by remodeling the gut microbiota structure and inhibiting CD4⁺ cell activation in mice.	Li J, Feng X, Jing Y, Qian H, Ji Y, Hao Y, Zhai Z.	Food Funct	10.1039/d5fo02302e	2025
	A novel multifunctional Lactiplantibacillus plantarum HMPM2111 strain: antibacterial and anti-inflammatory effects against stresses caused by pathogenic bacteria.	Liu Y, Wang J, Wang L, Cao J, Lu S, Li P, Wang Y, Wang J, Sheng K, Wang Y.	Food Funct	10.1039/d5fo02972d	2025
	Differential roles for Irgm1 in myeloid cells for immune resistance to pathogenic bacteria.	Fee BE, Fee LR, Sprouse AR, Vallance BA, Rai P, Fessler MB, Xue Y, Huang HI, Hammer GE, Taylor GA.	J Leukoc Biol	10.1093/jleuko/qiaf167	2025
	DR5 Governs Compound Exocytosis in Colonic Goblet Cells via TATA-Box Binding Protein-Dependent Bestrophin-2 Transcriptional Regulation.	Wang Y, Li X, Wang Y, Yang C, Gao X, Zhu K, Ren Y, Li J, Liu C, Xue B.	Adv Sci (Weinh)	10.1002/advs.202516789	2025
Metabolism	Acsbg1 maintains intestinal immune homeostasis and controls inflammation by regulating ST2⁺ Tregs.	Palatella M, Kruse F, Ji H, Loriani Fard AK, Becker M, Daniel C, Rohm M, Huehn J.	Mucosal Immunol	10.1016/j.mucimm.2025.10.009	2025
	STAT3 mediates an inflammation-induced microbial defense response and regulates pathogen control and clearance by macrophages.	Patel B, Zheng X, Kahn LM, Schneider SM, Pineda JE, Riba MN, Ouchen K, Meril S, Nash AP, Wang J, Watowich SS.	J Immunol	10.1093/jimmun/vkaf309	2025
	Enteropathogenic bacteria evade ROCK-driven epithelial cell extrusion.	Luchetti G, Miner MV, Peterson RM, Scott WP, Krishnamoorthy P, Kofoed EM, Jimenez AG, Zhang H, Tan MW, Reja R, Cheung TK, Skippington E, Liang Y, Rose CM, Kayagaki N, Newton K, Rauch I, Dixit VM.	Nature	10.1038/s41586-025-09645-0	2025
	Lactobacillus plantarum-derived extracellular vesicles from dietary barley leaf supplementation attenuate Citrobacter rodentium infection and intestinal inflammation.	Feng Y, Zhao Q, Zhao Y, Ma C, Tian M, Hu X, Chen F, Li D.	J Nanobiotechnology	10.1186/s12951-025-03504-w	2025
	IL-27 gut immunology: Mechanisms and potential value as a biomarker and therapeutic target in intestinal diseases.	Han Y, Wang S, Li C, Zhang S, Geng X, Zheng A, Zhou P, Ren F, Wang Q, Yin Z, Yang Z.	Int Immunopharmacol	10.1016/j.intimp.2025.115755	2025
	Defining enteric bacterial pathogenesis using organoids: Citrobacter rodentium uses EspC, an atypical mucinolytic protease, to penetrate mouse colonic mucus.	Chen Y, Gilliland A, Liang Q, Han X, Yang H, Chan J, Levesque D, Moon KM, Daneshgar P, Boisvert FM, Foster L, Zandberg WF, Bergstrom K, Yu HB, Vallance BA.	Gut Microbes	10.1080/19490976.2025.2494717	2025
	A type 4 resistant potato starch alters the cecal microbiome, gene expression and resistance to colitis in mice fed a Western diet based on NHANES data.	Pletsch EA, Dawson HD, Cheung L, Ragonese JS, Chen CT, Smith AD.	Food Funct	10.1039/d4fo04697h	2025
	Hyperglycemia worsens gut bacterial infection through intestinal Wnt, but independent of endotoxemia or obesity.	Bhatwa A, Lau TC, McPhee JB, Anhe FF, Anhe GF, Fang H, Barra NG, Li Y, Duggan BM, Chan DY, Gunn E, Gagnon C, Tchernof A, Marette A, Morrison KM, Coombes BK, Schertzer JD.	Am J Physiol Endocrinol Metab	10.1152/ajpendo.00251.2025	2025
	Citrobacter rodentium promotes brain cognitive dysfunction of type 2 diabetes mice by activating FXR mediated gut barrier damage.	Li Y, Chen ST, Zhang YY, Qin JF, Zhu X, Yin K.	Metab Brain Dis	10.1007/s11011-025-01529-6	2025
	Reactive Oxygen Species-Responsive Polymeric Chloroquine Nanogel for Targeted Oral Therapy of Ulcerative Colitis.	Kumari N, Panja S, Kumar B, Ahmad R, Kollala SS, Siddhanta K, Islam F, Joshi V, Talmon GA, Murry DJ, Singh AB, Oupicky D.	ACS Appl Mater Interfaces	10.1021/acsami.5c12328	2025
Pathogenicity	Inflammation-Induced Th17 Cells Synergize with the Inflammation-Trained Microbiota to Mediate Host Resiliency Against Intestinal Injury.	Golob JL, Hou G, Swanson BJ, Berinstein JA, Bishu S, Grasberger H, Zataari ME, Lee A, Kao JY, Kamada N, Bishu S.	Inflamm Bowel Dis	10.1093/ibd/izae293	2025
	Chlamydia muridarum Infection Impacts Murine Models of Intestinal Inflammation and Cancer.	Leung G, Carrasco SE, Mourino AJ, Aydin M, Mammone R, Sonnenberg GF, Diehl G, Artis D, Yano H, Ricart Arbona RJ, Lipman NS.	J Am Assoc Lab Anim Sci	10.30802/aalas-jaalas-25-078	2025
	Human cathelicidin LL-37 rapidly disrupted colonic epithelial integrity.	Kilari G, Tran J, Blyth GAD, Cobo ER.	Biochim Biophys Acta Biomembr	10.1016/j.bbamem.2025.184410	2025
	Innate lymphoid cells, immune functional dynamics, epithelial parallels, and therapeutic frontiers in infections.	Nouari W, Aribi M.	Int Rev Immunol	10.1080/08830185.2025.2490233	2025
	Development of intimin-enriched outer membrane vesicles (OMVs) as a vaccine to control intestinal carriage of Enterohemorrhagic Escherichia coli.	Garling A, Goursat C, Seguy C, Martin P, Goman A, Nougayrede JP, Oswald E, Auvray F, Branchu P.	Vaccine	10.1016/j.vaccine.2025.126899	2025
	ILC3s regulate the gut microbiota via host intestinal galactosylation to limit pathogen infection in mice.	Wang W, Li N, Xu H, Wei S, Li Y, Ou J, Hao J, Zhang J, Dong L, Qiu Y, Hu X, Fu YX, Guo X.	Nat Microbiol	10.1038/s41564-025-01933-9	2025
	Selenoproteome depletion enhances oxidative stress and alters neutrophil functions in Citrobacter rodentium infection leading to gastrointestinal inflammation.	Lee TJ, Liao HC, Salim A, Nettleford SK, Kleinman KL, Carlson BA, Prabhu KS.	Free Radic Biol Med	10.1016/j.freeradbiomed.2024.12.025	2025
	Bacteriophage Mu contamination impacts interbacterial competition.	Pick K, Tsviklist V, Stadel L, Raivio T.	Infect Immun	10.1128/iai.00268-25	2025
	Comparing Campylobacter jejuni to three other enteric pathogens in OligoMM¹² mice reveals pathogen-specific host and microbiota responses.	Herzog MK, Peters A, Shayya N, Cazzaniga M, Kaka Bra K, Arora T, Barthel M, Gul E, Maurer L, Kiefer P, Christen P, Endhardt K, Vorholt JA, Frankel G, Heimesaat MM, Bereswill S, Gahan CGM, Claesson MJ, Domingo-Almenara X, Hardt WD.	Gut Microbes	10.1080/19490976.2024.2447832	2025
	Microbiota-derived succinate promotes enterohaemorrhagic Escherichia coli virulence via lysine succinylation.	Li L, Liu Y, Liu D, Wang J, Wang M, Xiang B, Qin J, Yao T, Li W, Wu P, Wang Q, Zhang J, Xu Y, Liu M, Wang Y, Ma G, Liu R, Li X, Huai Z, Huang Y, Guo H, Yang B, Feng L, Huang D, Zhang K, Wang L, Liu B.	Nat Microbiol	10.1038/s41564-025-01931-x	2025
	IgA facilitates the persistence of the mucosal pathogen Helicobacter pylori.	Artola-Boran M, Kirsche L, Fallegger A, Leary P, Tanriover M, Goodwin T, Geiger G, Hapfelmeier S, Yousefi S, Simon HU, Arnold IC, Muller A.	Mucosal Immunol	10.1016/j.mucimm.2024.11.006	2025
	Ovomucin and its hydrolysates differentially influenced colitis severity in Citrobacter rodentium-infected mice.	Bao X, Ju T, Tollenaar S, Sergi C, Willing BP, Wu J.	Food Funct	10.1039/d4fo01813c	2024
	Possible link between colonization of the gastrointestinal tract by Citrobacter rodentium in C57BL/6 mice and microbiota composition.	Miki T, Haneda T, Okada N, Ito M.	Microbiol Immunol	10.1111/1348-0421.13128	2024
Pathogenicity	Impaired neutrophil migration underpins host susceptibility to infectious colitis.	Sanchez-Garrido J, Baghshomali YN, Kaushal P, Kozik Z, Perry RW, Williams HRT, Choudhary J, Frankel G.	Mucosal Immunol	10.1016/j.mucimm.2024.06.008	2024
	Evaluation of the protective effect of the intranasal vaccines adjuvanted with bacterium-like particles against intestinal infection.	Tsujii A, Takahashi K, Harada H, Kawashima S, Oikawa H, Fukushima H, Hayakawa Y, Koizumi J, Inoue N, Koshizuka T.	Vaccine	10.1016/j.vaccine.2024.05.023	2024
	GABA-producing Lactococcus lactis alleviates gut dysfunction and neurobehavioral abnormalities associated with irritable bowel syndrome.	Jin Z, Chen M, Ao L, Wang J, Sun J, Qian X, Tian P, Zhang H.	Microbiome Res Rep	10.20517/mrr.2025.56	2025
	Albumin binding domain fusion improved the therapeutic efficacy of Inhibitor of Differentiation-2 protein in colitis mice.	Xu L, Wang Y, Yan D, Li M, Qiao L, Chen Z, Wu M, Zhong G.	Life Sci	10.1016/j.lfs.2024.123237	2024
	DCLK1 isoform (DCLK1-S) as a critical player in promoting inflammation, tissue remodeling, and EMT in mouse models of colitis.	Yusuf K, Roy BC, Hauser WL, Al-Kasspooles M, Sanchez S, Attard TM, Pei D, Sampath V, Anant S, Umar S.	PLoS Pathog	10.1371/journal.ppat.1013360	2025
	Function of autophagy genes in innate immune defense against mucosal pathogens.	Cui X, Wang YT.	Curr Opin Microbiol	10.1016/j.mib.2024.102456	2024
Pathogenicity	Intestinal Epithelia and Myeloid Immune Cells Shape Colitis Severity and Colorectal Carcinogenesis via High-mobility Group Box Protein 1.	Foelsch K, Pelczar P, Zierz E, Kondratowicz S, Qi M, Mueller C, Alawi M, Huebener S, Clauditz T, Gagliani N, Huber S, Huebener P.	J Crohns Colitis	10.1093/ecco-jcc/jjae017	2024
	A hierarchical approach towards identification of novel inhibitors against L, D-transpeptidase YcbB as an anti-bacterial therapeutic target.	Alawam AS, M Alneghery L, Alwethaynani MS, Alamri MA.	J Biomol Struct Dyn	10.1080/07391102.2024.2322619	2025
	The gut microbiota-independent virulence of noninvasive bacterial pathogen Citrobacter rodentium.	Liu Y, Xu D, Guo S, Wang S, Ding H, Siu C, Wan F.	PLoS Pathog	10.1371/journal.ppat.1012758	2024
	A novel antibacterial strategy for targeting the bacterial methionine biosynthesis pathway.	Bin P, Liu W, Zhang X, Liu B, Zhu G.	Int J Antimicrob Agents	10.1016/j.ijantimicag.2023.107057	2024
	Citrobacter rodentium infection activates colonic lamina propria group 2 innate lymphoid cells.	Berkachy R, Mishra V, Biswas P, Frankel G.	PLoS Pathog	10.1371/journal.ppat.1013276	2025
	Gut permeability among Astronauts during Space missions.	Akinsuyi OS, Xhumari J, Ojeda A, Roesch LFW.	Life Sci Space Res (Amst)	10.1016/j.lssr.2024.03.003	2024
	Milk-derived osteopontin influences the composition of the intestinal intraepithelial lymphocyte compartment.	McClanahan KG, Capella J, Gaddy JA, Olivares-Villagomez D.	Immunohorizons	10.1093/immhor/vlaf057	2025
Pathogenicity	mSphere of Influence: Complement activity beyond systemic circulation-implications in the context of infections.	Desai JV.	mSphere	10.1128/msphere.00531-24	2025
Pathogenicity	LKB1 regulates ILC3 postnatal development and effector function through metabolic programming.	Zhang H, Zhao L, Zhang Q, Hu L, Su X, Sun J, Shen L.	Front Immunol	10.3389/fimmu.2025.1587256	2025
	Deficiency of interleukin-1 receptor antagonist aggravates Citrobacter rodentium infection in mice.	Yeoh BS, Saha P, Kushwaha V, Gohara AF, Vijay-Kumar M.	Immunohorizons	10.1093/immhor/vlaf034	2025
	Unique Regulation of Sed-1 beta-Lactamase in Citrobacter sedlakii: Insights on Resistance to Third-Generation Cephalosporin	Watanabe M, Nakano R, Yamamoto K, Nakano A, Suzuki Y, Saito K, Nakashima S, Endo K, Narita K, Yano H.	Antibiotics (Basel)		2025
	Helicobacter spp. are prevalent in wild mice and protect from lethal Citrobacter rodentium infection in the absence of adaptive immunity.	Zhao B, Osbelt L, Lesker TR, Wende M, Galvez EJC, Honicke L, Bublitz A, Greweling-Pils MC, Grassl GA, Neumann-Schaal M, Strowig T.	Cell Rep	10.1016/j.celrep.2023.112549	2023
	Effect of Propionate on Citrobacter rodentium Infection in Mice by Regulating NleH Expression.	Li Y, Mei W, Zhang Q, Li L, Ji Q.	J Cell Mol Med	10.1111/jcmm.70216	2024
	Evaluating the protective effects of Aurodox in a murine model of Shiga toxin-producing Escherichia coli.	McHugh RE, Rooney LM, Mark DR, Wale KR, Clapperton M, McConnell G, Hoskisson PA, Douce GR, Roe AJ.	NPJ Antimicrob Resist	10.1038/s44259-025-00094-3	2025
	Biological pathways via which the anthocyanin malvidin alleviated the murine colitis induced by Citrobacter rodentium.	Liu F, Smith AD, Wang TTY, Pham Q, Cheung L, Yang H, Li RW.	Food Funct	10.1039/d2fo02873e	2023
	Antihyperalgesic properties of gut microbiota: Parabacteroides distasonis as a new probiotic strategy to alleviate chronic abdominal pain.	Gervason S, Meleine M, Lolignier S, Meynier M, Daugey V, Birer A, Aissouni Y, Berthon JY, Ardid D, Filaire E, Carvalho FA.	Pain	10.1097/j.pain.0000000000003075	2024
Pathogenicity	A bacterial network of T3SS effectors counteracts host pro-inflammatory responses and cell death to promote infection.	Yeap HW, Goh GR, Rosli SN, Pung HS, Giogha C, Eng VV, Pearson JS, Hartland EL, Chen KW.	EMBO J	10.1038/s44318-025-00412-5	2025
Pathogenicity	Pericytes modulate endothelial inflammatory response during bacterial infection.	Carvalho TP, Toledo FAO, Bautista DFA, Silva MF, Oliveira JBS, Lima PA, Costa FB, Ribeiro NQ, Lee J-Y, Birbrair A, Paixao TA, Tsolis RM, Santos RL.	mBio	10.1128/mbio.03252-23	2024
	Whipworm Infection in Mice Increases Coinfection of Enteric Pathogens but Promotes Clearance of Ascaris Larvae From the Lungs.	Polakovicova N, Adji AV, Myhill LJ, Williams AR.	J Infect Dis	10.1093/infdis/jiad063	2023
Pathogenicity	Association between Toll-like receptor 9 signaling defect and developing post-infectious irritable bowel syndrome.	Kotani S, Mishima Y, Kishimoto K, Oka A, Oshima N, Kawashima K, Matsumoto K, Usuda H, Wada K, Ishihara S.	Front Immunol	10.3389/fimmu.2025.1672117	2025
Pathogenicity	Dietary Qiwenghuangbo powder-enriched Limosilactobacillus reuteri protects the intestinal epithelium and alleviates inflammation via a strain-specific mechanism.	Xu Q, Xue L, Wu Z, Kang S, Li J, Wu Y, Wu Y, Zhao J, Wu R, Lv H, Wang J, Han D.	Animal Model Exp Med	10.1002/ame2.70016	2025
	MHC class II antigen presentation by intestinal epithelial cells fine-tunes bacteria-reactive CD4 T-cell responses.	Heuberger CE, Janney A, Ilott N, Bertocchi A, Pott S, Gu Y, Pohin M, Friedrich M, Mann EH, Pearson C, Powrie FM, Pott J, Thornton E, Maloy KJ.	Mucosal Immunol	10.1016/j.mucimm.2023.05.001	2024
	Combinatorial effects of tryptophan derivatives serotonin and indole on virulence modulation of enteric pathogens.	Hoskan MA, Sperandio V.	mBio	10.1128/mbio.02067-25	2025
Pathogenicity	Reprogramming Targeted-Antibacterial-Plasmids (TAPs) to achieve broad-host range antibacterial activity.	Djermoun S, Reuter A, Derollez E, Lesterlin C, Bigot S.	Plasmid	10.1016/j.plasmid.2023.102680	2023
Pathogenicity	2-deoxy-D-glucose mitigates Citrobacter rodentium and dibenzazepine-induced gastrointestinal damage and colitis: novel implications of 2-DG polypharmacopea.	Ahmed I, Verma A, Umar S, Papineni RVL.	Int J Radiat Biol	10.1080/09553002.2022.2110297	2023
	Cathelicidin regulates goblet cell mucus secretion and mucus-associated proteins in Citrobacter rodentium-induced colitis.	Mirzadzare N, Blyth GAD, Hannawayya R, Cirone KM, Kilari G, Lahiri P, Tan YL, Herik AI, Fu Y, Gorman H, Petri B, Chadee K, Cobo ER.	Gut Microbes	10.1080/19490976.2025.2538696	2025
	Multi-omics analysis detected multiple pathways by which pomegranate punicalagin exerts its biological effects in modulating host-microbiota interactions in murine colitis models.	Liu F, Smith AD, Wang TTY, Pham Q, Yang H, Li RW.	Food Funct	10.1039/d3fo00286a	2023
	Rapid and relaying deleterious effects of a gastrointestinal pathogen, Citrobacter rodentium, on bone, an extra-intestinal organ.	Sharan K, Brandt C, Yusuf MA, Singh P, Halder N, Edwards ME, Mangu SR, Das A, Mishra A, Kumar SS, Sharma A, Gupta A, Liu XS, Guo EX, Monani UR, Ponnalagu D, Ivanov II, Lal G, Clare S, Dougan G, Yadav VK.	iScience	10.1016/j.isci.2025.111802	2025
	alpha-Ketoglutarate Restores Intestinal Barrier Function through Promoting Intestinal Stem Cells-Mediated Epithelial Regeneration in Colitis.	Si X, Song Z, Liu N, Jia H, Liu H, Wu Z.	J Agric Food Chem	10.1021/acs.jafc.2c04641	2022
Metabolism	Effects of myeloperoxidase on inflammatory responses with hypoxia in Citrobacter rodentium-infectious mice.	Gao X, Zhang Y, Zhu Q, Han Y, Jia R, Zhang W.	Immun Inflamm Dis	10.1002/iid3.1157	2024
	citrOgen: a synthesis-free polysaccharide and protein antigen-presentation to antibody-induction platform.	Wong JLC, Sanchez-Garrido J, Rattle J, Bradshaw J, Mishra V, Frankel G.	Nat Commun	10.1038/s41467-025-63922-0	2025
	Ellagitannin Punicalagin Disrupts the Pathways Related to Bacterial Growth and Affects Multiple Pattern Recognition Receptor Signaling by Acting as a Selective Histone Deacetylase Inhibitor.	Liu F, Smith AD, Wang TTY, Pham Q, Yang H, Li RW.	J Agric Food Chem	10.1021/acs.jafc.2c08738	2023
	Epithelial dysfunction is prevented by IL-22 treatment in a Citrobacter rodentium-induced colitis model that shares similarities with inflammatory bowel disease.	Zhu Q, Korenfeld D, Suarez-Fueyo A, Graham S, Jin L, Punit S, Duffy R, Puri M, Caruso A, Hu C, Tian Y, McRae BL, Kamath R, Phillips L, Schwartz-Sterman AJ, Westmoreland S, Cao X, Levesque MC, Bi Y, Paez-Cortez J, Goenka R.	Mucosal Immunol	10.1038/s41385-022-00577-w	2022
	Direct evidence of host-mediated glycosylation of NleA and its dependence on interaction with the COPII complex.	Burns L, Le Mauff F, Gruenheid S.	Gut Microbes	10.1080/19490976.2024.2305477	2024
	Fecal microbiome alterations of mice following immunization with gold nanoparticle vaccines against enterohemorrhagic Escherichia coli.	Bowser S, Chapartegui-Gonzalez I, Torres AG.	Gut Pathog	10.1186/s13099-024-00670-4	2024
	Trichinella spiralis infection ameliorates the severity of Citrobacter rodentium-induced experimental colitis in mice.	Xue Y, Xu YF, Zhang B, Huang HB, Pan TX, Li JY, Tang Y, Shi CW, Wang N, Yang GL, Wang CF.	Exp Parasitol	10.1016/j.exppara.2022.108264	2022
	Context-dependent role of group 3 innate lymphoid cells in mucosal protection.	Araujo LP, Edwards M, Irie K, Huang Y, Kawano Y, Tran A, De Michele S, Bhagat G, Wang HH, Ivanov II.	Sci Immunol	10.1126/sciimmunol.ade7530	2024
	Beneficial and detrimental consequences of AHR activation in intestinal infection.	Diaz OE, Zhou L, Barrington C, Lindqvist D, Graelmann F, Wincent E, Stockinger B.	Life Sci Alliance	10.26508/lsa.202503414	2025
	Bacterial membrane vesicles restore gut anaerobiosis.	Pitt N, Morrissette M, Gates MF, Bargabos R, Krumpoch M, Hawkins B, Lewis K.	NPJ Biofilms Microbiomes	10.1038/s41522-025-00676-z	2025
	Inducible transposon mutagenesis identifies bacterial fitness determinants during infection in mice.	Basta DW, Campbell IW, Sullivan EJ, Hotinger JA, Hullahalli K, Garg M, Waldor MK.	Nat Microbiol	10.1038/s41564-025-01975-z	2025
	Convergent evolution of distinct D-ribulose utilisation pathways in attaching and effacing pathogens.	Cottam C, Bowran K, White RT, Basle A, Josts I, Connolly JPR.	Nat Commun	10.1038/s41467-025-62476-5	2025
	In vivo studies on Citrobacter rodentium and host cell death pathways.	Eng VV, Pearson JS.	Curr Opin Microbiol	10.1016/j.mib.2021.09.005	2021
	Lactobacillus johnsonii Attenuates Citrobacter rodentium-Induced Colitis by Regulating Inflammatory Responses and Endoplasmic Reticulum Stress in Mice.	Zhang Y, Mu T, Yang Y, Zhang J, Ren F, Wu Z.	J Nutr	10.1093/jn/nxab250	2021
	Microbe-derived extracellular ATP via P2X7R signaling regulate macrophage heterogeneity in intestinal lymphoid tissue.	Tang YL, Tang Y.	Purinergic Signal	10.1007/s11302-024-10001-6	2025
Metabolism	Intimate Adhesion Is Essential for the Pathogen-Specific Inflammatory and Immune Responses in the Gut of Mice Infected with Citrobacter rodentium.	Takahashi K, Sugiyama T, Tokunoh N, Tsurumi S, Koshizuka T, Inoue N.	Immunohorizons	10.4049/immunohorizons.2100087	2021
	Type VI secretion systems of pathogenic and commensal bacteria mediate niche occupancy in the gut.	Serapio-Palacios A, Woodward SE, Vogt SL, Deng W, Creus-Cuadros A, Huus KE, Cirstea M, Gerrie M, Barcik W, Yu H, Finlay BB.	Cell Rep	10.1016/j.celrep.2022.110731	2022
	T cell subsets and environmental factors in Citrobacter rodentium infection.	Stockinger B.	Curr Opin Microbiol	10.1016/j.mib.2021.06.006	2021
	The bacterial virulence factor NleA undergoes host-mediated O-linked glycosylation.	Burns L, Giannakopoulou N, Zhu L, Xu YZ, Khan RH, Bekal S, Schurr E, Schmeing TM, Gruenheid S.	Mol Microbiol	10.1111/mmi.14989	2023
	The accessory type III secretion system effectors collectively shape intestinal inflammatory infection outcomes.	Biswas P, Sanchez-Garrido J, Kozik Z, Mishra V, Ruano-Gallego D, Berkachy R, Jordan S, Wong JLC, Choudhary JS, Frankel G.	Gut Microbes	10.1080/19490976.2025.2526134	2025
	The type III secretion system effector network hypothesis.	Sanchez-Garrido J, Ruano-Gallego D, Choudhary JS, Frankel G.	Trends Microbiol	10.1016/j.tim.2021.10.007	2022
Pathogenicity	Defects in the expression of colonic host defense factors associate with barrier dysfunction induced by a high-fat/high-cholesterol diet.	Valdes J, Gagne-Sansfacon J, Reyes V, Armas A, Marrero G, Moyo-Muamba M, Ramanathan S, Perreault N, Ilangumaran S, Rivard N, Fortier LC, Menendez A.	Anat Rec (Hoboken)	10.1002/ar.25083	2023
	Escherichia coli phage-inducible chromosomal island aids helper phage replication and represses the locus of enterocyte effacement pathogenicity island.	Pick K, Stadel L, Raivio TL.	ISME J	10.1093/ismejo/wrae258	2025
	Sufficient water intake maintains the gut microbiota and immune homeostasis and promotes pathogen elimination.	Sato K, Hara-Chikuma M, Yasui M, Inoue J, Kim YG.	iScience	10.1016/j.isci.2024.109903	2024
	A protective effect of inflammatory bowel disease on the severity of sclerosing cholangitis.	Stumme F, Steffens N, Steglich B, Mathies F, Nawrocki M, Sabihi M, Soukou-Wargalla S, Goke E, Kempski J, Frundt T, Weidemann S, Schramm C, Gagliani N, Huber S, Bedke T.	Front Immunol	10.3389/fimmu.2024.1307297	2024
Pathogenicity	Protegrin-1 Combats Multidrug-Resistant Porcine ExPEC: Potent Bactericidal Activity and Multimodal Immunometabolic Regulation In Vitro and in a Murine Model.	Xu J, He Y, Liang Z, Chen S, Tang B, Su F, Liu C.	Vet Sci	10.3390/vetsci12111030	2025
	Post-transcriptional regulation in attaching and effacing pathogens: integration of environmental cues and the impact on gene expression and host interactions.	Smallets S, Kendall MM.	Curr Opin Microbiol	10.1016/j.mib.2021.08.003	2021
Pathogenicity	The IL-21/IL-21R signaling axis regulates CD4+ T-cell responsiveness to IL-12 to promote bacterial-induced colitis.	Solaymani-Mohammadi S.	J Leukoc Biol	10.1093/jleuko/qiae069	2024
	Type III secretion system effector subnetworks elicit distinct host immune responses to infection.	Sanchez-Garrido J, Alberdi L, Chatterjee S, Frankel G, Mullineaux-Sanders C.	Curr Opin Microbiol	10.1016/j.mib.2021.08.008	2021
	What's for dinner? How Citrobacter rodentium's metabolism helps it thrive in the competitive gut.	Liang Q, Vallance BA.	Curr Opin Microbiol	10.1016/j.mib.2021.06.004	2021
Pathogenicity	Glycine Attenuates Citrobacter rodentium-Induced Colitis by Regulating ATF6-Mediated Endoplasmic Reticulum Stress in Mice.	Zhang Y, Jiang D, Jin Y, Jia H, Yang Y, Kim IH, Dai Z, Zhang J, Ren F, Wu Z.	Mol Nutr Food Res	10.1002/mnfr.202001065	2021
	Inhibition of Atg7 in intestinal epithelial cells drives resistance against Citrobacter rodentium.	Cune D, Pitasi CL, Rubiola A, Jamma T, Simula L, Boucher C, Fortun A, Adoux L, Letourneur F, Saintpierre B, Donnadieu E, Terris B, Bossard P, Chassaing B, Romagnolo B.	Cell Death Dis	10.1038/s41419-025-07422-5	2025
Pathogenicity	IL-22-dependent responses and their role during Citrobacter rodentium infection.	Melchior K, Gerner RR, Hossain S, Nuccio S-P, Moreira CG, Raffatellu M.	Infect Immun	10.1128/iai.00099-24	2024
	Glucuronic acid confers colonization advantage to enteric pathogens.	Rosay T, Jimenez AG, Sperandio V.	Proc Natl Acad Sci U S A	10.1073/pnas.2400226121	2024
	The neuropeptide VIP potentiates intestinal innate type 2 and type 3 immunity in response to feeding.	Pascal M, Kazakov A, Chevalier G, Dubrule L, Deyrat J, Dupin A, Saha S, Jagot F, Sailor K, Dulauroy S, Moigneu C, Belkaid Y, Lepousez G, Lledo PM, Wilhelm C, Eberl G.	Mucosal Immunol	10.1038/s41385-022-00516-9	2022
Transcriptome	Differential Correlation of Transcriptome Data Reveals Gene Pairs and Pathways Involved in Treatment of Citrobacter rodentium Infection with Bioactive Punicalagin.	Fleming DS, Liu F, Li RW.	Molecules	10.3390/molecules28217369	2023
Genetics	Genome-wide association study of cocoon-producing traits in four Henan silkworm strains revealed new candidate genes.	Song X, Lyu Y, Zhang Y, Ding W, Huang Y, Yang S.	Front Genet	10.3389/fgene.2025.1580806	2025
	Modulation of Host Immunity by Microbiome-Derived Indole-3-Propionic Acid and Other Bacterial Metabolites.	Schutz B, Krause FF, Taudte RV, Zaiss MM, Luu M, Visekruna A.	Eur J Immunol	10.1002/eji.202451594	2025
	Indole dysbiosis and mucosal inflammation.	Kim JY, Cartwright IM, Colgan SP.	Microbiota Host	10.1530/mah-25-0004	2025
	Plasmacytoid dendritic cells regulate host immune response to Citrobacter rodentium induced colitis in colon-draining lymph nodes.	Poysti S, Silojarvi S, Toivonen R, Hanninen A.	Eur J Immunol	10.1002/eji.202048714	2021
Pathogenicity	Overview of the Effect of Citrobacter rodentium Infection on Host Metabolism and the Microbiota.	Hopkins EGD, Frankel G.	Methods Mol Biol	10.1007/978-1-0716-1339-9_20	2021
Pathogenicity	Citrobacter rodentium Lysogenized with a Shiga Toxin-Producing Phage: A Murine Model for Shiga Toxin-Producing E. coli Infection.	Flowers LJ, Hu S, Shrestha A, Martinot AJ, Leong JM, Osburne MS.	Methods Mol Biol	10.1007/978-1-0716-1339-9_19	2021
	Microbial Respiration in the Colon: Using H₂O₂ to Catch Your Breath.	Crowley SM, Vallance BA.	Cell Host Microbe	10.1016/j.chom.2020.11.006	2020
	Turicibacterales protect mice from severe Citrobacter rodentium infection.	Hoek KL, McClanahan KG, Latour YL, Shealy N, Piazuelo MB, Vallance BA, Byndloss MX, Wilson KT, Olivares-Villagomez D.	Infect Immun	10.1128/iai.00322-23	2023
Pathogenicity	Supplementation with Rare Earth-Chitosan Chelate Improves Tibia Quality, Disease Resistance Capacity, and Performance in Nursery Pigs.	Hao S, Sun W, Wei P, Wu H, Lu W, He Y.	Int J Mol Sci	10.3390/ijms26062409	2025
Pathogenicity	Substance P receptor signaling contributes to host maladaptive responses during enteric bacterial infection.	Cremin M, Ramirez VT, Sanchez K, Tay E, Murray K, Brust-Mascher I, Reardon C.	Proc Natl Acad Sci U S A	10.1073/pnas.2415287122	2025
	Pectin limits epithelial barrier disruption by Citrobacter rodentium through anti-microbial effects.	Beukema M, Ishisono K, de Waard J, Faas MM, de Vos P, Kitaguchi K.	Food Funct	10.1039/d0fo02605k	2021
	Transcription factor c-Rel mediates communication between commensal bacteria and mucosal lymphocytes.	Luu M, Binder K, Hartmann S, Kespohl M, Bazant J, Romero R, Schutz B, Steinhoff U, Visekruna A.	J Leukoc Biol	10.1002/jlb.3ab0621-350r	2022
Pathogenicity	GPR120 promotes neutrophil control of intestinal bacterial infection.	Zhou Z, Yang W, Yu T, Yu Y, Zhao X, Yu Y, Gu C, Bilotta AJ, Yao S, Zhao Q, Golovko G, Li M, Cong Y.	Gut Microbes	10.1080/19490976.2023.2190311	2023
	Lrrk2 G2019S mutation incites increased cell-intrinsic neutrophil effector functions and intestinal inflammation in a model of infectious colitis.	Pei J, Oliveira NL, Recinto SJ, Kazanova A, Queiroz-Junior CM, Li Z, Couto K, Westfall S, Fahmy AM, Tiefensee-Ribeiro C, King IL, Milnerwood AJ, Desjardins M, Thanabalasuriar A, Stratton JA, Gruenheid S.	NPJ Parkinsons Dis	10.1038/s41531-025-01077-x	2025
Pathogenicity	Lactobacillus plantarum and Galacto-Oligosaccharides Synbiotic Relieve Irritable Bowel Syndrome by Reshaping Gut Microbiota and Attenuating Mast Cell Hyperactivation.	Yao Q, Zhang W, Wang Y, Shi L, Zhao Y, Liang J, Zhao Y, Kang J, Zheng X, Guo R, Yuan T, She Y, Liu Z.	Nutrients	10.3390/nu17101670	2025
	Breaking down barriers: is intestinal mucus degradation by Akkermansia muciniphila beneficial or harmful?	Tingler AM, Engevik MA.	Infect Immun	10.1128/iai.00503-24	2025
Pathogenicity	Saccharomyces boulardii CNCM I-745 Supernatant Improves Markers of Gut Barrier Function and Inflammatory Response in Small Intestinal Organoids	Filipe Rosa L, Gonda S, Roese N, Bischoff S.	Pharmaceuticals (Basel)		2025
Pathogenicity	Exploring the Role of Microglial Cells in the Gut-Brain Axis Communication: A Systematic Review.	Ortiz-Samur NS, Vijaya AK, Burokas A, Mela V.	J Neurochem	10.1111/jnc.70154	2025
	Lactobacillus plantarum-derived extracellular vesicles from dietary barley leaf supplementation attenuate Citrobacter rodentium infection and intestinal inflammation	Feng Y, Zhao Q, Zhao Y, Ma C, Tian M, Hu X, Chen F, Li D.	J Nanobiotechnology		2025
	IL-1R1-dependent signaling coordinates epithelial regeneration in response to intestinal damage.	Cox CB, Storm EE, Kapoor VN, Chavarria-Smith J, Lin DL, Wang L, Li Y, Kljavin N, Ota N, Bainbridge TW, Anderson K, Roose-Girma M, Warming S, Arron JR, Turley SJ, de Sauvage FJ, van Lookeren Campagne M.	Sci Immunol	10.1126/sciimmunol.abe8856	2021
	Histone demethylase JMJD2D protects against enteric bacterial infection via up-regulating colonic IL-17F to induce beta-defensin expression.	Zhang Y, Li B, Hong Y, Luo P, Hong Z, Xia X, Mo P, Yu C, Chen W.	PLoS Pathog	10.1371/journal.ppat.1012316	2024
Pathogenicity	Insufficient dietary choline aggravates disease severity in a mouse model of Citrobacter rodentium-induced colitis.	Ju T, Kennelly JP, Jacobs RL, Willing BP.	Br J Nutr	10.1017/s0007114520002639	2021
	Further Evaluation of Enterohemorrhagic Escherichia coli Gold Nanoparticle Vaccines Utilizing Citrobacter rodentium as the Model Organism.	Bowser S, Melton-Celsa A, Chapartegui-Gonzalez I, Torres AG.	Vaccines (Basel)	10.3390/vaccines12050508	2024
Pathogenicity	Host-Derived Reactive Oxygen Species in the Gut Epithelium: Defence Mechanism and Target of Bacterial Subversion.	Kansakar P, Gupta S, Mallick AI, Wren BW, Aksoy E, Elmi A, Gundogdu O.	Antioxidants (Basel)	10.3390/antiox14101156	2025
	Diet-driven differential response of Akkermansia muciniphila modulates pathogen susceptibility.	Wolter M, Grant ET, Boudaud M, Pudlo NA, Pereira GV, Eaton KA, Martens EC, Desai MS.	Mol Syst Biol	10.1038/s44320-024-00036-7	2024
Genetics	Genome-Based In Silico Analysis of the Structural and Functional Characteristics of the Type Three Secretion System (T3SS) and Core Effector Proteins in Enteropathogenic Escherichia coli (EPEC) Strains Isolated from Food-Producing Animals and Products of Animal Origin.	Malesa R, Pierneef R, Mafuna T, Magwedere K, Seakamela E, Matle I.	Pathogens	10.3390/pathogens14111099	2025
Pathogenicity	Protective Role of the Toll-Like Receptor 5 Agonist KMRC011 against Murine Colitis Induced by Citrobacter rodentium and Dextran Sulfate Sodium.	Kim JY, Seo SM, Kim HW, Lee WJ, Choi YK.	J Microbiol Biotechnol	10.4014/jmb.2209.09048	2023
	STING Promotes Intestinal IgA Production by Regulating Acetate-producing Bacteria to Maintain Host-microbiota Mutualism.	Yu T, Yang W, Yao S, Yu Y, Wakamiya M, Golovko G, Cong Y.	Inflamm Bowel Dis	10.1093/ibd/izac268	2023
Pathogenicity	Citrobacter rodentium possesses a functional type II secretion system necessary for successful host infection.	Krekhno Z, Woodward SE, Serapio-Palacios A, Pena-Diaz J, Moon KM, Foster LJ, Finlay BB.	Gut Microbes	10.1080/19490976.2024.2308049	2024
	Congenital iRHOM2 deficiency causes ADAM17 dysfunction and environmentally directed immunodysregulatory disease.	Kubo S, Fritz JM, Raquer-McKay HM, Kataria R, Vujkovic-Cvijin I, Al-Shaibi A, Yao Y, Zheng L, Zou J, Waldman AD, Jing X, Farley TK, Park AY, Oler AJ, Charles AK, Makhlouf M, AbouMoussa EH, Hasnah R, Saraiva LR, Ganesan S, Al-Subaiey AA, Matthews H, Flano E, Lee HH, Freeman AF, Sefer AP, Sayar E, Cakir E, Karakoc-Aydiner E, Baris S, Belkaid Y, Ozen A, Lo B, Lenardo MJ.	Nat Immunol	10.1038/s41590-021-01093-y	2022
	Starving out the Enemy.	Altier C.	Cell Host Microbe	10.1016/j.chom.2020.09.003	2020
	The Type III Secretion System (T3SS) of Escherichia Coli Promotes Atherosclerosis in Type 2 Diabetes Mellitus.	Zhang YY, Chen ST, Chen G, Zhou L, Zhou GL, Yu XY, Yuan L, Deng WQ, Wang ZB, Li J, Tu YF, Zhang DW, Li Y, Sammad A, Zhu X, Yin K.	Adv Sci (Weinh)	10.1002/advs.202413296	2025
	Low dietary fiber intake impairs small intestinal Th17 and intraepithelial T cell development over generations.	Royer CJ, Rodriguez-Marino N, Yaceczko MD, Rivera-Rodriguez DE, Ziegler TR, Cervantes-Barragan L.	Cell Rep	10.1016/j.celrep.2023.113140	2023
	Focal coagulative necrosis of the liver in a patient with sustained virologic response to anti-hepatitis C virus therapy.	Furuta A, Oura S, Shintani H, Kataoka N, Tanaka H, Takamatsu S, Ono W.	Radiol Case Rep	10.1016/j.radcr.2024.01.035	2024
	HOIL1 Regulates Group 3 Innate Lymphoid Cells in the Colon and Protects against Systemic Dissemination, Colonic Ulceration, and Lethality from Citrobacter rodentium Infection.	Hartley VL, Qaqish AM, Wood MJ, Studnicka BT, Iwai K, Liu TC, MacDuff DA.	J Immunol	10.4049/jimmunol.2300351	2023
	Attaching and effacing pathogens: the effector ABC of immune subversion.	Riebisch AK, Muhlen S.	Future Microbiol	10.2217/fmb-2019-0274	2020
Pathogenicity	Grimace scale assessment during Citrobacter rodentium inflammation and colitis development in laboratory mice.	Peppermuller PP, Gehring J, Zentrich E, Bleich A, Hager C, Buettner M.	Front Vet Sci	10.3389/fvets.2023.1173446	2023
	Structure of the outer membrane porin OmpW from the pervasive pathogen Klebsiella pneumoniae.	Seddon C, Frankel G, Beis K.	Acta Crystallogr F Struct Biol Commun	10.1107/s2053230x23010579	2024
Metabolism	Type III secretion system effectors form robust and flexible intracellular virulence networks.	Ruano-Gallego D, Sanchez-Garrido J, Kozik Z, Nunez-Berrueco E, Cepeda-Molero M, Mullineaux-Sanders C, Naemi Baghshomali Y, Slater SL, Wagner N, Glegola-Madejska I, Roumeliotis TI, Pupko T, Fernandez LA, Rodriguez-Paton A, Choudhary JS, Frankel G.	Science	10.1126/science.abc9531	2021
Metabolism	SRC-3 deficiency protects host from Listeria monocytogenes infection through increasing ROS production and decreasing lymphocyte apoptosis.	Xia X, Chen Y, Xu J, Yu C, Chen W.	Int Immunopharmacol	10.1016/j.intimp.2021.107625	2021
Pathogenicity	Citrobacter rodentium infection impairs dopamine metabolism and exacerbates the pathology of Parkinson's disease in mice.	He Y, Zhao J, Ma Y, Yan X, Duan Y, Zhang X, Dong H, Fang R, Zhang Y, Li Q, Yang P, Yu M, Fei J, Huang F.	J Neuroinflammation	10.1186/s12974-024-03145-0	2024
Pathogenicity	B4galnt2-mediated host glycosylation influences the susceptibility to Citrobacter rodentium infection.	Suwandi A, Alvarez KG, Galeev A, Steck N, Riedel CU, Puente JL, Baines JF, Grassl GA.	Front Microbiol	10.3389/fmicb.2022.980495	2022
	TRPV1 controls innate immunity during Citrobacter rodentium enteric infection.	Cremin M, Tay EXY, Ramirez VT, Murray K, Nichols RK, Brust-Mascher I, Reardon C.	PLoS Pathog	10.1371/journal.ppat.1011576	2023
	Subcutaneous white adipose tissue-derived extracellular vesicles maintain intestinal homeostasis via IgA biosynthesis in aging mice.	Long K, Liu P, Wang Y, Sulaiman JE, Hoque M, Li GHY, Zhao DD, Lee PK, Siu GK, Lee AW, Liu Z, So PK, Cai Y, Woo CW, Chan CB, Xu A, Cheng KK.	J Clin Invest	10.1172/jci188947	2025
	Ginkgo biloba Extract Preventively Intervenes in Citrobacter Rodentium-Induced Colitis in Mice.	Chen T, Chen Y, Li K, Chen Z, Zhao Q, Fan Y, Liu Y, Zhang S, Hao Z.	Nutrients	10.3390/nu15082008	2023
	Quorum sensing modulates bacterial virulence and colonization dynamics of the gastrointestinal pathogen Citrobacter rodentium.	Pena-Diaz J, Woodward SE, Creus-Cuadros A, Serapio-Palacios A, Ortiz-Jimenez S, Deng W, Finlay BB.	Gut Microbes	10.1080/19490976.2023.2267189	2023
Phylogeny	Potential role of salivary lactic acid bacteria in pathogenesis of oral lichen planus.	Ren X, Li D, Zhou M, Hua H, Li C.	BMC Microbiol	10.1186/s12866-024-03350-0	2024
	Gut Microbiota Diversity in 16 Stingless Bee Species (Hymenoptera: Apidae: Meliponini).	Ramirez-Ahuja ML, Pena-Carrillo KI, Gomez-Govea MA, Jimenez-Martinez ML, Trujillo-Rodriguez GJ, Espinoza-Ruiz M, Guzman Velasco A, Flores AE, Gonzalez-Rojas JI, Resendez-Perez D, Rodriguez-Sanchez IP.	Microorganisms	10.3390/microorganisms13071645	2025
	Effects of hypoxic exposure on immune responses of intestinal mucosa to Citrobacter colitis in mice.	Ji Q, Zhang Y, Zhou Y, Gamah M, Yuan Z, Liu J, Cao C, Gao X, Zhang H, Ren Y, Zhang W.	Biomed Pharmacother	10.1016/j.biopha.2020.110477	2020
	Efficacy of EHEC gold nanoparticle vaccines evaluated with the Shiga toxin-producing Citrobacter rodentium mouse model.	Bowser S, Melton-Celsa A, Chapartegui-Gonzalez I, Torres AG.	Microbiol Spectr	10.1128/spectrum.02261-23	2024
Genetics	Inferring bacterial transmission dynamics using deep sequencing genomic surveillance data.	Senghore M, Read H, Oza P, Johnson S, Passarelli-Araujo H, Taylor BP, Ashley S, Grey A, Callendrello A, Lee R, Goddard MR, Lumley T, Hanage WP, Wiles S.	Nat Commun	10.1038/s41467-023-42211-8	2023
Metabolism	Reversal of Pathogen-Induced Barrier Defects in Intestinal Epithelial Cells by Contra-pathogenicity Agents.	Choudhry N, Scott F, Edgar M, Sanger GJ, Kelly P.	Dig Dis Sci	10.1007/s10620-020-06121-9	2021
Pathogenicity	Citrobacter rodentium-host-microbiota interactions: immunity, bioenergetics and metabolism.	Mullineaux-Sanders C, Sanchez-Garrido J, Hopkins EGD, Shenoy AR, Barry R, Frankel G.	Nat Rev Microbiol	10.1038/s41579-019-0252-z	2019
Pathogenicity	Coumarin derivatives ameliorate the intestinal inflammation and pathogenic gut microbiome changes in the model of infectious colitis through antibacterial activity.	Jung HS, Park YJ, Gu BH, Han G, Ji W, Hwang SM, Kim M.	Front Cell Infect Microbiol	10.3389/fcimb.2024.1362773	2024
	[Commensal bacteria prevent pathogenic bacterial infection by inducing of activation of host immune system].	Goto Y.	Nihon Saikingaku Zasshi	10.3412/jsb.75.185	2020
Pathogenicity	Oral Administration with Live Attenuated Citrobacter rodentium Protects Immunocompromised Mice from Lethal Infection.	Wang S, Xia X, Liu Y, Wan F.	Infect Immun	10.1128/iai.00198-22	2022
	Crystal structures of QseE and QseG: elements of a three-component system from Escherichia coli.	Matsumoto K, Fukuda Y, Inoue T.	Acta Crystallogr F Struct Biol Commun	10.1107/s2053230x23009123	2023
	Magnesium Oxide Reduces Anxiety-like Behavior in Mice by Inhibiting Sulfate-Reducing Bacteria.	Coffman CN, Carroll-Portillo A, Alcock J, Singh SB, Rumsey K, Braun CA, Xue B, Lin HC.	Microorganisms	10.3390/microorganisms12071429	2024
	Epithelial IFNgamma signalling and compartmentalized antigen presentation orchestrate gut immunity.	Malik A, Sharma D, Aguirre-Gamboa R, McGrath S, Zabala S, Weber C, Jabri B.	Nature	10.1038/s41586-023-06721-1	2023
	Microbiota does not influence tumor development in two models of heritable cancer.	Spring J, Gurbuxani S, Golovkina T.	mBio	10.1128/mbio.03866-24	2025
	Evidence from comparative genomic analyses indicating that Lactobacillus-mediated irritable bowel syndrome alleviation is mediated by conjugated linoleic acid synthesis.	Liu Y, Xiao W, Yu L, Tian F, Wang G, Lu W, Narbad A, Chen W, Chen W, Zhai Q.	Food Funct	10.1039/d0fo02616f	2021
Pathogenicity	Pomegranate peel extract reduced colonic damage and bacterial translocation in a mouse model of infectious colitis induced by Citrobacter rodentium.	Smith AD, George NS, Cheung L, Bhagavathy GV, Luthria DL, John KM, Bhagwat AA.	Nutr Res	10.1016/j.nutres.2019.11.001	2020
	Evaluation of Direct Colony Sampling Compared with Sentinel-Free Soiled Bedding Testing for Murine Quarantine Programs.	Luchins KR, Holliday B, Rehman F, Bowers CJ, Ostdiek AM, Langan GP, Felgenhauer JL.	J Am Assoc Lab Anim Sci	10.30802/aalas-jaalas-25-099	2025
	Maternal Intake of Dietary Fat Pre-Programs Offspring's Gut Ecosystem Altering Colonization Resistance and Immunity to Infectious Colitis in Mice.	Quin C, Ghosh S, Dai C, Barnett JA, Garner AM, Yoo RKH, Zandberg WF, Botta A, Gorzelak MA, Gibson DL.	Mol Nutr Food Res	10.1002/mnfr.202000635	2021
	Intestinal Microbiota and Fecal Transplantation in Patients with Inflammatory Bowel Disease and Clostridioides difficile: An Updated Literature Review	Lahoud C, Habib T, Kalta D, Dimachkie R, El Sayegh S, Deeb L.	J Clin Med		2025
	Here, there, and everywhere: How pathogenic Escherichia coli sense and respond to gastrointestinal biogeography.	Woodward SE, Krekhno Z, Finlay BB.	Cell Microbiol	10.1111/cmi.13107	2019
Pathogenicity	RIPK3 and caspase-8 interpret cytokine signals to regulate ILC3 survival in the gut.	Joseph AM, Ahmed A, Goc J, Horn V, Fiedler B, Garone D, Grigg JB, Uddin J, Teng F, Fritsch M, Vivier E, Sonnenberg GF.	Mucosal Immunol	10.1016/j.mucimm.2024.08.004	2024
	Garlic-Derived Metabolites Exert Antioxidant Activity, Modulate Gut Microbiota Composition and Limit Citrobacter rodentium Infection in Mice.	Zhu L, Andersen-Civil AIS, Castro-Meija JL, Nielsen DS, Blanchard A, Olsen JE, Thamsborg SM, Williams AR.	Antioxidants (Basel)	10.3390/antiox11102033	2022
Pathogenicity	Plant- and Fish-Derived n-3 PUFAs Suppress Citrobacter Rodentium-Induced Colonic Inflammation.	Maattanen P, Lurz E, Botts SR, Wu RY, Robinson SC, Yeung CW, Colas R, Li B, Johnson-Henry KC, Surette ME, Dalli J, Sherman PM.	Mol Nutr Food Res	10.1002/mnfr.201900873	2020
	Deficiency of IL-22-binding protein enhances the ability of the gut microbiota to protect against enteric pathogens.	Fachi JL, Di Luccia B, Gilfillan S, Chang HW, Song C, Cheng J, Cella M, Vinolo MA, Gordon JI, Colonna M.	Proc Natl Acad Sci U S A	10.1073/pnas.2321836121	2024
Pathogenicity	Crosstalk between neutrophil extracellular traps and gut microbiota in ulcerative colitis: traditional Chinese medicine strategies.	Feng Y, Liu Y, Qiu X, Jiang J, Mo J, Xv Y.	Front Cell Infect Microbiol	10.3389/fcimb.2025.1692312	2025
Metabolism	Giardia spp. promote the production of antimicrobial peptides and attenuate disease severity induced by attaching and effacing enteropathogens via the induction of the NLRP3 inflammasome.	Manko-Prykhoda A, Allain T, Motta JP, Cotton JA, Feener T, Oyeyemi A, Bindra S, Vallance BA, Wallace JL, Beck P, Buret AG.	Int J Parasitol	10.1016/j.ijpara.2019.12.011	2020
Genetics	An obligate symbiont of Haematomyzus elephantis with a strongly reduced genome resembles symbiotic bacteria in sucking lice.	Martin Rihova J, Vodicka R, Hypsa V.	Appl Environ Microbiol	10.1128/aem.00220-25	2025
Pathogenicity	A lymphostatin homologue from Chlamydia pecorum inhibits mitogen-activated bovine T cell proliferation and IFNgamma production.	Blackburn EA, Chintoan-Uta C, Bease AG, Tuijtel MW, Hateley M, Wear M, Longbottom D, Cassady-Cain R, Stevens MP.	Virulence	10.1080/21505594.2025.2506500	2025
	The T3SS Effector Protease NleC Is Active within Citrobacter rodentium.	Hasan MK, El Qaidi S, Hardwidge PR.	Pathogens	10.3390/pathogens10050589	2021
	Interaction between gut microbiota and immunity in health and intestinal disease.	Wang Q, Meng Q, Chen Y, Liu Y, Li X, Zhou J, Ma Y, Yu Z, Chen X.	Front Immunol	10.3389/fimmu.2025.1673852	2025
	Intestinal microbiota-specific Th17 cells possess regulatory properties and suppress effector T cells via c-MAF and IL-10.	Brockmann L, Tran A, Huang Y, Edwards M, Ronda C, Wang HH, Ivanov II.	Immunity	10.1016/j.immuni.2023.11.003	2023
	The mysterious case of missing lymphocytes: a cautionary tale of interinstitutional variability in outcomes of lung dissociation protocols.	Harlow OS, Ravi VR, Ke F, Sanders NL, Armstrong E, Mizgerd JP, Shenoy AT.	Am J Physiol Lung Cell Mol Physiol	10.1152/ajplung.00323.2024	2025
Metabolism	Lypd8 inhibits attachment of pathogenic bacteria to colonic epithelia.	Okumura R, Kodama T, Hsu CC, Sahlgren BH, Hamano S, Kurakawa T, Iida T, Takeda K.	Mucosal Immunol	10.1038/s41385-019-0219-4	2020
	Dissecting the antibacterial functions of the T6SS-2 cluster in Xanthomonas oryzae for environment and plant protection.	Tan Z-M, Zheng X, Su J, Liu J-S, Liang X, Pei T-T, Dong T.	Appl Environ Microbiol	10.1128/aem.01021-25	2025
Pathogenicity	ZnT2 Is Critical for TLR4-Mediated Cytokine Expression in Colonocytes and Modulates Mucosal Inflammation in Mice.	McGourty K, Vijayakumar R, Wu T, Gagnon A, Kelleher SL.	Int J Mol Sci	10.3390/ijms231911467	2022
	Mechanism of TLR4-Mediated Anti-Inflammatory Response Induced by Exopolysaccharide from the Probiotic Bacillus subtilis.	Zamora-Pineda J, Kalinina O, Sperling AI, Knight KL.	J Immunol	10.4049/jimmunol.2200855	2023
Metabolism	IRF4 Expression Is Required for the Immunoregulatory Activity of Conventional Type 2 Dendritic Cells in Settings of Chronic Bacterial Infection and Cancer.	Zhang X, Artola-Boran M, Fallegger A, Arnold IC, Weber A, Reuter S, Taube C, Muller A.	J Immunol	10.4049/jimmunol.2000405	2020
	Genomic deletion of Bcl6 differentially affects conventional dendritic cell subsets and compromises Tfh/Tfr/Th17 cell responses.	Xiao H, Ulmert I, Bach L, Huber J, Narasimhan H, Kurochkin I, Chang Y, Holst S, Morbe U, Zhang L, Schlitzer A, Pereira CF, Schraml BU, Baumjohann D, Lahl K.	Nat Commun	10.1038/s41467-024-46966-6	2024
	Protective effects of oral immunization with formalin-inactivated whole-cell Citrobacter rodentium on Citrobacter rodentium infection in mice.	Takahashi K, Hanamura Y, Tokunoh N, Kassai K, Matsunishi M, Watanabe S, Sugiyama T, Inoue N.	J Microbiol Methods	10.1016/j.mimet.2019.02.016	2019
	Effects of intravenous morphine and lidocaine on bacterial growth.	Osoian CI, Pandrea SL, Flonta M, Florea A, Matros L, Ionescu D.	BMC Anesthesiol	10.1186/s12871-025-03070-6	2025
	Barley Leaf Ameliorates Citrobacter rodentium-Induced Colitis through Preventive Effects.	Feng Y, Li D, Ma C, Tian M, Hu X, Chen F.	Nutrients	10.3390/nu14183833	2022
	Distinct RORgammat-dependent Th17 immune responses are required for autoimmune pathogenesis and protection against bacterial infection.	Zhong X, Wu H, Zhang W, Shi Y, Gwack Y, Xue HH, Sun Z.	Cell Rep	10.1016/j.celrep.2024.114951	2024
	Complement in breast milk modifies offspring gut microbiota to promote infant health.	Xu D, Zhou S, Liu Y, Scott AL, Yang J, Wan F.	Cell	10.1016/j.cell.2023.12.019	2024
	TLR9 limits enteric antimicrobial responses and promotes microbiota-based colonisation resistance during Citrobacter rodentium infection.	Yang H, Yu HB, Bhinder G, Ryz NR, Lee J, Yang H, Fotovati A, Gibson DL, Turvey SE, Reid GS, Vallance BA.	Cell Microbiol	10.1111/cmi.13026	2019
	Utilizing novel Escherichia coli-specific conserved signature proteins for enhanced monitoring of recreational water quality.	Saleem F, Li E, Tran KL, Rudra B, Edge TA, Schellhorn HE, Gupta RS.	Microbiologyopen	10.1002/mbo3.1410	2024
	On the role of the sorting platform in hierarchical type III secretion regulation in enteropathogenic Escherichia coli.	Marcos-Vilchis A, Espinosa N, Alvarez AF, Puente JL, Soto JE, Gonzalez-Pedrajo B.	J Bacteriol	10.1128/jb.00446-24	2025
	Studies of C57BL/6J Mice Deficient in Receptors for IFNalpha/beta and IFNgamma as a Model for EV-D68 Acute Flaccid Myelitis	Watarastaporn T, Song W, Glenn J, Ooi Y, Carette J, Nagamine C.	Comp Med		2024
	Transcription factor Tox2 is required for metabolic adaptation and tissue residency of ILC3 in the gut.	Das A, Martinez-Ruiz GU, Bouladoux N, Stacy A, Moraly J, Vega-Sendino M, Zhao Y, Lavaert M, Ding Y, Morales-Sanchez A, Harly C, Seedhom MO, Chari R, Awasthi P, Ikeuchi T, Wang Y, Zhu J, Moutsopoulos NM, Chen W, Yewdell JW, Shapiro VS, Ruiz S, Taylor N, Belkaid Y, Bhandoola A.	Immunity	10.1016/j.immuni.2024.04.001	2024
	Aurodox inhibits type III secretion in multiple Gram-negative pathogens.	Mark DR, O'Boyle N, Wale KR, Tucker SK, McHugh RE, Roe AJ.	Open Biol	10.1098/rsob.240240	2024
Pathogenicity	High-Throughput Screen Identifies Host and Microbiota Regulators of Intestinal Barrier Function.	Grosheva I, Zheng D, Levy M, Polansky O, Lichtenstein A, Golani O, Dori-Bachash M, Moresi C, Shapiro H, Del Mare-Roumani S, Valdes-Mas R, He Y, Karbi H, Chen M, Harmelin A, Straussman R, Yissachar N, Elinav E, Geiger B.	Gastroenterology	10.1053/j.gastro.2020.07.003	2020
Metabolism	Endoplasmic reticulum stress in the intestinal epithelium initiates purine metabolite synthesis and promotes Th17 cell differentiation in the gut.	Duan J, Matute JD, Unger LW, Hanley T, Schnell A, Lin X, Krupka N, Griebel P, Lambden C, Sit B, Grootjans J, Pyzik M, Sommer F, Kaiser S, Falk-Paulsen M, Grasberger H, Kao JY, Fuhrer T, Li H, Paik D, Lee Y, Refetoff S, Glickman JN, Paton AW, Bry L, Paton JC, Sauer U, Macpherson AJ, Rosenstiel P, Kuchroo VK, Waldor MK, Huh JR, Kaser A, Blumberg RS.	Immunity	10.1016/j.immuni.2023.02.018	2023
	The clinical outcomes of gut-brain axis (GBA) microbiota influence on psychiatric disorders.	Navidinia M, Goudarzi M, Seyfi E.	Iran J Microbiol	10.18502/ijm.v15i1.11912	2023
	Myeloid deletion of talin-1 reduces mucosal macrophages and protects mice from colonic inflammation.	Latour YL, McNamara KM, Allaman MM, Barry DP, Smith TM, Asim M, Williams KJ, Hawkins CV, Jacobse J, Goettel JA, Delgado AG, Piazuelo MB, Washington MK, Gobert AP, Wilson KT.	Sci Rep	10.1038/s41598-023-49614-z	2023
	A Comprehensive Review of the Role of Virulence Factors in Enteropathogenic Escherichia coli-Induced Intestinal Injury	Ahmad O, Rukh S, Dos Santos Pereira S, Saran A, Chandran V, Muneeb A, Banderas Echeverry W, Shoyoye M, Akintunde D, Hassan D, Morani Z, Masood L.	Cureus
	Roles of zinc and zinc transporters in development, progression, and treatment of inflammatory bowel disease (IBD).	Mitchell SB, Aydemir TB.	Front Nutr	10.3389/fnut.2025.1649658	2025
	The gut commensal Blautia maintains colonic mucus function under low-fiber consumption through secretion of short-chain fatty acids.	Holmberg SM, Feeney RH, Prasoodanan P K V, Puertolas-Balint F, Singh DK, Wongkuna S, Zandbergen L, Hauner H, Brandl B, Nieminen AI, Skurk T, Schroeder BO.	Nat Commun	10.1038/s41467-024-47594-w	2024
	Collective dynamics of Escherichia coli growth under near-lethal acid stress.	Segura Munoz RR, Sourjik V.	mBio	10.1128/mbio.01932-25	2025
	Epigenetic programming mediates abnormal gut microbiota and disease susceptibility in offspring with prenatal dexamethasone exposure.	Lu X, Chen B, Xu D, Hu W, Wang X, Dai Y, Wang Q, Peng Y, Chen K, Zhao D, Wang H.	Cell Rep Med	10.1016/j.xcrm.2024.101398	2024
	IL-23 and IL-2 activation of STAT5 is required for optimal IL-22 production in ILC3s during colitis.	Bauche D, Joyce-Shaikh B, Fong J, Villarino AV, Ku KS, Jain R, Lee YC, Annamalai L, Yearley JH, Cua DJ.	Sci Immunol	10.1126/sciimmunol.aav1080	2020
Pathogenicity	Hypusination in intestinal epithelial cells protects mice from infectious colitis.	Gobert AP, Hawkins CV, Williams KJ, Snyder LA, Barry DP, Asim M, Allaman MM, McNamara KM, Delgado AG, Wang Y, Zhao S, Rose KL, Piazuelo MB, Wilson KT.	Gut Microbes	10.1080/19490976.2024.2438828	2024
Metabolism	Characterization of the Citrobacter rodentium Cpx regulon and its role in host infection.	Vogt SL, Scholz R, Peng Y, Guest RL, Scott NE, Woodward SE, Foster LJ, Raivio TL, Finlay BB.	Mol Microbiol	10.1111/mmi.14182	2019
	Mmp17-deficient mice exhibit heightened goblet cell effector expression in the colon and increased resistance to chronic Trichuris muris infection.	Vornewald PM, Forman R, Yao R, Parmar N, Lindholm HT, Lee LSK, Martin-Alonso M, Else KJ, Oudhoff MJ.	Front Immunol	10.3389/fimmu.2023.1243528	2023
Metabolism	NINJ1 mediates plasma membrane rupture during lytic cell death.	Kayagaki N, Kornfeld OS, Lee BL, Stowe IB, O'Rourke K, Li Q, Sandoval W, Yan D, Kang J, Xu M, Zhang J, Lee WP, McKenzie BS, Ulas G, Payandeh J, Roose-Girma M, Modrusan Z, Reja R, Sagolla M, Webster JD, Cho V, Andrews TD, Morris LX, Miosge LA, Goodnow CC, Bertram EM, Dixit VM.	Nature	10.1038/s41586-021-03218-7	2021
Transcriptome	The transcriptional response to low temperature is weakly conserved across the Enterobacteriaceae.	Hoang J, Stoebel DM.	mSystems	10.1128/msystems.00785-24	2024
	Pathologic copulatory lock in a genetically engineered laboratory mouse breeding pair.	Leung G, Ricart-Arbona R, Monette S, Lipman NS.	Lab Anim	10.1177/00236772231168185	2023
	Evaluation of Serum L-FABP as a Biomarker and Hepatoprotective Effect of L-FABP Using Wild-Type and Human L-FABP Chromosome Transgenic Mice.	Ohata K, Ryu K, Uno K, Teoh SH, Sugaya T, Kamijo-Ikemori A, Suzuki-Kemuriyama N, Miyajima K.	J Am Assoc Lab Anim Sci	10.30802/aalas-jaalas-25-003	2025
	Cytochrome bd-II oxidase CyxA promotes the pathogenicity of Klebsiella pneumoniae by resisting oxidative stress.	Xiao X, Song G, Lu H, Zheng W, Meng P, Peng W, Yang J, Wang M, Zhu J, Wang J, Li B, Li M.	Virulence	10.1080/21505594.2025.2590244	2025
	Dexmedetomidine attenuates acute stress-impaired learning and memory in mice by maintaining the homeostasis of intestinal flora.	Feng H, Hu X, Lin Y, Xiao J, Dai C, Hu Z, Feng H, Qin J, Chen L.	Eur J Med Res	10.1186/s40001-024-01832-5	2024
	Gavage-Needle Voluntary Consumption Administration of a Dose-Specific Measure to Mice (Mus musculus)	Punger E, Norris S, Stevens S, Santos K, Christy A.	J Am Assoc Lab Anim Sci		2025
	Environmental Enrichment Attenuates Reproductive Adversity in a Mouse Model of Parkinson Disease.	Walsh CA, Johnson L, Cirillo PA, Smith PC, Wilson SR.	J Am Assoc Lab Anim Sci	10.30802/aalas-jaalas-24-000032	2025
Pathogenicity	Both pathogen and host dynamically adapt pH responses along the intestinal tract during enteric bacterial infection.	Woodward SE, Neufeld LMP, Pena-Diaz J, Feng W, Serapio-Palacios A, Tarrant I, Deng W, Finlay BB.	PLoS Biol	10.1371/journal.pbio.3002761	2024
	Citrobacter rodentium infection at the gut-brain axis interface.	Martins FH, Cuesta S.	Curr Opin Microbiol	10.1016/j.mib.2021.06.003	2021
Metabolism	Salmonella, E. coli, and Citrobacter Type III Secretion System Effector Proteins that Alter Host Innate Immunity.	El Qaidi S, Wu M, Zhu C, Hardwidge PR.	Adv Exp Med Biol	10.1007/5584_2018_289	2019
	Intestinal epithelial Gasdermin C is induced by IL-4R/STAT6 signaling but is dispensable for gut immune homeostasis.	Gamez-Belmonte R, Wagner Y, Mahapatro M, Wang R, Erkert L, Gonzalez-Acera M, Cineus R, Hainbuch S, Patankar JV, Voehringer D, Hegazy AN, Neurath MF, Wirtz S, Becker C.	Sci Rep	10.1038/s41598-024-78336-z	2024
Pathogenicity	Pea polyphenolics and hydrolysis processing alter microbial community structure and early pathogen colonization in mice.	Forgie AJ, Gao Y, Ju T, Pepin DM, Yang K, Ganzle MG, Ozga JA, Chan CB, Willing BP.	J Nutr Biochem	10.1016/j.jnutbio.2019.01.012	2019
	Effects of Lonicera japonica Flower Bud Extract on Citrobacter rodentium-Induced Digestive Tract Infection.	Minami M, Makino T.	Medicines (Basel)	10.3390/medicines7090052	2020
	Indole signaling in Escherichia coli: a target for antivirulence therapy?	Razzaq Meo S, Van de Wiele T, Defoirdt T.	Gut Microbes	10.1080/19490976.2025.2499573	2025
Pathogenicity	Microbiota-derived indoles alleviate intestinal inflammation and modulate microbiome by microbial cross-feeding.	Wang G, Fan Y, Zhang G, Cai S, Ma Y, Yang L, Wang Y, Yu H, Qiao S, Zeng X.	Microbiome	10.1186/s40168-024-01750-y	2024
	Curcumin Oxidation Is Required for Inhibition of Helicobacter pylori Growth, Translocation and Phosphorylation of Cag A.	Ray AK, Luis PB, Mishra SK, Barry DP, Asim M, Pandey A, Chaturvedi M, Gupta J, Gupta S, Mahant S, Das R, Kumar P, Shalimar, Wilson KT, Schneider C, Chaturvedi R.	Front Cell Infect Microbiol	10.3389/fcimb.2021.765842	2021
Metabolism	IRE1alpha-Driven Inflammation Promotes Clearance of Citrobacter rodentium Infection.	Sweet LA, Kuss-Duerkop SK, Keestra-Gounder AM.	Infect Immun	10.1128/iai.00481-21	2022
Genetics	LoniComp: a platform for gene function comparison and analysis between Lonicera japonica and Lonicera macranthoides.	Zhang J, Pan B, Yang J, Pan Q, Zhu P, Yang J, Zhang M, Xiao Q.	BMC Genomics	10.1186/s12864-025-11507-y	2025
	Citrobacter rodentium alters the mouse colonic miRNome.	Wen B, Tokar T, Taibi A, Chen J, Jurisica I, Comelli EM.	Genes Immun	10.1038/s41435-018-0026-z	2019
	Fecal fermentation behaviors of Konjac glucomannan and its impacts on human gut microbiota.	Tan X, Wang B, Zhou X, Liu C, Wang C, Bai J.	Food Chem X	10.1016/j.fochx.2024.101610	2024
	alpha-Ketoglutarate for Preventing and Managing Intestinal Epithelial Dysfunction.	Bravo Iniguez A, Du M, Zhu MJ.	Adv Nutr	10.1016/j.advnut.2024.100200	2024
	Effect of Cage Change Frequency on Perinatal Mortality in C57BL/6J Mice.	Wharton KN, Walsh C, Bauer-Pisani TJ, Smith PC, Wilson SR.	J Am Assoc Lab Anim Sci	10.30802/aalas-jaalas-23-000055	2024
Metabolism	Modulation of virulence and metabolic profiles in Klebsiella pneumoniae under indole-mediated stress response.	Fang X, Chen Y, Hu L, Gu S, Zhu J, Hang Y, Cao X, Xiao Y, Luo H, Zhao C, Xiao L, Zhong Q.	Front Cell Infect Microbiol	10.3389/fcimb.2025.1546991	2025
Pathogenicity	Omptin Proteases of Enterobacterales Show Conserved Regulation by the PhoPQ Two-Component System but Exhibit Divergent Protection from Antimicrobial Host Peptides and Complement.	Cho YH, Fadle Aziz MR, Malpass A, Sutradhar T, Bashal J, Cojocari V, McPhee JB.	Infect Immun	10.1128/iai.00518-22	2023
	PurA is the main target of aurodox, a type III secretion system inhibitor.	Watanabe Y, Haneda T, Kimishima A, Kuwae A, Suga T, Suzuki T, Iwabuchi Y, Honsho M, Honma S, Iwatsuki M, Matsui H, Hanaki H, Kanoh N, Abe A, Asami Y, Omura S.	Proc Natl Acad Sci U S A	10.1073/pnas.2322363121	2024
Phenotype	IMPACT: interpretable microbial phenotype analysis via microbial characteristic traits.	Mechtersheimer D, Ding W, Xu X, Kim S, Sue C, Cao Y, Yang J.	Bioinformatics	10.1093/bioinformatics/btae702	2024
	Pea-protein alginate encapsulation adversely affects development of clinical signs of Citrobacter rodentium-induced colitis in mice treated with probiotics.	Varankovich N, Grigoryan A, Brown K, Inglis GD, Uwiera RRE, Nickerson MT, Korber DR.	Can J Microbiol	10.1139/cjm-2018-0166	2018
	The transcription factor IRF4 regulates the homeostasis and function of intestinal ILC3s.	Gao X, Shen X, Xu Q, Zeng Y, Dong L, Hong S, Jin H, Wang Q, Wang D, Lu L, Wang L.	iScience	10.1016/j.isci.2025.112800	2025
Genetics	Microbiota and environmental health monitoring of mouse colonies by metagenomic shotgun sequencing.	Lupini L, Bassi C, Guerriero P, Raspa M, Scavizzi F, Sabbioni S.	World J Microbiol Biotechnol	10.1007/s11274-022-03469-0	2022
Pathogenicity	Working together: gut microbe-microbe interactions shape host inflammation.	Lawing A, Bleich R.	Infect Immun	10.1128/iai.00512-24	2025
Pathogenicity	Exploring the mechanism of intestinal bacterial translocation after severe acute pancreatitis: the role of Toll-like receptor 5.	Zhang C, Chen S, Wang Z, Zhang J, Yu W, Wang Y, Si W, Zhang Y, Zhang Y, Liang T.	Gut Microbes	10.1080/19490976.2025.2489768	2025
	Citrobacter rodentium Infection Model for the Analysis of Bacterial Pathogenesis and Mucosal Immunology.	Kennedy CL, Hartland EL.	Methods Mol Biol	10.1007/978-1-4939-7568-6_7	2018
Pathogenicity	mSphere of Influence: Drivers of Host-Associated Microbial Community Structure and Change.	Hale VL.	mSphere	10.1128/msphere.00248-21	2021
	Self-sealing MEMS spray-nozzles to prevent bacterial contamination of portable inhalers for aqueous drug delivery.	Last TS, Winkler TE, Stemme G, Roxhed N.	Biomed Microdevices	10.1007/s10544-022-00628-w	2022
	The arginine methyltransferase PRMT5 promotes mucosal defense in the intestine.	Hernandez JE, Llorente C, Ma S, Miyamoto KT, Sinha S, Steele S, Xiao Z, Lai CJ, Zuniga EI, Ghosh P, Schnabl B, Huang WJM.	Life Sci Alliance	10.26508/lsa.202302026	2023
Pathogenicity	Cytoskeletal mechanisms regulating attaching/effacing bacteria interactions with host cells: It takes a village to build the pedestal.	Naydenov NG, Marino-Melendez A, Campellone KG, Ivanov AI.	Bioessays	10.1002/bies.202400160	2024
	Analysis of Individually Ventilated Cage (IVC) Microenvironments During 21-d Cage Change Frequency for Mice Using Two Different Bedding Types.	Felgenhauer JL, Copio JN, Suri AM, Turcios R, Ostdiek AM, Langan GP, Luchins KR.	J Am Assoc Lab Anim Sci	10.30802/aalas-jaalas-24-101	2025
	A Prospective Assessment of the Etiology of Murine Dystocia.	Cheleuitte-Nieves C, Ritter A, Palillo MB, Miranda IC, Carrasco SE, Monette S, Atmane MI, Lipman NS.	J Am Assoc Lab Anim Sci	10.30802/aalas-jaalas-24-090	2025
	Colitis induced by IL-17A-inhibitors.	Grumme L, Dombret S, Knosel T, Skapenko A, Schulze-Koops H.	Clin J Gastroenterol	10.1007/s12328-023-01893-9	2024
	Exploring the fate of Listeria monocytogenes in an in vitro digestion and fecal fermentation model: insights into survival during digestion and interaction with gut microbiota.	Kim DW, Singh S, Kim UI, An SH, Je HJ, Lee DY, Yun EJ, Koo OK.	Front Microbiol	10.3389/fmicb.2025.1616720	2025
	A master regulator of central carbon metabolism directly activates virulence gene expression in attaching and effacing pathogens.	Wale KR, O'Boyle N, McHugh RE, Serrano E, Mark DR, Douce GR, Connolly JPR, Roe AJ.	PLoS Pathog	10.1371/journal.ppat.1012451	2024
Phylogeny	Enterotoxigenic Escherichia coli as a Modulator of the Entero-Pulmonary Axis in Piglets: Impacts on the Microbiota and Immune Responses.	Breyer GM, Carli S, da Silva MERJ, Dias ME, Varela APM, Mann MB, Frazzon J, Mayer FQ, Junior IDSV, Siqueira FM.	Transbound Emerg Dis	10.1155/tbed/8865503	2025
	Regulation of Citrobacter rodentium colonization: virulence, immune response and microbiota interactions.	Caballero-Flores G, Pickard JM, Nunez G.	Curr Opin Microbiol	10.1016/j.mib.2021.07.003	2021
	Amino Acid-Based Diet Prevents Lethal Infectious Diarrhea by Maintaining Body Water Balance in a Murine Citrobacter rodentium Infection Model.	Kimizuka T, Seki N, Yamaguchi G, Akiyama M, Higashi S, Hase K, Kim YG.	Nutrients	10.3390/nu13061896	2021
	Secretion of functional interferon by the type 3 secretion system of enteropathogenic Escherichia coli.	Rostovsky I, Wieler U, Kuzmina A, Taube R, Sal-Man N.	Microb Cell Fact	10.1186/s12934-024-02397-y	2024
	Effects of Taurine on Gut Microbiota Homeostasis: An Evaluation Based on Two Models of Gut Dysbiosis.	Qian W, Li M, Yu L, Tian F, Zhao J, Zhai Q.	Biomedicines	10.3390/biomedicines11041048	2023
	In situ deposition of nanobodies by an engineered commensal microbe promotes survival in a mouse model of enterohemorrhagic E. coli.	Srivastava R, Gonzalez-Prieto C, Lynch JP, Muscolo ME, Lin CY, Brown MA, Lemos L, Shrestha A, Osburne MS, Leong JM, Lesser CF.	PNAS Nexus	10.1093/pnasnexus/pgae374	2024
Pathogenicity	STING controls intestinal homeostasis through promoting antimicrobial peptide expression in epithelial cells.	Yu Y, Yang W, Bilotta AJ, Yu Y, Zhao X, Zhou Z, Yao S, Xu J, Zhou J, Dann SM, Li Y, Cong Y.	FASEB J	10.1096/fj.202001524r	2020
Metabolism	Evidence for the butyrate metabolism as key pathway improving ulcerative colitis in both pediatric and adult patients.	Zhou Z, Cao J, Liu X, Li M.	Bioengineered	10.1080/21655979.2021.1985815	2021
Phylogeny	Gut microbiota in preterm infants with late-onset sepsis and pneumonia: a pilot case-control study.	Ma Y, Peng X, Zhang J, Zhu Y, Huang R, Li G, Wu Y, Zhou C, You J, Fang S, Xiang S, Qiu J.	BMC Microbiol	10.1186/s12866-024-03419-w	2024
	Portulaca Oleracea L. as a Potential Therapeutic Drug Intervention in Ulcerative Colitis: Mechanisms of Action and Clinical Studies.	Liu XY, Liu ZX, Tan WW, Zhang WB, Zhang YL, Zheng L, Que RY, Wen HZ, Dai YC.	Drug Des Devel Ther	10.2147/dddt.s486407	2024
	IRF4 is required for migration of CD4⁺ T cells to the intestine but not for Th2 and Th17 cell maintenance.	Schmidt C, Harberts A, Reimers D, Bertram T, Voss LC, Schmid J, Lory NC, Spohn M, Koch-Nolte F, Huber S, Raczkowski F, Breloer M, Mittrucker HW.	Front Immunol	10.3389/fimmu.2023.1182502	2023
Pathogenicity	Molecular mechanisms of co-infections.	Walch PDK, Broz P.	EMBO Rep	10.1038/s44319-025-00517-2	2025
	Bacterial species to be considered in quality assurance of mice and rats.	Hansen AK, Nielsen DS, Krych L, Hansen CHF.	Lab Anim	10.1177/0023677219834324	2019
Pathogenicity	A discovery platform for identification of host-induced bacterial biosensors from diverse sources.	Robinson CM, Carreno D, Weber T, Chen Y, Riglar DT.	Mol Syst Biol	10.1038/s44320-025-00123-3	2025
	Gut microbiota as a regulator of vaccine efficacy: implications for personalized vaccination.	Lu Q, Feng Y, Wang H, Zhu K, Teng L, Yue M, Li Y.	Gut Microbes	10.1080/19490976.2025.2563709	2025
Pathogenicity	Ground flaxseed reverses protection of a reduced-fat diet against Citrobacter rodentium-induced colitis.	Maattanen P, Lurz E, Botts SR, Wu RY, Yeung CW, Li B, Abiff S, Johnson-Henry KC, Lepp D, Power KA, Pierro A, Surette ME, Sherman PM.	Am J Physiol Gastrointest Liver Physiol	10.1152/ajpgi.00101.2018	2018
	A generalizable Cas9/sgRNA prediction model using machine transfer learning with small high-quality datasets.	Ham DT, Browne TS, Banglorewala PN, Wilson TL, Michael RK, Gloor GB, Edgell DR.	Nat Commun	10.1038/s41467-023-41143-7	2023
	Short-Chain Fatty Acid and FFAR2 Activation - A New Option for Treating Infections?	Schlatterer K, Peschel A, Kretschmer D.	Front Cell Infect Microbiol	10.3389/fcimb.2021.785833	2021
Pathogenicity	A cross talk between dysbiosis and gut-associated immune system governs the development of inflammatory arthropathies.	Kalinkovich A, Livshits G.	Semin Arthritis Rheum	10.1016/j.semarthrit.2019.05.007	2019
Pathogenicity	The autoinflammation-associated NLRC4^V341A mutation increases microbiota-independent IL-18 production but does not recapitulate human autoinflammatory symptoms in mice.	Eeckhout E, Asaoka T, Van Gorp H, Demon D, Girard-Guyonvarc'h C, Andries V, Vereecke L, Gabay C, Lamkanfi M, van Loo G, Wullaert A.	Front Immunol	10.3389/fimmu.2023.1272639	2023
	Berberine ameliorates dextran sulfate sodium -induced colitis through tuft cells and bitter taste signalling.	Yang Y, Li W, Sun K, Sun S, Zhang Y, Chen L, Ni Y, Hou M, Xu Z, Chen L, Ji M.	BMC Biol	10.1186/s12915-024-02078-7	2024
	Gut complement induced by the microbiota combats pathogens and spares commensals.	Wu M, Zheng W, Song X, Bao B, Wang Y, Ramanan D, Yang D, Liu R, Macbeth JC, Do EA, Andrade WA, Yang T, Cho HS, Gazzaniga FS, Ilves M, Coronado D, Thompson C, Hang S, Chiu IM, Moffitt JR, Hsiao A, Mekalanos JJ, Benoist C, Kasper DL.	Cell	10.1016/j.cell.2023.12.036	2024
	Administration of a bacterial lysate to the airway compartment is sufficient to inhibit allergen-induced lung eosinophilia in germ-free mice.	Michael AN, Pivniouk O, Ezeh PC, Banskar S, Hahn S, DeVries A, O'Connell K, Pivniouk V, Vercelli D.	J Leukoc Biol	10.1093/jleuko/qiae047	2024
Pathogenicity	Gut metabolite L-lactate supports Campylobacter jejuni population expansion during acute infection.	Sinha R, LeVeque RM, Callahan SM, Chatterjee S, Stopnisek N, Kuipel M, Johnson JG, DiRita VJ.	Proc Natl Acad Sci U S A	10.1073/pnas.2316540120	2024
	2'-Fucosyllactose Modulates the Intestinal Immune Response to Gut Microbiota and Buffers Experimental Colitis in Mice: An Integrating Investigation of Colonic Proteomics and Gut Microbiota Analysis.	Dong J, Qian M, Zhou D, Zhu A, Zhang W.	Food Sci Nutr	10.1002/fsn3.70418	2025
	Dietary phytate primes epithelial antibacterial immunity in the intestine.	Hashimoto-Hill S, Colapietro L, Woo V, Antonacci S, Whitt J, Engleman L, Alenghat T.	Front Immunol	10.3389/fimmu.2022.952994	2022
	Identification and Treatment of Fur Mites (Radfordia lemnina) in California Deer Mice (Peromyscus californicus) Using Selamectin.	Capria VM, Freed CL.	J Am Assoc Lab Anim Sci	10.30802/aalas-jaalas-24-055	2024
	Noncanonical inflammasome signaling elicits gasdermin D-dependent neutrophil extracellular traps.	Chen KW, Monteleone M, Boucher D, Sollberger G, Ramnath D, Condon ND, von Pein JB, Broz P, Sweet MJ, Schroder K.	Sci Immunol	10.1126/sciimmunol.aar6676	2018
Pathogenicity	Oral Treatment with BT-11 Ameliorates Inflammatory Bowel Disease by Enhancing Regulatory T Cell Responses in the Gut.	Leber A, Hontecillas R, Zoccoli-Rodriguez V, Chauhan J, Bassaganya-Riera J.	J Immunol	10.4049/jimmunol.1801446	2019
	Unveiling the gut-heart potential connection: microbiota's role in kawasaki disease and coronary artery lesions.	Yang Q, Tang W, Ren J, Li M, Zhao C.	Front Cell Infect Microbiol	10.3389/fcimb.2025.1560083	2025
	Optimization of Ketamine/Xylazine Anesthesia in Geriatric Mice.	Beecy S, Meuse D, Kizielewicz N, Beale C, Molk D.	J Am Assoc Lab Anim Sci	10.30802/aalas-jaalas-25-010	2025
	A murine colitis model developed using a combination of dextran sulfate sodium and Citrobacter rodentium.	Park JI, Seo SM, Park JH, Jeon HY, Kim JY, Ryu SH, Choi YK.	J Microbiol	10.1007/s12275-018-7504-x	2018
Pathogenicity	ETEC biofilms are regulated by magnesium and lactate bioavailability.	Hollifield IE, Clement KL, Fernando KA, Blythe MD, Bitoun JP.	Infect Immun	10.1128/iai.00243-25	2025
	Pilots, Astronauts, and the Aerospace Microbiota: A Narrative Review of Occupational Impact.	Minoretti P, Fontana JM, Yilmaz Y.	Cureus	10.7759/cureus.72268	2024
	Trained ILC3 responses promote intestinal defense.	Serafini N, Jarade A, Surace L, Goncalves P, Sismeiro O, Varet H, Legendre R, Coppee JY, Disson O, Durum SK, Frankel G, Di Santo JP.	Science	10.1126/science.aaz8777	2022
	mSphere of Influence: Discovering New Layers of Complexity in the Immune System.	Drummond RA.	mSphere	10.1128/msphere.00359-21	2021
	Muc2-dependent microbial colonization of the jejunal mucus layer is diet sensitive and confers local resistance to enteric pathogen infection.	Birchenough GMH, Schroeder BO, Sharba S, Arike L, Recktenwald CV, Puertolas-Balint F, Subramani MV, Hansson KT, Yilmaz B, Linden SK, Backhed F, Hansson GC.	Cell Rep	10.1016/j.celrep.2023.112084	2023
	The impact of butyrate on group B Streptococcus-induced intestinal barrier disruption.	Dominguez K, Pearah AN, Lindon AK, Worthington L-AM, Carter RR, John-Lewis Edwards N, Ho TTB, Darch SE, Randis TM.	Infect Immun	10.1128/iai.00200-24	2024
	Characterization of the intestinal microbiota during Citrobacter rodentium infection in a mouse model of infection-triggered Parkinson's disease.	Cannon T, Sinha A, Trudeau LE, Maurice CF, Gruenheid S.	Gut Microbes	10.1080/19490976.2020.1830694	2020
	Genomic insights into antimicrobial potential and optimization of fermentation conditions of pig-derived Bacillus subtilis BS21.	Wu D, Fu L, Cao Y, Dong N, Li D.	Front Microbiol	10.3389/fmicb.2023.1239837	2023
Genetics	De Novo Synthesis of a Conjugative System from Human Gut Metagenomic Data for Targeted Delivery of Cas9 Antimicrobials.	Hamilton TA, Joris BR, Shrestha A, Browne TS, Rodrigue S, Karas BJ, Gloor GB, Edgell DR.	ACS Synth Biol	10.1021/acssynbio.3c00319	2023
	The PAD4 inhibitor GSK484 diminishes neutrophil extracellular trap in the colon mucosa but fails to improve inflammatory biomarkers in experimental colitis.	Xie K, Hunter J, Lee A, Ahmad G, Witting PK, Ortiz-Cerda T.	Biosci Rep	10.1042/bsr20253205	2025
	Traditional Chinese Medicine Compounds Containing Lonicera japonica, Chrysanthemum morifolium, and Siraitia grosvenorii Inhibits the Growth of Streptococcus mutans.	Zhou X, Reheman A, Kang Z, Long A, Wang T.	Evid Based Complement Alternat Med	10.1155/2022/5802343	2022
	The thin line between conventional dendritic cells (cDCs) and group 3 innate lymphoid cells (ILC3s) in the gut.	Ulezko Antonova A, Fachi JL, Gilfillan S, Colonna M.	Int Immunol	10.1093/intimm/dxac054	2023
	Sialic acid plays a pivotal role in licensing Citrobacter rodentium's transition from the intestinal lumen to a mucosal adherent niche.	Liang Q, Ma C, Crowley SM, Allaire JM, Han X, Chong RWW, Packer NH, Yu HB, Vallance BA.	Proc Natl Acad Sci U S A	10.1073/pnas.2301115120	2023
	Metabolism of L-arabinose converges with virulence regulation to promote enteric pathogen fitness.	Cottam C, White RT, Beck LC, Stewart CJ, Beatson SA, Lowe EC, Grinter R, Connolly JPR.	Nat Commun	10.1038/s41467-024-48933-7	2024
Pathogenicity	REG/Reg family proteins: mediating gut microbiota homeostasis and implications in digestive diseases.	Qi Z, Pang W, Zha X, Liu Y, Liu S, Xiao F, Wang X, Zhou J, Wang W, Liu X.	Gut Microbes	10.1080/19490976.2025.2568055	2025
Metabolism	STAT1 coordinates intestinal epithelial cell death during gastrointestinal infection upstream of Caspase-8.	Stolzer I, Schickedanz L, Chiriac MT, Lopez-Posadas R, Grassl GA, Mattner J, Wirtz S, Winner B, Neurath MF, Gunther C.	Mucosal Immunol	10.1038/s41385-021-00450-2	2022
	Enteric bacterial infection stimulates remodelling of bile metabolites to promote intestinal homeostasis.	Zhang T, Hasegawa Y, Waldor MK.	Nat Microbiol	10.1038/s41564-024-01862-z	2024
Genetics	Nationwide molecular epidemiology of carbapenemase-producing Citrobacter spp. in France in 2019 and 2020.	Biez L, Bonnin RA, Emeraud C, Birer A, Jousset AB, Naas T, Dortet L.	mSphere	10.1128/msphere.00366-23	2023
Pathogenicity	Tannic Acid and Ethacridine Lactate Attenuate Markers of Stress-Induced Intestinal Barrier Dysfunctions in Murine Small Intestinal Organoids.	Filipe Rosa L, Gonda S, Roese N, Bischoff SC.	Biomolecules	10.3390/biom15050650	2025
	Amelioration of Citrobacter rodentium proliferation in early stage of infection in mice by pretreatment with Lactobacillus brevis KB290 and verification using in vivo bioluminescence imaging.	Waki N, Kuwabara Y, Yoshikawa Y, Suganuma H, Koide H, Oku N, Ohashi N.	FEMS Microbiol Lett	10.1093/femsle/fnw254	2017
	Epithelial talin-1 protects mice from citrobacter rodentium-induced colitis by restricting bacterial crypt intrusion and enhancing t cell immunity.	Latour YL, Allaman MM, Barry DP, Smith TM, Williams KJ, McNamara KM, Jacobse J, Goettel JA, Delgado AG, Piazuelo MB, Zhao S, Gobert AP, Wilson KT.	Gut Microbes	10.1080/19490976.2023.2192623	2023
	Key Interleukins in Inflammatory Bowel Disease-A Review of Recent Studies.	Aebisher D, Bartusik-Aebisher D, Przygorzewska A, Oles P, Woznicki P, Kawczyk-Krupka A.	Int J Mol Sci	10.3390/ijms26010121	2024
Pathogenicity	Dysregulation of CD177⁺ neutrophils on intraepithelial lymphocytes exacerbates gut inflammation via decreasing microbiota-derived DMF.	Chen H, Wu X, Sun R, Lu H, Lin R, Gao X, Li G, Feng Z, Zhu R, Yao Y, Feng B, Liu Z.	Gut Microbes	10.1080/19490976.2023.2172668	2023
	Indole Sensing Regulator (IsrR) Promotes Virulence Gene Expression in Enteric Pathogens.	Kumar A, Russell RM, Hoskan MA, Sperandio V.	mBio	10.1128/mbio.01939-22	2022
	Endogenous Hyaluronan Promotes Intestinal Homeostasis and Protects against Murine Necrotizing Enterocolitis.	Eckert JV, Moshal KS, Burge K, Wilson A, Chaaban H.	Cells	10.3390/cells13141179	2024
	Cooperative defenses during enteropathogenic infection.	Troha K, Ayres JS.	Curr Opin Microbiol	10.1016/j.mib.2021.11.003	2022
Metabolism	Inflammasome Activation by ATP Enhances Citrobacter rodentium Clearance through ROS Generation.	Bording-Jorgensen M, Alipour M, Danesh G, Wine E.	Cell Physiol Biochem	10.1159/000455988	2017
	Sensory Nociceptive Neurons Contribute to Host Protection During Enteric Infection With Citrobacter rodentium.	Ramirez VT, Sladek J, Godinez DR, Rude KM, Chicco P, Murray K, Brust-Mascher I, Gareau MG, Reardon C.	J Infect Dis	10.1093/infdis/jiaa014	2020
Phylogeny	Assessing Fecal Microbial Diversity and Hormone Levels as Indicators of Gastrointestinal Health in Reintroduced Przewalski's Horses (Equus ferus przewalskii).	Li Z, Luo Z, Hu D.	Animals (Basel)	10.3390/ani14172616	2024
	Interferon regulatory factor 1 (IRF-1) promotes intestinal group 3 innate lymphoid responses during Citrobacter rodentium infection.	Schmalzl A, Leupold T, Kreiss L, Waldner M, Schurmann S, Neurath MF, Becker C, Wirtz S.	Nat Commun	10.1038/s41467-022-33326-5	2022
Genetics	Biological Characteristics and Whole-Genome Analysis of a Porcine E. coli Phage.	Wan S, Li N, Habib S, Zheng P, Li Y, Liang Y, Qu Y.	Vet Sci	10.3390/vetsci12010057	2025
	Strain-resolved metagenomic analysis and qPCR validation suggest Clostridium cuniculi is the etiologic agent for infectious diarrhea in severely immunodeficient mice.	Barouch-Bentov R, Merrill BD, Reineking W, Moorhead R, Herberg de Alonso F, Fazel M, Uzal FA, Felt SA, Sonnenburg JL, Casey KM, Nagamine CM.	J Vet Diagn Invest	10.1177/10406387251378688	2025
Pathogenicity	Deficiency of cannabinoid receptors enhances host susceptibility to bacterial infection.	Barker HA, Bhimani S, Tirado D, Canas JJ, Lemos LN, Roesch LFW, Ferraro MJ.	mBio	10.1128/mbio.02088-25	2025
	Dietary Pea Fibre Improves Obesity, Intestinal Barrier, Reproductive Performance, Offspring Health of Parent Mice Deprived of Dietary Fibre.	Tian S, Zhang M, Chen Y, Sun H, Li Q, Yang Y, Guo A.	Animals (Basel)	10.3390/ani15050655	2025
	USP2 promotes experimental colitis and bacterial infections by inhibiting the proliferation of myeloid cells and remodeling the extracellular matrix network.	An R, Wang P, Guo H, Liuyu T, Zhong B, Zhang ZD.	Cell Insight	10.1016/j.cellin.2022.100047	2022
	The Postbiotic Butyrate Mitigates Gut Mucosal Disruption Caused by Acute Ethanol Exposure.	Siddiqui MT, Han Y, Shapiro D, West G, Fiocchi C, Cresci GAM.	Int J Mol Sci	10.3390/ijms25031665	2024
	Simulated Colonic Fluid Replicates the In Vivo Growth Capabilities of Citrobacter rodentium cpxRA Mutants and Uncovers Additive Effects of Cpx-Regulated Genes on Fitness.	Gilliland A, Gavino C, Gruenheid S, Raivio T.	Infect Immun	10.1128/iai.00314-22	2022
Genetics	High genetic diversity and different type VI secretion systems in Enterobacter species revealed by comparative genomics analysis.	Peng M, Lin W, Zhou A, Jiang Z, Zhou F, Wang Z.	BMC Microbiol	10.1186/s12866-023-03164-6	2024
Metabolism	AhR/IL-22 pathway as new target for the treatment of post-infectious irritable bowel syndrome symptoms.	Meynier M, Baudu E, Rolhion N, Defaye M, Straube M, Daugey V, Modoux M, Wawrzyniak I, Delbac F, Villeger R, Meleine M, Borras Nogues E, Godfraind C, Barnich N, Ardid D, Poirier P, Sokol H, Chatel JM, Langella P, Livrelli V, Bonnet M, Carvalho FA.	Gut Microbes	10.1080/19490976.2021.2022997	2022
	Gasdermin D independent canonical inflammasome responses cooperate with caspase-8 to establish host defense against gastrointestinal Citrobacter rodentium infection.	Eeckhout E, Hamerlinck L, Jonckheere V, Van Damme P, van Loo G, Wullaert A.	Cell Death Dis	10.1038/s41419-023-05801-4	2023
	Molecular Insights Into the Role of Gut Microbiota in Antibiotic Therapy Selection and Resistance Mitigation.	Andreescu M.	Cureus	10.7759/cureus.50318	2023
	The regenerating family member 3 beta instigates IL-17A-mediated neutrophil recruitment downstream of NOD1/2 signalling for controlling colonisation resistance independently of microbiota community structure.	Waldschmitt N, Kitamoto S, Secher T, Zacharioudaki V, Boulard O, Floquet E, Delacre M, Lamas B, Pham HP, Six A, Richard ML, Dagorn JC, Eberl G, Langella P, Chatel JM, Ryffel B, Iovanna JL, Poulin LF, Sokol H, Kamada N, Chamaillard M.	Gut	10.1136/gutjnl-2018-316757	2019
	Characterization of Effect of Enterovirus D68 in 129/Sv Mice Deficient in IFN-alpha/beta and/or IFN-gamma Receptors.	Song W, Watarastaporn T, Ooi YS, Nguyen K, Glenn JS, Carette JE, Casey KM, Nagamine CM.	Comp Med	10.30802/aalas-cm-24-044	2024
	Over supplementation with vitamin B12 alters microbe-host interactions in the gut leading to accelerated Citrobacter rodentium colonization and pathogenesis in mice.	Forgie AJ, Pepin DM, Ju T, Tollenaar S, Sergi CM, Gruenheid S, Willing BP.	Microbiome	10.1186/s40168-023-01461-w	2023
	Batf stabilizes Th17 cell development via impaired Stat5 recruitment of Ets1-Runx1 complexes.	Pham D, Silberger DJ, Nguyen KN, Gao M, Weaver CT, Hatton RD.	EMBO J	10.15252/embj.2021109803	2023
	In Situ Expression of Yak IL-22 in Mammary Glands as a Treatment for Bovine Staphylococcus aureus-Induced Mastitis in Mice.	Wang Z, Riqing D, Ma L, Jiang M, Zhuoma C, Li X, Liu Y.	Vet Sci	10.3390/vetsci11100515	2024
	A specialized bacterial group II intron is a highly efficient retrotransposon.	Gomes L, Toffano-Nioche C, Gautheret D, Costa M.	Mob DNA	10.1186/s13100-025-00380-x	2025
	Lactobacillus delbrueckii subsp. lactis (strain CIDCA 133) stimulates murine macrophages infected with Citrobacter rodentium.	Hugo AA, Rolny IS, Romanin D, Perez PF.	World J Microbiol Biotechnol	10.1007/s11274-017-2219-4	2017
Enzymology	Development of a real-time PCR assay for quantification of Citrobacter rodentium.	Sagaidak S, Taibi A, Wen B, Comelli EM.	J Microbiol Methods	10.1016/j.mimet.2016.05.008	2016
	Chronic binge drinking-induced susceptibility to colonic inflammation is microbiome-dependent.	Fonseca-Pereira D, Bae S, Michaud M, Glickman JN, Garrett WS.	Gut Microbes	10.1080/19490976.2024.2392874	2024
Metabolism	Caspase-6 promotes activation of the caspase-11-NLRP3 inflammasome during gram-negative bacterial infections.	Zheng M, Karki R, Kancharana B, Berns H, Pruett-Miller SM, Kanneganti TD.	J Biol Chem	10.1016/j.jbc.2021.101379	2021
	Proton Pump Inhibitors Increase the Susceptibility of Mice to Oral Infection with Enteropathogenic Bacteria.	Yasutomi E, Hoshi N, Adachi S, Otsuka T, Kong L, Ku Y, Yamairi H, Inoue J, Ishida T, Watanabe D, Ooi M, Yoshida M, Tsukimi T, Fukuda S, Azuma T.	Dig Dis Sci	10.1007/s10620-017-4905-3	2018
Metabolism	Swarm motility inhibitory and antioxidant activities of pomegranate peel processed under three drying conditions.	John KMM, Bhagwat AA, Luthria DL.	Food Chem	10.1016/j.foodchem.2017.04.143	2017
	Linking Pathogen Virulence, Host Immunity and The Microbiota at the Intestinal Barrier.	Nunez G.	Keio J Med	10.2302/kjm.66-001-abst	2017
	Development of a novel complex inflammatory bowel disease mouse model: Reproducing human inflammatory bowel disease etiologies in mice.	Seo SM, Kim NW, Yoo ES, Lee JH, Kang AR, Jeong HB, Shim WY, Kim DH, Park YJ, Bae K, Yoon KA, Choi YK.	PLoS One	10.1371/journal.pone.0311310	2024
Phylogeny	A mouse model of Citrobacter rodentium oral infection and evaluation of innate and adaptive immune responses.	Wang W, Li Y, Guo X.	STAR Protoc	10.1016/j.xpro.2020.100218	2020
	Citrobacter rodentium mouse model of bacterial infection.	Crepin VF, Collins JW, Habibzay M, Frankel G.	Nat Protoc	10.1038/nprot.2016.100	2016
	Conjugative RP4 Plasmid-Mediated Transfer of Antibiotic Resistance Genes to Commensal and Multidrug-Resistant Enteric Bacteria In Vitro.	Sher AA, VanAllen ME, Ahmed H, Whitehead-Tillery C, Rafique S, Bell JA, Zhang L, Mansfield LS.	Microorganisms	10.3390/microorganisms11010193	2023
	Neutralizing antibodies in the intestinal mucosa are essential to control gastrointestinal infection by Shiga toxin-producing Escherichia coli.	Bernal AM, Sosa FN, Carpintero-Polanco YM, Cancino CD, Fernandez-Brando RJ, Ramos MV, Podhozer A, Errea A, Rumbo M, Palermo MS.	mLife	10.1002/mlf2.70026	2025
Enzymology	R18C is a new viable P2-like bacteriophage of rabbit origin infecting Citrobacter rodentium and Shigella sonnei strains.	Svab D, Horvath B, Rohde M, Maroti G, Toth I.	Arch Virol	10.1007/s00705-019-04424-5	2019
	Clostridium butyricum relieve the visceral hypersensitivity in mice induced by Citrobacter rodentium infection with chronic stress.	Wang T, Li L, Li S, Zhao H, Qu J, Xia Y, Li Y.	PeerJ	10.7717/peerj.11585	2021
	Effects of Intermittent Harem Mating on Parturition-induced Stress and Success Rate of Weaning in C57BL/6JNarl Mice.	Chang TK, Wang CH, Lin TY, Su YC.	J Am Assoc Lab Anim Sci	10.30802/aalas-jaalas-24-000003	2024
	Weichang' an pill alleviates functional dyspepsia through modulating brain-gut peptides and gut microbiota.	Mengting L, Tao LI, Fuhao C, Yan C, Ni L, Yuan Z, Rongqiang BO, Xia D.	J Tradit Chin Med	10.19852/j.cnki.jtcm.2024.06.006	2024
	The role of selenoproteins in neutrophils during inflammation.	Lee TJ, Nettleford SK, McGlynn A, Carlson BA, Kirimanjeswara GS, Prabhu KS.	Arch Biochem Biophys	10.1016/j.abb.2022.109452	2022
	Gastric acid and escape to systemic circulation represent major bottlenecks to host infection by Citrobacter rodentium.	Woodward SE, Vogt SL, Pena-Diaz J, Melnyk RA, Cirstea M, Serapio-Palacios A, Neufeld LMP, Huus KE, Wang MA, Haney CH, Finlay BB.	ISME J	10.1038/s41396-022-01321-9	2023
	Fluorescence Detection of Type III Secretion Using a Glu-CyFur Reporter System in Citrobacter rodentium.	Pendergrass HA, Johnson AL, Hotinger JA, May AE.	Microorganisms	10.3390/microorganisms8121953	2020
	Distinct Molecular Features of NleG Type 3 Secreted Effectors Allow for Different Roles during Citrobacter rodentium Infection in Mice.	Popov G, Fiebig-Comyn A, Syriste L, Little DJ, Skarina T, Stogios PJ, Birstonas S, Coombes BK, Savchenko A.	Infect Immun	10.1128/iai.00505-22	2023
Phylogeny	Diversity, Distribution and Structural Prediction of the Pathogenic Bacterial Effectors EspN and EspS.	Li Z, Hu Y, Song Y, Li D, Yang X, Zhang L, Li T, Wang H.	Genes (Basel)	10.3390/genes15101250	2024
	IL-22: Scavenging beyond the barrier.	Datta SK.	Sci Immunol	10.1126/sciimmunol.aam7039	2017
	Evaluation of a Novel Battery-Operated Tumbler Device for Use in the Detection of Mouse Pathogens for Rodent Health Monitoring.	Sidhu HK, Perkins CL, Henderson KS, Hibl BM, Nouer SS, Tolley EA, Hamilton DJ.	J Am Assoc Lab Anim Sci	10.30802/aalas-jaalas-23-000053	2024
	Modified Tn7 transposon vectors for controlled chromosomal gene expression.	Chang C, Phan M-D, Schembri MA.	Appl Environ Microbiol	10.1128/aem.01556-24	2024
	The Interaction of the F-Like Plasmid-Encoded TraN Isoforms with Their Cognate Outer Membrane Receptors.	Low WW, Seddon C, Beis K, Frankel G.	J Bacteriol	10.1128/jb.00061-23	2023
	Card9 mediates susceptibility to intestinal pathogens through microbiota modulation and control of bacterial virulence.	Lamas B, Michel ML, Waldschmitt N, Pham HP, Zacharioudaki V, Dupraz L, Delacre M, Natividad JM, Costa GD, Planchais J, Sovran B, Bridonneau C, Six A, Langella P, Richard ML, Chamaillard M, Sokol H.	Gut	10.1136/gutjnl-2017-314195	2018
	Pectins that Structurally Differ in the Distribution of Methyl-Esters Attenuate Citrobacter rodentium-Induced Colitis.	Beukema M, Akkerman R, Jermendi E, Koster T, Laskewitz A, Kong C, Schols HA, Faas MM, de Vos P.	Mol Nutr Food Res	10.1002/mnfr.202100346	2021
	Cecal microbiome transplantation without antibiotic preconditioning standardizes murine microbiomes.	Howard-Stone R, Gerwin P, Capunitan D, Driscoll M, Jackson E, Tran TDB, Mandoiu I, Oziolor E.	Front Microbiol	10.3389/fmicb.2025.1632210	2025
	Immunological mechanisms involved in probiotic-mediated protection against Citrobacter rodentium-induced colitis.	Jiang Y, Yang G, Meng F, Yang W, Hu J, Ye L, Shi C, Wang C.	Benef Microbes	10.3920/bm2015.0119	2016
	A chemogenetic screen reveals that Trpv1-expressing neurons control regulatory T cells in the gut.	Zhu Y, Meerschaert KA, Galvan-Pena S, Bin NR, Yang D, Basu H, Kawamoto R, Shalaby A, Liberles SD, Mathis D, Benoist C, Chiu IM.	Science	10.1126/science.adk1679	2024
	Citrobacter rodentium Infection Inhibits Colonic P-glycoprotein Expression.	Patel M, Kumar A, Jayawardena D, Priyamvada S, Anbazhagan AN, Alrefai WA, Gill RK, Dudeja PK, Saksena S.	Gene Rep	10.1016/j.genrep.2019.100549	2020
	The adjuvant effect of bacterium-like particles depends on the route of administration.	Sudo H, Tokunoh N, Tsujii A, Kawashima S, Hayakawa Y, Fukushima H, Takahashi K, Koshizuka T, Inoue N.	Front Immunol	10.3389/fimmu.2023.1082273	2023
	Pyruvate-GPR31 axis induces LysoDC dendrite protrusion to M-cell pockets for effective immune responses.	Nakanishi K, Ajiro T, Yukishima K, Tsukamoto Y, Kikuta J, Sawa S, Tomura M, Kinoshita N, Shimanuki W, Suzuki A, Arai S, Maeshima K, Ichisawa T, Katakai T, Hayasaka H, Ishii M, Umemoto E.	Gut Microbes	10.1080/19490976.2025.2536089	2025
Metabolism	Desmoglein 2, but not desmocollin 2, protects intestinal epithelia from injury.	Gross A, Pack LAP, Schacht GM, Kant S, Ungewiss H, Meir M, Schlegel N, Preisinger C, Boor P, Guldiken N, Krusche CA, Sellge G, Trautwein C, Waschke J, Heuser A, Leube RE, Strnad P.	Mucosal Immunol	10.1038/s41385-018-0062-z	2018
	The Impact of Athymic Nude Mouse Stock and Colony Source on the Severity of Corynebacterium-Associated Hyperkeratosis.	Michelson A, Cheleuitte-Nieves C, Miranda IC, Ricart Arbona R, Dobtsis I, Wipf J, Lipman NS.	J Am Assoc Lab Anim Sci	10.30802/aalas-jaalas-24-100	2025
	Case Report: Resolution of high grade anal squamous intraepithelial lesion with antibiotics proposes a new role for syphilitic infection in potentiation of HPV-associated ASCC.	Ranabhotu A, Habibian N, Patel B, Farrell E, Do J, Sedghi S, Sedghi L.	Front Oncol	10.3389/fonc.2023.1226202	2023
	Intestinal Inflammation Promotes MDL-1⁺ Osteoclast Precursor Expansion to Trigger Osteoclastogenesis and Bone Loss.	Peek CT, Ford CA, Eichelberger KR, Jacobse J, Torres TP, Maseda D, Latour YL, Piazuelo MB, Johnson JR, Byndloss MX, Wilson KT, Rathmell JC, Goettel JA, Cassat JE.	Cell Mol Gastroenterol Hepatol	10.1016/j.jcmgh.2022.07.002	2022
Pathogenicity	Viral-bacterial co-infections screen in vitro reveals molecular processes affecting pathogen proliferation and host cell viability.	Walch P, Broz P.	Nat Commun	10.1038/s41467-024-52905-2	2024
	Elevated muramyl dipeptide by sialic acid-facilitated postantibiotic pathobiont expansion contributes to gut dysbiosis-induced mastitis in mice.	Qiu M, Ye C, Bao L, Wu K, Zhao Y, Zhao X, Tang R, Shang R, Shang S, Yuan C, Hu X, Zhang N, Fu Y, Wang J, Zhao C.	J Adv Res	10.1016/j.jare.2024.09.023	2025
	Ornithine decarboxylase supports ILC3 responses in infectious and autoimmune colitis through positive regulation of IL-22 transcription.	Peng V, Cao S, Trsan T, Bando JK, Avila-Pacheco J, Cleveland JL, Clish C, Xavier RJ, Colonna M.	Proc Natl Acad Sci U S A	10.1073/pnas.2214900119	2022
	Muribaculum intestinale restricts Salmonella Typhimurium colonization by converting succinate to propionate.	Wang Z, Kang S, Wu Z, Liu X, Zhang X, Wu Y, Wen Y, Zhou X, Zhang G, Wang J, Han D.	ISME J	10.1093/ismejo/wraf069	2025
	Prevalence and Pathologic Characterization of Mouse Kidney Parvovirus in Sentinel CD1 Mice.	Ge Z, Feng Y, Parry NM, Annamalai D, Carrasco SE, Guo M, Muthupalani S, Erdman SE, Fox JG.	Comp Med	10.30802/aalas-cm-24-000015	2024
	_D-Tryptophan suppresses enteric pathogen and pathobionts and prevents colitis by modulating microbial tryptophan metabolism.	Seki N, Kimizuka T, Gondo M, Yamaguchi G, Sugiura Y, Akiyama M, Yakabe K, Uchiyama J, Higashi S, Haneda T, Suematsu M, Hase K, Kim YG.	iScience	10.1016/j.isci.2022.104838	2022
Pathogenicity	PTPN2 regulates bacterial clearance in a mouse model of enteropathogenic and enterohemorrhagic E. coli infection.	Spalinger MR, Canale V, Becerra A, Shawki A, Crawford M, Santos AN, Chatterjee P, Li J, Nair MG, McCole DF.	JCI Insight	10.1172/jci.insight.156909	2023
Metabolism	Novel non-flagellated surface motility mediated by chemical signaling in Citrobacter rodentium.	Melchior K, Moreira CG.	Braz J Microbiol	10.1007/s42770-019-00123-0	2019
Pathogenicity	Gut colonization by Proteobacteria alters host metabolism and modulates cocaine neurobehavioral responses.	Cuesta S, Burdisso P, Segev A, Kourrich S, Sperandio V.	Cell Host Microbe	10.1016/j.chom.2022.09.014	2022
Metabolism	The Probiotic Lactobacillus Prevents Citrobacter rodentium-Induced Murine Colitis in a TLR2-Dependent Manner.	Ryu SH, Park JH, Choi SY, Jeon HY, Park JI, Kim JY, Ham SH, Choi YK.	J Microbiol Biotechnol	10.4014/jmb.1602.02004	2016
Metabolism	Investigation of Host and Pathogen Contributions to Infectious Colitis Using the Citrobacter rodentium Mouse Model of Infection.	Bosman ES, Chan JM, Bhullar K, Vallance BA.	Methods Mol Biol	10.1007/978-1-4939-3603-8_21	2016
	Infection leaves a genetic and functional mark on the gut population of a commensal bacterium.	Tawk C, Lim B, Bencivenga-Barry NA, Lees HJ, Ramos RJF, Cross J, Goodman AL.	Cell Host Microbe	10.1016/j.chom.2023.04.005	2023
	Activation of Plasmacytoid Dendritic Cells in Colon-Draining Lymph Nodes during Citrobacter rodentium Infection Involves Pathogen-Sensing and Inflammatory Pathways Distinct from Conventional Dendritic Cells.	Toivonen R, Kong L, Rasool O, Lund RJ, Lahesmaa R, Hanninen A.	J Immunol	10.4049/jimmunol.1600235	2016
	2023 Workshop: Neuroimmune Crosstalk in the Gut - Impact on Local, Autonomic and Gut-Brain Function.	Margolis KG, Shea-Donohue T, Cummings DM, Greenwel P, Lunsford RD, Gulbransen BD, Chiu IM.	Gastroenterology	10.1053/j.gastro.2024.03.023	2024
	Genetic insight into the relationship between inflammatory bowel disease and Clostridioides difficile infection.	Cushing-Damm KC, Chen Y, Du X, Kuppa A, Raut C, Oliveri A, Chen VL, Vanderwerff B, Zawistowski M, Rao K, Higgins P, Speliotes EK.	mSphere	10.1128/msphere.00567-24	2024
	Intranasal Administration of a Polymeric Biodegradable Film to C57BL/6 Mice.	Balafas EG, Papakyriakopoulou PI, Kostomitsopoulos NG, Valsami GN.	J Am Assoc Lab Anim Sci	10.30802/aalas-jaalas-22-000091	2023
Metabolism	The Ethanolamine-Sensing Transcription Factor EutR Promotes Virulence and Transmission during Citrobacter rodentium Intestinal Infection.	Rowley CA, Sauder AB, Kendall MM.	Infect Immun	10.1128/iai.00137-20	2020
	Genotoxins: The Mechanistic Links between Escherichia coli and Colorectal Cancer.	Wang Y, Fu K.	Cancers (Basel)	10.3390/cancers15041152	2023
Metabolism	Bap180/Baf180 is required to maintain homeostasis of intestinal innate immune response in Drosophila and mice.	He X, Yu J, Wang M, Cheng Y, Han Y, Yang S, Shi G, Sun L, Fang Y, Gong ST, Wang Z, Fu YX, Pan L, Tang H.	Nat Microbiol	10.1038/nmicrobiol.2017.56	2017
	A Macroporous Magnesium Oxide-Templated Carbon Adsorbs Shiga Toxins and Type III Secretory Proteins in Enterohemorrhagic Escherichia coli, Which Attenuates Virulence.	Hirakawa H, Suzue K, Uchida M, Takita A, Kamitani W, Tomita H.	Front Microbiol	10.3389/fmicb.2022.883689	2022
Metabolism	Protease-activated Receptor 1 Plays a Proinflammatory Role in Colitis by Promoting Th17-related Immunity.	Saeed MA, Ng GZ, Dabritz J, Wagner J, Judd L, Han JX, Dhar P, Kirkwood CD, Sutton P.	Inflamm Bowel Dis	10.1097/mib.0000000000001045	2017
	Salmonella multimutants enable efficient identification of SPI-2 effector protein function in gut inflammation and systemic colonization.	Newson JPM, Gurtler F, Piffaretti P, Barbieri N, Meyer A, Sintsova A, Barthel M, Steiger Y, McHugh SC, Enz U, Alto NM, Sunagawa S, Hardt WD.	Nat Commun	10.1038/s41467-025-64760-w	2025
	Non-canonical inflammasome activation analysis in a mouse model of Citrobacter rodentium infection.	Tsutsuki H, Zhang T, Yahiro K, Toyomoto T, Sawa T.	STAR Protoc	10.1016/j.xpro.2022.101741	2022
Pathogenicity	Effect of genetic background and postinfectious stress on visceral sensitivity in Citrobacter rodentium-infected mice.	Mondelaers SU, Theofanous SA, Florens MV, Perna E, Aguilera-Lizarraga J, Boeckxstaens GE, Wouters MM.	Neurogastroenterol Motil	10.1111/nmo.12759	2016
	Transcriptional Profiling of the Small Intestine and the Colon Reveals Modulation of Gut Infection with Citrobacter rodentium According to the Vitamin A Status.	Chai Z, Lyu Y, Chen Q, Wei CH, Snyder LM, Weaver V, Sebastian A, Albert I, Li Q, Cantorna MT, Ross C.	Nutrients	10.3390/nu14081563	2022
	Multiparametric Sensing of Outer Membrane Vesicle-Derived Supported Lipid Bilayers Demonstrates the Specificity of Bacteriophage Interactions.	Bali K, McCoy R, Lu Z, Treiber J, Savva A, Kaminski CF, Salmond G, Salleo A, Mela I, Monson R, Owens RM.	ACS Biomater Sci Eng	10.1021/acsbiomaterials.3c00021	2023
Metabolism	Intestinal colonization regulates systemic anti-commensal immune sensitivity and hyperreactivity.	Burkhard R, Koegler M, Brown K, Wilson K, Mager LF, Zucoloto AZ, Thomson C, Hebbandi Nanjundappa R, Skalosky I, Ahmadi S, McDonald B, Geuking MB.	Front Immunol	10.3389/fimmu.2023.1030395	2023
	Armenian Hamsters (Nothocricetulus migratorius): A New Host Susceptible to Corynebacterium bovis Infection and Disease.	Cheleuitte-Nieves C, Miranda IC, Michelson A, Walton K, Geist GE, Nickerson K, Wipf JR, Carrasco SE, Monette S, Mammone R, Lipman NS.	J Am Assoc Lab Anim Sci	10.30802/aalas-jaalas-25-054	2025
	Dietary Interventions Ameliorate Infectious Colitis by Restoring the Microbiome and Promoting Stem Cell Proliferation in Mice.	Ahmed I, Yusuf K, Roy BC, Stubbs J, Anant S, Attard TM, Sampath V, Umar S.	Int J Mol Sci	10.3390/ijms23010339	2021
	The Small RNA MicF Represses ObgE and SeqA in Escherichia coli.	Stibelman AY, Sariles AY, Takahashi MK.	Microorganisms	10.3390/microorganisms12122397	2024
Metabolism	Tandem tyrosine phosphosites in the Enteropathogenic Escherichia coli chaperone CesT are required for differential type III effector translocation and virulence.	Runte CS, Jain U, Getz LJ, Secord S, Kuwae A, Abe A, LeBlanc JJ, Stadnyk AW, Kaper JB, Hansen AM, Thomas NA.	Mol Microbiol	10.1111/mmi.13948	2018
Transcriptome	Understanding the host-adapted state of Citrobacter rodentium by transcriptomic analysis.	Smith AD, Yan X, Chen C, Dawson HD, Bhagwat AA.	Arch Microbiol	10.1007/s00203-016-1191-y	2016
	Microbiota and metabolome dynamics induced by Shiga toxin-producing E. coli in an in vitro model of an infant's colon.	Izquierdo M, O'Sullivan D, Uriot O, Brun M, Durif C, Denis S, Gallardo P, Gahan CGM, Etienne-Mesmin L, Blanquet-Diot S, Farfan MJ.	Microb Cell	10.15698/mic2025.04.847	2025
Pathogenicity	Bergapten inhibits NLRP3 inflammasome activation and pyroptosis via promoting mitophagy.	Luo T, Jia X, Feng WD, Wang JY, Xie F, Kong LD, Wang XJ, Lian R, Liu X, Chu YJ, Wang Y, Xu AL.	Acta Pharmacol Sin	10.1038/s41401-023-01094-7	2023
	Escherichia coli infection indicates favorable outcomes in patients with infected pancreatic necrosis.	Huang H, Peng J, Ning C, Wei Q, Li J, Lin C, Sun Z, Chen L, Zhu S, Shen D, Huang G.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1107326	2023
	Ecophysiology and interactions of a taurine-respiring bacterium in the mouse gut.	Ye H, Borusak S, Eberl C, Krasenbrink J, Weiss AS, Chen SC, Hanson BT, Hausmann B, Herbold CW, Pristner M, Zwirzitz B, Warth B, Pjevac P, Schleheck D, Stecher B, Loy A.	Nat Commun	10.1038/s41467-023-41008-z	2023
	Colonic phosphocholine is correlated with Candida tropicalis and promotes diarrhea and pathogen clearance.	Zhou X, He Y, Chen J, Xiong X, Yin J, Liang J, Peng C, Huang C, Guan G, Yin Y.	NPJ Biofilms Microbiomes	10.1038/s41522-023-00433-0	2023
	Dietary Indole-3-Carbinol Alleviated Spleen Enlargement, Enhanced IgG Response in C3H/HeN Mice Infected with Citrobacter rodentium.	Wu Y, Wang J, He Q, Yu L, Pham Q, Cheung L, Zhang Z, Kim YS, Smith AD, Wang TTY.	Nutrients	10.3390/nu12103148	2020
Pathogenicity	Macrophages regulate gastrointestinal motility through complement component 1q.	Pendse M, De Selle H, Vo N, Quinn G, Dende C, Li Y, Salinas CN, Srinivasan T, Propheter DC, Crofts AA, Koo E, Hassell B, Ruhn KA, Raj P, Obata Y, Hooper LV.	Elife	10.7554/elife.78558	2023
	Gut Microbiota-mediated Alleviation of Dextran Sulfate Sodium-induced Colitis in Mice.	Ikeda E, Yamaguchi M, Kawabata S.	Gastro Hep Adv	10.1016/j.gastha.2024.01.016	2024
	An Enteric Pathogen Subverts Colonization Resistance by Evading Competition for Amino Acids in the Gut.	Caballero-Flores G, Pickard JM, Fukuda S, Inohara N, Nunez G.	Cell Host Microbe	10.1016/j.chom.2020.06.018	2020
	The C-terminal proline-rich repeats of Enteropathogenic E. coli effector EspF are sufficient for the depletion of tight junction membrane proteins and interactions with early and recycling endosomes.	Ansari I, Mandal A, Kansal K, Walling P, Khan S, Aijaz S.	Gut Pathog	10.1186/s13099-024-00626-8	2024
Pathogenicity	Eosinophils respond to, but are not essential for control of an acute Salmonella enterica serovar Typhimurium infection in mice.	FitzPatrick RD, Noone JR, Cartwright RA, Gatti DM, Brosschot TP, Lane JM, Jensen EL, Kroker Kimber I, Reynolds LA.	Infect Immun	10.1128/iai.00325-24	2024
	Disruption of the biorhythm in gastric epithelial cell triggers inflammation in Helicobacter pylori-associated gastritis by aberrantly regulating NFIL3 via CagA activated ERK-SP1 pathway.	Teng Y, Lv Y, Chen W, Mao F, Peng L, Huang H, Li H, Shi L, Zou Q, Zhuang Y, Tian W, Guo H.	Cell Commun Signal	10.1186/s12964-025-02302-z	2025
	Agent-based model of the human colon to investigate mechanisms of pathogen colonization resistance.	Fletcher SJ, Ching C, Suprenant MP, Desai D, Zaman MH.	Biophys J	10.1016/j.bpj.2025.03.022	2025
Pathogenicity	Host immunity and the colon microbiota of mice infected with Citrobacter rodentium are beneficially modulated by lipid-soluble extract from late-cutting alfalfa in the early stages of infection.	Fries-Craft K, Anast JM, Schmitz-Esser S, Bobeck EA.	PLoS One	10.1371/journal.pone.0236106	2020
Pathogenicity	Analysis of the effect of hypusination in myeloid cells on colitis and colitis-associated cancer.	Gobert AP, Finley J, Asim M, Barry DP, Allaman MM, Hawkins CV, Williams KJ, Delagado AG, Mirmira RG, Zhao S, Piazuelo MB, Washington MK, Coburn LA, Wilson KT.	Heliyon	10.1016/j.heliyon.2024.e33838	2024
	Modulation of host defence against bacterial and viral infections by omega-3 polyunsaturated fatty acids.	Husson MO, Ley D, Portal C, Gottrand M, Hueso T, Desseyn JL, Gottrand F.	J Infect	10.1016/j.jinf.2016.10.001	2016
	Dopamine receptor D2 confers colonization resistance via microbial metabolites.	Scott SA, Fu J, Chang PV.	Nature	10.1038/s41586-024-07179-5	2024
Pathogenicity	Immune regulator IRF1 contributes to ZBP1-, AIM2-, RIPK1-, and NLRP12-PANoptosome activation and inflammatory cell death (PANoptosis).	Sharma BR, Karki R, Rajesh Y, Kanneganti TD.	J Biol Chem	10.1016/j.jbc.2023.105141	2023
	LACC1 regulates changes in the intestinal flora in a mouse model of inflammatory bowel disease.	Xu ZY, Wang JC.	BMC Gastroenterol	10.1186/s12876-023-02971-5	2023
	MARCH5-dependent NLRP3 ubiquitination is required for mitochondrial NLRP3-NEK7 complex formation and NLRP3 inflammasome activation.	Park YJ, Dodantenna N, Kim Y, Kim TH, Lee HS, Yoo YS, Heo J, Lee JH, Kwon MH, Kang HC, Lee JS, Cho H.	EMBO J	10.15252/embj.2023113481	2023
	The CpxAR signaling system confers a fitness advantage for flea gut colonization by the plague bacillus.	Robin B, Dewitte A, Alaimo V, Lecoeur C, Pierre F, Billon G, Sebbane F, Bontemps-Gallo S.	J Bacteriol	10.1128/jb.00173-24	2024
	Catechol-O-Methyltransferase Loss Drives Cell-Specific Nociceptive Signaling via the Enteric Catechol-O-Methyltransferase/microRNA-155/Tumor Necrosis Factor alpha Axis.	Zhou Q, Yang L, Verne ML, Zhang BB, Fields J, Verne GN.	Gastroenterology	10.1053/j.gastro.2022.12.041	2023
	Clostridium butyricum ameliorates indomethacin-induced enteropathy by promoting MUC2 secretion via suppressing the Notch pathway.	Zhu L, Luo Y, Liu Y, Sun S, Yuan J, Zhang L, Zhong W, Ma S, Yu Z, Zhou J, Chen X, Zhao J.	Front Microbiol	10.3389/fmicb.2025.1509876	2025
	Gut-Antimicrobial Peptides: Synergistic Co-Evolution with Antibiotics to Combat Multi-Antibiotic Resistance.	Baindara P, Mandal SM.	Antibiotics (Basel)	10.3390/antibiotics12121732	2023
Pathogenicity	Dietary Lipid Type, Rather Than Total Number of Calories, Alters Outcomes of Enteric Infection in Mice.	DeCoffe D, Quin C, Gill SK, Tasnim N, Brown K, Godovannyi A, Dai C, Abulizi N, Chan YK, Ghosh S, Gibson DL.	J Infect Dis	10.1093/infdis/jiw084	2016
	Type IV pili of Enterobacteriaceae species.	Little JI, Singh PK, Zhao J, Dunn S, Matz H, Donnenberg MS.	EcoSal Plus	10.1128/ecosalplus.esp-0003-2023	2024
	Heterocyclic Antidepressants with Antimicrobial and Fungicide Activity.	Zolotareva D, Zazybin A, Belyankova Y, Bayazit S, Dauletbakov A, Seilkhanov T, Kemelbekov U, Aydemir M.	Molecules	10.3390/molecules30051102	2025
	High Serum miR-361-3p Predicts Early Postdischarge Infections after Autologous Stem Cell Transplantation.	Mikulski D, Koscielny K, Drozdz I, Nowicki M, Misiewicz M, Perdas E, Strzalka P, Wierzbowska A, Fendler W.	Infect Chemother	10.3947/ic.2024.0021	2024
	Dietary Quercetin Increases Colonic Microbial Diversity and Attenuates Colitis Severity in Citrobacter rodentium-Infected Mice.	Lin R, Piao M, Song Y.	Front Microbiol	10.3389/fmicb.2019.01092	2019
	Mast cell modulation: A novel therapeutic strategy for abdominal pain in irritable bowel syndrome.	Van Remoortel S, Hussein H, Boeckxstaens G.	Cell Rep Med	10.1016/j.xcrm.2024.101780	2024
	Attaching and effacing pathogens modulate host mitochondrial structure and function.	Harishankar A, Viswanathan VK.	Int Rev Cell Mol Biol	10.1016/bs.ircmb.2023.03.001	2023
	Venipuncture Site Influences Blood-drop Volume in C57BL/6 Mice.	Lavin ES, Feldman ER, Soprano SM, Moore ES.	J Am Assoc Lab Anim Sci	10.30802/aalas-jaalas-23-000083	2024
	Epithelial GPR35 protects from Citrobacter rodentium infection by preserving goblet cells and mucosal barrier integrity.	Melhem H, Kaya B, Kaymak T, Wuggenig P, Flint E, Roux J, Oost KC, Cavelti-Weder C, Balmer ML, Walser JC, Morales RA, Riedel CU, Liberali P, Villablanca EJ, Niess JH.	Mucosal Immunol	10.1038/s41385-022-00494-y	2022
Phylogeny	Endoscopic healing in pediatric IBD perpetuates a persistent signature defined by Th17 cells with molecular and microbial drivers of disease.	Siebert K, Faro T, Kohler N, Holz H, Jarosch S, Matchado M, Hacker D, De Zen F, Hajji MS, Lurz E, Koletzko S, Pauling JK, Steiger K, Neuhaus K, Ohnmacht C, List M, Busch DH, Haller D, Schwerd T.	Cell Rep Med	10.1016/j.xcrm.2025.102236	2025
	Selective enrichment of commensal gut bacteria protects against Citrobacter rodentium-induced colitis.	Vong L, Pinnell LJ, Maattanen P, Yeung CW, Lurz E, Sherman PM.	Am J Physiol Gastrointest Liver Physiol	10.1152/ajpgi.00053.2015	2015
	Quantitative dose-response analysis untangles host bottlenecks to enteric infection.	Campbell IW, Hullahalli K, Turner JR, Waldor MK.	Nat Commun	10.1038/s41467-023-36162-3	2023
Metabolism	Granzyme B prevents aberrant IL-17 production and intestinal pathogenicity in CD4⁺ T cells.	Hoek KL, Greer MJ, McClanahan KG, Nazmi A, Piazuelo MB, Singh K, Wilson KT, Olivares-Villagomez D.	Mucosal Immunol	10.1038/s41385-021-00427-1	2021
	Deprivation of dietary fiber in specific-pathogen-free mice promotes susceptibility to the intestinal mucosal pathogen Citrobacter rodentium.	Neumann M, Steimle A, Grant ET, Wolter M, Parrish A, Willieme S, Brenner D, Martens EC, Desai MS.	Gut Microbes	10.1080/19490976.2021.1966263	2021
Pathogenicity	Differential antibiosis predisposes mice to Campylobacter jejuni infection: Deeper insights into the impact of the gut microbiota composition in colonization resistance.	Shayya NW, Mousavi S, Stingl K, Bereswill S, Heimesaat MM.	Eur J Microbiol Immunol (Bp)	10.1556/1886.2024.00140	2025
	The gut microbiota is essential for Trichinella spiralis-evoked suppression of colitis.	Sun H, Long SR, Jiang M, Zhang HR, Wang JJ, Liao ZX, Cui J, Wang ZQ.	PLoS Negl Trop Dis	10.1371/journal.pntd.0012645	2024
Pathogenicity	Citrobacter rodentium-induced colitis: A robust model to study mucosal immune responses in the gut.	Koroleva EP, Halperin S, Gubernatorova EO, Macho-Fernandez E, Spencer CM, Tumanov AV.	J Immunol Methods	10.1016/j.jim.2015.02.003	2015
	SLAMF7 regulates goblet cell mucus production and negatively impacts gut homeostasis and commensalism.	Zhou D, Wu C, Li C, Li M, Li Z, Li J, Zhang Y, Zhao H, Wang Y, Liang L, Xu L, Li Y, Zhong LL, Feng S, Tian GB.	Gut Microbes	10.1080/19490976.2025.2527857	2025
Metabolism	Retinoid Signaling in Intestinal Epithelial Cells Is Essential for Early Survival From Gastrointestinal Infection.	Snyder LM, Arora J, Kennett MJ, Weaver V, Cantorna MT.	Front Immunol	10.3389/fimmu.2020.559635	2020
	Structural and Cellular Insights into the l,d-Transpeptidase YcbB as a Therapeutic Target in Citrobacter rodentium, Salmonella Typhimurium, and Salmonella Typhi Infections.	Caveney NA, Serapio-Palacios A, Woodward SE, Bozorgmehr T, Caballero G, Vuckovic M, Deng W, Finlay BB, Strynadka NCJ.	Antimicrob Agents Chemother	10.1128/aac.01592-20	2021
	Using weight loss to predict outcome and define a humane endpoint in preclinical sepsis studies.	Brochut M, Heinonen T, Snaka T, Gilbert C, Le Roy D, Roger T.	Sci Rep	10.1038/s41598-024-72039-1	2024
	Investigating the Effect of Enterally Administered Capromorelin on Body Weight in Mice (Mus musculus).	Punger EM, Norris SLW, Stevens SC, Santos KH, Christy AC.	Comp Med	10.30802/aalas-cm-24-031	2024
	Genetic Diversity and Expression of Intimin in Escherichia albertii Isolated from Humans, Animals, and Food.	Liu Q, Yang X, Sun H, Wang H, Sui X, Zhang P, Bai X, Xiong Y.	Microorganisms	10.3390/microorganisms11122843	2023
Phylogeny	Isolation and Characterization of Bacteriophages That Infect Citrobacter rodentium, a Model Pathogen for Intestinal Diseases.	Mizuno CM, Luong T, Cederstrom R, Krupovic M, Debarbieux L, Roach DR.	Viruses	10.3390/v12070737	2020
	Duodenal macrophages control dietary iron absorption via local degradation of transferrin.	Sukhbaatar N, Scholler M, Fritsch SD, Linke M, Horer S, Trager M, Mazic M, Forisch S, Gonzales K, Kahler JP, Binder C, Lassnig C, Strobl B, Muller M, Scheiber-Mojdehkar B, Gundacker C, Dabsch S, Kain R, Hengstschlager M, Verhelst SHL, Weiss G, Theurl I, Weichhart T.	Blood	10.1182/blood.2022016632	2023
Pathogenicity	mSphere of Influence: a Controlled Burn-Pathogen Manipulation of the Dynamic Chemistry That Results from Inflammation.	Hammer ND.	mSphere	10.1128/msphere.00110-20	2020
	Influence of Intestinal Microbiota Transplantation and NleH Expression on Citrobacter rodentium Colonization of Mice.	Wang G, Feuerbacher LA, Hardwidge PR.	Pathogens	10.3390/pathogens7020035	2018
	Gut microbiome, T cell subsets, and cytokine analysis identify differential biomarkers in tuberculosis.	Chai Y, Liu X, Bai G, Zhou N, Liu D, Zhang X, Li M, Li K, Lei H.	Front Immunol	10.3389/fimmu.2024.1323723	2024
Pathogenicity	Intestinal luminal anion transporters and their interplay with gut microbiome and inflammation.	Husain N, Kumar A, Anbazhagan AN, Gill RK, Dudeja PK.	Am J Physiol Cell Physiol	10.1152/ajpcell.00026.2025	2025
	Fecal Proteolytic Bacteria and Staphylococcal Superantigens Are Associated With Abdominal Pain Severity in Irritable Bowel Syndrome.	Quan R, Decraecker L, Appeltans I, Cuende-Estevez M, Van Remoortel S, Aguilera-Lizarraga J, Wang Z, Hicks G, Wykosky J, McLean P, Denadai-Souza A, Hussein H, Boeckxstaens GE.	Am J Gastroenterol	10.14309/ajg.0000000000003042	2025
	IL-36alpha expression is elevated in ulcerative colitis and promotes colonic inflammation.	Russell SE, Horan RM, Stefanska AM, Carey A, Leon G, Aguilera M, Statovci D, Moran T, Fallon PG, Shanahan F, Shanahan F, Brint EK, Melgar S, Hussey S, Walsh PT.	Mucosal Immunol	10.1038/mi.2015.134	2016
	Assessing Reuse of Hypodermic Needles in Mice by means of Digital Imaging, Photomicrography, Bacterial Culture, Analysis of Nest Building, and Animal Vocalization.	Bennett TE, Rizzo J, Yang S, Rosfjord E.	J Am Assoc Lab Anim Sci	10.30802/aalas-jaalas-22-000094	2023
	Cathelicidin-related antimicrobial peptide protects against enteric pathogen-accelerated type 1 diabetes in mice.	Jia L, Li J, Zhang M, Liu H, Ren Z, Dong XL, Pan X, Qiu J, Pan LL, Sun J.	Theranostics	10.7150/thno.61433	2022
	Pseudomonas aeruginosa population dynamics in a vancomycin-induced murine model of gastrointestinal carriage.	Lebrun-Corbin M, Cheung BH, Hullahalli K, Dailey KG, Bailey K, Waldor MK, Wunderink RG, Bachta KER, Hauser AR.	mBio	10.1128/mbio.03136-24	2025
Pathogenicity	Crosstalk between circadian clocks and pathogen niche.	Borrmann H, Rijo-Ferreira F.	PLoS Pathog	10.1371/journal.ppat.1012157	2024
	Bacterial Genotoxin Accelerates Transient Infection-Driven Murine Colon Tumorigenesis.	Liu Y, Fu K, Wier EM, Lei Y, Hodgson A, Xu D, Xia X, Zheng D, Ding H, Sears CL, Yang J, Wan F.	Cancer Discov	10.1158/2159-8290.cd-21-0912	2022
	Pseudomonas aeruginosa aggregates elicit neutrophil swarming.	Drenkard E, Godfrey C, Hopke A, Thundivalappil SR, Li MC, Irimia D, Hurley BP.	iScience	10.1016/j.isci.2025.111805	2025
	Failure of colonization following gut microbiota transfer exacerbates DSS-induced colitis.	Gustafson KL, Rodriguez TR, McAdams ZL, Coghill LM, Ericsson AC, Franklin CL.	Gut Microbes	10.1080/19490976.2024.2447815	2025
Pathogenicity	Drosophila symbionts in infection: when a friend becomes an enemy.	Yu Y, Iatsenko I.	Infect Immun	10.1128/iai.00511-24	2025
	Infrared Thermography for Temperature Measurement in Adult Female C57BL/6NCrl Mice: A Comparison with Rectal Probe and Subcutaneous Transponder.	Fiebig K, Jourdan T, Kock M, Krehl K, Merle R, Thone-Reineke C.	J Am Assoc Lab Anim Sci	10.30802/aalas-jaalas-23-000114	2025
Pathogenicity	Dietary fiber pectin: challenges and potential anti-inflammatory benefits for preterms and newborns.	Donadio JLS, Fabi JP, Sztein MB, Salerno-Goncalves R.	Front Nutr	10.3389/fnut.2023.1286138	2023
Metabolism	Detection of gut microbiota and pathogen produced N-acyl homoserine in host circulation and tissues.	Xue J, Chi L, Tu P, Lai Y, Liu CW, Ru H, Lu K.	NPJ Biofilms Microbiomes	10.1038/s41522-021-00224-5	2021
	Fecal metabolite profiling identifies critically ill patients with increased 30-day mortality	de Porto A, Dylla N, Stutz M, Lin H, Khalid M, Mullowney M, Little J, Rose A, Moran D, McMillin M, Burgo V, Smith R, Woodson C, Metcalfe C, Ramaswamy R, Lehmann C, Odenwald M, Bandealy N, Zhao J, Kim M, Adler E, Sundararajan A, Sidebottom A, Kress J, Wolfe K, Pamer E, Patel B.	Sci Adv		2025
	NINJ1 mediates inflammatory cell death, PANoptosis, and lethality during infection conditions and heat stress.	Han JH, Karki R, Malireddi RKS, Mall R, Sarkar R, Sharma BR, Klein J, Berns H, Pisharath H, Pruett-Miller SM, Bae SJ, Kanneganti TD.	Nat Commun	10.1038/s41467-024-45466-x	2024
Pathogenicity	Network Analysis of Gut Microbial Communities Reveals Key Reason for Quercetin Protects against Colitis.	Lv Y, Peng J, Ma X, Liang Z, Salekdeh GH, Ke Q, Shen W, Yan Z, Li H, Wang S, Ding X.	Microorganisms	10.3390/microorganisms12101973	2024
	Bacillus subtilis ensures high spore quality in competition with Salmonella Typhimurium via the SigB-dependent pathway.	Podnar E, Dendinovic K, Danevcic T, Lories B, Kovacec E, Steenackers H, Mandic-Mulec I.	ISME J	10.1093/ismejo/wraf052	2025
Metabolism	Properdin provides protection from Citrobacter rodentium-induced intestinal inflammation in a C5a/IL-6-dependent manner.	Jain U, Cao Q, Thomas NA, Woodruff TM, Schwaeble WJ, Stover CM, Stadnyk AW.	J Immunol	10.4049/jimmunol.1401814	2015
	Origin and Evolution of Bacterial Periplasmic Force Transducers.	Williams-Jones DP, Webby MN, Bray JE, Maiden MCJ, Kleanthous C, Szczepaniak J.	Mol Biol Evol	10.1093/molbev/msaf138	2025
	Bcl-2 supports survival and metabolic fitness of quiescent tissue-resident ILC3.	King JI, Melo-Gonzalez F, Malengier-Devlies B, Tacho-Pinot R, Magalhaes MS, Hodge SH, Romero Ros X, Gentek R, Hepworth MR.	Mucosal Immunol	10.1016/j.mucimm.2023.07.001	2023
Metabolism	T Follicular Helper Cells Regulate Humoral Response for Host Protection against Intestinal Citrobacter rodentium Infection.	Bai X, Chi X, Qiao Q, Xie S, Wan S, Ni L, Wang P, Jin W, Dong C.	J Immunol	10.4049/jimmunol.2000046	2020
Genetics	Genetic and Microbial Analysis of Invasiveness for Escherichia coli Strains Associated With Inflammatory Bowel Disease.	Kim J, Zhang J, Kinch L, Shen J, Field S, Khan S, Klapproth JM, Forsberg KJ, Harris-Tryon T, Orth K, Cong Q, Ni J.	Cell Mol Gastroenterol Hepatol	10.1016/j.jcmgh.2024.101451	2025
Pathogenicity	Insight into the effects of Omega-3 fatty acids on gut microbiota: impact of a balanced tissue Omega-6/Omega-3 ratio	Zou B, Zhao D, Zhou S, Kang J, Wang B.	Front Nutr		2025
Pathogenicity	Egg Protein Transferrin-Derived Peptides IRW and IQW Regulate Citrobacter rodentium-Induced, Inflammation-Related Microbial and Metabolomic Profiles.	Ma Y, Ding S, Liu G, Fang J, Yan W, Duraipandiyan V, Al-Dhabi NA, Esmail GA, Jiang H.	Front Microbiol	10.3389/fmicb.2019.00643	2019
	Assessment of Antimicrobial Therapy in Eradicating Chlamydia muridarum in Research Mice: Immune Status and Its Impact on Outcomes.	Palillo MB, Carrasco SE, Mishkin N, Palillo JA, Lynch DB, Lawton S, Aydin M, Mourino A, Lipman NS, Ricart Arbona RJ.	J Am Assoc Lab Anim Sci	10.30802/aalas-jaalas-24-069	2025
	Evaluation of Sentinel-Free Soiled Bedding as a Replacement for Direct Sampling in PCR Detection of Rodent Pathogens during Quarantine.	Feinberg A, Nickerson KP, Woods CL, Reimer D, Henderson KS, Andersen RP, Singh B.	J Am Assoc Lab Anim Sci	10.30802/aalas-jaalas-25-028	2025
Metabolism	Aspartate Metabolism Facilitates IL-1beta Production in Inflammatory Macrophages.	Wang H, Zheng X, Liu B, Xia Y, Xin Z, Deng B, He L, Deng J, Ren W.	Front Immunol	10.3389/fimmu.2021.753092	2021
	Concurrent psychological stress and infectious colitis is key to sustaining enhanced peripheral sensory signaling.	Spreadbury I, Ochoa-Cortes F, Ibeakanma C, Martin N, Hurlbut D, Vanner SJ.	Neurogastroenterol Motil	10.1111/nmo.12497	2015
	Uremia Coupled with Mucosal Damage Predisposes Mice with Kidney Disease to Systemic Infection by Commensal Candida albicans.	Jawale CV, Li DD, Ramani K, Lin L, Li K, Methe B, Biswas PS.	Immunohorizons	10.4049/immunohorizons.2000114	2021
	Assembly and dynamic regulation of the tip filament of the Bordetella type III secretion system injectisome.	Malcova I, Zmuda M, Valecka J, Kamanova J.	mBio	10.1128/mbio.01135-25	2025
Genetics	Selected commensals educate the intestinal vascular and immune system for immunocompetence.	Romero R, Zarzycka A, Preussner M, Fischer F, Hain T, Herrmann JP, Roth K, Keber CU, Suryamohan K, Raifer H, Luu M, Leister H, Bertrams W, Klein M, Shams-Eldin H, Jacob R, Mollenkopf HJ, Rajalingam K, Visekruna A, Steinhoff U.	Microbiome	10.1186/s40168-022-01353-5	2022
	Effects of Bifidobacterium bifidum in Mice Infected with Citrobacter rodentium.	Wen B, Taibi A, Villa CR, Lee SH, Sagaidak S, Comelli EM.	Microorganisms	10.3390/microorganisms7020051	2019
	MUC17 is an essential small intestinal glycocalyx component that is disrupted in Crohn's disease.	Layunta E, Javerfelt S, van de Koolwijk FC, Sivertsson M, Dolan B, Arike L, Thulin SI, Vallance BA, Pelaseyed T.	JCI Insight	10.1172/jci.insight.181481	2024
Metabolism	IL-21 Promotes Intestinal Memory IgA Responses.	Huang X, Yang W, Yao S, Bilotta AJ, Lu Y, Zhou Z, Kumar P, Dann SM, Cong Y.	J Immunol	10.4049/jimmunol.1900766	2020
	Raw potato starch alters the microbiome, colon and cecal gene expression, and resistance to Citrobacter rodentium infection in mice fed a Western diet.	Smith AD, Chen C, Cheung L, Dawson HD.	Front Nutr	10.3389/fnut.2022.1057318	2022
	Mouse models for bacterial enteropathogen infections: insights into the role of colonization resistance.	Herzog MK, Cazzaniga M, Peters A, Shayya N, Beldi L, Hapfelmeier S, Heimesaat MM, Bereswill S, Frankel G, Gahan CGM, Hardt WD.	Gut Microbes	10.1080/19490976.2023.2172667	2023
Pathogenicity	Citrobacter rodentium: infection, inflammation and the microbiota.	Collins JW, Keeney KM, Crepin VF, Rathinam VA, Fitzgerald KA, Finlay BB, Frankel G.	Nat Rev Microbiol	10.1038/nrmicro3315	2014
	The CpxRA two-component system of adherent and invasive Escherichia coli contributes to epithelial cell invasion and early-stage intestinal fitness in a dysbiotic mouse model mediated by type 1 fimbriae expression.	Miki T, Ito M, Okada N, Haneda T.	Infect Immun	10.1128/iai.00132-24	2024
	YM155 Inhibits NleB and SseK Arginine Glycosyltransferase Activity.	Zhu C, El Qaidi S, McDonald P, Roy A, Hardwidge PR.	Pathogens	10.3390/pathogens10020253	2021
	Diet composition drives tissue-specific intensity of murine enteric infections.	Israelson H, Vedsted-Jakobsen A, Zhu L, Gagnaire A, von Munchow A, Polakovicova N, Valente AH, Raza A, Andersen-Civil AIS, Olsen JE, Myhill LJ, Geldhof P, Williams AR.	mBio	10.1128/mbio.02603-23	2024
	Bioprospecting of inhibitors of EPEC virulence from metabolites of marine actinobacteria from the Arctic Sea.	Pylkko T, Schneider YK, Rama T, Andersen JH, Tammela P.	Front Microbiol	10.3389/fmicb.2024.1432475	2024
	Infection with the enteric pathogen C. rodentium promotes islet-specific autoimmunity by activating a lymphatic route from the gut to pancreatic lymph node.	Poysti S, Toivonen R, Takeda A, Silojarvi S, Yatkin E, Miyasaka M, Hanninen A.	Mucosal Immunol	10.1038/s41385-022-00490-2	2022
	FTY720 Reduces the Biomass of Biofilms in Pseudomonas aeruginosa in a Dose-Dependent Manner.	Niazy AA, Lambarte RNA, Sumague TS, Vigilla MGB, Bin Shwish NM, Kamalan R, Daeab EK, Aljehani NM.	Antibiotics (Basel)	10.3390/antibiotics13070621	2024
	Roles of OmpA in Type III Secretion System-Mediated Virulence of Enterohemorrhagic Escherichia coli.	Hirakawa H, Suzue K, Takita A, Tomita H.	Pathogens	10.3390/pathogens10111496	2021
	Effect of Bojanggunbi-tang and its primary constituent herbs on the gastrointestinal tract: a scoping review.	Park C, Kim M, Park JW, Kim J, Bu Y, Ko SJ.	Front Pharmacol	10.3389/fphar.2025.1543194	2025
	Escherichia coli O157:H7 senses microbiota-produced riboflavin to increase its virulence in the gut.	Liu B, Liu Y, Yang B, Wang Q, Liu X, Qin J, Zhao K, Li F, Feng X, Li L, Wu P, Liu M, Zhu S, Feng L, Wang L.	Proc Natl Acad Sci U S A	10.1073/pnas.2212436119	2022
	Vaccination with O-linked Mannans Protects against Systemic Candidiasis through Innate Lymphocyte Populations.	Taira CL, Dos Santos Dias L, Lichtenberger S, Whitehead AJ, Kischkel B, Netea MG, Klein BS, Wuthrich M.	J Immunol	10.4049/jimmunol.2400065	2024
	Dietary L-Tryptophan consumption determines the number of colonic regulatory T cells and susceptibility to colitis via GPR15.	Van NT, Zhang K, Wigmore RM, Kennedy AI, DaSilva CR, Huang J, Ambelil M, Villagomez JH, O'Connor GJ, Longman RS, Cao M, Snook AE, Platten M, Kasenty G, Sigal LJ, Prendergast GC, Kim SV.	Nat Commun	10.1038/s41467-023-43211-4	2023
	Microbial interactions and the homeostasis of the gut microbiome: the role of Bifidobacterium.	Martin AJM, Serebrinsky-Duek K, Riquelme E, Saa PA, Garrido D.	Microbiome Res Rep	10.20517/mrr.2023.10	2023
	¹H, ¹³C, and ¹⁵N NMR chemical shift assignment of the complex formed by the first EPEC EspF repeat and N-WASP GTPase binding domain.	Karjalainen M, Hellman M, Tossavainen H, Permi P.	Biomol NMR Assign	10.1007/s12104-021-10008-9	2021
	Systematic investigation of recipient cell genetic requirements reveals important surface receptors for conjugative transfer of IncI2 plasmids.	Allard N, Collette A, Paquette J, Rodrigue S, Cote JP.	Commun Biol	10.1038/s42003-023-05534-2	2023
	The gut-kidney axis in high-altitude hypoxia: pathophysiological mechanisms and the central role of hypoxia inducible factor.	Wu P, Li X, Long W, Ma Y, Xue B, Xie W, Ma X.	Ann Med	10.1080/07853890.2025.2557514	2025
Pathogenicity	Dietary prevention of antibiotic-induced dysbiosis and mortality upon aging in mice.	Smith KM, Francisco SG, Zhu Y, LeRoith T, Davis ML, Crott JW, Barger K, Greenberg AS, Smith DE, Taylor A, Yeruva L, Rowan S.	FASEB J	10.1096/fj.202402262r	2024
	Examining Intercage Transmission of Chlamydia muridarum: Impact of Barrier Husbandry and Cage Sanitization.	Palillo MB, Mishkin N, Aydin M, Mourino A, Ricart Arbona RJ, Lipman NS.	J Am Assoc Lab Anim Sci	10.30802/aalas-jaalas-24-043	2024
	Induction of Endometriosis in a Menstruating Mouse Model (Mus musculus): A Translational Animal Disease Model.	Howe CA, Cote JJ, Stoos CT, Hallgren JJ, Bredehoeft MR, Gelineau-van Waes JB.	J Am Assoc Lab Anim Sci	10.30802/aalas-jaalas-24-160	2025
	Social Stress Affects Colonic Inflammation, the Gut Microbiome, and Short-chain Fatty Acid Levels and Receptors.	Maltz RM, Keirsey J, Kim SC, Mackos AR, Gharaibeh RZ, Moore CC, Xu J, Somogyi A, Bailey MT.	J Pediatr Gastroenterol Nutr	10.1097/mpg.0000000000002226	2019
	Gene Expression Analysis before and after the Pelvic Flexure in the Epithelium of the Equine Hindgut.	Moss CD, Wilson AL, Reed KJ, Jennings KJ, Kunz IGZ, Landolt GA, Metcalf J, Engle TE, Coleman SJ.	Animals (Basel)	10.3390/ani14162303	2024
	GATA4 controls regionalization of tissue immunity and commensal-driven immunopathology.	Earley ZM, Lisicka W, Sifakis JJ, Aguirre-Gamboa R, Kowalczyk A, Barlow JT, Shaw DG, Discepolo V, Tan IL, Gona S, Ernest JD, Matzinger P, Barreiro LB, Morgun A, Bendelac A, Ismagilov RF, Shulzhenko N, Riesenfeld SJ, Jabri B.	Immunity	10.1016/j.immuni.2022.12.009	2023
Metabolism	Arginine glycosylation enhances methylglyoxal detoxification.	El Qaidi S, Scott NE, Hardwidge PR.	Sci Rep	10.1038/s41598-021-83437-0	2021
Pathogenicity	Indole-3-Carbinol Inhibits Citrobacter rodentium Infection through Multiple Pathways Including Reduction of Bacterial Adhesion and Enhancement of Cytotoxic T Cell Activity.	Wu Y, He Q, Yu L, Pham Q, Cheung L, Kim YS, Wang TTY, Smith AD.	Nutrients	10.3390/nu12040917	2020
	Maternal gut microbiome-induced IgG regulates neonatal gut microbiome and immunity.	Sanidad KZ, Amir M, Ananthanarayanan A, Singaraju A, Shiland NB, Hong HS, Kamada N, Inohara N, Nunez G, Zeng MY.	Sci Immunol	10.1126/sciimmunol.abh3816	2022
	Microbiota as a New Target in Cancer Pathogenesis and Treatment.	Algrafi AS, Jamal AA, Ismaeel DM.	Cureus	10.7759/cureus.47072	2023
	Draft Genome Sequence of Citrobacter rodentium DBS100 (ATCC 51459), a Primary Model of Enterohemorrhagic Escherichia coli Virulence.	Lenz A, Tomkins J, Fabich AJ.	Genome Announc	10.1128/genomea.00415-15	2015
	Twin-Arginine Translocation System Is Involved in Citrobacter rodentium Fitness in the Intestinal Tract.	Otake T, Fujimoto M, Hoshino Y, Ishihara T, Haneda T, Okada N, Miki T.	Infect Immun	10.1128/iai.00892-19	2020
	IL-17-dependent fibroblastic reticular cell training boosts tissue protective mucosal immunity through IL-10-producing B cells.	Wu D, Poholek CH, Majumder S, Liu Q, Revu SK, Mohib K, Rothstein DM, McGeachy MJ.	Sci Immunol	10.1126/sciimmunol.aao3669	2021
	Understanding The Regulatory Role of USP32 and SHMT2 in The Progression of Gastric Cancer.	Li J, Bo Y, Ding B, Wang L.	Cell J	10.22074/cellj.2022.557384.1046	2023
	Bacterial Sphingolipids Exacerbate Colitis by Inhibiting ILC3-derived IL-22 Production.	Bao B, Wang Y, Boudreau P, Song X, Wu M, Chen X, Patik I, Tang Y, Ouahed J, Ringel A, Barends J, Wu C, Balskus E, Thiagarajah J, Liu J, Wessels MR, Lencer WI, Kasper DL, An D, Horwitz BH, Snapper SB.	Cell Mol Gastroenterol Hepatol	10.1016/j.jcmgh.2024.04.007	2024
Pathogenicity	Detection of typical indigenous gut bacteria related to kanpyo Lagenaria siceraria var. hispida powder in murine caecum and human faecal cultures.	Yamamoto M, Ogura H, Kuda T, Xia Y, Nakamura A, Takahashi H, Inoue J, Takayanagi S.	3 Biotech	10.1007/s13205-024-03960-5	2024
Pathogenicity	Geographic differences in gut microbiota composition impact susceptibility to enteric infection.	Porras AM, Shi Q, Zhou H, Callahan R, Montenegro-Bethancourt G, Solomons N, Brito IL.	Cell Rep	10.1016/j.celrep.2021.109457	2021
Pathogenicity	Alpha hemolysin enhances the immune response by modulating dendritic cell differentiation via ADAM10-Notch signaling.	Wang K, Liao J, Yuan Y, Chen Z, Gou Q, Jing H, Liang M, Tang Y, Yan P, Yu X, Zhao Z, Sun T, Xia Z, Yu T, Liao Y, Zeng H, Zhang X, Zou Q, Zhang J.	Signal Transduct Target Ther	10.1038/s41392-025-02432-3	2025
	Effects of Supplemental Diet during Breeding on Fertility, Litter Size, Survival Rate, and Weaning Weight in Mice (Mus musculus).	Wong RK, Carriero SJ, Wadsworth BC, Raiciulescu S, Field AE, Cadieux CL.	J Am Assoc Lab Anim Sci	10.30802/aalas-jaalas-23-000128	2024
	Dynamic Spread of Antibiotic Resistance Determinants by Conjugation to a Human-Derived Gut Microbiota in a Transplanted Mouse Model.	Sher AA, Whitehead-Tillery CE, Peer AM, Bell JA, Vocelle DB, Dippel JT, Zhang L, Mansfield LS.	Antibiotics (Basel)	10.3390/antibiotics14020152	2025
	Bcl6 is a subset-defining transcription factor of lymphoid tissue inducer-like ILC3.	Tacho-Pinot R, Stamper CT, King JI, Matei-Rascu V, Richardson E, Li Z, Roberts LB, Bassett JW, Melo-Gonzalez F, Fiancette R, Lin IH, Dent A, Harada Y, Finlay C, Mjosberg J, Withers DR, Hepworth MR.	Cell Rep	10.1016/j.celrep.2023.113425	2023
	Epithelial NAD⁺ depletion drives mitochondrial dysfunction and contributes to intestinal inflammation.	Novak EA, Crawford EC, Mentrup HL, Griffith BD, Fletcher DM, Flanagan MR, Schneider C, Firek B, Rogers MB, Morowitz MJ, Piganelli JD, Wang Q, Mollen KP.	Front Immunol	10.3389/fimmu.2023.1231700	2023
Pathogenicity	IL-17 links the tumor suppressor LKB1 to gastrointestinal inflammation and polyposis.	Compton SE, DeCamp LM, Oswald BM, Kitchen-Goosen SM, Lau KH, Fillinger R, Dahabieh MS, Ark AV, Krawczyk CM, Jones RG.	Sci Adv	10.1126/sciadv.adt5933	2025
	Western-style diet impedes colonization and clearance of Citrobacter rodentium.	An J, Zhao X, Wang Y, Noriega J, Gewirtz AT, Zou J.	PLoS Pathog	10.1371/journal.ppat.1009497	2021
	A Study of NLRC4 in Patients with Leprosy.	Batta SM, Far NNE, Soliman NA, Nassar SO.	Indian J Dermatol	10.4103/ijd.ijd_781_22	2023
	Maternal consumption of yoghurt activating the aryl hydrocarbon receptor increases group 3 innate lymphoid cells in murine offspring.	Pimentel G, Roder T, Bar C, Christensen S, Sattari Z, Kalbermatter C, von Ah U, Robert CAM, Mateo P, Bruggmann R, Ganal-Vonarburg SC, Vergeres G.	Microbiol Spectr	10.1128/spectrum.00393-24	2024
Pathogenicity	Citrobacter rodentium induces rapid and unique metabolic and inflammatory responses in mice suffering from severe disease.	Carson D, Barry R, Hopkins EGD, Roumeliotis TI, Garcia-Weber D, Mullineaux-Sanders C, Elinav E, Arrieumerlou C, Choudhary JS, Frankel G.	Cell Microbiol	10.1111/cmi.13126	2020
	Pantoea ananatis, A New Bacterial Pathogen Affecting Wheat Plants (Triticum L.) in Poland.	Krawczyk K, Wielkopolan B, Obrepalska-Steplowska A.	Pathogens	10.3390/pathogens9121079	2020
	The Microbiome in Pancreatic Cancer-Implications for Diagnosis and Precision Bacteriophage Therapy for This Low Survival Disease.	Kabwe M, Dashper S, Tucci J.	Front Cell Infect Microbiol	10.3389/fcimb.2022.871293	2022
	Fas regulates neutrophil lifespan during viral and bacterial infection.	O'Donnell JA, Kennedy CL, Pellegrini M, Nowell CJ, Zhang JG, O'Reilly LA, Cengia L, Dias S, Masters SL, Hartland EL, Roberts AW, Gerlic M, Croker BA.	J Leukoc Biol	10.1189/jlb.3ab1113-594rr	2015
	Exogenous indole modulates several CpxRA-mediated virulence-related parameters of Edwardsiella piscicida in vitro.	Gou Y, Fang Q, Gu H, Tian A, Li J, Wang Y, Hu Y.	Mar Life Sci Technol	10.1007/s42995-024-00238-w	2024
	Hemopexin regulates acute-phase inflammatory response against pathogenetic infections in black rockfish (Sebastes schlegelii)	Gao C, Sun P, Cai X, Tian M, Li C.	Comparative Immunology Reports		2024
	Trained Immunity Confers Broad-Spectrum Protection Against Bacterial Infections.	Ciarlo E, Heinonen T, Theroude C, Asgari F, Le Roy D, Netea MG, Roger T.	J Infect Dis	10.1093/infdis/jiz692	2020
	Laboratory mice engrafted with natural gut microbiota possess a wildling-like phenotype.	Runge S, von Zedtwitz S, Maucher AM, Bruno P, Osbelt L, Zhao B, Gernand AM, Lesker TR, Grawe K, Rogg M, Schell C, Boerries M, Strowig T, Andrieux G, Hild B, Rosshart SP.	Nat Commun	10.1038/s41467-025-60554-2	2025
Pathogenicity	Interleukin-4 Programmed Macrophages Suppress Colitis and Do Not Enhance Infectious-Colitis, Inflammation-Associated Colon Cancer or Airway Hypersensitivity.	Callejas BE, Blyth GAD, Jendzjowsky N, Wang A, Babbar A, Koro K, Wilson RJA, Kelly MM, Cobo ER, McKay DM.	Front Immunol	10.3389/fimmu.2021.744738	2021
	NLRP6 negatively regulates host defense against polymicrobial sepsis.	Ghimire L, Paudel S, Le J, Jin L, Cai S, Bhattarai D, Jeyaseelan S.	Front Immunol	10.3389/fimmu.2024.1248907	2024
Genetics	Investigation of Citrobacter freundii clinical isolates in a Chinese hospital during 2020-2022 revealed genomic characterization of an extremely drug-resistant C. freundii ST257 clinical strain GMU8049 co-carrying bla_NDM-1 and a novel bla_CMY variant.	Zhang M, Yin Z, Chen B, Yu Z, Liang J, Tian X, Li D, Deng X, Peng L.	Microbiol Spectr	10.1128/spectrum.04254-23	2024
Pathogenicity	Targeting macrophage autophagy for inflammation resolution and tissue repair in inflammatory bowel disease.	Wang EJ, Wu MY, Ren ZY, Zheng Y, Ye RD, Tan CSH, Wang Y, Lu JH.	Burns Trauma	10.1093/burnst/tkad004	2023
	Surface-mediated bacteriophage defense incurs fitness tradeoffs for interbacterial antagonism.	Tsai CE, Wang FQ, Yang CW, Yang LL, Nguyen TV, Chen YC, Chen PY, Hwang IS, Ting SY.	EMBO J	10.1038/s44318-025-00406-3	2025
	Live and Diet by Your Gut Microbiota.	Bassis CM.	mBio	10.1128/mbio.02335-19	2019
	Transient Glycolytic Complexation of Arsenate Enhances Resistance in the Enteropathogen Vibrio cholerae.	Bueno E, Pinedo V, Shinde DD, Mateus A, Typas A, Savitski MM, Thomas VC, Cava F.	mBio	10.1128/mbio.01654-22	2022
	Heat Tolerance Differences Between Hu Sheep and Hu Crossbred Sheep in Microbial Community Structure and Metabolism.	Yuan JD, Wang LW, Fu SY, E RG, Ren XQ, Sun H, Liu F, Wang B, An JH, Zhao MR, He JF, He XL.	Metabolites	10.3390/metabo15010040	2025
	Complete-genome sequencing and comparative genomic characterization of bla_NDM-5 carrying Citrobacter freundii isolates from a patient with multiple infections.	Ye J, Jin L, Li Y, Xu H, Lin Y, Zhou T, Zheng B, Wang M, Wang Z.	BMC Genomics	10.1186/s12864-023-09579-9	2023
Metabolism	The inhibition of COPII trafficking is important for intestinal epithelial tight junction disruption during enteropathogenic Escherichia coli and Citrobacter rodentium infection.	Thanabalasuriar A, Kim J, Gruenheid S.	Microbes Infect	10.1016/j.micinf.2013.05.001	2013
Genetics	A comprehensive approach for microbiota and health monitoring in mouse colonies using metagenomic shotgun sequencing.	Scavizzi F, Bassi C, Lupini L, Guerriero P, Raspa M, Sabbioni S.	Anim Microbiome	10.1186/s42523-021-00113-4	2021
Enzymology	Severe Acute Respiratory Syndrome Coronavirus 2 Attachment Receptor Angiotensin-Converting Enzyme 2 Is Decreased in Crohn's Disease and Regulated By Microbial and Inflammatory Signaling.	Patankar JV, Chiriac MT, Lehmann M, Kuhl AA, Atreya R, Becker C, Callaborators, Gonzalez-Acera M, Schmitt H, Gamez-Belmonte R, Mahapatro M, Diemand L, Hartmann L, Mascia F, Hracsko Z, Thonn V, Schodel L, Zielinska M, Yu Y, Erkert L, Li W, Zeitler M, Ruder B, Ganzleben I, Gunther C, Voehringer D, Zundler S, Neurath MF, Siegmund B.	Gastroenterology	10.1053/j.gastro.2020.10.021	2021
	Cutaneous Application of Capsaicin Cream Reduces Clinical Signs of Experimental Colitis and Repairs Intestinal Barrier Integrity by Modulating the Gut Microbiota and Tight Junction Proteins.	Santos EA, Silva JL, Leocadio PCL, Andrade MER, Queiroz-Junior CM, Oliveira NSS, Alves JL, Oliveira JS, Aguilar EC, Boujour K, Cogliati B, Cardoso VN, Fernandes SOA, Faria AMC, Alvarez-Leite JI.	ACS Pharmacol Transl Sci	10.1021/acsptsci.4c00207	2024
Pathogenicity	Removal of the cecum affects intestinal fermentation, enteric bacterial community structure, and acute colitis in mice.	Brown K, Abbott DW, Uwiera RRE, Inglis GD.	Gut Microbes	10.1080/19490976.2017.1408763	2018
	The formidable guardian: Type 3 immunity in the intestine of pigs.	Yang Z, Zhang D, Jiang Z, Peng J, Wei H.	Virulence	10.1080/21505594.2024.2424325	2024
	Modulative effect of Physalis alkekengi on both gut bacterial and fungal micro-ecosystem.	Yang Y, Zhao X, Xie Y, Wu C.	Chin Herb Med	10.1016/j.chmed.2023.02.003	2023
Pathogenicity	Modulation of Macrophages TLR4-Mediated Transcriptional Response by Lacticaseibacillus rhamnosus CRL1505 and Lactiplantibacillus plantarum CRL1506.	Suzuki M, Baillo A, Albarracin L, Elean M, Serda R, Suda Y, Namai F, Nishiyama K, Kitazawa H, Villena J.	Int J Mol Sci	10.3390/ijms26062688	2025
Pathogenicity	Gut microbiota in gastric cancer: from pathogenesis to precision medicine	Huo S, Lv K, Han L, Zhao Y, Jiang J.	Front Microbiol		2025
	A comparison of feeding acetylated high-amylose maize starch and zinc oxide in weaned pigs experimentally inoculated with an enterotoxigenic strain of Escherichia coli.	Evans D, Bowring B, Collins A, Clarke J, Kim JC, Mansfield J, Pluske JR.	J Anim Sci	10.1093/jas/skaf181	2025
	Interleukin-23 receptor signaling impairs the stability and function of colonic regulatory T cells.	Jacobse J, Brown RE, Li J, Pilat JM, Pham L, Short SP, Peek CT, Rolong A, Washington MK, Martinez-Barricarte R, Byndloss MX, Shelton C, Markle JG, Latour YL, Allaman MM, Cassat JE, Wilson KT, Choksi YA, Williams CS, Lau KS, Flynn CR, Casanova JL, Rings EHHM, Samsom JN, Goettel JA.	Cell Rep	10.1016/j.celrep.2023.112128	2023
Metabolism	An iron-containing dodecameric heptosyltransferase family modifies bacterial autotransporters in pathogenesis.	Lu Q, Yao Q, Xu Y, Li L, Li S, Liu Y, Gao W, Niu M, Sharon M, Ben-Nissan G, Zamyatina A, Liu X, Chen S, Shao F.	Cell Host Microbe	10.1016/j.chom.2014.08.008	2014
	STAT3 activation in Th17 and Th22 cells controls IL-22-mediated epithelial host defense during infectious colitis.	Backert I, Koralov SB, Wirtz S, Kitowski V, Billmeier U, Martini E, Hofmann K, Hildner K, Wittkopf N, Brecht K, Waldner M, Rajewsky K, Neurath MF, Becker C, Neufert C.	J Immunol	10.4049/jimmunol.1303076	2014
	Chlamydia muridarum Associated Pulmonary and Urogenital Disease and Pathology in a Colony of Enzootically Infected Il12rb2 Deficient and Stat1 Knockout Mice.	Mishkin N, Miranda IC, Carrasco SE, Cheleuitte-Nieves C, Arbona RRJ, Wingert C, Sun JC, Lipman NS.	Comp Med	10.30802/aalas-cm-24-000002	2024
	Catalytic DxD motif caged in Asx-turn and Met-aromatic interaction attenuates the pathogenic glycosylation of SseK2/NleB2 effectors.	Koh E, Kim U, Cho HS.	Sci Rep	10.1038/s41598-022-22803-y	2022
Metabolism	Hypervirulent-host-associated Citrobacter rodentium cells have poor acid tolerance.	Smith A, Bhagwat AA.	Curr Microbiol	10.1007/s00284-012-0298-x	2013
	Enhancement of subunit vaccine delivery with zinc-carnosine coordination polymer through the addition of mannan.	Roque JA, Lukesh NR, Hendy DA, Dixon TA, Islam MJ, Ontiveros-Padilla L, Pena ES, Lifshits LM, Simpson SR, Batty CJ, Bachelder EM, Ainslie KM.	Int J Pharm	10.1016/j.ijpharm.2024.124076	2024
Pathogenicity	Antibiotic-Induced Dysbiosis of the Gut Microbiota Shifts Host Tryptophan Metabolism and Increases the Susceptibility of Mice to Pulmonary Infection With Pseudomonas aeruginosa.	de Brito CB, do Nascimento Arifa RD, de Oliveira Bezerra R, Dias Igidio CE, de Amorim-Santos BM, de Menezes Santos ACP, Barbosa LM, Barbosa JPP, Cassiano LMG, Kohlhoff M, Fagundes M, Batista RRA, Queiroz-Junior CM, Saliba AM, Raposo JDA, Braga FC, Coimbra RS, Teixeira MM, Fagundes CT, Souza DG.	Immunology	10.1111/imm.13932	2025
	Regulatory T cells promote a protective Th17-associated immune response to intestinal bacterial infection with C. rodentium.	Wang Z, Friedrich C, Hagemann SC, Korte WH, Goharani N, Cording S, Eberl G, Sparwasser T, Lochner M.	Mucosal Immunol	10.1038/mi.2014.17	2014
	The role of RHIM in necroptosis.	Riebeling T, Kunzendorf U, Krautwald S.	Biochem Soc Trans	10.1042/bst20220535	2022
	To die or not to die: Gasdermins in intestinal health and disease.	Lin Z, Chen Q, Ruan HB.	Semin Immunol	10.1016/j.smim.2024.101865	2024
Pathogenicity	GPR120 Inhibits Colitis Through Regulation of CD4⁺ T Cell Interleukin 10 Production.	Yang W, Liu H, Xu L, Yu T, Zhao X, Yao S, Zhao Q, Barnes S, Cohn SM, Dann SM, Zhang H, Zuo X, Li Y, Cong Y.	Gastroenterology	10.1053/j.gastro.2021.09.018	2022
Phylogeny	Pomegranate peel extract alters the microbiome in mice and dysbiosis caused by Citrobacter rodentium infection.	George NS, Cheung L, Luthria DL, Santin M, Dawson HD, Bhagwat AA, Smith AD.	Food Sci Nutr	10.1002/fsn3.1106	2019
	pLxIS-containing domains are biochemically flexible regulators of interferons and metabolism.	Landau LM, Chaudhary N, Tien YC, Rogozinska M, Joshi S, Yao C, Crowley J, Hullahalli K, Campbell IW, Waldor MK, Haigis M, Kagan JC.	Mol Cell	10.1016/j.molcel.2024.05.030	2024
Enzymology	Assessing the Biosecurity Risk of Footwear as a Fomite for Transmission of Adventitious Infectious Agents to Mice	Palillo M, Mishkin N, Atmane M, Palillo J, Carrasco S, Woods C, Henderson K, Lipman N, Ricart Arbona R.	J Am Assoc Lab Anim Sci		2025
	Inter-individual and inter-regional variability of breast milk antibody reactivity to bacterial lipopolysaccharides.	Crone L, Sobek J, Muller N, Restin T, Bassler D, Paganini D, Zimmermann MB, Zarnovican P, Routier FH, Romero-Urunuela T, Izquierdo L, Hennet T.	Front Immunol	10.3389/fimmu.2024.1404192	2024
	An Antibiotic-Impacted Microbiota Compromises the Development of Colonic Regulatory T Cells and Predisposes to Dysregulated Immune Responses.	Zhang X, Borbet TC, Fallegger A, Wipperman MF, Blaser MJ, Muller A.	mBio	10.1128/mbio.03335-20	2021
Pathogenicity	EspF is crucial for Citrobacter rodentium-induced tight junction disruption and lethality in immunocompromised animals.	Xia X, Liu Y, Hodgson A, Xu D, Guo W, Yu H, She W, Zhou C, Lan L, Fu K, Vallance BA, Wan F.	PLoS Pathog	10.1371/journal.ppat.1007898	2019
	CEACAM1 regulates CD8⁺ T cell immunity and protects from severe pathology during Citrobacter rodentium induced colitis.	Zoller J, Ebel JF, Khairnar V, Schmitt V, Klopfleisch R, Meiners J, Seiffart V, Hansen W, Buer J, Singer BB, Lang KS, Westendorf AM.	Gut Microbes	10.1080/19490976.2020.1775464	2020
	Cathelicidins Induce Toll-Interacting Protein Synthesis to Prevent Apoptosis in Colonic Epithelium.	Holani R, Rathnayaka C, Blyth GAD, Babbar A, Lahiri P, Young D, Dufour A, Hollenberg MD, McKay DM, Cobo ER.	J Innate Immun	10.1159/000526121	2023
	Highly Sensitive, Flow Cytometry-Based Measurement of Intestinal Permeability in Models of Experimental Colitis.	Tsai K, Ma C, Han X, Allaire J, Lunken GR, Crowley SM, Yu H, Jacobson K, Xia L, Priatel JJ, Vallance BA.	Cell Mol Gastroenterol Hepatol	10.1016/j.jcmgh.2022.10.004	2023
Metabolism	Complex interplay of gut microbiota between obesity and asthma in children.	Hu M, Zhao X, Liu Y, Zhou H, You Y, Xue Z.	Front Microbiol	10.3389/fmicb.2023.1264356	2023
	Lyn deficiency leads to increased microbiota-dependent intestinal inflammation and susceptibility to enteric pathogens.	Roberts ME, Bishop JL, Fan X, Beer JL, Kum WW, Krebs DL, Huang M, Gill N, Priatel JJ, Finlay BB, Harder KW.	J Immunol	10.4049/jimmunol.1302832	2014
	F4/80⁺Ly6C^high Macrophages Lead to Cell Plasticity and Cancer Initiation in Colitis.	Shin AE, Tesfagiorgis Y, Larsen F, Derouet M, Zeng PYF, Good HJ, Zhang L, Rubinstein MR, Han YW, Kerfoot SM, Nichols AC, Hayakawa Y, Howlett CJ, Wang TC, Asfaha S.	Gastroenterology	10.1053/j.gastro.2023.01.002	2023
Pathogenicity	Activated sympathetic nerve post stroke downregulates Toll-like receptor 5 and disrupts the gut mucosal barrier.	Wang H, Li J, Wu G, Lin X, Chen J, Liang J, Zhang J, Luo X, Mao H, Xie J, Li Z, Zhou H, Xu K, Yin J, He Y.	Cell Rep Med	10.1016/j.xcrm.2024.101754	2024
Pathogenicity	Promotion of Colitis in B Cell-Deficient C57BL/6 Mice Infected with Enterotoxigenic Bacteroides fragilis.	Jo M, Hwang S, Lee CG, Hong JE, Kang DH, Yoo SH, Kim WS, Yoo JY, Rhee KJ.	Int J Mol Sci	10.3390/ijms25010364	2023
	Constitutive induction of intestinal Tc17 cells in the absence of hematopoietic cell-specific MHC class II expression.	Rubino SJ, Geddes K, Magalhaes JG, Streutker C, Philpott DJ, Girardin SE.	Eur J Immunol	10.1002/eji.201243028	2013
Metabolism	Interleukin-22 alleviates metabolic disorders and restores mucosal immunity in diabetes.	Wang X, Ota N, Manzanillo P, Kates L, Zavala-Solorio J, Eidenschenk C, Zhang J, Lesch J, Lee WP, Ross J, Diehl L, van Bruggen N, Kolumam G, Ouyang W.	Nature	10.1038/nature13564	2014
	Insights Into Inflammatory Bowel Disease and Effects of Dietary Fatty Acid Intake With a Focus on Polyunsaturated Fatty Acids Using Preclinical Models.	Smyth M, Lunken G, Jacobson K.	J Can Assoc Gastroenterol	10.1093/jcag/gwad058	2024
Pathogenicity	Nicotinamide treatment ameliorates the course of experimental colitis mediated by enhanced neutrophil-specific antibacterial clearance.	Bettenworth D, Nowacki TM, Ross M, Kyme P, Schwammbach D, Kerstiens L, Thoennissen GB, Bokemeyer C, Hengst K, Berdel WE, Heidemann J, Thoennissen NH.	Mol Nutr Food Res	10.1002/mnfr.201300818	2014
Metabolism	PmrC (EptA) and CptA Negatively Affect Outer Membrane Vesicle Production in Citrobacter rodentium.	Sinha A, Nyongesa S, Viau C, Gruenheid S, Veyrier FJ, Le Moual H.	J Bacteriol	10.1128/jb.00454-18	2019
Metabolism	The Virulence Effect of CpxRA in Citrobacter rodentium Is Independent of the Auxiliary Proteins NlpE and CpxP.	Giannakopoulou N, Mendis N, Zhu L, Gruenheid S, Faucher SP, Le Moual H.	Front Cell Infect Microbiol	10.3389/fcimb.2018.00320	2018
Metabolism	Vitamin D deficiency promotes epithelial barrier dysfunction and intestinal inflammation.	Assa A, Vong L, Pinnell LJ, Avitzur N, Johnson-Henry KC, Sherman PM.	J Infect Dis	10.1093/infdis/jiu235	2014
	Detection of chimeric alpha-defensin transcripts and peptides in mouse Paneth cells.	Timmermans S, Wallaeys C, De Beul S, Garcia-Gonzales N, Libert C.	Front Immunol	10.3389/fimmu.2025.1543059	2025
	The type III secretion system effector EspO of enterohaemorrhagic Escherichia coli inhibits apoptosis through an interaction with HAX-1.	Chatterjee S, Lekmeechai S, Constantinou N, Grzybowska EA, Kozik Z, Choudhary JS, Berger CN, Frankel G, Clements A.	Cell Microbiol	10.1111/cmi.13366	2021
	Extracellular Vesicles of the Probiotic Escherichia coli Nissle 1917 Reduce PepT1 Levels in IL-1beta-Treated Caco-2 Cells via Upregulation of miR-193a-3p.	Olivo-Martinez Y, Martinez-Ruiz S, Cordero C, Badia J, Baldoma L.	Nutrients	10.3390/nu16162719	2024
	SLAMF7 and SLAMF8 receptors shape human plasmacytoid dendritic cell responses to intracellular bacteria.	Pellegrini JM, Keriel A, Gorvel L, Hanniffy S, Arce-Gorvel V, Bosilkovski M, Solera J, Meresse S, Memet S, Gorvel JP.	J Clin Invest	10.1172/jci182467	2025
Metabolism	l-Arginine sensing regulates virulence gene expression and disease progression in enteric pathogens.	Menezes-Garcia Z, Kumar A, Zhu W, Winter SE, Sperandio V.	Proc Natl Acad Sci U S A	10.1073/pnas.1919683117	2020
Metabolism	Tpl2 Promotes Innate Cell Recruitment and Effector T Cell Differentiation To Limit Citrobacter rodentium Burden and Dissemination.	Acuff NV, Li X, Latha K, Nagy T, Watford WT.	Infect Immun	10.1128/iai.00193-17	2017
Pathogenicity	The RNA helicase Dhx15 mediates Wnt-induced antimicrobial protein expression in Paneth cells.	Wang Y, He K, Sheng B, Lei X, Tao W, Zhu X, Wei Z, Fu R, Wang A, Bai S, Zhang Z, Hong N, Ye C, Tian Y, Wang J, Li M, Zhang K, Li L, Yang H, Li HB, Flavell RA, Zhu S.	Proc Natl Acad Sci U S A	10.1073/pnas.2017432118	2021
	The interplay between innate lymphoid cells and microbiota.	Wang R, Cui W, Yang H.	mBio	10.1128/mbio.00399-23	2023
	Bacteroides fragilis Enterotoxin Induces Autophagy through an AMPK and FoxO3-Pathway, Leading to the Inhibition of Apoptosis in Intestinal Epithelial Cells.	Ko SH, Choi JH, Kim JM.	Toxins (Basel)	10.3390/toxins15090544	2023
	Alterations in Gut Microbiota as Early Biomarkers for Predicting Inflammatory Bowel Disease Onset and Progression: A Systematic Review.	Boppana K, Almansouri NE, Bakkannavar S, Faheem Y, Jaiswal A, Shergill K, Nath TS.	Cureus	10.7759/cureus.58080	2024
Genetics	Research progress concerning the involvement of the intestinal microbiota in the occurrence and development of inflammatory bowel disease.	Zheng L, Duan SL, Wang K.	World J Gastroenterol	10.3748/wjg.v31.i42.113170	2025
	Amino acid competition shapes Acinetobacter baumannii gut carriage.	Ren X, Clark RM, Bansah DA, Varner EN, Tiffany CR, Jaswal K, Geary JH, Todd OA, Winkelman JD, Friedman ES, Jarrett RN, Zemel BS, Wu GD, Zackular JP, DePas WH, Behnsen J, Palmer LD.	Cell Host Microbe	10.1016/j.chom.2025.07.003	2025
	Salmonella T3SS effector SseK1 arginine-glycosylates the two-component response regulator OmpR to alter bile salt resistance.	Hasan MK, Scott NE, Hays MP, Hardwidge PR, El Qaidi S.	Sci Rep	10.1038/s41598-023-36057-9	2023
Pathogenicity	HIC1 links retinoic acid signalling to group 3 innate lymphoid cell-dependent regulation of intestinal immunity and homeostasis.	Burrows K, Antignano F, Chenery A, Bramhall M, Korinek V, Underhill TM, Zaph C.	PLoS Pathog	10.1371/journal.ppat.1006869	2018
	Mechanistic insights into the attenuation of intestinal inflammation and modulation of the gut microbiome by krill oil using in vitro and in vivo models.	Liu F, Smith AD, Solano-Aguilar G, Wang TTY, Pham Q, Beshah E, Tang Q, Urban JF, Xue C, Li RW.	Microbiome	10.1186/s40168-020-00843-8	2020
	Disentangling the impact of obesity, diet, host factors, and microbiota on small intestinal antimicrobial peptide expression.	Puertolas-Balint F, Prasoodanan P K V, Holmberg SM, Schroeder BO.	Gut Microbes	10.1080/19490976.2025.2536095	2025
Metabolism	Distinct Immunomodulatory Effects of Spermine Oxidase in Colitis Induced by Epithelial Injury or Infection.	Gobert AP, Al-Greene NT, Singh K, Coburn LA, Sierra JC, Verriere TG, Luis PB, Schneider C, Asim M, Allaman MM, Barry DP, Cleveland JL, Destefano Shields CE, Casero RA, Washington MK, Piazuelo MB, Wilson KT.	Front Immunol	10.3389/fimmu.2018.01242	2018
	Mef2d potentiates type-2 immune responses and allergic lung inflammation.	Szeto ACH, Clark PA, Ferreira ACF, Heycock M, Griffiths EL, Jou E, Mannion J, Luan SL, Storrar S, Knolle MD, Kozik P, Jolin HE, Fallon PG, McKenzie ANJ.	Science	10.1126/science.adl0370	2024
	Electropenetrography with Alternating Current Reveals In Situ Changes of Aedes aegypti Probing Behaviors Associated with Dengue Virus Infection.	Jameson SB, Vaughan LD, de Verges JE, Carter BH, Dobek GL, Londono-Renteria B, Wesson DM.	Comp Med	10.30802/aalas-cm-24-030	2024
	Small-molecule probe for IBD risk variant GPR65 I231L alters cytokine signaling networks through positive allosteric modulation.	Neale I, Reddy C, Tan ZY, Li B, Nag PP, Park J, Park J, Carey KL, Graham DB, Xavier RJ.	Sci Adv	10.1126/sciadv.adn2339	2024
Pathogenicity	Effect of coiled-coil peptides on the function of the type III secretion system-dependent activity of enterohemorragic Escherichia coli O157:H7 and Citrobacter rodentium.	Larzabal M, Zotta E, Ibarra C, Rabinovitz BC, Vilte DA, Mercado EC, Cataldi A.	Int J Med Microbiol	10.1016/j.ijmm.2012.12.001	2013
	IL-1R8 as Pathoimmunological Marker for Severity of Canine Chronic Enteropathy.	Riva F, Bianchessi L, Recordati C, Inglesi A, Castiglioni V, Turin L.	Vet Sci	10.3390/vetsci9060295	2022
	Inflammasome activation and evasion by bacterial pathogens.	Ta A, Vanaja SK.	Curr Opin Immunol	10.1016/j.coi.2020.11.006	2021
Metabolism	A purified diet affects intestinal epithelial proliferation and barrier functions through gut microbial alterations.	Shiratori H, Hattori KM, Nakata K, Okawa T, Komiyama S, Kinashi Y, Kabumoto Y, Kaneko Y, Nagai M, Shindo T, Moritoki N, Kawamura YI, Dohi T, Takahashi D, Kimura S, Hase K.	Int Immunol	10.1093/intimm/dxae003	2024
	Complete Genome Sequences of Two Citrobacter rodentium Bacteriophages, CR8 and CR44b.	Toribio AL, Pickard D, Cerdeno-Tarraga AM, Petty NK, Thomson N, Salmond G, Dougan G.	Genome Announc	10.1128/genomea.00146-14	2014
	Akkermansia muciniphila MucT attenuates sodium valproate-induced hepatotoxicity and upregulation of Akkermansia muciniphila in rats.	Cui Z, Xu L, Zhao M, Zhou L.	J Cell Mol Med	10.1111/jcmm.18026	2024
Metabolism	Variations in microbiota composition of laboratory mice influence Citrobacter rodentium infection via variable short-chain fatty acid production.	Osbelt L, Thiemann S, Smit N, Lesker TR, Schroter M, Galvez EJC, Schmidt-Hohagen K, Pils MC, Muhlen S, Dersch P, Hiller K, Schluter D, Neumann-Schaal M, Strowig T.	PLoS Pathog	10.1371/journal.ppat.1008448	2020
Metabolism	Infection with enteric pathogens Salmonella typhimurium and Citrobacter rodentium modulate TGF-beta/Smad signaling pathways in the intestine.	Zhang YG, Singhal M, Lin Z, Manzella C, Kumar A, Alrefai WA, Dudeja PK, Saksena S, Sun J, Gill RK.	Gut Microbes	10.1080/19490976.2018.1429878	2018
	Cooperation between physiological defenses and immune resistance produces asymptomatic carriage of a lethal bacterial pathogen.	Chen GY, Thorup NR, Miller AJ, Li YC, Ayres JS.	Sci Adv	10.1126/sciadv.adg8719	2023
	A nonredundant role for T cell-derived interleukin 22 in antibacterial defense of colonic crypts.	Zindl CL, Witte SJ, Laufer VA, Gao M, Yue Z, Janowski KM, Cai B, Frey BF, Silberger DJ, Harbour SN, Singer JR, Turner H, Lund FE, Vallance BA, Rosenberg AF, Schoeb TR, Chen JY, Hatton RD, Weaver CT.	Immunity	10.1016/j.immuni.2022.02.003	2022
	Layer segmented filamentous bacteria colonize and impact gut health of broiler chickens.	Meinen-Jochum J, Skow CJ, Mellata M.	mSphere	10.1128/msphere.00492-24	2024
Pathogenicity	Opioid use potentiates the virulence of hospital-acquired infection, increases systemic bacterial dissemination and exacerbates gut dysbiosis in a murine model of Citrobacter rodentium infection.	Wang F, Meng J, Zhang L, Roy S.	Gut Microbes	10.1080/19490976.2019.1629237	2020
	Evaluation of Pain and Distress and Therapeutic Interventions for Rectal Prolapse in Mice to Reduce Early Study Removal.	Mitchell CM, Salyards GW, Theriault BR, Langan GP, Luchins KR.	J Am Assoc Lab Anim Sci	10.30802/aalas-jaalas-21-000038	2021
	PINK1 deficiency rewires early immune responses in a mouse model of Parkinson's disease triggered by intestinal infection.	Recinto SJ, Kazanova A, Liu L, Cordeiro B, Premachandran S, Bessaiah H, Allot A, Afanasiev E, Mukherjee S, Pei J, MacDonald A, Yaqubi M, McBride HM, Matheoud D, Trudeau LE, Gruenheid S, Stratton JA.	NPJ Parkinsons Dis	10.1038/s41531-025-00945-w	2025
	T cell plasticity in renal autoimmune disease.	Soukou S, Huber S, Krebs CF.	Cell Tissue Res	10.1007/s00441-021-03466-z	2021
	Mechanistic Insights into the Multiple Functions of Niacinamide: Therapeutic Implications and Cosmeceutical Applications in Functional Skincare Products.	Marques C, Hadjab F, Porcello A, Lourenco K, Scaletta C, Abdel-Sayed P, Hirt-Burri N, Applegate LA, Laurent A.	Antioxidants (Basel)	10.3390/antiox13040425	2024
Metabolism	Dietary L-arabinose-induced gut dysbiosis exacerbates Salmonella infection outcome.	Yu J, Tang H, Zhou N, Wang Z, Huang W, Chen Y, Wang D, Ni J, Lu J, Yao Y-F.	mSystems	10.1128/msystems.00522-24	2024
	Controversial role of ILC3s in intestinal diseases: A novelty perspective on immunotherapy.	Zhang Y, Feng X, Chen J, Liu J, Wu J, Tan H, Mi Z, Rong P.	Front Immunol	10.3389/fimmu.2023.1134636	2023
Metabolism	TCF-1 controls ILC2 and NKp46+RORgammat+ innate lymphocyte differentiation and protection in intestinal inflammation.	Mielke LA, Groom JR, Rankin LC, Seillet C, Masson F, Putoczki T, Belz GT.	J Immunol	10.4049/jimmunol.1301228	2013
	Reduced alpha diversity of the oral microbiome correlates with short progression-free survival in patients with relapsed/refractory multiple myeloma treated with ixazomib-based therapy (AGMT MM 1, phase II trial).	Ludwig H, Hausmann B, Schreder M, Ponisch W, Zojer N, Knop S, Gunsilius E, Egle A, Petzer A, Einsele H, Hajek R, Weisel K, Krenosz KJ, Lang A, Lechner D, Greil R, Berry D.	EJHaem	10.1002/jha2.130	2021
	The Gut Microbiome Regulates the Psychomotor Effects and Context-Dependent Rewarding Responses to Cocaine in Germ-Free and Antibiotic-Treated Animal Models.	Winters AD, Francescutti DM, Kracht DJ, Chaudhari DS, Zagorac B, Angoa-Perez M.	Microorganisms	10.3390/microorganisms13010077	2025
	The Tol-Pal system of Acinetobacter baumannii is important for cell morphology, antibiotic resistance and virulence.	Hubloher JJ, Van der Sande L, Schaudinn C, Muller V, Averhoff B.	Int Microbiol	10.1007/s10123-022-00319-9	2023
	Role of the gut microbiota in nutrient competition and protection against intestinal pathogen colonization.	Horrocks V, King OG, Yip AYG, Marques IM, McDonald JAK.	Microbiology (Reading)	10.1099/mic.0.001377	2023
Pathogenicity	Comparative analysis of single-cell transcriptome reveals heterogeneity and commonality in the immune microenvironment of colorectal cancer and inflammatory bowel disease.	Lv H, Mu Y, Zhang C, Zhao M, Jiang P, Xiao S, Sun H, Wu N, Sun D, Jin Y.	Front Immunol	10.3389/fimmu.2024.1356075	2024
	Formyl peptide receptor 2 orchestrates mucosal protection against Citrobacter rodentium infection.	Sharba S, Venkatakrishnan V, Padra M, Winther M, Gabl M, Sundqvist M, Wang J, Forsman H, Linden SK.	Virulence	10.1080/21505594.2019.1635417	2019
	Ketogenic Diet High in Saturated Fat Promotes Colonic Claudin Expression without Changes in Intestinal Permeability to Iohexol in Healthy Mice.	Toivio L, Launonen H, Linden J, Lehto M, Vapaatalo H, Salmenkari H, Korpela R.	Nutrients	10.3390/nu16010018	2023
	Intratumoral Microbiota: Insights from Anatomical, Molecular, and Clinical Perspectives.	Lombardo C, Fazio R, Sinagra M, Gattuso G, Longo F, Lombardo C, Salmeri M, Zanghi GN, Loreto CAE.	J Pers Med	10.3390/jpm14111083	2024
Metabolism	Identification of Antibiotics That Diminish Disease in a Murine Model of Enterohemorrhagic Escherichia coli Infection.	Muhlen S, Ramming I, Pils MC, Koeppel M, Glaser J, Leong J, Flieger A, Stecher B, Dersch P.	Antimicrob Agents Chemother	10.1128/aac.02159-19	2020
	Highly-conserved regulatory activity of the ANR family in the virulence of diarrheagenic bacteria through interaction with master and global regulators.	Rodriguez-Valverde D, Giron JA, Hu Y, Nataro JP, Ruiz-Perez F, Santiago AE.	Sci Rep	10.1038/s41598-023-33997-0	2023
	Increased Listeria monocytogenes Dissemination and Altered Population Dynamics in Muc2-Deficient Mice.	Zhang T, Sasabe J, Hullahalli K, Sit B, Waldor MK.	Infect Immun	10.1128/iai.00667-20	2021
Genetics	Positive Synergistic Effects of Quercetin and Rice Bran on Human Gut Microbiota Reduces Enterobacteriaceae Family Abundance and Elevates Propionate in a Bioreactor Model.	Ghimire S, Wongkuna S, Sankaranarayanan R, Ryan EP, Bhat GJ, Scaria J.	Front Microbiol	10.3389/fmicb.2021.751225	2021
	The Role of the Microbiome in the Pathogenesis and Treatment of Ulcerative Colitis-A Literature Review.	Swirkosz G, Szczygiel A, Logon K, Wrzesniewska M, Gomulka K.	Biomedicines	10.3390/biomedicines11123144	2023
	Notch2 with retinoic acid license IL-23 expression by intestinal EpCAM+ DCIR2+ cDC2s in mice.	Ohara D, Takeuchi Y, Watanabe H, Lee Y, Mukoyama H, Ohteki T, Kondoh G, Hirota K.	J Exp Med	10.1084/jem.20230923	2024
	Phenotypic diversity of type III secretion system activity in enteropathogenic Escherichia coli clinical isolates.	Contreras CA, Hazen TH, Guadarrama C, Cervantes-Rivera R, Ochoa TJ, Vinuesa P, Rasko DA, Puente JL.	J Med Microbiol	10.1099/jmm.0.001907	2024
Pathogenicity	Chlamydia muridarum Causes Persistent Subclinical Infection and Elicits Innate and Adaptive Immune Responses in C57BL/6J, BALB/cJ, and J:ARC(S) Mice Following Exposure to Shedding Mice.	Mishkin N, Carrasco SE, Palillo M, Momtsios P, Woods C, Henderson KS, Longhini ALF, Otis C, Gardner R, Joseph AM, Sonnenberg GF, Palillo J, Arbona RJR, Lipman NS.	Comp Med	10.30802/aalas-cm-24-057	2024
	The role and significance of the oncobiota in selected cancers: a review.	Walczak LJ, Kosikowska U, Herbet M.	Clin Exp Med	10.1007/s10238-025-01598-y	2025
	Citrobacter rodentium Induces Tissue-Resident Memory CD4⁺ T Cells.	Bishu S, Hou G, El Zaatari M, Bishu SR, Popke D, Zhang M, Grasberger H, Zou W, Stidham RW, Higgins PDR, Spence JR, Kamada N, Kao JY.	Infect Immun	10.1128/iai.00295-19	2019
	Isolation and Characterization of a Novel Alpha-Hemolytic Streptococcus spp. from the Oral Cavity and Blood of Septicemic Periparturient Immunodeficient Mice.	Funk A, Jia Q, Janke L, Crawford A, Iverson A, Rosch J, Emmons J, Savage C, Glasgow H, Hayden R, Margolis E, Pisharath H.	Comp Med	10.30802/aalas-cm-23-000020	2023
	IL-22 from T cells: better late than never.	Honda K.	Immunity	10.1016/j.immuni.2012.11.006	2012
	Comparative genomic analysis of Citrobacter sp. XT1-2-2 reveals insights into the molecular mechanism of microbial immobilization of heavy metals.	Shan S, Cheng W, Li Y, Zhang M, Liu Z, Wang Y, Wei X, Fu Z, Wu S, Du D, Guo Z.	BMC Genomics	10.1186/s12864-022-09069-4	2022
	From In Vitro to In Vivo: A Rational Flowchart for the Selection and Characterization of Candidate Probiotic Strains in Intestinal Disorders.	Maillard F, Meynier M, Mondot S, Pepke F, Galbert C, Torres Maravilla E, Kropp C, Sokol H, Carvalho FA, Jacouton E, Holowacz S, Langella P, Chain F, Martin R.	Microorganisms	10.3390/microorganisms11040906	2023
	Spatial recovery of the murine gut microbiota after antibiotics perturbation.	Taguer M, Xiao J, Crawford R, Shi H, Cheng MP, Citron M, Hannigan GD, Kasper SH.	mBio	10.1128/mbio.00707-24	2024
Metabolism	Faecal neutrophil elastase-antiprotease balance reflects colitis severity.	Barry R, Ruano-Gallego D, Radhakrishnan ST, Lovell S, Yu L, Kotik O, Glegola-Madejska I, Tate EW, Choudhary JS, Williams HRT, Frankel G.	Mucosal Immunol	10.1038/s41385-019-0235-4	2020
	Role of IL-22 in microbial host defense.	Eidenschenk C, Rutz S, Liesenfeld O, Ouyang W.	Curr Top Microbiol Immunol	10.1007/978-3-662-43492-5_10	2014
	Effect size of delayed freezing, diurnal variation, and hindgut location on the mouse fecal microbiome.	Gustafson KL, McAdams ZL, Russell AL, Dorfmeyer RA, Turner GM, Ericsson AC.	iScience	10.1016/j.isci.2024.109090	2024
	DCLK1 isoforms and aberrant Notch signaling in the regulation of human and murine colitis.	Roy BC, Ahmed I, Stubbs J, Zhang J, Attard T, Septer S, Welch D, Anant S, Sampath V, Umar S.	Cell Death Discov	10.1038/s41420-021-00526-9	2021
	Gut microbiota and derived metabolomic profiling in glaucoma with progressive neurodegeneration.	Zhang Y, Zhou X, Lu Y.	Front Cell Infect Microbiol	10.3389/fcimb.2022.968992	2022
	Short-chain fatty acids of various lengths differentially inhibit Klebsiella pneumoniae and Enterobacteriaceae species.	Chang KC, Nagarajan N, Gan Y-H.	mSphere	10.1128/msphere.00781-23	2024
	Irgm1-deficiency leads to myeloid dysfunction in colon lamina propria and susceptibility to the intestinal pathogen Citrobacter rodentium.	Taylor GA, Huang HI, Fee BE, Youssef N, Jewell ML, Cantillana V, Schoenborn AA, Rogala AR, Buckley AF, Feng CG, Vallance BA, Gulati AS, Hammer GE.	PLoS Pathog	10.1371/journal.ppat.1008553	2020
Pathogenicity	Unveiling the immune dynamics of Neisseria persistent oral colonization.	Alles M, Gunasena M, Zia T, D'Mello A, Bhattarai S, Mulhern W, Terry L, Scherger T, Wijeratne S, Singh S, Wijeratne AJ, Kasturiratna D, Tettelin H, Weyand NJ, Liyanage NPM.	Infect Immun	10.1128/iai.00048-24	2024
	Pathometagenomics reveals susceptibility to intestinal infection by Morganella to be mediated by the blood group-related B4galnt2 gene in wild mice.	Vallier M, Suwandi A, Ehrhardt K, Belheouane M, Berry D, Cepic A, Galeev A, Johnsen JM, Grassl GA, Baines JF.	Gut Microbes	10.1080/19490976.2022.2164448	2023
	Glycomics of cervicovaginal fluid from women at risk of preterm birth reveals immuno-regulatory epitopes that are hallmarks of cancer and viral glycosylation.	Wu G, Grassi P, Molina BG, MacIntyre DA, Sykes L, Bennett PR, Dell A, Haslam SM.	Sci Rep	10.1038/s41598-024-71950-x	2024
	Medicinal lavender modulates the enteric microbiota to protect against Citrobacter rodentium-induced colitis.	Baker J, Brown K, Rajendiran E, Yip A, DeCoffe D, Dai C, Molcan E, Chittick SA, Ghosh S, Mahmoud S, Gibson DL.	Am J Physiol Gastrointest Liver Physiol	10.1152/ajpgi.00327.2011	2012
Metabolism	Direct and indirect control of Lrp on LEE pathogenicity genes of Citrobacter rodentium.	Cordone A, Lucchini S, De Felice M, Ricca E.	FEMS Microbiol Lett	10.1111/j.1574-6968.2011.02411.x	2011
Pathogenicity	Determining distinct roles of IL-1alpha through generation of an IL-1alpha knockout mouse with no defect in IL-1beta expression.	Malireddi RKS, Bynigeri RR, Kancharana B, Sharma BR, Burton AR, Pelletier S, Kanneganti TD.	Front Immunol	10.3389/fimmu.2022.1068230	2022
	Probiotics are effective for the prevention and treatment of Citrobacter rodentium-induced colitis in mice.	Rodrigues DM, Sousa AJ, Johnson-Henry KC, Sherman PM, Gareau MG.	J Infect Dis	10.1093/infdis/jis177	2012
	Inhibition of TLR signaling by a bacterial protein containing immunoreceptor tyrosine-based inhibitory motifs.	Yan D, Wang X, Luo L, Cao X, Ge B.	Nat Immunol	10.1038/ni.2417	2012
	Effects of Housing Density on Reproductive Performance, Intracage Ammonia, and Welfare of Mice Continuously Housed as Breeders in Standard Mouse and Rat Caging.	Cho E, Walsh CA, D'Angelo-Gavrish NM, Wilson SR, Cirillo PA, Smith PC.	J Am Assoc Lab Anim Sci	10.30802/aalas-jaalas-22-000069	2023
	IL-22 bridges the lymphotoxin pathway with the maintenance of colonic lymphoid structures during infection with Citrobacter rodentium.	Ota N, Wong K, Valdez PA, Zheng Y, Crellin NK, Diehl L, Ouyang W.	Nat Immunol	10.1038/ni.2089	2011
	TNFRSF13B polymorphisms counter microbial adaptation to enteric IgA.	Platt JL, de Mattos Barbosa MG, Huynh D, Lefferts AR, Katta J, Kharas C, Freddolino P, Bassis CM, Wobus C, Geha R, Bram R, Nunez G, Kamada N, Cascalho M.	JCI Insight	10.1172/jci.insight.148208	2021
Metabolism	Bifidobacterium breve UCC2003 surface exopolysaccharide production is a beneficial trait mediating commensal-host interaction through immune modulation and pathogen protection.	Fanning S, Hall LJ, van Sinderen D.	Gut Microbes	10.4161/gmic.20630	2012
Metabolism	Mucins Dynamics in Physiological and Pathological Conditions.	Melhem H, Regan-Komito D, Niess JH.	Int J Mol Sci	10.3390/ijms222413642	2021
Metabolism	Functional consequences of genetic variations in DgoR, a GntR/FadR family transcriptional repressor of D-galactonate metabolism in Escherichia coli.	Singh S, Mishra R, Kakkar RA, Singla S, Pratap A, Sharma G, Sharma M, Chaba R.	J Bacteriol	10.1128/jb.00103-25	2025
	Sublytic Activity of a Pore-Forming Protein From Commensal Bacteria Causes Epigenetic Modulation of Tumour-Affiliated Protein Expression.	Toh E, Baryalai P, Nadeem A, Aung KM, Myint SL, Zlatkov N, Alidadi H, Zhu S, Mateus A, Raina DB, Ramstedt M, Uhlin BE, Wai SN.	J Extracell Vesicles	10.1002/jev2.70149	2025
	Scalable Reporter Assays to Analyze the Regulation of stx2 Expression in Shiga Toxin-Producing Enteropathogens.	Koeppel MB, Glaser J, Baumgartner T, Spriewald S, Gerlach RG, von Armansperg B, Leong JM, Stecher B.	Toxins (Basel)	10.3390/toxins13080534	2021
Transcriptome	Bacillus amyloliquefaciens attenuates the intestinal permeability, oxidative stress and endoplasmic reticulum stress: transcriptome and microbiome analyses in weaned piglets.	Yuan J, Meng H, Liu Y, Wang L, Zhu Q, Wang Z, Liu H, Zhang K, Zhao J, Li W, Wang Y.	Front Microbiol	10.3389/fmicb.2024.1362487	2024
Metabolism	Diet-derived galacturonic acid regulates virulence and intestinal colonization in enterohaemorrhagic Escherichia coli and Citrobacter rodentium.	Jimenez AG, Ellermann M, Abbott W, Sperandio V.	Nat Microbiol	10.1038/s41564-019-0641-0	2020
Metabolism	Anaerobic Respiration of NOX1-Derived Hydrogen Peroxide Licenses Bacterial Growth at the Colonic Surface.	Miller BM, Liou MJ, Zhang LF, Nguyen H, Litvak Y, Schorr EM, Jang KK, Tiffany CR, Butler BP, Baumler AJ.	Cell Host Microbe	10.1016/j.chom.2020.10.009	2020
	Neglected gut microbiome: interactions of the non-bacterial gut microbiota with enteric pathogens.	Jaswal K, Todd OA, Behnsen J.	Gut Microbes	10.1080/19490976.2023.2226916	2023
	Psidium guajava leaf extract prevents intestinal colonization of Citrobacter rodentium in the mouse model.	Gupta P, Birdi T.	J Ayurveda Integr Med	10.4103/0975-9476.146557	2015
	Tibetan Pig-Derived Probiotic Lactobacillus amylovorus SLZX20-1 Improved Intestinal Function via Producing Enzymes and Regulating Intestinal Microflora.	Shen J, Zhang J, Zhao Y, Lin Z, Ji L, Ma X.	Front Nutr	10.3389/fnut.2022.846991	2022
Genetics	Draft genomes of novel avian Chlamydia abortus strains from Australian Torresian crows (Corvus orru) shed light on possible reservoir hosts and evolutionary pathways.	Kasimov V, White RT, Jelocnik M.	Microb Genom	10.1099/mgen.0.001134	2023
Pathogenicity	The mitochondrial UPR regulator ATF5 promotes intestinal barrier function via control of the satiety response.	Chamseddine D, Mahmud SA, Westfall AK, Castoe TA, Berg RE, Pellegrino MW.	Cell Rep	10.1016/j.celrep.2022.111789	2022
Metabolism	Hyaluronan 35kDa treatment protects mice from Citrobacter rodentium infection and induces epithelial tight junction protein ZO-1 in vivo.	Kim Y, Kessler SP, Obery DR, Homer CR, McDonald C, de la Motte CA.	Matrix Biol	10.1016/j.matbio.2016.11.001	2017
	CexE Is a Coat Protein and Virulence Factor of Diarrheagenic Pathogens.	Rivas ZP, Talbot KM, Merselis LC, McCormack RM, Adkins B, Munson GP.	Front Microbiol	10.3389/fmicb.2020.01374	2020
Metabolism	Characterization of the Mode of Action of Aurodox, a Type III Secretion System Inhibitor from Streptomyces goldiniensis.	McHugh RE, O'Boyle N, Connolly JPR, Hoskisson PA, Roe AJ.	Infect Immun	10.1128/iai.00595-18	2019
Metabolism	Intestinal Epithelial Expression of MHCII Determines Severity of Chemical, T-Cell-Induced, and Infectious Colitis in Mice.	Jamwal DR, Laubitz D, Harrison CA, Figliuolo da Paz V, Cox CM, Wong R, Midura-Kiela M, Gurney MA, Besselsen DG, Setty P, Lybarger L, Bhattacharya D, Wilson JM, Ghishan FK, Kiela PR.	Gastroenterology	10.1053/j.gastro.2020.06.049	2020
Metabolism	Vitamin D Is Required for ILC3 Derived IL-22 and Protection From Citrobacter rodentium Infection.	Lin YD, Arora J, Diehl K, Bora SA, Cantorna MT.	Front Immunol	10.3389/fimmu.2019.00001	2019
	Evaluation of topical oclacitinib and nail trimming as a treatment for murine ulcerative dermatitis in laboratory mice.	Davison SE, Emmer KM, Ugiliweneza B, Sherwood LC.	PLoS One	10.1371/journal.pone.0276333	2022
	Bovine milk derived skimmed milk powder and whey protein concentrate modulates Citrobacter rodentium shedding in the mouse intestinal tract.	Cakebread J, Hodgkinson A, Wallace O, Callaghan M, Hurford D, Wieliczko R, Harris P, Haigh B.	PeerJ	10.7717/peerj.5359	2018
Metabolism	The multifaceted role of CARD9 in inflammatory bowel disease.	Luo P, Yang Z, Chen B, Zhong X.	J Cell Mol Med	10.1111/jcmm.14770	2020
	Notch inhibitors induce diarrhea, hypercrinia and secretory cell metaplasia in the human colon.	Collins M, Michot JM, Bellanger C, Mussini C, Benhadji K, Massard C, Carbonnel F.	EXCLI J	10.17179/excli2021-3572	2021
Metabolism	Retinoic Acid Mediated Clearance of Citrobacter rodentium in Vitamin A Deficient Mice Requires CD11b+ and T Cells.	Snyder LM, McDaniel KL, Tian Y, Wei CH, Kennett MJ, Patterson AD, Ross AC, Cantorna MT.	Front Immunol	10.3389/fimmu.2018.03090	2018
	The Cri1 locus is the common genetic cause of susceptibility to Citrobacter rodentium infection in C3H and FVB mouse strains.	Teatero SA, Thomassin JL, Zhu L, Diez E, Malo D, Gruenheid S.	Gut Microbes	10.4161/gmic.2.3.16297	2011
	Vitamin D/Vitamin D Receptor Signaling Is Required for Normal Development and Function of Group 3 Innate Lymphoid Cells in the Gut.	He L, Zhou M, Li YC.	iScience	10.1016/j.isci.2019.06.026	2019
	The arginine/ornithine binding protein ArgT plays an essential role in Brucella neotomae/Brucella melitensis to prevent intracellular killing and contribute to chronic persistence in the host.	Mallik SR, Joshi K, Radhakrishnan GK.	Virulence	10.1080/21505594.2024.2421983	2024
	Intestinal epithelial pH-sensing receptor GPR65 maintains mucosal homeostasis via regulating antimicrobial defense and restrains gut inflammation in inflammatory bowel disease.	Li G, Lin J, Gao X, Su H, Lin R, Gao H, Feng Z, Wu H, Feng B, Zuo K, Li Y, Wu W, Fang L, Liu Z.	Gut Microbes	10.1080/19490976.2023.2257269	2023
	How does Quorum Sensing of Intestinal Bacteria Affect Our Health and Mental Status?	Dicks LMT.	Microorganisms	10.3390/microorganisms10101969	2022
	Association between intestinal microbiota and inflammatory bowel disease.	Zhang Y, Si X, Yang L, Wang H, Sun Y, Liu N.	Animal Model Exp Med	10.1002/ame2.12255	2022
	Ileal Crohn's Disease Exhibits Reduced Activity of Phospholipase C-beta3-Dependent Wnt/beta-Catenin Signaling Pathway.	Ando T, Takazawa I, Spencer ZT, Ito R, Tomimori Y, Mikulski Z, Matsumoto K, Ishitani T, Denson LA, Kawakami Y, Kawakami Y, Kitaura J, Ahmed Y, Kawakami T.	Cells	10.3390/cells13110986	2024
Metabolism	IFN-gamma and IL-17A regulate intestinal crypt production of CXCL10 in the healthy and inflamed colon.	Walrath T, Malizia RA, Zhu X, Sharp SP, D'Souza SS, Lopez-Soler R, Parr B, Kartchner B, Lee EC, Stain SC, Iwakura Y, O'Connor W.	Am J Physiol Gastrointest Liver Physiol	10.1152/ajpgi.00208.2019	2020
	Microbial collaborations and conflicts: unraveling interactions in the gut ecosystem.	Wang S, Mu L, Yu C, He Y, Hu X, Jiao Y, Xu Z, You S, Liu SL, Bao H.	Gut Microbes	10.1080/19490976.2023.2296603	2024
	Oral immunization with Shigella sonnei WRSs2 and WRSs3 vaccine strains elicits systemic and mucosal antibodies with functional anti-microbial activity.	Shrivastava S, Agnememel AB, Ndungo E, Islam D, Liang Y, Frenck RW, Pasetti MF.	mSphere	10.1128/msphere.00419-23	2024
Metabolism	Enterobacteriaceae Growth Promotion by Intestinal Acylcarnitines, a Biomarker of Dysbiosis in Inflammatory Bowel Disease.	Lemons JMS, Conrad M, Tanes C, Chen J, Friedman ES, Roggiani M, Curry D, Chau L, Hecht AL, Harling L, Vales J, Kachelries KE, Baldassano RN, Goulian M, Bittinger K, Master SR, Liu L, Wu GD.	Cell Mol Gastroenterol Hepatol	10.1016/j.jcmgh.2023.09.005	2024
	From Nutrient to Nanocarrier: The Multifaceted Role of Vitamin B12 in Drug Delivery.	Kuldyushev NA, Simonenko SY, Goreninskii SI, Pallaeva TN, Zamyatnin AA, Parodi A.	Int J Mol Sci	10.3390/ijms26115119	2025
	Application of Lactobacillus reuteri B1/1 (Limosilactobacillus reuteri) Improves Immunological Profile of the Non-Carcinogenic Porcine-Derived Enterocytes.	Karaffova V, Teleky J, Pintaric M, Langerholc T, Mudronova D, Hudec E, Sevcikova Z.	Life (Basel)	10.3390/life13051090	2023
Pathogenicity	Hyaluronan-induced alterations of the gut microbiome protects mice against Citrobacter rodentium infection and intestinal inflammation.	Mao T, Su CW, Ji Q, Chen CY, Wang R, Vijaya Kumar D, Lan J, Jiao L, Shi HN.	Gut Microbes	10.1080/19490976.2021.1972757	2021
	Redefining the Role of Lymphotoxin Beta Receptor in the Maintenance of Lymphoid Organs and Immune Cell Homeostasis in Adulthood.	Shou Y, Koroleva E, Spencer CM, Shein SA, Korchagina AA, Yusoof KA, Parthasarathy R, Leadbetter EA, Akopian AN, Munoz AR, Tumanov AV.	Front Immunol	10.3389/fimmu.2021.712632	2021
	GrlR, a negative regulator in enteropathogenic E. coli, also represses the expression of LEE virulence genes independently of its interaction with its cognate partner GrlA.	Lara-Ochoa C, Huerta-Saquero A, Medrano-Lopez A, Deng W, Finlay BB, Martinez-Laguna Y, Puente JL.	Front Microbiol	10.3389/fmicb.2023.1063368	2023
	Quantifying the intra- and inter-species community interactions in microbiomes by dynamic covariance mapping.	Gencel M, Cofino GM, Hui C, Sahaf Z, Gauthier L, Matta C, Gagne-Leroux D, Tsang DKL, Philpott DP, Ramathan S, Menendez A, Bershtein S, Serohijos AWR.	Nat Commun	10.1038/s41467-025-61368-y	2025
Metabolism	Interleukin-33 signaling exacerbates experimental infectious colitis by enhancing gut permeability and inhibiting protective Th17 immunity.	Palmieri V, Ebel JF, Ngo Thi Phuong N, Klopfleisch R, Vu VP, Adamczyk A, Zoller J, Riedel C, Buer J, Krebs P, Hansen W, Pastille E, Westendorf AM.	Mucosal Immunol	10.1038/s41385-021-00386-7	2021
	What Can Go Wrong When Applying Immune Modulation Therapies to Target Persistent Bacterial Infections.	Micheva-Viteva S, Hong-Geller E.	J Cell Immunol	10.33696/immunology.2.011	2020
Phylogeny	Comparative analysis of intestinal microbiota composition and transcriptome in diploid and triploid Carassius auratus.	Cai Y, Wei K.	BMC Microbiol	10.1186/s12866-022-02709-5	2023
	Cuts Both Ways: Proteases Modulate Virulence of Enterohemorrhagic Escherichia coli.	Palmer LD, Skaar EP.	mBio	10.1128/mbio.00115-19	2019
Pathogenicity	Infection-induced signals generated at the plasma membrane epigenetically regulate Wnt signaling in vitro and in vivo.	Ahmed I, Roy BC, Rao Jakkula LUM, Subramaniam D, Dandawate P, Anant S, Sampath V, Umar S.	J Biol Chem	10.1074/jbc.ra119.010285	2020
Metabolism	An intra-bacterial activity for a T3SS effector.	El Qaidi S, Scott NE, Hays MP, Geisbrecht BV, Watkins S, Hardwidge PR.	Sci Rep	10.1038/s41598-020-58062-y	2020
	Conserved patterns of sequence diversification provide insight into the evolution of two-component systems in Enterobacteriaceae.	Barretto LAF, Van PT, Fowler CC.	Microb Genom	10.1099/mgen.0.001215	2024
Metabolism	T-cell derived acetylcholine aids host defenses during enteric bacterial infection with Citrobacter rodentium.	Ramirez VT, Godinez DR, Brust-Mascher I, Nonnecke EB, Castillo PA, Gardner MB, Tu D, Sladek JA, Miller EN, Lebrilla CB, Bevins CL, Gareau MG, Reardon C.	PLoS Pathog	10.1371/journal.ppat.1007719	2019
	Identification and characterization of Cri1, a locus controlling mortality during Citrobacter rodentium infection in mice.	Diez E, Zhu L, Teatero SA, Paquet M, Roy MF, Loredo-Osti JC, Malo D, Gruenheid S.	Genes Immun	10.1038/gene.2010.76	2011
	Nfkb2 deficiency and its impact on plasma cells and immunoglobulin expression in murine small intestinal mucosa.	Papoutsopoulou S, Tang J, Elramli AH, Williams JM, Gupta N, Ikuomola FI, Sheibani-Tezerji R, Alam MT, Hernandez-Fernaud JR, Caamano JH, Probert CS, Muller W, Duckworth CA, Pritchard DM.	Am J Physiol Gastrointest Liver Physiol	10.1152/ajpgi.00037.2022	2022
	The microbiome and the immune system in critical illness.	Miniet AA, Grunwell JR, Coopersmith CM.	Curr Opin Crit Care	10.1097/mcc.0000000000000800	2021
	EspB and HtpG interact with the type III-A CRISPR/Cas system of Mycobacterium tuberculosis.	Shi M, Zhang H, Fleming J, Wei W, Chen H, Dai X, Liu Y, Li C, Ran F, Wu Z, Wang Y, Zhang X, Zhang H, Bi L.	Front Mol Biosci	10.3389/fmolb.2023.1261613	2023
Pathogenicity	Microbiota-nourishing Immunity and Its Relevance for Ulcerative Colitis.	Byndloss MX, Litvak Y, Baumler AJ.	Inflamm Bowel Dis	10.1093/ibd/izz004	2019
	Examination of Horizontal Transmission of Nippostrongylus brasiliensis in Mice to Assess Biosecurity Risks.	Floyd RJ, Ricart Arbona RJ, Carrasco SE, Lipman NS.	J Am Assoc Lab Anim Sci	10.30802/aalas-jaalas-23-000004	2023
	Long-term selenium deficiency increases the pathogenicity of a Citrobacter rodentium infection in mice.	Smith AD, Cheung L, Botero S.	Biol Trace Elem Res	10.1007/s12011-011-9071-4	2011
Metabolism	Natural aryl hydrocarbon receptor ligands control organogenesis of intestinal lymphoid follicles.	Kiss EA, Vonarbourg C, Kopfmann S, Hobeika E, Finke D, Esser C, Diefenbach A.	Science	10.1126/science.1214914	2011
	ECDD-S16 targets vacuolar ATPase: A potential inhibitor compound for pyroptosis-induced inflammation.	Ekchariyawat P, Saengfak R, Sanongkiet S, Charoenwongpaiboon T, Khongpraphan S, Mala S, Luangjindarat C, Munyoo B, Chabang N, Charoensutthivarakul S, Borwornpinyo S, Tuchinda P, Ponpuak M, Pudla M, Utaisincharoen P.	PLoS One	10.1371/journal.pone.0292340	2023
Metabolism	Disrupted Iron Metabolism and Mortality during Co-infection with Malaria and an Intestinal Gram-Negative Extracellular Pathogen.	Dos Santos LI, Torres TA, Diniz SQ, Goncalves R, Caballero-Flores G, Nunez G, Gazzinelli RT, Maloy KJ, Ribeiro do V Antonelli L.	Cell Rep	10.1016/j.celrep.2020.108613	2021
Genetics	Characterizing arginine, ornithine, and putrescine pathways in enteric pathobionts.	Lillie IM, Booth CE, Horvath AE, Mondragon M, Engevik MA, Horvath TD.	Microbiologyopen	10.1002/mbo3.1408	2024
	Preventing the Transmission of Murine Norovirus to Mice (Mus musculus) by Using Dry-heat Sterilization.	Lee JC, Bidot WA, Nunamaker EA.	J Am Assoc Lab Anim Sci	10.30802/aalas-jaalas-21-000138	2022
	Gut microbiota and intestinal immunity interaction in ulcerative colitis and its application in treatment.	Bu F, Chen K, Chen S, Jiang Y.	Front Cell Infect Microbiol	10.3389/fcimb.2025.1565082	2025
	Plasmacytoid Dendritic Cells Provide Protection Against Bacterial-Induced Colitis.	Rahman T, Brown AS, Hartland EL, van Driel IR, Fung KY.	Front Immunol	10.3389/fimmu.2019.00608	2019
	Prolonged restraint stressor exposure in outbred CD-1 mice impacts microbiota, colonic inflammation, and short chain fatty acids.	Maltz RM, Keirsey J, Kim SC, Mackos AR, Gharaibeh RZ, Moore CC, Xu J, Bakthavatchalu V, Somogyi A, Bailey MT.	PLoS One	10.1371/journal.pone.0196961	2018
	IL-33 Deficiency Attenuates Lung Inflammation by Inducing Th17 Response and Impacting the Th17/Treg Balance in LPS-Induced ARDS Mice via Dendritic Cells.	Cheng L, Jiao Y, Jiang W, Zhang X, Zhang L, Jia G.	J Immunol Res	10.1155/2022/9543083	2022
Pathogenicity	Psychoactive Drugs Induce the SOS Response and Shiga Toxin Production in Escherichia coli.	Crane JK, Salehi M, Alvarado CL.	Toxins (Basel)	10.3390/toxins13070437	2021
	Effects of Pelleted and Extruded Feed on Growth Performance, Intestinal Histology and Microbiota of Juvenile Red Swamp Crayfish (Procambarus clarkii).	Wan J, Xi Q, Tang J, Liu T, Liu C, Li H, Gu X, Shen M, Zhang M, Fang J, Meng X.	Animals (Basel)	10.3390/ani12172252	2022
	Structure of lymphostatin, a large multi-functional virulence factor of pathogenic Escherichia coli.	Griessmann M, Rasmussen T, Flegler VJ, Kraft C, Schneider R, Hateley M, Spantzel L, Stevens MP, Borsch M, Bottcher B.	Nat Commun	10.1038/s41467-025-60995-9	2025
Metabolism	Commensal segmented filamentous bacteria-derived retinoic acid primes host defense to intestinal infection.	Woo V, Eshleman EM, Hashimoto-Hill S, Whitt J, Wu SE, Engleman L, Rice T, Karns R, Qualls JE, Haslam DB, Vallance BA, Alenghat T.	Cell Host Microbe	10.1016/j.chom.2021.09.010	2021
	Co-localization of autophagy-related protein p62 with cancer stem cell marker dclk1 may hamper dclk1's elimination during colon cancer development and progression.	Roy BC, Ahmed I, Ramalingam S, Jala V, Haribabu B, Ramamoorthy P, Ashcraft J, Valentino J, Anant S, Sampath V, Umar S.	Oncotarget	10.18632/oncotarget.26684	2019
	Cell type-specific mechanisms coupling protease-activated receptor-1 to infectious colitis pathogenesis.	Boucher AA, Rosenfeldt L, Mureb D, Shafer J, Sharma BK, Lane A, Crowther RR, McKell MC, Whitt J, Alenghat T, Qualls J, Antoniak S, Mackman N, Flick MJ, Steinbrecher KA, Palumbo JS.	J Thromb Haemost	10.1111/jth.14641	2020
Pathogenicity	Long-Term Effects of Early-Life Antibiotic Exposure on Resistance to Subsequent Bacterial Infection.	Roubaud-Baudron C, Ruiz VE, Swan AM, Vallance BA, Ozkul C, Pei Z, Li J, Battaglia TW, Perez-Perez GI, Blaser MJ.	mBio	10.1128/mbio.02820-19	2019
Metabolism	Interleukin-1beta secretion induced by mucosa-associated gut commensal bacteria promotes intestinal barrier repair.	Wu WH, Kim M, Chang LC, Assie A, Saldana-Morales FB, Zegarra-Ruiz DF, Norwood K, Samuel BS, Diehl GE.	Gut Microbes	10.1080/19490976.2021.2014772	2022
	Oat Beta-Glucans Modulate the Gut Microbiome, Barrier Function, and Immune Responses in an In Vivo Model of Early-Stage Colorectal Cancer.	Guzowska M, Dziendzikowska K, Kopiasz L, Gajewska M, Wilczak J, Harasym J, Czerwinska M, Gromadzka-Ostrowska J.	Int J Mol Sci	10.3390/ijms252413586	2024
Metabolism	PAD4-dependent NETs generation are indispensable for intestinal clearance of Citrobacter rodentium.	Saha P, Yeoh BS, Xiao X, Golonka RM, Singh V, Wang Y, Vijay-Kumar M.	Mucosal Immunol	10.1038/s41385-019-0139-3	2019
	Dysbiosis: from fiction to function.	Tiffany CR, Baumler AJ.	Am J Physiol Gastrointest Liver Physiol	10.1152/ajpgi.00230.2019	2019
Pathogenicity	Galactooligosaccharide supplementation provides protection against Citrobacter rodentium-induced colitis without limiting pathogen burden.	Kittana H, Quintero-Villegas MI, Bindels LB, Gomes-Neto JC, Schmaltz RJ, Segura Munoz RR, Cody LA, Moxley RA, Hostetter J, Hutkins RW, Ramer-Tait AE.	Microbiology (Reading)	10.1099/mic.0.000593	2018
	Lacticaseibacillus rhamnosus P118 enhances host tolerance to Salmonella infection by promoting microbe-derived indole metabolites.	Wang B, Peng X, Zhou X, Jin X, Siddique A, Yao J, Zhang H, Li W, Li Y, Yue M.	Elife	10.7554/elife.101198	2025
	Unveiling the Important Role of Gut Microbiota and Diet in Multiple Sclerosis.	Dzidic Krivic A, Begagic E, Hadzic S, Becirovic A, Becirovic E, Hibic H, Tandir Lihic L, Kadic Vukas S, Beculic H, Kasapovic T, Pojskic M.	Brain Sci	10.3390/brainsci15030253	2025
	Citrobacter amalonaticus Inhibits the Growth of Citrobacter rodentium in the Gut Lumen.	Mullineaux-Sanders C, Carson D, Hopkins EGD, Glegola-Madejska I, Escobar-Zepeda A, Browne HP, Lawley TD, Frankel G.	mBio	10.1128/mbio.02410-21	2021
Metabolism	Sec24 interaction is essential for localization and virulence-associated function of the bacterial effector protein NleA.	Thanabalasuriar A, Bergeron J, Gillingham A, Mimee M, Thomassin JL, Strynadka N, Kim J, Gruenheid S.	Cell Microbiol	10.1111/j.1462-5822.2012.01789.x	2012
	The interaction between ginseng and gut microbiota.	Zhao L, Sui M, Zhang T, Zhang K.	Front Nutr	10.3389/fnut.2023.1301468	2023
Pathogenicity	Short-chain fatty acids activate GPR41 and GPR43 on intestinal epithelial cells to promote inflammatory responses in mice.	Kim MH, Kang SG, Park JH, Yanagisawa M, Kim CH.	Gastroenterology	10.1053/j.gastro.2013.04.056	2013
Metabolism	Vasoactive intestinal peptide promotes host defense against enteric pathogens by modulating the recruitment of group 3 innate lymphoid cells.	Yu HB, Yang H, Allaire JM, Ma C, Graef FA, Mortha A, Liang Q, Bosman ES, Reid GS, Waschek JA, Osborne LC, Sokol H, Vallance BA, Jacobson K.	Proc Natl Acad Sci U S A	10.1073/pnas.2106634118	2021
	Distal colonocytes targeted by C. rodentium recruit T-cell help for barrier defence.	Zindl CL, Wilson CG, Chadha AS, Duck LW, Cai B, Harbour SN, Nagaoka-Kamata Y, Hatton RD, Gao M, Figge DA, Weaver CT.	Nature	10.1038/s41586-024-07288-1	2024
Metabolism	Dual-function quorum-sensing systems in bacterial pathogens and symbionts.	Barrasso K, Watve S, Simpson CA, Geyman LJ, van Kessel JC, Ng WL.	PLoS Pathog	10.1371/journal.ppat.1008934	2020
Metabolism	Defective IgA response to atypical intestinal commensals in IL-21 receptor deficiency reshapes immune cell homeostasis and mucosal immunity.	Cho H, Jaime H, de Oliveira RP, Kang B, Spolski R, Vaziri T, Myers TG, Thovarai V, Shen Z, Fox JG, Leonard WJ, Kelsall BL.	Mucosal Immunol	10.1038/s41385-018-0056-x	2019
	Formation of a membraneless compartment regulates bacterial virulence.	Aroeti L, Elbaz N, Faigenbaum-Romm R, Yakovian O, Altuvia Y, Argaman L, Katsowich N, Bejerano-Sagie M, Ravins M, Margalit H, Ben-Yehuda S, Rosenshine I.	Nat Commun	10.1038/s41467-025-58829-9	2025
Metabolism	Roles of the Tol-Pal system in the Type III secretion system and flagella-mediated virulence in enterohemorrhagic Escherichia coli.	Hirakawa H, Suzue K, Takita A, Awazu C, Kurushima J, Tomita H.	Sci Rep	10.1038/s41598-020-72412-w	2020
	Up-regulation of NHE8 by somatostatin ameliorates the diarrhea symptom in infectious colitis mice model.	Lei X, Cai L, Li X, Xu H, Geng C, Wang C.	Korean J Physiol Pharmacol	10.4196/kjpp.2018.22.3.269	2018
Metabolism	IL-17RE is the functional receptor for IL-17C and mediates mucosal immunity to infection with intestinal pathogens.	Song X, Zhu S, Shi P, Liu Y, Shi Y, Levin SD, Qian Y.	Nat Immunol	10.1038/ni.2155	2011
	Combinatorial Click Chemistry Labeling to Study Live Human Gut-Derived Microbiota Communities.	Hajjo H, Bhardwaj N, Gefen T, Geva-Zatorsky N.	Front Microbiol	10.3389/fmicb.2021.750624	2021
	Maternal Immunization Confers Protection to the Offspring against an Attaching and Effacing Pathogen through Delivery of IgG in Breast Milk.	Caballero-Flores G, Sakamoto K, Zeng MY, Wang Y, Hakim J, Matus-Acuna V, Inohara N, Nunez G.	Cell Host Microbe	10.1016/j.chom.2018.12.015	2019
	Hypusination Orchestrates the Antimicrobial Response of Macrophages.	Gobert AP, Finley JL, Latour YL, Asim M, Smith TM, Verriere TG, Barry DP, Allaman MM, Delagado AG, Rose KL, Calcutt MW, Schey KL, Sierra JC, Piazuelo MB, Mirmira RG, Wilson KT.	Cell Rep	10.1016/j.celrep.2020.108510	2020
Enzymology	A structural motif is the recognition site for a new family of bacterial protein O-glycosyltransferases.	Charbonneau ME, Cote JP, Haurat MF, Reiz B, Crepin S, Berthiaume F, Dozois CM, Feldman MF, Mourez M.	Mol Microbiol	10.1111/j.1365-2958.2012.07973.x	2012
	Advancements and progress in juvenile idiopathic arthritis: A Review of pathophysiology and treatment.	Huang HYR, Wireko AA, Miteu GD, Khan A, Roy S, Ferreira T, Garg T, Aji N, Haroon F, Zakariya F, Alshareefy Y, Pujari AG, Madani D, Papadakis M.	Medicine (Baltimore)	10.1097/md.0000000000037567	2024
	Association between risk of brucellosis and genetic variations in MicroRNA-146a.	Kazemi S, Afshar S, Karami M, Saidijam M, Keramat F, Hashemi SH, Alikhani MY.	BMC Infect Dis	10.1186/s12879-021-06775-4	2021
Metabolism	Interleukin-33 Promotes REG3gamma Expression in Intestinal Epithelial Cells and Regulates Gut Microbiota.	Xiao Y, Huang X, Zhao Y, Chen F, Sun M, Yang W, Chen L, Yao S, Peniche A, Dann SM, Sun J, Golovko G, Fofanov Y, Miao Y, Liu Z, Chen D, Cong Y.	Cell Mol Gastroenterol Hepatol	10.1016/j.jcmgh.2019.02.006	2019
	Citrobacter rodentium Infection Induces Persistent Molecular Changes and Interferon Gamma-Dependent Major Histocompatibility Complex Class II Expression in the Colonic Epithelium.	Mullineaux-Sanders C, Kozik Z, Sanchez-Garrido J, Hopkins EGD, Choudhary JS, Frankel G.	mBio	10.1128/mbio.03233-21	2021
Pathogenicity	GPR4 Knockout Attenuates Intestinal Inflammation and Forestalls the Development of Colitis-Associated Colorectal Cancer in Murine Models.	Marie MA, Sanderlin EJ, Hoffman AP, Cashwell KD, Satturwar S, Hong H, Sun Y, Yang LV.	Cancers (Basel)	10.3390/cancers15204974	2023
	Lung type 3 innate lymphoid cells respond early following Mycobacterium tuberculosis infection.	Das S, Chauhan KS, Ahmed M, Akter S, Lu L, Colonna M, Khader SA.	mBio	10.1128/mbio.03299-23	2024
	Noncanonical inflammasome activation by intracellular LPS independent of TLR4.	Kayagaki N, Wong MT, Stowe IB, Ramani SR, Gonzalez LC, Akashi-Takamura S, Miyake K, Zhang J, Lee WP, Muszynski A, Forsberg LS, Carlson RW, Dixit VM.	Science	10.1126/science.1240248	2013
Pathogenicity	Specialized Proresolving Mediators Rescue Infant Mice from Lethal Citrobacter rodentium Infection and Promote Immunity against Reinfection.	Diaz LA, Altman NH, Khan WN, Serhan CN, Adkins B.	Infect Immun	10.1128/iai.00464-17	2017
Metabolism	RNAseq studies reveal distinct transcriptional response to vitamin A deficiency in small intestine versus colon, uncovering novel vitamin A-regulated genes.	Chai Z, Lyu Y, Chen Q, Wei CH, Snyder LM, Weaver V, Sebastian A, Albert I, Li Q, Cantorna MT, Ross AC.	J Nutr Biochem	10.1016/j.jnutbio.2021.108814	2021
	DOCK2 confers immunity and intestinal colonization resistance to Citrobacter rodentium infection.	Liu Z, Man SM, Zhu Q, Vogel P, Frase S, Fukui Y, Kanneganti TD.	Sci Rep	10.1038/srep27814	2016
	Protamine cleavage specificity of the avian pathogen Escherichia coli OmpT reveals two substrate-binding sites related to virulence.	Liu J, Jiang L, Wang H, Wu J, Gao Q, Huan C, Gao S.	Front Vet Sci	10.3389/fvets.2024.1410113	2024
Metabolism	IRF8 Regulates Gram-Negative Bacteria-Mediated NLRP3 Inflammasome Activation and Cell Death.	Karki R, Lee E, Sharma BR, Banoth B, Kanneganti TD.	J Immunol	10.4049/jimmunol.1901508	2020
Metabolism	Exploring the Molecular Mechanisms Underlying the Protective Effects of Microbial SCFAs on Intestinal Tolerance and Food Allergy.	Luu M, Monning H, Visekruna A.	Front Immunol	10.3389/fimmu.2020.01225	2020
Pathogenicity	Screening of Anti-Adhesion Agents for Pathogenic Escherichia coli O157:H7 by Targeting the GrlA Activator.	Hong SY, Kim BS.	J Microbiol Biotechnol	10.4014/jmb.2207.07065	2023
Metabolism	Dendritic cell-derived nitric oxide inhibits the differentiation of effector dendritic cells.	Si C, Zhang R, Wu T, Lu G, Hu Y, Zhang H, Xu F, Wei P, Chen K, Tang H, Yeretssian G, Xiong H.	Oncotarget	10.18632/oncotarget.11361	2016
	Cutting Edge: Check Your Mice-A Point Mutation in the Ncr1 Locus Identified in CD45.1 Congenic Mice with Consequences in Mouse Susceptibility to Infection.	Jang Y, Gerbec ZJ, Won T, Choi B, Podsiad A, B Moore B, Malarkannan S, Laouar Y.	J Immunol	10.4049/jimmunol.1701676	2018
Phylogeny	Microbiome analysis in women with endometriosis: Does a microbiome exist in peritoneal fluid and ovarian cystic fluid?	Oishi S, Mekaru K, Tanaka SE, Arai W, Ashikawa K, Sakuraba Y, Nishioka M, Nakamura R, Miyagi M, Akamine K, Aoki Y.	Reprod Med Biol	10.1002/rmb2.12441	2022
	Artificial intelligence-rationalized balanced PPARalpha/gamma dual agonism resets dysregulated macrophage processes in inflammatory bowel disease.	Katkar GD, Sayed IM, Anandachar MS, Castillo V, Vidales E, Toobian D, Usmani F, Sawires JR, Leriche G, Yang J, Sandborn WJ, Das S, Sahoo D, Ghosh P.	Commun Biol	10.1038/s42003-022-03168-4	2022
	Intestinal and Mucosal Microbiome Response to Oral Challenge of Enterotoxigenic Escherichia coli in Weaned Pigs.	Peng SS, Li Y, Chen Q, Hu Q, He Y, Che L, Jiang PP.	Pathogens	10.3390/pathogens11020160	2022
Metabolism	Citrobacter rodentium infection induces MyD88-dependent formation of ubiquitinated protein aggregates in the intestinal epithelium.	Kaniuk NA, Lam GY, Ma C, Galindo-Mata E, Jones N, Vallance BA, Brumell JH.	J Innate Immun	10.1159/000320644	2011
	The Critical Role of Acyl Hydrocarbon Receptor on the Combined Benefits of Postbiotic Propionate on Active Vitamin D3-Orchestrated Innate Immunity in Salmonella Colitis.	Huang FC, Huang SC.	Biomedicines	10.3390/biomedicines11010195	2023
Pathogenicity	Microbiota-derived small molecule genotoxins: host interactions and ecological impact in the gut ecosystem.	Zechner EL, Kienesberger S.	Gut Microbes	10.1080/19490976.2024.2430423	2024
Pathogenicity	CD73 blockade alleviates intestinal inflammatory responses by regulating macrophage differentiation in ulcerative colitis.	Wang R, Wang Y, Wu C, Jin G, Zhu F, Yang Y, Wang Y, Zhou G.	Exp Ther Med	10.3892/etm.2023.11972	2023
	Dietary Chitosan Supplementation Increases Microbial Diversity and Attenuates the Severity of Citrobacter rodentium Infection in Mice.	Guan G, Wang H, Chen S, Liu G, Xiong X, Tan B, Duraipandiyan V, Al-Dhabi NA, Fang J.	Mediators Inflamm	10.1155/2016/9236196	2016
	Mucosal IgG in inflammatory bowel disease - a question of (sub)class?	Castro-Dopico T, Clatworthy MR.	Gut Microbes	10.1080/19490976.2019.1651596	2020
	Fcµ Receptor Promotes the Survival and Activation of Marginal Zone B Cells and Protects Mice against Bacterial Sepsis.	Liu J, Zhu H, Qian J, Xiong E, Zhang L, Wang YQ, Chu Y, Kubagawa H, Tsubata T, Wang JY.	Front Immunol	10.3389/fimmu.2018.00160	2018
	Bacteria That Cause Enteric Diseases Stimulate Distinct Humoral Immune Responses.	Amadou Amani S, Lang ML.	Front Immunol	10.3389/fimmu.2020.565648	2020
	The Use of Hypochlorous Acid, Test-and-removal, and Cross-fostering to Eradicate Mouse Pathogens in an Animal Facility.	Shih HY, Chen YC, Liao CF.	J Am Assoc Lab Anim Sci	10.30802/aalas-jaalas-22-000115	2023
	Quercetin Reduces Inflammation and Protects Gut Microbiota in Broilers.	Sun L, Guo L, Xu G, Li Z, Appiah MO, Yang L, Lu W.	Molecules	10.3390/molecules27103269	2022
Pathogenicity	A small-molecule inhibitor of the bacterial type III secretion system protects against in vivo infection with Citrobacter rodentium.	Kimura K, Iwatsuki M, Nagai T, Matsumoto A, Takahashi Y, Shiomi K, Omura S, Abe A.	J Antibiot (Tokyo)	10.1038/ja.2010.155	2011
	The Pivotal Role of Aryl Hydrocarbon Receptor-Regulated Tight Junction Proteins and Innate Immunity on the Synergistic Effects of Postbiotic Butyrate and Active Vitamin D3 to Defense against Microbial Invasion in Salmonella Colitis.	Huang FC, Huang SC.	Nutrients	10.3390/nu15020305	2023
	Indole derivatives, microbiome and graft versus host disease.	Qayed M, Michonneau D, Socie G, Waller EK.	Curr Opin Immunol	10.1016/j.coi.2021.02.006	2021
	Intestinal microbiota and metabolome perturbations in ischemic and idiopathic dilated cardiomyopathy.	Wang Y, Xie Y, Mahara G, Xiong Y, Xiong Y, Zheng Q, Chen J, Zhang W, Zhou H, Li Q.	J Transl Med	10.1186/s12967-023-04605-6	2024
Pathogenicity	A gut commensal bacterium promotes black soldier fly larval growth and development partly via modulation of intestinal protein metabolism.	Luo X, Fang G, Chen K, Song Y, Lu T, Tomberlin JK, Zhan S, Huang Y.	mBio	10.1128/mbio.01174-23	2023
	Immune chromatin reader SP140 regulates microbiota and risk for inflammatory bowel disease.	Fraschilla I, Amatullah H, Rahman RU, Jeffrey KL.	Cell Host Microbe	10.1016/j.chom.2022.08.018	2022
	Maintenance of caecal homeostasis by diverse adaptive immune cells in the rhesus macaque.	Castro Dopico X, Guryleva M, Mandolesi M, Corcoran M, Coquet JM, Murrell B, Karlsson Hedestam GB.	Clin Transl Immunology	10.1002/cti2.1508	2024
	Serological and molecular epidemiology of leptospirosis and the role of dogs as sentinel for human infection in Nigeria.	Pilau NN, Lubar AA, Daneji AI, Mera UM, Magaji AA, Abiayi EA, Chaiboonma KL, Busayo EI, Vinetz JM, Matthias MA.	Heliyon	10.1016/j.heliyon.2022.e09484	2022
	Blocking GARP-mediated activation of TGF-beta1 did not alter innate or adaptive immune responses to bacterial infection or protein immunization in mice.	Gaignage M, Zhang X, Stockis J, Dedobbeleer O, Michiels C, Cochez P, Dumoutier L, Coulie PG, Lucas S.	Cancer Immunol Immunother	10.1007/s00262-021-03119-8	2022
	SRC2 controls CD4⁺ T cell activation via stimulating c-Myc-mediated upregulation of amino acid transporter Slc7a5.	Zhang W, Cao X, Cao X, Zhong X, Wu H, Shi Y, Feng M, Wang YC, Ann D, Gwack Y, Yuan YC, Shang W, Sun Z.	Proc Natl Acad Sci U S A	10.1073/pnas.2221352120	2023
	The IRE1alpha/XBP1 pathway sustains cytokine responses of group 3 innate lymphoid cells in inflammatory bowel disease.	Cao S, Fachi JL, Ma K, Ulezko Antonova A, Wang Q, Cai Z, Kaufman RJ, Ciorba MA, Deepak P, Colonna M.	J Clin Invest	10.1172/jci174198	2024
	Modulation of colonic immunometabolic responses during Clostridioides difficile infection ameliorates disease severity and inflammation.	Tubau-Juni N, Bassaganya-Riera J, Leber AJ, Alva SS, Baker R, Hontecillas R.	Sci Rep	10.1038/s41598-023-41847-2	2023
Metabolism	Discovery of an archetypal protein transport system in bacterial outer membranes.	Selkrig J, Mosbahi K, Webb CT, Belousoff MJ, Perry AJ, Wells TJ, Morris F, Leyton DL, Totsika M, Phan MD, Celik N, Kelly M, Oates C, Hartland EL, Robins-Browne RM, Ramarathinam SH, Purcell AW, Schembri MA, Strugnell RA, Henderson IR, Walker D, Lithgow T.	Nat Struct Mol Biol	10.1038/nsmb.2261	2012
	Activator-induced conformational changes regulate division-associated peptidoglycan amidases.	Cook J, Baverstock TC, McAndrew MBL, Roper DI, Stansfeld PJ, Crow A.	Proc Natl Acad Sci U S A	10.1073/pnas.2302580120	2023
	Temporary consumption of western diet trains the immune system to reduce future gut inflammation.	Wu D, Wang X, Yang X, Gu L, McGeachy MJ, Liu X.	iScience	10.1016/j.isci.2023.106915	2023
Pathogenicity	Cytochrome P450 1A1 is essential for the microbial metabolite, Urolithin A-mediated protection against colitis.	Ghosh S, Moorthy B, Haribabu B, Jala VR.	Front Immunol	10.3389/fimmu.2022.1004603	2022
	Intestinal microbiota-derived short-chain fatty acids regulation of immune cell IL-22 production and gut immunity.	Yang W, Yu T, Huang X, Bilotta AJ, Xu L, Lu Y, Sun J, Pan F, Zhou J, Zhang W, Yao S, Maynard CL, Singh N, Dann SM, Liu Z, Cong Y.	Nat Commun	10.1038/s41467-020-18262-6	2020
	Microalgae-based Intestinal villi-targeting multistage biosystem for irritable bowel syndrome treatment	Ye J, Sun H, Zhang Q, He J, Zhou M.	Nat Commun		2025
	Impact of IBD-Associated Dysbiosis on Bacterial Quorum Sensing Mediated by Acyl-Homoserine Lactone in Human Gut Microbiota.	Grellier N, Suzuki MT, Brot L, Rodrigues AMS, Humbert L, Escoubeyrou K, Rainteau D, Grill JP, Lami R, Seksik P.	Int J Mol Sci	10.3390/ijms232315404	2022
Genetics	Colicins and T6SS-based competition systems enhance enterotoxigenic E. coli (ETEC) competitiveness.	Kjellin J, Lee D, Steinsland H, Dwane R, Barth Vedoy O, Hanevik K, Koskiniemi S.	Gut Microbes	10.1080/19490976.2023.2295891	2024
	Spontaneous Loss-of-Function Dock2 Mutation Alters Murine Colitis Sensitivity and Is a Confounding Variable in Inflammatory Bowel Disease Research.	Peters DE, Norris LD, Slusher BS.	Crohns Colitis 360	10.1093/crocol/otz030	2019
	From Gut to Blood: Spatial and Temporal Pathobiome Dynamics during Acute Abdominal Murine Sepsis.	Hartwig C, Drechsler S, Vainshtein Y, Maneth M, Schmitt T, Ehling-Schulz M, Osuchowski M, Sohn K.	Microorganisms	10.3390/microorganisms11030627	2023
	Gut microbiota links to cognitive impairment in bipolar disorder via modulating synaptic plasticity	Tang A, Jiang H, Li J, Chen Y, Zhang J, Wang D, Hu S, Lai J.	BMC Med		2025
Metabolism	Intestinal tryptophan metabolism in disease prevention and swine production.	Hu Z, Feng L, Jiang Q, Wang W, Tan B, Tang X, Yin Y.	Anim Nutr	10.1016/j.aninu.2023.08.002	2023
Metabolism	Non-canonical inflammasome activation targets caspase-11.	Kayagaki N, Warming S, Lamkanfi M, Vande Walle L, Louie S, Dong J, Newton K, Qu Y, Liu J, Heldens S, Zhang J, Lee WP, Roose-Girma M, Dixit VM.	Nature	10.1038/nature10558	2011
	Porcine Interleukin-17 and 22 Co-Expressed by Yarrowia lipolytica Enhance Immunity and Increase Protection against Bacterial Challenge in Mice and Piglets	Peng J, Yang F, Chen J, Guo S, Zhang L, Deng D, Li J, Lv X, Gao R.	Biology (Basel)	10.3390/biology11121747	2022
Phylogeny	Gut Microbiota and Sunitinib-Induced Diarrhea in Metastatic Renal Cell Carcinoma: A Pilot Study.	Su Z, Lu L, Chen F, Chen J, Chen X.	Cancer Manag Res	10.2147/cmar.s328451	2021
Pathogenicity	Shigella type-III secretion system effectors counteract the induction of host inflammation and cell death.	Ashida H, Okano T, Iida T, Onsoi P, Sasakawa C, Suzuki T.	EMBO J	10.1038/s44318-025-00561-7	2025
Pathogenicity	Bicarbonate-mediated stimulation of RegA, the global virulence regulator from Citrobacter rodentium.	Yang J, Dogovski C, Hocking D, Tauschek M, Perugini M, Robins-Browne RM.	J Mol Biol	10.1016/j.jmb.2009.10.033	2009
	Unraveling the Molecular Mechanisms of Fructus Anisi Stellati as a Remedy for Infantile Colic by Network Pharmacology.	Li X, Xu Y.	Evid Based Complement Alternat Med	10.1155/2020/9210304	2020
Metabolism	IL-36R signaling integrates innate and adaptive immune-mediated protection against enteropathogenic bacteria.	Ngo VL, Abo H, Kuczma M, Szurek E, Moore N, Medina-Contreras O, Nusrat A, Merlin D, Gewirtz AT, Ignatowicz L, Denning TL.	Proc Natl Acad Sci U S A	10.1073/pnas.2004484117	2020
	Standardized Complex Gut Microbiomes Influence Fetal Growth, Food Intake, and Adult Body Weight in Outbred Mice.	Cheatham CN, Gustafson KL, McAdams ZL, Turner GM, Dorfmeyer RA, Ericsson AC.	Microorganisms	10.3390/microorganisms11020484	2023
	The Assembly of Flagella in Enteropathogenic Escherichia coli Requires the Presence of a Functional Type III Secretion System.	Soria-Bustos J, Saldana-Ahuactzi Z, Samadder P, Yanez-Santos JA, Laguna YM, Cedillo-Ramirez ML, Giron JA.	Int J Mol Sci	10.3390/ijms232213705	2022
	Brain-gut interactions increase peripheral nociceptive signaling in mice with postinfectious irritable bowel syndrome.	Ibeakanma C, Ochoa-Cortes F, Miranda-Morales M, McDonald T, Spreadbury I, Cenac N, Cattaruzza F, Hurlbut D, Vanner S, Bunnett N, Vergnolle N, Vanner S.	Gastroenterology	10.1053/j.gastro.2011.08.006	2011
Metabolism	Chlamydia muridarum Alleviates Colitis via the IL-22/Occludin Signal Pathway.	Wang X, Zeng HC, Huang YR, He QZ.	Biomed Res Int	10.1155/2020/8894331	2020
Proteome	Differential Impact of Hexuronate Regulators ExuR and UxuR on the Escherichia coli Proteome.	Bessonova TA, Fando MS, Kostareva OS, Tutukina MN, Ozoline ON, Gelfand MS, Nikulin AD, Tishchenko SV.	Int J Mol Sci	10.3390/ijms23158379	2022
	Rhubarb extract rebuilding the mucus homeostasis and regulating mucin-associated flora to relieve constipation.	Gao H, He C, Xin S, Hua R, Du Y, Wang B, Gong F, Yu X, Pan L, Liang C, Gao L, Shang H, Xu JD.	Exp Biol Med (Maywood)	10.1177/15353702231211859	2023
Metabolism	Stressor-Induced Increases in Circulating, but Not Colonic, Cytokines Are Related to Anxiety-like Behavior and Hippocampal Inflammation in a Murine Colitis Model.	Maltz RM, Marte-Ortiz P, Rajasekera TA, Loman BR, Gur TL, Bailey MT.	Int J Mol Sci	10.3390/ijms23042000	2022
Genetics	Complete Genome Sequence of the Type Strain Citrobacter rodentium DSM 16636.	Wahl A, Neuhaus K	Microbiol Resour Announc	10.1128/mra.01237-21	2022
Metabolism	Genetic and biochemical characterization of Citrobacter rodentium sp. nov.	Schauer DB, Zabel BA, Pedraza IF, O'Hara CM, Steigerwalt AG, Brenner DJ.	J Clin Microbiol	10.1128/jcm.33.8.2064-2068.1995	1995
	Safety evaluation of Akkermansia massiliensis sp. nov. DSM 33459.	Pitt J, Bauter MR, Kumar R, Hasselwander O, Hibberd AA, Kane H, Wang Q, Auzanneau I, Bry S, David E, Seguinot P, Burns F, Smith AB.	Toxicol Rep	10.1016/j.toxrep.2025.102042	2025
Phylogeny	Superficieibacter electus gen. nov., sp. nov., an Extended-Spectrum beta-Lactamase Possessing Member of the Enterobacteriaceae Family, Isolated From Intensive Care Unit Surfaces.	Potter RF, D'Souza AW, Wallace MA, Shupe A, Patel S, Gul D, Kwon JH, Beatty W, Andleeb S, Burnham CD, Dantas G	Front Microbiol	10.3389/fmicb.2018.01629	2018

References

#6539	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16636
#20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#38514	; Curators of the CIP;
#50275	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 30795
#66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68368	Automatically annotated from API 20E .
#68382	Automatically annotated from API zym .
#122246	Collection of Institut Pasteur ; Curators of the CIP; CIP 104675
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Citrobacter rodentium (DSM 16636, ATCC 51116, CDC 1843-73)

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