Escherichia fergusonii (DSM 13698, ATCC 35469, CDC 0568-73)

Name: Escherichia fergusonii (DSM 13698, ATCC 35469, CDC 0568-73)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 4930

Type strain

Strain Designation 568-73

Culture col. no. DSM 13698 ATCC 35469 CDC 0568-73 CCUG 18766 NCTC 12128 7 more

NCBI tax ID(s) 585054 564

Special Collections DSMZ CCUG JCM CIP

History <- ATCC <- CDC <- Missouri State Health Dept. IAM 14443 <-- ATCC 35469 <-- CDC 0568-73 <-- Missouri State Health Dept., USA. CIP <- 1996, PAD Grimont, Inst. Pasteur, Paris, France <- CDC: strain 568-73 <- Missouri State Hlth. Dept.

Links

Escherichia fergusonii 568-73 is a facultative anaerobe, Gram-negative, motile human pathogen that was isolated from faeces of 1-year-old boy.

Gram-negative motile rod-shaped facultative anaerobe human pathogen genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 2807

LMG 7866,ATCC 35469,CCUG 18766,DSM 13698,CIP 104947,CIP 103357,NCTC 12128,BCRC 15582,CCRC 15582,IAM 14443,NBRC 102419,JCM 21226

@ref 20215

Last LPSN update 2026-02-09 11:18:50

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Enterobacterales

Family Enterobacteriaceae

Genus Escherichia

Species Escherichia fergusonii

Full scientific name Escherichia fergusonii Farmer et al. 1985

BacDive ID	Other strains from **Escherichia fergusonii** (24)	Type strain
4931	E. fergusonii Ef137, DSM 25831
137175	E. fergusonii 3296-73, CIP 104948, ATCC 35470
143723	E. fergusonii CCUG 21144
143724	E. fergusonii CCUG 21145
143725	E. fergusonii CCUG 21146
143726	E. fergusonii CCUG 21147
143768	E. fergusonii CCUG 21203
143769	E. fergusonii CCUG 21204
145930	E. fergusonii CCUG 29925
145931	E. fergusonii CCUG 29926
145932	E. fergusonii CCUG 29927
145933	E. fergusonii CCUG 29928
145934	E. fergusonii CCUG 29929
145935	E. fergusonii CCUG 29930
145936	E. fergusonii CCUG 29931
145937	E. fergusonii CCUG 29932
145938	E. fergusonii CCUG 29933
145939	E. fergusonii CCUG 29934
145940	E. fergusonii CCUG 29935
145941	E. fergusonii CCUG 29936
145942	E. fergusonii CCUG 29937
145943	E. fergusonii CCUG 29938
165317	E. fergusonii JCM 5897, ATCC 35471, CDC 1016-74
165318	E. fergusonii JCM 5899, ATCC 35473, CDC 3458-74

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility	Confidence
119305	negative	rod-shaped
125438	negative			99.75

Colony morphology

119305

Hemolysis ability1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
5121	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
5121	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
39147	MEDIUM 3 - Columbia agar		Columbia agar (39.000 g);distilled water (1000.000 ml)
119305	CIP Medium 3	Medium recipe at CIP
119305	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
5121	positive	growth	37
39147	positive	growth	30
67770	positive	growth	30
119305	positive	growth	5-41

Physiology and metabolism

Oxygen tolerance

119305

Oxygen tolerancefacultative anaerobe

Spore formation

@ref	Spore formation	Confidence
125439		92.6

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
68371	17057 ChEBI	cellobiose	+	builds acid from	from API 50CH acid
119305	16947 ChEBI	citrate	-	carbon source
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	+	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16988 ChEBI	D-ribose	+	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68371	65327 ChEBI	D-xylose	+	builds acid from	from API 50CH acid
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
119305	4853 ChEBI	esculin	+	hydrolysis
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	+	builds acid from	from API 50CH acid
119305	17234 ChEBI	glucose	+	fermentation
119305	17234 ChEBI	glucose	+	degradation
68371	28087 ChEBI	glycogen	-	builds acid from	from API 50CH acid
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	30849 ChEBI	L-arabinose	+	builds acid from	from API 50CH acid
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	-	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	+	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
119305	17716 ChEBI	lactose	-	fermentation
119305	15792 ChEBI	malonate	+	assimilation
68371	17306 ChEBI	maltose	+	builds acid from	from API 50CH acid
119305	29864 ChEBI	mannitol	+	fermentation
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68371	59640 ChEBI	N-acetylglucosamine	+	builds acid from	from API 50CH acid
119305	17632 ChEBI	nitrate	+	reduction
119305	16301 ChEBI	nitrite	-	reduction
68371		Potassium 2-ketogluconate	+	builds acid from	from API 50CH acid
68371		Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
119305	132112 ChEBI	sodium thiosulfate	-	builds gas from
68371	28017 ChEBI	starch	-	builds acid from	from API 50CH acid
68371	17992 ChEBI	sucrose	-	builds acid from	from API 50CH acid
68371	27082 ChEBI	trehalose	+	builds acid from	from API 50CH acid
68371	32528 ChEBI	turanose	-	builds acid from	from API 50CH acid
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
119305	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
119305	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
119305	15688 ChEBI	acetoin	-
119305	17234 ChEBI	glucose		+

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
119305	alcohol dehydrogenase	-	1.1.1.1
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
68382	beta-galactosidase	+	3.2.1.23	from API zym
119305	beta-galactosidase	+	3.2.1.23
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
119305	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
119305	gelatinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
119305	lysine decarboxylase	+	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
119305	ornithine decarboxylase	+	4.1.1.17
119305	oxidase	-
119305	phenylalanine ammonia-lyase	-	4.3.1.24
68382	trypsin	-	3.4.21.4	from API zym
119305	tryptophan deaminase	-
119305	urease	-	3.5.1.5
68382	valine arylamidase	-		from API zym

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
119305	-	+	+	+	-	+	-	-	-	-	+	+	-	+	-	+	-	-	-	-

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
119305	not determinedn.d.	+/-	-	-	+	+	+	-	+/-	-	+/-	+/-	+/-	+/-	-	+	-	-	+/-	-	-	-	+	-	+/-	+/-	+/-	+	+	+/-	+/-	-	+	-	-	+/-	-	-	-	+/-	-	-	-	-	-	+	-	+	+	-

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
119305	not determinedn.d.	+	+	+	+	-	-	-	-	-	+	-	-	-	-	-	+	-	+	-	+	+	+	-	+	-	-	+	-	-	-	-	+	-	+	-	-	-	+	-	-	+	-	-	+	+	-	-	-	-	+	-	-	-	-	+	+	+	-	-	+	+	+	+	-	-	-	-	+	-	-	-	-	-	-	-	+	-	-	-	+	+	-	-	-	-	-	+	-	-	+	+	+	+	+	+	-	+	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Infection	#Patient	-
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)
#Host	#Human	#Child

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
5121	faeces of 1-year-old boy	Missouri	USA	USA	North America
46882	Feces,1-yr-old boy		USA	USA	North America
67770	Human stool
119305	Human, Child, feces	Michigan	United States of America	USA	North America

Taxonmaps

69479

Global distribution of 16S sequence AF530475 (>99% sequence identity) for Enterobacteriaceae from Microbeatlas

Aquatic Samples	5613
Soil Samples	2111
Animal Samples	88071
Plant Samples	1835
Total Samples	97630

Interaction and safety

Risk assessment

@ref	Pathogenicity human	Pathogenicity animal	Biosafety level	Biosafety level comment
5121			2	Risk group (German classification) According to TRBA 466
119305			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	Escherichia fergusonii strain FDAARGOS_1499	complete		564.336		564	98.71
66792	Escherichia fergusonii strain FDAARGOS_1499	complete		564.246		564	98.71
66792	Escherichia fergusonii strain FDAARGOS_1499	complete		564.285		564	98.71
124043	ASM2009747v1 assembly for Escherichia fergusonii FDAARGOS_1499	complete	GCA_020097475	564.206	8120691386	564	98.15
66792	ASM2622v1 assembly for Escherichia fergusonii ATCC 35469 ATCC 35469T	complete	GCA_000026225	585054.5	643692022	585054	96.77
67770	28869_D01 assembly for Escherichia fergusonii NCTC12128	contig	GCA_900450565	564.28	8117503729	564	46.92

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Escherichia fergusonii 16S ribosomal RNA gene, partial sequence	AF530475	1473	585054
20218	Escherichia fergusonii gene for 16S rRNA, partial sequence, strain: NBRC 102419	AB681775	1467	564
67770	Escherichia fergusonii strain ATCC 35469 16S ribosomal RNA gene, partial sequence	KP941767	882	564
124043	Escherichia fergusonii ATCC 35469 gene for 16S rRNA, partial sequence.	LC752358	587	585054
124043	Escherichia fergusonii ATCC 35469 16S ribosomal RNA gene, partial sequence.	OR660252	1092	585054
124043	Escherichia fergusonii ATCC 35469 16S ribosomal RNA gene, partial sequence.	PP858996	717	585054
124043	Escherichia fergusonii ATCC 35469 16S ribosomal RNA gene, partial sequence.	PP858826	703	585054
124043	Escherichia fergusonii strain BIU GLSF10 16S ribosomal RNA gene, partial sequence.	MN544280	410	564
124043	Escherichia fergusonii ATCC 35469 16S ribosomal RNA gene, partial sequence.	PP858976	767	585054
124043	Escherichia fergusonii ATCC 35469 16S ribosomal RNA gene, partial sequence.	PP859347	730	585054
124043	Escherichia fergusonii ATCC 35469 16S ribosomal RNA gene, partial sequence.	PP858409	715	585054
124043	Escherichia fergusonii ATCC 35469 16S ribosomal RNA gene, partial sequence.	PP859339	727	585054
124043	Escherichia fergusonii ATCC 35469 16S ribosomal RNA gene, partial sequence.	PQ373115	731	585054
124043	Escherichia fergusonii ATCC 35469 16S ribosomal RNA gene, partial sequence.	PP859293	715	585054
124043	Escherichia fergusonii ATCC 35469 16S ribosomal RNA gene, partial sequence.	PP858831	728	585054
124043	Escherichia fergusonii strain ATCC -35469 16S ribosomal RNA gene, partial sequence.	MN587901	1108	564
124043	Escherichia fergusonii ATCC 35469 16S ribosomal RNA gene, partial sequence.	MT940977	1050	585054
124043	Escherichia fergusonii ATCC 35469 16S ribosomal RNA gene, partial sequence.	MW012853	1399	585054
124043	Escherichia fergusonii ATCC 35469 16S ribosomal RNA gene, partial sequence.	PP859012	732	585054
124043	Escherichia fergusonii ATCC 35469 16S ribosomal RNA gene, partial sequence.	PP859362	563	585054

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Escherichia fergusonii ATCC 35469 ATCC 35469T
NCBI: GCA_000026225

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	92.60	no
125439	motility	BacteriaNetⓘ	no	50.60	no
125439	gram_stain	BacteriaNetⓘ	negative	88.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	88.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Escherichia fergusonii ATCC 35469 ATCC 35469T
NCBI: GCA_000026225.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.75	no
125438	anaerobic	anaerobicⓘ	no	96.91	no
125438	aerobic	aerobicⓘ	no	72.92	yes
125438	spore-forming	spore-formingⓘ	no	87.83	no
125438	thermophilic	thermophileⓘ	no	97.00	yes
125438	flagellated	motile2+ⓘ	yes	77.85	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	A new understanding of Acanthamoeba castellanii: dispelling the role of bacterial pore-forming toxins in cyst formation and amoebicidal actions.	Yabrag A, Ullah N, Baryalai P, Ahmad I, Zlatkov N, Toh E, Lindback T, Uhlin BE, Wai SN, Nadeem A.	Cell Death Discov	10.1038/s41420-025-02345-8	2025
	Development of a Droplet Digital Polymerase Chain Reaction for Rapid and Simultaneous Identification of Common Foodborne Pathogens in Soft Cheese.	Cremonesi P, Cortimiglia C, Picozzi C, Minozzi G, Malvisi M, Luini M, Castiglioni B.	Front Microbiol	10.3389/fmicb.2016.01725	2016
Phylogeny	Phylogenetic profiling: how much input data is enough?	Skunca N, Dessimoz C.	PLoS One	10.1371/journal.pone.0114701	2015
Enzymology	Multiplex detection of nine food-borne pathogens by mPCR and capillary electrophoresis after using a universal pre-enrichment medium.	Villamizar-Rodriguez G, Fernandez J, Marin L, Muniz J, Gonzalez I, Lombo F.	Front Microbiol	10.3389/fmicb.2015.01194	2015
Phylogeny	Molecular Characterization and Antibiogram Profiling of Bacteria Isolated From Sewage and Surface Water in Bangladesh.	Polash MA, Islam MS, Zahan N, Sarker S, Haque MH.	Scientifica (Cairo)	10.1155/sci5/1848058	2025
Phylogeny	Gut microbiome profile to the level species in diarrheic protozoan-carrier patients in Italy.	Marangi M, Boughattas S, Benslimane F.	Life Sci	10.1016/j.lfs.2024.123182	2024
	Comprehensive analysis of Eimeria necatrix infection: From intestinal lesions to gut microbiota and metabolic disturbances.	Chen YM, Wei P, Liao HY, Tsai YW, Cheng MC, Lien YY.	Poult Sci	10.1016/j.psj.2025.105412	2025
	Dietary Methionine Restriction Alleviates Choline-Induced Tri-Methylamine-N-Oxide (TMAO) Elevation by Manipulating Gut Microbiota in Mice.	Lu M, Yang Y, Xu Y, Wang X, Li B, Le G, Xie Y.	Nutrients	10.3390/nu15010206	2023
Phylogeny	Identification of acacia gum fermenting bacteria from pooled human feces using anaerobic enrichment culture.	Rawi MH, Tan HY, Sarbini SR.	Front Microbiol	10.3389/fmicb.2023.1245042	2023
	Intestinal colonization with Escherichia fergusonii enhances infectivity of GII.12 human norovirus in gnotobiotic pigs.	Jung K, Wang Q, Chang KO, Saif LJ.	Virus Res	10.1016/j.virusres.2023.199219	2023
	Assembling the anaerobic gamma-butyrobetaine to TMA metabolic pathway in Escherichia fergusonii and confirming its role in TMA production from dietary L-carnitine in murine models.	Dwidar M, Buffa JA, Wang Z, Santos A, Tittle AN, Fu X, Hajjar AM, DiDonato JA, Hazen SL.	mBio	10.1128/mbio.00937-23	2023
	Identification of a genomic cluster related to hypersecretion of intestinal mucus and mucinolytic activity of atypical enteropathogenic Escherichia coli (aEPEC).	Trovao LO, Vieira MAM, Santos ACM, Puno-Sarmiento JJ, Nunes PHS, Santos FF, Rocha VGP, Knobl T, Navarro-Garcia F, Gomes TAT.	Front Cell Infect Microbiol	10.3389/fcimb.2024.1393369	2024
	Enhanced Antibiotic Tolerance of an In Vitro Multispecies Uropathogen Biofilm Model, Useful for Studies of Catheter-Associated Urinary Tract Infections.	Hou J, Wang L, Alm M, Thomsen P, Monsen T, Ramstedt M, Burmolle M.	Microorganisms	10.3390/microorganisms10061207	2022
	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
	Outer Membrane Porin F in E. coli Is Critical for Effective Predation by Bdellovibrio.	Mun W, Upatissa S, Lim S, Dwidar M, Mitchell RJ.	Microbiol Spectr	10.1128/spectrum.03094-22	2022
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Phylogeny	Deciphering Bacterial Community Succession and Pathogen Dynamics in ICU Ventilator Circuits Through Full-Length 16S rRNA Sequencing for Mitigating the Risk of Nosocomial Infections.	Tsai HC, Chen JS, Hsu GJ, Hussain B, Lin IC, Hsu TK, Han J, Huang SW, Wu CC, Hsu BM.	Microorganisms	10.3390/microorganisms13091982	2025
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Genetics	Genomic Dissection of an Enteroaggregative Escherichia coli Strain Isolated from Bacteremia Reveals Insights into Its Hybrid Pathogenic Potential.	Del Carpio AMG, Freire CA, Andrade FB, Piazza RMF, Silva RM, Carvalho E, Elias WP.	Int J Mol Sci	10.3390/ijms25179238	2024
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Pathogenicity	Appelmans protocol - A directed in vitro evolution enables induction and recombination of prophages with expanded host range.	Vu TN, Clark JR, Jang E, D'Souza R, Nguyen LP, Pinto NA, Yoo S, Abadie R, Maresso AW, Yong D.	Virus Res	10.1016/j.virusres.2023.199272	2024
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Genetics	Extended Spectrum Beta-Lactamase-Producing Gram-Negative Bacteria Recovered From an Amazonian Lake Near the City of Belém, Brazil.	Freitas DY, Araujo S, Folador ARC, Ramos RTJ, Azevedo JSN, Tacao M, Silva A, Henriques I, Barauna RA.	Front Microbiol	10.3389/fmicb.2019.00364	2019
Genetics	Distribution and genomic characterization of tigecycline-resistant tet(X4)-positive Escherichia coli of swine farm origin.	Li Y, Wang Q, Peng K, Liu Y, Xiao X, Mohsin M, Li R, Wang Z.	Microb Genom	10.1099/mgen.0.000667	2021
Genetics	Specificities and Commonalities of Carbapenemase-Producing Escherichia coli Isolated in France from 2012 to 2015.	Patino-Navarrete R, Rosinski-Chupin I, Cabanel N, Zongo PD, Hery M, Oueslati S, Girlich D, Dortet L, Bonnin RA, Naas T, Glaser P.	mSystems	10.1128/msystems.01169-21	2022
Genetics	Survey and Sequence Characterization of Bovine Mastitis-Associated Escherichia coli in Dairy Herds.	Alawneh JI, Vezina B, Ramay HR, Al-Harbi H, James AS, Soust M, Moore RJ, Olchowy TWJ.	Front Vet Sci	10.3389/fvets.2020.582297	2020
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Genetics	Classification of a Hypervirulent Aeromonas hydrophila Pathotype Responsible for Epidemic Outbreaks in Warm-Water Fishes.	Rasmussen-Ivey CR, Hossain MJ, Odom SE, Terhune JS, Hemstreet WG, Shoemaker CA, Zhang D, Xu DH, Griffin MJ, Liu YJ, Figueras MJ, Santos SR, Newton JC, Liles MR.	Front Microbiol	10.3389/fmicb.2016.01615	2016
Metabolism	Bioremediation of a Common Product of Food Processing by a Human Gut Bacterium.	Wolf AR, Wesener DA, Cheng J, Houston-Ludlam AN, Beller ZW, Hibberd MC, Giannone RJ, Peters SL, Hettich RL, Leyn SA, Rodionov DA, Osterman AL, Gordon JI.	Cell Host Microbe	10.1016/j.chom.2019.09.001	2019
Genetics	The genome sequence of E. coli W (ATCC 9637): comparative genome analysis and an improved genome-scale reconstruction of E. coli.	Archer CT, Kim JF, Jeong H, Park JH, Vickers CE, Lee SY, Nielsen LK.	BMC Genomics	10.1186/1471-2164-12-9	2011
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Phylogeny	Variation of the ribosomal operon 16S-23S gene spacer region in representatives of Salmonella enterica subspecies.	Perez Luz S, Rodriguez-Valera F, Lan R, Reeves PR.	J Bacteriol	10.1128/jb.180.8.2144-2151.1998	1998
Enzymology	Intergeneric transfer and recombination of the 6-phosphogluconate dehydrogenase gene (gnd) in enteric bacteria.	Nelson K, Selander RK.	Proc Natl Acad Sci U S A	10.1073/pnas.91.21.10227	1994
Phylogeny	High-resolution microbial community reconstruction by integrating short reads from multiple 16S rRNA regions.	Amir A, Zeisel A, Zuk O, Elgart M, Stern S, Shamir O, Turnbaugh PJ, Soen Y, Shental N.	Nucleic Acids Res	10.1093/nar/gkt1070	2013
Genetics	Rapid determination of nucleotide content and its application to the study of genome structure.	Krane DE, Hartl DL, Ochman H.	Nucleic Acids Res	10.1093/nar/19.19.5181	1991
Enzymology	Phosphatase activity is a constant feature of all isolates of all major species of the family Enterobacteriaceae.	Satta G, Pompei R, Grazi G, Cornaglia G.	J Clin Microbiol	10.1128/jcm.26.12.2637-2641.1988	1988
	Bioinformatic characterization of the trimeric intracellular cation-specific channel protein family.	Silverio AL, Saier MH.	J Membr Biol	10.1007/s00232-011-9364-8	2011
	The evolution of insertion sequences within enteric bacteria.	Lawrence JG, Ochman H, Hartl DL.	Genetics	10.1093/genetics/131.1.9	1992
Metabolism	Evolution of coenzyme B12 synthesis among enteric bacteria: evidence for loss and reacquisition of a multigene complex.	Lawrence JG, Roth JR.	Genetics	10.1093/genetics/142.1.11	1996
	Insertion sequences.	Mahillon J, Chandler M.	Microbiol Mol Biol Rev	10.1128/mmbr.62.3.725-774.1998	1998
	Global phylogenetic analysis and emergence of carbapenem-resistant Escherichia fergusonii carrying blaNDM-5 in clinic	Wang X, Zhang Y, Sheng J, Zhou L, Yao J, Hu Y, Xu X, Yu Y, Li X.	One Health.		2025
	Global phylogenetic analysis and emergence of carbapenem-resistant Escherichia fergusonii carrying bla _NDM-5 in clinic.	Wang X, Zhang Y, Sheng J, Zhou L, Yao J, Hu Y, Xu X, Yu Y, Li X.	One Health	10.1016/j.onehlt.2025.101069	2025
	Characterisation of bla_NDM-5-bearing IncHI2 plasmid from Escherichia fergusonii in China.	Shi Y, Yang Y, Song Y, Zhu Y, Zhao G, Tang B.	J Glob Antimicrob Resist	10.1016/j.jgar.2025.03.008	2025
	Biofilm associated growth inhibition of XDR Escherichia fergusonii strain ACE12 isolated from soil.	Bhowmik B, Chowdhury A, Bhuiyan MNI, Afrin S, Sarkar R, Dey SS, Siddique S, Satter Miah MA.	Microb Pathog	10.1016/j.micpath.2025.107400	2025
	Mycogenic synthesis of silver nanoparticles using endophytic fungi and their characterization, biological activities, including in-silico studies with special reference to Fusarium wilt of tomato.	Jana S, Das D, Bhattacharyya S, Raha S.	Fungal Biol	10.1016/j.funbio.2025.101610	2025
Genetics	Aetiology and environmental factors of the Watery Mouth Disease associated with neonatal diarrhoea in lambs.	Canete-Reyes A, Gonzalez JG, Alteio LV, Rodriguez-Lazaro D, Hernandez M.	Vet Microbiol	10.1016/j.vetmic.2025.110542	2025
	Adenylate kinase gene polymerase chain reaction-restriction fragment length polymorphism to differentiate Escherichia coli, Escherichia fergusonii, and Citrobacter freundii: a molecular diagnostic study.	Dahal RH, Choi YJ, Kim B, Rana MS, Shin JH, Kim J, Kim S.	J Yeungnam Med Sci	10.12701/jyms.2025.42.52	2025
	Investigating the virulence-associated genes and antimicrobial resistance of Escherichia fergusonii Isolated from diseased ostrich chicks.	Torkan A, Askari Badouei M.	Comp Immunol Microbiol Infect Dis	10.1016/j.cimid.2024.102226	2024
	Occurrence of Antibiotic-Resistant Bacteria in Urban Surface Water Sources in Bangladesh.	Islam MMM, Islam MA, Neela FA, Hasanuzzaman AFM.	Curr Microbiol	10.1007/s00284-025-04082-8	2025
	Effect of tannin-degrading bacteria isolated from the rumen of some ruminants on the in vitro digestibility and gas production of fruits residues silage.	Gheibipour M, Ghiasi SE, Vaghar Seyedin SM, Zeidi A, Motamedi H.	Vet Res Forum	10.30466/vrf.2025.2038543.4405	2025
Enzymology	Isolation and characterization of novel cadmium-resistant Escherichia fergusonii ZSF-15 from industrial effluent for flocculant production and antioxidant enzyme activity.	Zafar S, Ashraf A, Hayat S, Siddique MH, Waseem M, Hassan M, Qaisar H, Muzammil S.	Environ Monit Assess	10.1007/s10661-024-12545-x	2024
Genetics	Isolation and whole-genome sequencing analysis of Escherichia fergusonii harboring a heat-labile enterotoxin gene from retail chicken meat in Okinawa, Japan.	Kakita T, Lee K, Morita M, Okuno M, Kyan H, Okano S, Maeshiro N, Ishizu M, Kudeken T, Taira H, Teruya M, Ogura Y, Akeda Y, Ohnishi M.	Microbiol Immunol	10.1111/1348-0421.13115	2024
Phylogeny	Assessing the impact of broiler genotype on cecal and tracheal microbiome composition using full-length 16S rRNA sequencing.	Poudel S, Rahman FA, Granados EAF, Adhikari Y, Naeem M, Rochell SJ, Bourassa D.	Poult Sci	10.1016/j.psj.2025.106072	2025
	Lipopolysaccharide-producing Veillonella infantium and Escherichia fergusonii cause vagus nerve-mediated cognitive impairment in mice.	Ma X, Kim JK, Shin YJ, Park HS, Lee DY, Yim SV, Kim DH.	Brain Behav Immun	10.1016/j.bbi.2024.02.031	2024
Genetics	Metagenomic Analysis of Biliary Microbial Flora in Patients with Gallbladder Cancer or Gallstones-Associated Chronic Cholecystitis.	Shukla R, Tsuchiya Y, Behari A, Ikoma T, Nakamura K, Kapoor VK.	Cancer Invest	10.1080/07357907.2024.2361305	2024
Biotechnology	Microbiological quality assessment of Clarias gariepinus, Bagrus bajad, and Pangasianodon hypophthalmus fillets.	El-Gendy NM, Amer A, Ibrahim HA, Abou-Okada M.	Sci Rep	10.1038/s41598-024-62730-8	2024
Phylogeny	Molecular diagnosis of hen eggs microbiota.	Al-Hejin AM, Ahmed MMM, Alattasa SG, Al Karaim S.	Cell Mol Biol (Noisy-le-grand)	10.14715/cmb/2024.70.5.6	2024
Enzymology	Modified DNA substrate selectivity by GmrSD-family Type IV restriction enzyme BrxU.	Readshaw JJ, Lee YJ, Weigele P, Blower TR.	Philos Trans R Soc Lond B Biol Sci	10.1098/rstb.2024.0072	2025
	Eco-friendly silver nanoparticles from garlic: a novel therapeutic approach for treating Escherichia fergusonii wound infections.	Abdelkhalig SM, Ali AG, Ghaly MF, Alharbi NK, Alharbi M, Bendary MM, Abousaty AI.	Front Cell Infect Microbiol	10.3389/fcimb.2025.1604507	2025
	Preliminary Study to Understand the Role of Gut Microbiota in Coronary Slow Flow Phenomenon (CSFP).	Gurol T, Karaman T, Gurol Y, Sezerman OU, Oktem Okullu S.	Metabolites	10.3390/metabo15070475	2025
Phylogeny	Dynamic changes in the gut microbiota after bismuth quadruple therapy and high-dose dual therapy for Helicobacter pylori eradication.	Chen J, Zhang Y, Min H, Zhi J, Ma S, Dong H, Yan J, Chi X, Zhang X, Yang Y.	Helicobacter	10.1111/hel.13077	2024
	Complete genomic analysis of Escherichia phage Mangalyan infecting Escherichia fergusonii.	Manohar P, Young R.	Microbiol Resour Announc	10.1128/mra.00963-23	2024
Phylogeny	Qualitative detection of E. coli in distributed drinking water using real-time reverse transcription PCR targeting 16S rRNA: Validation and practical experiences.	Heijnen L, de Vries HJ, van Pelt G, Stroobach E, Atsma A, Vranken J, De Maeyer K, Vissers L, Medema G.	Water Res	10.1016/j.watres.2024.121843	2024
	The Spread of Heat-Labile Enterotoxin-Harboring Escherichia fergusonii in Broiler Chickens and Pigs in Okinawa, Japan.	Kakita T, Kudeken T, Taira H, Okano S, Kyan H, Ohnishi M.	Jpn J Infect Dis	10.7883/yoken.jjid.2022.625	2023
	Differential Cytotoxic Effects of Cell-Free Supernatants of Emerging Pathogens Escherichia albertii and Escherichia fergusonii on Four Cell Lines Reveal Vero Cells as a Putative Candidate for Cytotoxicity Analysis.	Srinivas K, Ghatak S, Puro KU, Hussain Z, Prasad MCB, Milton AAP, Pakyntein CL, Bhargavi D, Das S, Angappan M, Lyngdoh V, Khan S, Kader NA, Ramshon U.	Microorganisms	10.3390/microorganisms12112370	2024
Phylogeny	The variation of gut microbiota in captive Sichuan golden snub-nosed monkeys (Rhinopithecus roxellana) from infancy to adulthood.	Chen R, Liu X, Wang S, Guo L, Li M, Xu X, Lv R, Hong L, Wang G, Deng C, Sun W, Liu G.	Front Vet Sci	10.3389/fvets.2025.1683047	2025
	Prophylactic application of vaginal lactic acid bacteria against urogenital pathogens and its prospective use in sanitary suppositories.	Das S, Konwar BK.	Int Microbiol	10.1007/s10123-023-00376-8	2024
Biotechnology	Prevalence of extended-spectrum beta-lactamase-producing Enterobacterales in edible ice in Thailand.	Amornchai P, Wuthiekanun V, Langla S, Wongsuvan G, Aramrueang P, Day NPJ, Limmathurotsakul D.	Int Health	10.1093/inthealth/ihae050	2025
	Intestinal microecological transplantation for a patient with chronic radiation enteritis: A case report.	Wang L, Li Y, Zhang YJ, Peng LH.	World J Gastroenterol	10.3748/wjg.v30.i19.2603	2024
	Microbiological quality, antibiotic resistant bacteria and relevant resistance genes in ready-to-eat Pacific oysters (Magallana gigas).	Guedes B, Godinho O, Lage OM, Quinteira S.	FEMS Microbiol Lett	10.1093/femsle/fnad053	2023
	Prenatal depression-associated gut microbiota induces depressive-like behaviors and hippocampal neuroinflammation in germ-free mice.	Cao Y, Fan X, Zang T, Qiu T, Fang Q, Bai J, Liu Y.	Transl Psychiatry	10.1038/s41398-025-03606-x	2025
Genetics	Emergence of plasmid-mediated tigecycline resistance gene, tet(X4), in Escherichia fergusonii from pigs.	Guan C, Tang B, Yang H, Ma J, Huang Y, Liu C.	J Glob Antimicrob Resist	10.1016/j.jgar.2022.06.029	2022
	Role of Gut and Urinary Microbiome in Children with Urinary Tract Infections: A Systematic Review.	Srivastava A, Shete O, Gulia A, Aggarwal S, Ghosh TS, Ahuja V, Anand S.	Diagnostics (Basel)	10.3390/diagnostics15010093	2025
	Case report: Fatal neonatal sepsis associated with Escherichia fergusonii infection in a common bottlenose dolphin (Tursiops truncatus).	Baek SM, Lee SW, Kim TU, Kim JH, Lee YJ, Yim JH, Kim WJ, Choi SK, Han JE, Jeong KS, Park JK.	Front Vet Sci	10.3389/fvets.2023.1242599	2023
	First report of Escherichia albertii in Iran: a case study highlighting diagnostic challenges in pediatric gastroenteritis.	Dadvar A, Nemati A, Hafiz M, Khammar Z, Romling U, Askari Badouei M, Hashemi Tabar G.	ASM Case Rep	10.1128/asmcr.00046-25	2025
Genetics	Whole-genome characterization and antibiotic resistance phenotype of Escherichia marmotae first isolated from Berylmys bowersi.	Liu Y, Zhou J, Gu T, Ai W, Zhou J, Ma Q, Hu Y, Li S.	Microbiol Spectr	10.1128/spectrum.02946-24	2025
	Emergence of Incl2 plasmid-mediated colistin resistance in avian Escherichia fergusonii.	Lin J, Tang B, Zheng X, Chang J, Ma J, He Y, Yang H, Wu Y.	FEMS Microbiol Lett	10.1093/femsle/fnac016	2022
	Screening the Rumen of Balochi Camel (Camelus dromedarius) and Cashmere Goat (Capra hircus) to Isolate Enzyme-Producing Bacteria as Potential Additives for Animal Feed.	Gheibipour M, Ghiasi SE, Bashtani M, Torbati MBM, Motamedi H.	Indian J Microbiol	10.1007/s12088-024-01197-7	2024
Genetics	Long-term adaptation of ParA, RelE/ParE partition system, replication protein and phage proteins encoding low-cost plasmids of Escherichia species isolated from diarrheic children of North East India.	Sarma S, Bhattacharjee A, Devi MV, Panyang PP, Singh AK.	J Appl Microbiol	10.1093/jambio/lxac065	2023
Phylogeny	Optimized extraction and kinetic study of cholesterol oxidase from a newly isolated Escherichia fergusonii strain from local whey samples: insights through a combined experimental study and artificial neural network modeling.	Khataee S, Dehghan G, Rashtbari S, Marefat A, Jamei S, Farzi-Khajeh H.	BMC Microbiol	10.1186/s12866-024-03728-0	2025
	Escherichia fergusonii bacteremia after esophagectomy: a case report and literature review.	Jiang YY, Zhang Y, Hu Y, Guo Y.	J Int Med Res	10.1177/03000605231167316	2023
	The extracellular vesicle of depressive patient-derived Escherichia fergusonii induces vagus nerve-mediated neuroinflammation in mice.	Ma X, Park HS, Shin YJ, Kim JK, Hong JK, Han SW, Yoon IY, Kim DH.	J Neuroinflammation	10.1186/s12974-024-03211-7	2024
	High antimicrobial resistance rates and multidrug resistance in Enterobacteriaceae isolates from poultry in Souk Ahras region, Algeria.	Kamel K, Merghad A, Barour D, Eddine Gherissi D, Khenenou T.	Vet World	10.14202/vetworld.2024.2709-2718	2024
Phylogeny	Isolation and characterization of chitinolytic bacterium, Escherichia fergusonii AMC01 from insectivorous bat, Taphozous melanopogon.	Gracy Jenifer S, Marimuthu G, Raghuram H.	J Basic Microbiol	10.1002/jobm.202100271	2021
	Studies on antimicrobial stress with reference to biofilm formation of faecal microbial communities from Apatani tribe of Arunachal Pradesh.	Hazarika P, Chattopadhyay I, Umpo M, Choudhury Y, Sharma I.	Indian J Med Microbiol	10.1016/j.ijmmb.2022.09.011	2023
	Lung Microenvironment Among Patients with Nontuberculous Mycobacterial Pulmonary Disease by Metagenomic Sequencing Technique.	Qin L, Chen Y, Luan S, Yin X, Pan J, Wang L, Yao Y, Zhou C, Bao R, Shen J, Miao Q, Hu B.	Biomedicines	10.3390/biomedicines13040818	2025
	Filamentation activates bacterial Avs5 antiviral protein.	Wang Y, Tian Y, Yang X, Yu F, Zheng J.	Nat Commun	10.1038/s41467-025-57732-7	2025
	Effects of different composting methods on antibiotic-resistant bacteria, antibiotic resistance genes, and microbial diversity in dairy cattle manures.	Tang M, Wu Z, Li W, Shoaib M, Aqib AI, Shang R, Yang Z, Pu W.	J Dairy Sci	10.3168/jds.2022-22193	2023
Phylogeny	Analysis of Alterations in Intestinal Flora in Chinese Elderly with Cardiovascular Disease and Its Association with Trimethylamine.	He Y, Chen S, Xue Y, Lu H, Li Z, Jia X, Ning Y, Yuan Q, Wang S.	Nutrients	10.3390/nu16121864	2024
Genetics	Isolation and Genomic Characterization of a Heat-Labile Enterotoxin 1-Producing Escherichia fergusonii Strain from a Human.	Okuno M, Tsuru N, Yoshino S, Gotoh Y, Yamamoto T, Hayashi T, Ogura Y.	Microbiol Spectr	10.1128/spectrum.00491-23	2023
Genetics	Genomic analysis of Enterobacteriaceae from colorectal cancer patients at a tertiary hospital in Ghana: a case-control study.	Bachelle SV, Bah SY, Addo RT, Bediako-Bowan AAA, Egyir B, Tsatsu SE, Dzudzor B, Amarh V.	Sci Rep	10.1038/s41598-024-74299-3	2024
	Detection of pathogenic bacteria in retailed shrimp from Bangladesh.	Khan M, Rahman MM, Paul SI, Lively JA.	Food Sci Nutr	10.1002/fsn3.4260	2024
	The first case of Escherichia fergusonii with biofilm in China and literature review.	Zang YM, Liu JF, Li G, Zhao M, Yin GM, Zhang ZP, Jia W.	BMC Infect Dis	10.1186/s12879-023-07985-8	2023
Phylogeny	A novel clinically relevant human fecal microbial transplantation model in humanized mice.	Yang S, Tong L, Li X, Zhang Y, Chen H, Zhang W, Zhang H, Chen Y, Chen R.	Microbiol Spectr	10.1128/spectrum.00436-24	2024
Enzymology	Differences in chlorine and peracetic acid disinfection kinetics of Enterococcus faecalis and Escherichia fergusonii and their susceptible strains based on gene expressions and genomics.	Sahulka SQ, Bhattarai B, Bhattacharjee AS, Tanner W, Mahar RB, Goel R.	Water Res	10.1016/j.watres.2021.117480	2021
	Zoonotic bacteria in clinically healthy goats in petting zoo settings of zoological gardens in Germany.	Gottling J, Heckel JO, Hotzel H, Fruth A, Pfeifer Y, Henning K, Kopp P, Mertens-Scholz K, Rietschel W, Pfeffer M.	Zoonoses Public Health	10.1111/zph.12922	2022
	Efflux Pumps and Different Genetic Contexts of tet(X4) Contribute to High Tigecycline Resistance in Escherichia fergusonii from Pigs.	Wang J, Wan X, Meng H, Olsen RH, Chen X, Li L.	Int J Mol Sci	10.3390/ijms24086923	2023
	A Case of Resembling Hemolytic Uremic Syndrome Caused by Escherichia fergusonii in an Immunocompetent Adult.	Hwang S, Chang HH, Bae S, Kim YK, Kim J.	Chonnam Med J	10.4068/cmj.2022.58.1.64	2022
	Lipid Nanoparticle-Mediated CRISPR-Cas13a Delivery for the Control of Bacterial Infection.	Kim B, Seo HW, Lee K, Yong D, Park YK, Lee Y, Lee S, Kim DW, Kim D, Ryu CM.	Adv Healthc Mater	10.1002/adhm.202403281	2025
	First case report of pustules associated with Escherichia fergusonii in the chinese pangolin (Manis pentadactyla aurita).	An F, Wang K, Wei S, Yan H, Xu X, Xu J, Sun S, Zou J, Hou F, Hua Y.	BMC Vet Res	10.1186/s12917-023-03622-3	2023
	The Vaginally Exposed Extracellular Vesicle of Gardnerella vaginalis Induces RANK/RANKL-Involved Systemic Inflammation in Mice.	Shin YJ, Ma X, Baek JS, Kim DH.	Microorganisms	10.3390/microorganisms13040955	2025
	Potentially Virulent Multi-Drug Resistant Escherichia fergusonii Isolated from Inanimate Surface in a Medical University: Omphisa fuscidentalis as an Alternative for Bacterial Virulence Determination.	Ilsan NA, Yunita M, Dewi NK, Irham LM, Sipriyadi, Nurfajriah S, Inggraini M.	Diagnostics (Basel)	10.3390/diagnostics13020279	2023
	Remediation of textile effluents for water reuse: Decolorization and desalination using Escherichia fergusonii followed by detoxification with activated charcoal.	Santhana Raj D, Nagarajan SV, Raman T, Venkatachalam P, Parthasarathy M.	J Environ Manage	10.1016/j.jenvman.2020.111406	2021
	Prevalence and Antimicrobial Resistance of Enterobacteriaceae in Wild Birds Across Europe: A Systematic Review.	Cocos DI, Dumitrescu E, Muselin F, Brezovan D, Degi J, Boldura OM, Cristina RT.	Antibiotics (Basel)	10.3390/antibiotics14090905	2025
Pathogenicity	Comprehensive discovery and functional characterization of diverse prophages in the pig gut microbiome.	Wei C, Wang Y, Chen Z.	Front Microbiol	10.3389/fmicb.2025.1662087	2025
	Impact of short-chain fatty acid supplementation on gut inflammation and microbiota composition in a murine colitis model.	Lee JG, Lee J, Lee AR, Jo SV, Park CH, Han DS, Eun CS.	J Nutr Biochem	10.1016/j.jnutbio.2021.108926	2022
Pathogenicity	Letter to the Editor: Escherichia fergusonii Harboring IncHI2 Plasmid Containing mcr-1 Gene-A Novel Reservoir for Colistin Resistance in Brazil.	Pontes LDS, Pimenta R, Silveira MC, Tavares-Teixeira CB, Pereira NF, da Conceicao Neto OC, de Oliveira Santos IC, da Costa BS, Carvalho-Assef APD, de Souza MMS, Rocha-de-Souza CM.	Microb Drug Resist	10.1089/mdr.2020.0041	2021
	Molecular Evidence of Clonal Salmonella Enteritidis Persistence in Poultry Cold-Chain Environments Under Environmental Stress.	Gazi KS, Alshehri WA, Alkhammash AM, Alqadri N, Bahwerth FS, Baty RS, Albakri NN, Khalel AF, Alpakistany TA, Melebari M.	Foods	10.3390/foods14223943	2025
	Is systemic inflammation a missing link between oral microbiome and oral squamous cell carcinoma? Results from multi-omics integration analyses.	Yan L, He B, Deng Q, Qiu Y, Lin L, Shi B, Wang J, Chen F.	J Oral Microbiol	10.1080/20002297.2025.2574326	2025
Genetics	Mapping the spread of fluoroquinolone resistance: continued presence of non-susceptible Escherichia coli in broilers.	Ringenier M, Boyen F, Bogaerts B, Gand M, Vanneste K, De Keersmaecker SCJ, Chantziaras I, Ibrahim N, Devreese M, Dewulf J.	Front Vet Sci	10.3389/fvets.2025.1610997	2025
	Identification of Arg32Ser, His92Tyr and Leu147Phe novel mutations in chromosomally mediated beta-lactamase SHV and in silico characterization to understand their substrate activity imparting resistance.	Sarma S, Deka B, Panyang PP, Singh AK.	J Biomol Struct Dyn	10.1080/07391102.2021.1978321	2022
	The Gut Microbiome Profile Predicts the Severe Acute Toxicities in Patients With Locally Advanced Rectal Cancer Undergoing Neoadjuvant Chemoradiation.	Yi Y, Shen L, Xia F, Wang Y, Zhang H, Zhang J, Wang Y, Sun X, Zhang Z.	Int J Radiat Oncol Biol Phys	10.1016/j.ijrobp.2021.07.240	2021
	Highly Sensitive and Specific Detection of Mobilized Colistin Resistance Gene mcr-1 by CRISPR-Based Platform.	Gong L, Jin Z, Liu E, Tang F, Yuan F, Liang J, Wang Y, Liu X, Wang Y.	Microbiol Spectr	10.1128/spectrum.01884-22	2022
	Loop-Mediated Isothermal Amplification for Detecting Four Major Foodborne Pathogens in Meat and Meat Products.	Li X, Zhu M, Wang S, Li W, Ren B, Qu L, Zhang X.	Foods	10.3390/foods14132321	2025
	The Prevalence of Multidrug-Resistant Uropathogenic Bacterial Profile With Antibiotic Susceptibility Patterns Among the Community and Hospitalized Patients During COVID Waves.	Shawkat ND, Yassin NA.	Cureus	10.7759/cureus.60613	2024
	Escherichia fergusonii in a patient with a traumatic amputation of the right pelvic limb.	Vanegas-Rodriguez ES, Lopez-Jacome LE, Becerra-Lobato N, Colin-Castro CA, Franco-Cendejas R.	Cir Cir	10.24875/ciru.20001455	2020
Phylogeny	Avian strains of emerging pathogen Escherichia fergusonii are phylogenetically diverse and harbor the greatest AMR dissemination potential among different sources: Comparative genomic evidence.	Srinivas K, Ghatak S, Pyngrope DA, Angappan M, Milton AAP, Das S, Lyngdoh V, Lamare JP, Prasad MCB, Sen A.	Front Microbiol	10.3389/fmicb.2022.1080677	2022
Genetics	Influence of Seasonality and Pollution on the Presence of Antibiotic Resistance Genes and Potentially Pathogenic Bacteria in a Tropical Urban River	Barrantes-Jimenez K, Mendoza-Guido B, Morales-Mora E, Rivera-Montero L, Montiel-Mora J, Chacon-Jimenez L, Rojas-Jimenez K, Arias-Andres M.	Antibiotics (Basel)		2025
	Migratory birds as the vehicle of transmission of multi drug resistant extended spectrum beta lactamase producing Escherichia fergusonii, an emerging zoonotic pathogen.	Shah A, Alam S, Kabir M, Fazal S, Khurshid A, Iqbal A, Khan MM, Khan W, Qayyum A, Hussain M, El Askary A, Gharib AF, Elesawy BH, Bibi Y.	Saudi J Biol Sci	10.1016/j.sjbs.2022.01.057	2022
	Survival Disparity and the Unique Genomic and Microbiome Profiles of Colon Cancer in Appalachian Kentucky.	McDonald HG, Reagan AM, Faisal ASM, Goettl R, Wang C, Hoyd R, Spakowicz D, Evers BM, Kim J, Bhakta AS.	J Am Coll Surg	10.1097/xcs.0000000000001299	2025
Genetics	Deep culturing the fecal microbiota of healthy laying hens.	Feng Z, Lorenc N, O'Brien B, Sun G, Li Z, Jung D, Ronholm J.	Anim Microbiome	10.1186/s42523-025-00395-y	2025
	Computational Elucidation of Phylogenetic, Functional and Structural Features of Methioninase from Pseudomonas, Escherichia, Clostridium and Citrobacter Strains.	Irajie C, Mohkam M, Vakili B, Nezafat N.	Recent Pat Biotechnol	10.2174/1872208315666210910091438	2021
	Investigating the Role of Invasive Streptococcus Constellatus Infection in Severe Systemic Disease Manifestations: A Case Report.	Momoh R, Nagarajan A.	Cureus	10.7759/cureus.67088	2024
	Differentiation of Escherichia fergusonii and Escherichia coli Isolated from Patients with Inflammatory Bowel Disease/Ischemic Colitis and Their Antimicrobial Susceptibility Patterns.	Dahal RH, Choi YJ, Kim S, Kim J.	Antibiotics (Basel)	10.3390/antibiotics12010154	2023
	Geospatial mapping of microbial contaminants and public health risks in Lahore's municipal water.	Rashid R, Shah FA, Munir R, Iqbal A, Javed W, Batool R, Lutfi A, Zaidi N.	Sci Rep	10.1038/s41598-025-98687-5	2025
Genetics	Evidence Supporting Oral Hygiene Management by Owners through a Genetic Analysis of Dental Plaque Bacteria in Dogs.	Yu JS, Kim M, Cho IH, Sim YM, Hwang YS.	Vet Sci	10.3390/vetsci11020096	2024
	The role of Anvillea garcinii and its compounds in health and disease: An overview.	Zarei A, Rasekh F, Ahmadpour Khorrami S, Masmouei B, Changizi-Ashtiyani S, Ramezani M, Zarei A.	Avicenna J Phytomed	10.22038/ajp.2024.25131	2025
Proteome	Design of a novel multi-epitopes vaccine against Escherichia fergusonii: a pan-proteome based in- silico approach.	Almanaa TN.	Front Immunol	10.3389/fimmu.2023.1332378	2023
	Bioactivity and antibacterial effect of star anise biosynthesized silver nanoparticles against Streptococcus mutans: an in vitro study.	Elchaghaby MA, Rashad S, Wassef NM.	BMC Complement Med Ther	10.1186/s12906-024-04550-x	2024
	Fecal Bacterial Community and Metagenome Function in Asians with Type 2 Diabetes, According to Enterotypes.	Wu X, Park S.	Biomedicines	10.3390/biomedicines10112998	2022
	First report of a bloodstream infection caused by Trabulsiella odontotermitis in a low-birth-weight newborn undergoing surgery for intestinal obstruction: a fatal case.	Yu J, Pan S, Tai S, Yuan E, Duan Y.	Emerg Microbes Infect	10.1080/22221751.2023.2259002	2023
	Screening of natural compounds for identification of novel inhibitors against beta-lactamase CTX-M-152 reported among Kluyvera georgiana isolates: An in vitro and in silico study.	Hemlata, Bhat MA, Kumar V, Ahmed MZ, Alqahtani AS, Alqahtani MS, Jan AT, Rahman S, Tiwari A.	Microb Pathog	10.1016/j.micpath.2020.104688	2021
Genetics	Genomic insights and epidemiology of mcr-1-Carrying Escherichia albertii isolated from agricultural soil in China.	Yang Y, Liu W, Zhao Z, Guo K, Wang X, Lou Z, Yang X, Gong L, Wang K, Liu X, Xu H, Liu Q, Zheng B, Jiang X.	BMC Genomics	10.1186/s12864-025-11493-1	2025
	Genomic diversity of uropathogenic Escherichia coli in clinical isolates from six latin american countries, 2018-2023.	Caballero F, Martinez-Ventura A, Cuicapuza D, Fajardo-Loyola A, Gutierrez-Ajalcrina R, Soto-Pastrana J, Asmat-Marrufo P, Barco-Yaipen de Vera E, Meza-Fernandez H, Chambi-Quispe M, Pino-Duenas J, Laura-Rivas N, Briones-Alejo A, Diaz-Rengifo P, Peralta-Siesquen C, Salvatierra G, Tsukayama P, Marcos-Carbajal P.	Rev Peru Med Exp Salud Publica	10.17843/rpmesp.2025.422.14299	2025
Genetics	Cell Compartment is a Predictor of Protein Rate of Evolution, but not in the Manner Expected: Evidence Against the Extended Complexity Hypothesis.	Rivas-Santisteban J, Yubero P, Hurst LD.	Genome Biol Evol	10.1093/gbe/evaf126	2025
Genetics	Genomic Characterization of Two Escherichia fergusonii Isolates Harboring mcr-1 Gene From Farm Environment.	Liu R, Xu H, Guo X, Liu S, Qiao J, Ge H, Zheng B, Gou J.	Front Cell Infect Microbiol	10.3389/fcimb.2022.774494	2022
Phylogeny	Delineating the fecal microbiome of healthy domestic short-hair cats in South Korea.	Cho HY, Park HJ, Choi JS, Kim SH, Ryu MO, Seo KW.	Front Vet Sci	10.3389/fvets.2025.1571107	2025
Genetics	Centrifuger: lossless compression of microbial genomes for efficient and accurate metagenomic sequence classification.	Song L, Langmead B.	Genome Biol	10.1186/s13059-024-03244-4	2024
Genetics	Multiresistant Enterobacteriaceae in yellow-legged gull chicks in their first weeks of life.	Vittecoq M, Brazier L, Elguero E, Bravo IG, Renaud N, Manzano-Marin A, Prugnolle F, Godreuil S, Blanchon T, Roux F, Durand P, Renaud F, Thomas F.	Ecol Evol	10.1002/ece3.8974	2022
Pathogenicity	Spatial host-microbiome profiling demonstrates bacterial-associated host transcriptional alterations in pediatric ileal Crohn's disease.	Jang S, Lee EJ, Park S, Lim H, Ahn B, Huh Y, Koh H, Park YR.	Microbiome	10.1186/s40168-025-02178-8	2025
	Isolation, Identification, and Antibiotic Resistance, CRISPR System Analysis of Escherichia coli from Forest Musk Deer in Western China.	Yang K, Wu X, Ding H, Ma B, Li Z, Wang Y, Yang Z, Yao X, Luo Y.	Microorganisms	10.3390/microorganisms13071683	2025
Genetics	Comparative genomic and phenotypic description of Escherichia ruysiae: a newly identified member of the gut microbiome of the domestic dog.	Dione N, Mlaga KD, Liang S, Jospin G, Marfori Z, Alvarado N, Scarsella E, Uttarwar R, Ganz HH.	Front Microbiol	10.3389/fmicb.2025.1558802	2025
	A virulent escherichia coli O121-B2-ST131 strain causes hemorrhagic pneumonia in mink: evidence from pathogenicity and animal challenge experiments.	Lin Y, Wang F, YanYang, Ma D, Wen S, Wang X, Yang J, Guan Z, Chen H, Ge J, Zhao L.	BMC Vet Res	10.1186/s12917-025-04817-6	2025
	Renal pelvis urobiome dysbiosis is associated with postoperative systemic inflammatory response syndrome after percutaneous nephrolithotomy.	Wang Q, Chen X, Deng G, Huang K, Hong S, Jiang K.	mSystems	10.1128/msystems.00780-25	2025
Biotechnology	Biogenic amines' residues in meat products with a reference to their microbial status.	Elgaffry O, Darwish WS, El Bayoumi RM, Hussein MA, Megahed A, Reda LM, Basiony A, Dawod YF.	Open Vet J	10.5455/ovj.2024.v14.i6.7	2024
	Modulation of the Gut Microbiota in Memory Impairment and Alzheimer's Disease via the Inhibition of the Parasympathetic Nervous System.	Park S, Wu X.	Int J Mol Sci	10.3390/ijms232113574	2022
	Gold nanoparticles synthesised by flavonoid tricetin as a potential antibacterial nanomedicine to treat respiratory infections causing opportunistic bacterial pathogens.	Alsamhary K, Al-Enazi N, Alshehri WA, Ameen F.	Microb Pathog	10.1016/j.micpath.2019.103928	2020
Genetics	Microbial and Metabolic Gut Profiling across Seven Malignancies Identifies Fecal Faecalibacillus intestinalis and Formic Acid as Commonly Altered in Cancer Patients.	Kulecka M, Czarnowski P, Balabas A, Turkot M, Kruczkowska-Tarantowicz K, Zeber-Lubecka N, Dabrowska M, Paszkiewicz-Kozik E, Walewski J, Lugowska I, Kosela-Paterczyk H, Rutkowski P, Kluska A, Piatkowska M, Jagiello-Gruszfeld A, Tenderenda M, Gawinski C, Wyrwicz L, Borucka M, Krzakowski M, Zajac L, Kaminski M, Mikula M, Ostrowski J.	Int J Mol Sci	10.3390/ijms25158026	2024
	Decoding the Gut Microbiota in Multiple Sclerosis Using Nanopore Long-Read Sequencing: Insights into Disease Severity and Subtypes.	Alshinnawy AS, Badiea EA, Swelam MS, Sayed AA, Mohamed MR.	Mol Neurobiol	10.1007/s12035-025-05194-9	2025
	COVID-19 association with multidrug-resistant bacteria superinfections: Lessons for future challenges.	Susan M, Susan R, Lazar V, Bagiu IC, Mihu AG, Bagiu RV, Ionescu A, Iana AN, Dehelean CA, Lighezan D, Marti DT.	Exp Ther Med	10.3892/etm.2023.11953	2023
Genetics	Genomic Features of an MDR Escherichia coli ST5506 Harboring an IncHI2/In229/bla_CTX-M-2 Array Isolated from a Migratory Black Skimmer.	Moura Q, Fernandes MR, Sellera FP, Cardoso B, Nascimento CL, Dutra GHP, Lincopan N.	Pathogens	10.3390/pathogens13010063	2024
	Sodium butyrate reduces ammonia production in the cecum of laying hens by regulating ammonia-producing bacteria.	Liu S, Hu J, Li L, Xing S, Yang Y, Liao X.	Poult Sci	10.1016/j.psj.2022.102241	2023
	An exploratory in silico analysis of bacteriocin gene clusters in the urobiome.	Jones J, Murphy CP, Sleator RD, Culligan EP.	Microbiome Res Rep	10.20517/mrr.2023.78	2024
	Culturable Human Microorganisms and the Impact of Transportation Conditions on Cultivability.	Fan X, Lv N, Quan Z.	Microorganisms	10.3390/microorganisms13030549	2025
Enzymology	Production of chitinase from Escherichia fergusonii, chitosanase from Chryseobacterium indologenes, Comamonas koreensis and its application in N-acetylglucosamine production.	Kim TI, Lim DH, Baek KS, Jang SS, Park BY, Mayakrishnan V.	Int J Biol Macromol	10.1016/j.ijbiomac.2018.02.056	2018
Metabolism	Plasmids associated with heavy metal resistance and herbicide degradation potential in bacterial isolates obtained from two Brazilian regions.	Moretto JAS, Braz VS, Furlan JPR, Stehling EG.	Environ Monit Assess	10.1007/s10661-019-7461-9	2019
Enzymology	Within-host heterogeneity and flexibility of mcr-1 transmission in chicken gut.	Li XP, Sun RY, Song JQ, Fang LX, Zhang RM, Lian XL, Liao XP, Liu YH, Lin J, Sun J.	Int J Antimicrob Agents	10.1016/j.ijantimicag.2019.09.010	2020
Pathogenicity	Bat guano-dwelling microbes and antimicrobial properties of the pygidial gland secretion of a troglophilic ground beetle against them.	Dimkic I, Stankovic S, Kabic J, Stupar M, Nenadic M, Ljaljevic-Grbic M, Zikic V, Vujisic L, Tesevic V, Vesovic N, Pantelic D, Savic-Sevic S, Vukojevic J, Curcic S.	Appl Microbiol Biotechnol	10.1007/s00253-020-10498-y	2020
Pathogenicity	First Report of KPC-2 and KPC-3-Producing Enterobacteriaceae in Wild Birds in Africa.	Ben Yahia H, Chairat S, Gharsa H, Alonso CA, Ben Sallem R, Porres-Osante N, Hamdi N, Torres C, Ben Slama K.	Microb Ecol	10.1007/s00248-019-01375-x	2020
	PglZ from Type I BREX phage defence systems is a metal-dependent nuclease that forms a sub-complex with BrxB.	Readshaw JJ, Doyle LA, Puiu M, Kelly A, Nelson A, Kaiser AJ, McGuire SF, Peralta Acosta J, Smith DL, Stoddard BL, Kaiser BK, Blower TR.	Nucleic Acids Res	10.1093/nar/gkaf540	2025
	The association between the gut microbiota metabolite trimethylamine N-oxide and heart failure.	Jarmukhanov Z, Mukhanbetzhanov N, Kozhakhmetov S, Nurgaziyev M, Sailybayeva A, Bekbossynova M, Kushugulova A.	Front Microbiol	10.3389/fmicb.2024.1440241	2024
	gammaBMGC: A Comprehensive and Accurate Database for Screening TMAO-Associated Cardiovascular Diseases.	Yang G, Tao T, Yu G, Zhang H, Wu Y, Sun S, Guo K, Jia S.	Microorganisms	10.3390/microorganisms13020225	2025
Genetics	Trimethylamine N-oxide and risk of inflammatory bowel disease: A Mendelian randomization study.	Banno Y, Nomura M, Hara R, Asami M, Tanaka K, Mukai Y, Tomata Y.	Medicine (Baltimore)	10.1097/md.0000000000034758	2023
	Flavonoids, Isoquinoline Alkaloids, and Their Combinations Affect Growth Performance, Inflammatory Status, and Gut Microbiome of Broilers Under High Stocking Density and Heat Stress.	Insawake K, Songserm T, Songserm O, Theapparat Y, Adeyemi KD, Rassmidatta K, Ruangpanit Y.	Animals (Basel)	10.3390/ani15010071	2024
	The global distribution of the macrolide esterase EstX from the alpha/beta hydrolase superfamily.	Lin J, Lv H, Wang T, Tao H, Zhong Y, Zhou Y, Tang Y, Xie F, Zhuang G, Xu C, Chu Y, Wang X, Yang Y, Song T.	Commun Biol	10.1038/s42003-024-06473-2	2024
	Genome analysis of Bifidobacterium adolescentis and investigation of its effects on inflammation and intestinal barrier function.	Li B, Wang H, Wang M, Liang H, Hu T, Yang J, Li S, You X, Xia B, Yuan Y, Zou Y, Miao Y, Sun Y.	Front Microbiol	10.3389/fmicb.2024.1496280	2024
	The vibriophage-encoded inhibitor OrbA abrogates BREX-mediated defense through the ATPase BrxC.	Oshiro RT, Dunham DT, Seed KD.	J Bacteriol	10.1128/jb.00206-24	2024
	A droplet microfluidic strategy for cultivation, investigation, and high-throughput isolation of mouse gut microbiome bacteria.	Hengoju S, Abdissa K, Boto ST, Samimi A, Martin K, Jacobsen ID, Rosenbaum MA.	Appl Environ Microbiol	10.1128/aem.00695-25	2025
	Antibiotic resistance and heavy metal tolerance plasmids: the antimicrobial bulletproof properties of Escherichia fergusonii isolated from poultry.	Galetti R, Penha Filho RAC, Ferreira JC, Varani AM, Darini ALC.	Infect Drug Resist	10.2147/idr.s196411	2019
	Nasal microbiome inhabitants with anti-Staphylococcus aureus activity.	Cole AL, Marzahn MR, Valdespino EL, Patel R, Cole AM.	Microbiol Spectr	10.1128/spectrum.01024-25	2025
Pathogenicity	Escherichia fergusonii, an Underrated Repository for Antimicrobial Resistance in Food Animals.	Tang B, Chang J, Chen Y, Lin J, Xiao X, Xia X, Lin J, Yang H, Zhao G.	Microbiol Spectr	10.1128/spectrum.01617-21	2022
	Dose-Responsive Effects of Iron Supplementation on the Gut Microbiota in Middle-Aged Women.	Shearer J, Shah S, MacInnis MJ, Shen-Tu G, Mu C.	Nutrients	10.3390/nu16060786	2024
Genetics	Whole-genome-based characterization of Escherichia albertii strains isolated from paediatric diarrhoeal cases in Kolkata, India.	Chowdhury G, Hoshiko Y, Okuno M, Kitahara K, Albert MJ, Miyoshi SI, Ogura Y, Dutta S, Ramamurthy T, Mukhopadhyay AK.	Microb Genom	10.1099/mgen.0.001363	2025
	Novel Acylated Naringin Enhances Propionate Release and Stimulates the Growth of Flavanone-Metabolizing Bacteria in an In Vitro Batch Fermentation Model.	Ruiz-Alvarez BE, Padilla-de la Rosa JD, Gonzalez Avila M, Sandoval G, Desjardins Y.	Life (Basel)	10.3390/life15060967	2025
	The Interaction between Human Microbes and Advanced Glycation End Products: The Role of Klebsiella X15 on Advanced Glycation End Products' Degradation.	Shi A, Ji X, Li W, Dong L, Wu Y, Zhang Y, Liu X, Zhang Y, Wang S.	Nutrients	10.3390/nu16050754	2024
	Label-Free Sequence-Specific Visualization of LAMP Amplified Salmonella via DNA Machine Produces G-Quadruplex DNAzyme.	Zeng H, Huang S, Chen Y, Chen M, He K, Fu C, Wang Q, Zhang F, Wang L, Xu X.	Biosensors (Basel)	10.3390/bios13050503	2023
	Draft Genome Sequences of Escherichia albertii, Escherichia fergusonii, and Strains Belonging to Six Cryptic Lineages of Escherichia spp.	Gangiredla J, Mammel MK, Barnaba TJ, Tartera C, Gebru ST, Patel IR, Leonard SR, Kotewicz ML, Lampel KA, Elkins CA, Lacher DW.	Genome Announc	10.1128/genomea.00271-18	2018
Genetics	GenomeFISH: genome-based fluorescence in situ hybridization for strain-level visualization of microbial communities.	Engelberts JP, Ye J, Parks DH, McMaster ES, McInnes AS, Woodcroft BJ, Volmer JG, McIlroy SJ, Tyson GW.	ISME J	10.1093/ismejo/wraf138	2025
	Low-frequency transmission and persistence of antimicrobial-resistant bacteria and genes from livestock to agricultural soil and crops through compost application.	Fukuda A, Suzuki M, Makita K, Usui M.	PLoS One	10.1371/journal.pone.0301972	2024
	Evaluation of the efficacy of sulbactam combination therapy for monomicrobial and polymicrobial pulmonary infections caused by multidrug-resistant Acinetobacter baumannii.	Peng L, Yang X, Qiu X, Wang L, Chen L, Wei J, Jing C, Wu X, Li W, Wang D, Qian Q, Sun W.	Microbiol Spectr	10.1128/spectrum.03355-24	2025
	Exploring the epidemiology of mcr genes, genetic context and plasmids in Enterobacteriaceae originating from pigs and humans on farms in Thailand.	Leangapichart T, Stosic MS, Hickman RA, Lunha K, Jiwakanon J, Angkititrakul S, Magnusson U, Van Boeckel TP, Jarhult JD, Sunde M.	J Antimicrob Chemother	10.1093/jac/dkad097	2023
	May Sulfites in Wine Affect Gut Microbiota? An In Vitro Study of Their Digestion and Interplay with Wine Polyphenols.	Relano de la Guia E, Cueva C, Molinero N, Ruano A, Motilva MJ, Bartolome B, Moreno-Arribas MV.	J Agric Food Chem	10.1021/acs.jafc.5c02710	2025
	Effects of second-line anti-tuberculosis drugs on the intestinal microbiota of patients with rifampicin-resistant tuberculosis.	Wu C, Yi H, Hu Y, Luo D, Tang Z, Wen X, Zhang Y, Tang M, Zhang L, Wu S, Chen M.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1127916	2023
	Tryptophan was metabolized into beneficial metabolites against coronary heart disease or prevented from producing harmful metabolites by the in vitro drug screening model based on Clostridium sporogenes.	Tian X, Wu Y, Duan C, Zhou X, Li Y, Zheng J, Lai W, Zhang S, Cao L, Zhong S.	Front Microbiol	10.3389/fmicb.2022.1013973	2022
	Identifying potential novel widespread determinants of bacterial pathogenicity using phylogenetic-based orthology analysis.	Ribeiro S, Alves K, Nourikyan J, Lavergne JP, de Bernard S, Buffat L.	Front Microbiol	10.3389/fmicb.2025.1494490	2025
Genetics	Characterizing microbial diversity and metabolic pathways in yak milk and fermented yak milk based on metagenomics: A study from Ganzi Tibetan autonomous prefecture.	Zhang J, Jiao Y, Liu K, Situ W, Menghe B, Chen Y, Zha M.	Food Chem X	10.1016/j.fochx.2025.102198	2025
	Antimicrobial Resistance of Escherichia fergusonii Isolated from Broiler Chickens.	Simmons K, Islam MR, Rempel H, Block G, Topp E, Diarra MS.	J Food Prot	10.4315/0362-028x.jfp-15-575	2016
Genetics	Metagenomic Insight into Cecal Microbiota Shifts in Broiler Chicks Following Eimeria spp. Vaccination.	Karadedos DM, Mantzios T, Kiousi DE, Tsifintaris M, Giannenas I, Sakkas P, Papadopoulos GA, Antonissen G, Pappa A, Galanis A, Tsiouris V.	Microorganisms	10.3390/microorganisms13071470	2025
Metabolism	Dietary Supplementation of Microbial Dextran and Inulin Exerts Hypocholesterolemic Effects and Modulates Gut Microbiota in BALB/c Mice Models.	Jawad I, Bin Tawseen H, Irfan M, Ahmad W, Hassan M, Sattar F, Awan FR, Khaliq S, Akhtar N, Akhtar K, Anwar MA, Munawar N.	Int J Mol Sci	10.3390/ijms24065314	2023
	The Small RNA MicF Represses ObgE and SeqA in Escherichia coli.	Stibelman AY, Sariles AY, Takahashi MK.	Microorganisms	10.3390/microorganisms12122397	2024
	Rapid detection of multiple resistance genes to last-resort antibiotics in Enterobacteriaceae pathogens by recombinase polymerase amplification combined with lateral flow dipstick.	Lu C, Wang J, Pan L, Gu X, Lu W, Chen D, Zhang C, Ye Q, Xiao C, Liu P, Tang Y, Tang B, Huang G, Fang J, Jiang H.	Front Microbiol	10.3389/fmicb.2022.1062577	2022
	The gut-lung axis and microbiome dysbiosis in non-tuberculous mycobacterial infections: immune mechanisms, clinical implications, and therapeutic frontiers	Zhu F, Ying H, Siadat S, Fateh A.	Gut Pathog		2025
	The Impact of Chlorine Disinfection of Hospital Wastewater on Clonal Similarity and ESBL-Production in Selected Bacteria of the Family Enterobacteriaceae.	Rolbiecki D, Korzeniewska E, Czatzkowska M, Harnisz M.	Int J Environ Res Public Health	10.3390/ijerph192113868	2022
Phylogeny	Microbiota analysis of perimenopausal women experiencing recurrent vaginitis in conjunction with urinary tract infection.	Bi Y, Wang Y, Li W, Chen Y, Qin J, Zheng H.	BMC Microbiol	10.1186/s12866-024-03709-3	2025
Genetics	Antimicrobial Resistance and Genomic Epidemiology of tet(X4)-Bearing Bacteria of Pork Origin in Jiangsu, China.	Li Y, Li Y, Bu K, Wang M, Wang Z, Li R.	Genes (Basel)	10.3390/genes14010036	2022
Enzymology	Development and Optimization of a Rapid Colorimetric Membrane Immunoassay for Porphyromonas gingivalis.	Lee J, Choi MK, Kim J, Chun S, Kim HG, Lee H, Kim J, Lee D, Han SH, Yoon DY.	J Microbiol Biotechnol	10.4014/jmb.2103.03029	2021
	Clinical Impact of Microbiome Characteristics in Treatment-Naïve Extranodal NK/T-Cell Lymphoma Patients.	Yoon SE, Kang W, Cho J, Chalita M, Lee JH, Hyun DW, Kim H, Kim SJ, Kim WS.	Cancer Res Treat	10.4143/crt.2024.675	2025
	Metal-based nanoparticles in antibacterial application in biomedical field: Current development and potential mechanisms.	Jiang H, Li L, Li Z, Chu X.	Biomed Microdevices	10.1007/s10544-023-00686-8	2024
	Development of a loop-mediated isothermal amplification assay combined with a nanoparticle-based lateral flow biosensor for rapid detection of plasmid-mediated colistin resistance gene mcr-1.	Gong L, Tang F, Liu E, Liu X, Xu H, Wang Y, Song Y, Liang J.	PLoS One	10.1371/journal.pone.0249582	2021
Enzymology	Multiple Cross Displacement Amplification Coupled With Gold Nanoparticles-Based Lateral Flow Biosensor for Detection of the Mobilized Colistin Resistance Gene mcr-1.	Gong L, Liu E, Che J, Li J, Liu X, Xu H, Liang J.	Front Cell Infect Microbiol	10.3389/fcimb.2019.00226	2019
	A Study of the Antimicrobial Activity of Combined Black Pepper and Cinnamon Essential Oils against Escherichia fergusonii in Traditional African Yoghurt.	Ogwaro BA, O'Gara EA, Hill DJ, Gibson H.	Foods	10.3390/foods10112847	2021
Pathogenicity	Identification and characterization of plasmid-mediated quinolone resistance determinants in Enterobacteriaceae isolated from healthy poultry in Brazil.	Ferreira JC, Penha Filho RAC, Kuaye APY, Andrade LN, Berchieri Junior A, Darini ALDC.	Infect Genet Evol	10.1016/j.meegid.2018.02.003	2018
Metabolism	Gut Microbiome: The Interplay of an "Invisible Organ" with Herbal Medicine and Its Derived Compounds in Chronic Metabolic Disorders.	Lim DW, Wang JH.	Int J Environ Res Public Health	10.3390/ijerph192013076	2022
	Investigation of the human-gut-kidney axis by fecal proteomics, highlights molecular mechanisms affected in CKD.	Lohia S, Valkenburg S, Stroggilos R, Lygirou V, Makridakis M, Zoidakis J, Verbeke F, Glorieux G, Vlahou A.	Heliyon	10.1016/j.heliyon.2024.e32828	2024
	Ureaplasma and Prevotella colonization with Lactobacillus abundance during pregnancy facilitates term birth.	Park S, You YA, Kim YH, Kwon E, Ansari A, Kim SM, Lee G, Hur YM, Jung YJ, Kim K, Kim YJ.	Sci Rep	10.1038/s41598-022-13871-1	2022
	Changes in the diversity of local cervical bacteria in women with cervical cancer receiving antineoplastic treatment.	Manzanares-Leal GL, Coronel-Martinez J, Rodriguez-Morales M, Bustamante-Montes LP, Sandoval-Trujillo H, Ramirez-Duran N.	J Res Med Sci	10.4103/jrms.jrms_757_19	2021
	Incidence of bactibilia and related factors in patients who undergo cholecystectomy.	Moon DK, Kang JS, Byun Y, Choi YJ, Lee HW, Jang JY, Lim CS.	Ann Surg Treat Res	10.4174/astr.2023.104.1.10	2023
	Gut microbiota: a novel strategy affecting atherosclerosis.	Yang L, Yang J, Zhang T, Xie X, Wu Q.	Microbiol Spectr	10.1128/spectrum.00482-24	2025
	Wastewater-based surveillance in Italy leading to the first detection of mcr-10-positive Klebsiella quasipneumoniae.	Formenti N, Guarneri F, Bertasio C, Parisio G, Romeo C, Scali F, Birbes L, Boniotti MB, Diegoli G, Candela L, Romeo GA, Pasquali P, Alborali GL.	Antimicrob Resist Infect Control	10.1186/s13756-022-01194-9	2022
	Preliminary Identification of the Aerobic Cervicovaginal Microbiota in Mexican Women With Cervical Cancer as the First Step Towards Metagenomic Studies.	Manzanares-Leal GL, Coronel-Martinez JA, Rodriguez-Morales M, Rangel-Cuevas I, Bustamante-Montes LP, Sandoval-Trujillo H, Ramirez-Duran N.	Front Cell Infect Microbiol	10.3389/fcimb.2022.838491	2022
	Novel multiplex-PCR test for Escherichia coli detection.	Zimon B, Psujek M, Matczak J, Guzinski A, Wojcik E, Dastych J.	Microbiol Spectr	10.1128/spectrum.03773-23	2024
Phylogeny	Preliminary Studies of Lactic Acid Bacteria Isolated from Feces of Thai Newborns.	Chotelersak K, Thamacharoensuk T, Tanasupawat S, Nantavisai K, Taweechotipatr M, Puttikamonkul S.	J Med Assoc Thai		2016
	Molecular basis of foreign DNA recognition by BREX anti-phage immunity system.	Drobiazko A, Adams MC, Skutel M, Potekhina K, Kotovskaya O, Trofimova A, Matlashov M, Yatselenko D, Maxwell KL, Blower TR, Severinov K, Ghilarov D, Isaev A.	Nat Commun	10.1038/s41467-025-57006-2	2025
	Impressive pan-genomic diversity of E. coli from a wild animal community near urban development reflects human impacts.	Lagerstrom KM, Scales NC, Hadly EA.	iScience	10.1016/j.isci.2024.109072	2024
	The Detrimental Impact of Ultra-Processed Foods on the Human Gut Microbiome and Gut Barrier.	Rondinella D, Raoul PC, Valeriani E, Venturini I, Cintoni M, Severino A, Galli FS, Mora V, Mele MC, Cammarota G, Gasbarrini A, Rinninella E, Ianiro G.	Nutrients	10.3390/nu17050859	2025
Genetics	Escherichia fergusonii.	Gaastra W, Kusters JG, van Duijkeren E, Lipman LJ.	Vet Microbiol	10.1016/j.vetmic.2014.04.016	2014
	Draft Whole-Genome Sequences of Escherichia fergusonii Strains Isolated from Beef Trim (GTA-EF02), Ground Beef (GTA-EF03), and Chopped Kale (GTA-EF04).	Manninger P, Koziol A, Carrillo CD.	Genome Announc	10.1128/genomea.00185-16	2016
	High Frequency of Antibiotic Resistance Genes (ARGs) in the Lerma River Basin, Mexico.	Tapia-Arreola AK, Ruiz-Garcia DA, Rodulfo H, Sharma A, De Donato M.	Int J Environ Res Public Health	10.3390/ijerph192113988	2022
	Probiotic supplementation as an alternative to antibiotics in broiler chickens.	Tomczyk G, Niczyporuk JS, Kozdrun W, Sawicka-Durkalec A, Bocian L, Barabasz M, Michalski M.	J Vet Res	10.2478/jvetres-2024-0009	2024
	Corynebacterium parakroppenstedtii secretes a novel glycolipid to promote the development of granulomatous lobular mastitis.	Liu R, Luo Z, Dai C, Wei Y, Yan S, Kuang X, Qi K, Fu A, Li Y, Fu S, Ma Z, Dai W, Xiao X, Wu Q, Zhou H, Rao Y, Yuan J, Shi T, Deng Z, Chen C, Liu T.	Signal Transduct Target Ther	10.1038/s41392-024-01984-0	2024
	Emergence of Carbapenem- and Tigecycline-Resistant Proteus cibarius of Animal Origin.	Li Y, Wang Q, Peng K, Liu Y, Li R, Wang Z.	Front Microbiol	10.3389/fmicb.2020.01940	2020
	Antibiotic Resistance Profile of Uropathogenic Bacteria in Diabetic Patients at the Bafoussam Regional Hospital, West Cameroon Region.	Signing AT, Marbou WJT, Penlap Beng V, Kuete V.	Cureus	10.7759/cureus.9345	2020
Pathogenicity	Neonates exposed to HIV but uninfected exhibit an altered gut microbiota and inflammation associated with impaired breast milk antibody function.	Byrne A, Diener C, Brown BP, Maust BS, Feng C, Alinde BL, Gibbons SM, Koch M, Gray CM, Jaspan HB, Nyangahu DD.	Microbiome	10.1186/s40168-024-01973-z	2024
	Effect of food additives on key bacterial taxa and the mucosa-associated microbiota in Crohn's disease. The ENIGMA study.	Loayza JJJ, Kang S, Schooth L, Teh JJ, de Klerk A, Noon EK, Zhang J, Hu J, Hamilton AL, Wilson-O'Brien A, Trakman GL, Lin W, Ching J, Or L, Sung JJY, Yu J, Ng SC, Kamm MA, Morrison M.	Gut Microbes	10.1080/19490976.2023.2172670	2023
Phylogeny	A novel barcoded nanopore sequencing workflow of high-quality, full-length bacterial 16S amplicons for taxonomic annotation of bacterial isolates and complex microbial communities.	Dommann J, Kerbl-Knapp J, Albertos Torres D, Egli A, Keiser J, Schneeberger PHH.	mSystems	10.1128/msystems.00859-24	2024
Genetics	MBCN: A novel reference database for Effcient Metagenomic analysis of human gut microbiome.	Zheng B, Xu J, Zhang Y, Qin J, Yuan D, Fan T, Wu W, Chen Y, Jiang Y.	Heliyon	10.1016/j.heliyon.2024.e37422	2024
Genetics	Occurrence and Characterisation of Colistin-Resistant Escherichia coli in Raw Meat in Southern Italy in 2018-2020.	Nobili G, La Bella G, Basanisi MG, Damato AM, Coppola R, Migliorelli R, Rondinone V, Leekitcharoenphon P, Bortolaia V, La Salandra G.	Microorganisms	10.3390/microorganisms10091805	2022
	Gut microbiota-mediated polyphenol metabolism is restrained by parasitic whipworm infection and associated with altered immune function in mice.	Schytz Andersen-Civil AI, Arora P, Zhu L, Myhill LJ, Budeyri Gokgoz N, Castro-Mejia JL, Leppa MM, Hansen LH, Lessard-Lord J, Salminen JP, Thamsborg SM, Sandris Nielsen D, Desjardins Y, Williams AR.	Gut Microbes	10.1080/19490976.2024.2370917	2024
	Diversity and adaptation properties of actinobacteria associated with Tunisian stone ruins.	Saadouli I, Marasco R, Mejri L, Hamden H, Guerfali MM, Stathopoulou P, Daffonchio D, Cherif A, Ouzari HI, Tsiamis G, Mosbah A.	Front Microbiol	10.3389/fmicb.2022.997832	2022
Enzymology	Evaluation and characterization of plasmids carrying CTX-M genes in a non-clonal population of multidrug-resistant Enterobacteriaceae isolated from poultry in Brazil.	Ferreira JC, Penha Filho RA, Andrade LN, Berchieri Junior A, Darini AL.	Diagn Microbiol Infect Dis	10.1016/j.diagmicrobio.2016.05.011	2016
Enzymology	Detection of Escherichia fergusonii by PCR-based DNA sequencing in a case of delayed-onset chronic endophthalmitis after cataract surgery.	Gokhale VV, Therese KL, Bagyalakshmi R, Biswas J.	J Cataract Refract Surg	10.1016/j.jcrs.2013.12.006	2014
	An enterococcal phage protein inhibits type IV restriction enzymes involved in antiphage defense.	Bullen NP, Johnson CN, Andersen SE, Arya G, Marotta SR, Lee YJ, Weigele PR, Whitney JC, Duerkop BA.	Nat Commun	10.1038/s41467-024-51346-1	2024
Metabolism	Biological production of silver nanoparticles by soil isolated bacteria and preliminary study of their cytotoxicity and cutaneous wound healing efficiency in rat.	Pourali P, Yahyaei B.	J Trace Elem Med Biol	10.1016/j.jtemb.2015.11.004	2016
Biotechnology	Inoculation of paperboard mill sludge versus mixed culture bacteria for hydrogen production from paperboard mill wastewater.	Farghaly A, Tawfik A, Tawfik A, Danial A.	Environ Sci Pollut Res Int	10.1007/s11356-015-5652-7	2016
	Distribution of Antibiotic-Resistant Enterobacteriaceae Pathogens in Potable Spring Water of Eastern Indian Himalayas: Emphasis on Virulence Gene and Antibiotic Resistance Genes in Escherichia coli.	Singh AK, Das S, Kumar S, Gajamer VR, Najar IN, Lepcha YD, Tiwari HK, Singh S.	Front Microbiol	10.3389/fmicb.2020.581072	2020
Phylogeny	Characterization of Escherichia fergusonii and Escherichia albertii isolated from water.	Maheux AF, Boudreau DK, Bergeron MG, Rodriguez MJ.	J Appl Microbiol	10.1111/jam.12551	2014
Metabolism	Biodegradation of crude oil by Pseudomonas aeruginosa and Escherichia fergusonii isolated from the Goan coast.	Pasumarthi R, Chandrasekaran S, Mutnuri S.	Mar Pollut Bull	10.1016/j.marpolbul.2013.08.026	2013
	Colistin resistance plasmids dually enhance bacterial virulence and antibiotic resistance via surface polysaccharide biosynthesis.	Ahn E, Kim J, Jiang J, Kim J, Muszynski A, Kasperkiewicz K, Shin H, Cao Y, Soh Y, Park Y, Heiss C, Fernando LDP, Azadi P, Wang Y, Jeon B, Ryu S.	Nat Commun	10.1038/s41467-025-65412-9	2025
	Comparison of the New VITEK MS PRIME System with the Matrix-Assisted Laser Desorption Ionization Biotyper Microflex LT for the Identification of Microorganisms.	Grohs P, Remaud E, Lath C, Vuong K, Parolini ML, Dannaoui E, Podglajen I.	Ann Lab Med	10.3343/alm.2023.43.6.574	2023
Pathogenicity	Exercise Preconditioning Attenuates the Response to Experimental Colitis and Modifies Composition of Gut Microbiota in Wild-Type Mice.	Cho J, Kim D, Kang H.	Life (Basel)	10.3390/life10090200	2020
	OrthoRefine: automated enhancement of prior ortholog identification via synteny.	Ludwig J, Mrazek J.	BMC Bioinformatics	10.1186/s12859-024-05786-7	2024
	Isolation, Characterization and Chemical Synthesis of Large Spectrum Antimicrobial Cyclic Dipeptide (l-leu-l-pro) from Streptomyces misionensisV16R3Y1 Bacteria Extracts. A Novel ¹H NMR Metabolomic Approach.	Saadouli I, Zendah El Euch I, Trabelsi E, Mosbah A, Redissi A, Ferjani R, Fhoula I, Cherif A, Sabatier JM, Sewald N, Ouzari HI.	Antibiotics (Basel)	10.3390/antibiotics9050270	2020
Genetics	Promiscuous and genome-wide recombination underlies the sequence-discrete species of the SAR11 lineage in the deep ocean.	Zhao J, Pachiadaki M, Conrad RE, Hatt JK, Bristow LA, Rodriguez-R LM, Rossello-Mora R, Stewart FJ, Konstantinidis KT.	ISME J	10.1093/ismejo/wraf072	2025
	Isolation of a polyethylene-degrading bacterium, Acinetobacter guillouiae, using a novel screening method based on a redox indicator.	Kim HR, Lee C, Shin H, Kim J, Jeong M, Choi D.	Heliyon	10.1016/j.heliyon.2023.e15731	2023
	Maternal Faecalibacterium pathobionts and low-fiber diets synergize to impact offspring health: implications for atopic dermatitis	Lee D, Park J, Park S, Hwang J, Kim S, Kee S, Kim H.	Microbiome		2025
Phylogeny	Identification of enterobacteria in viscera of pigs afflicted with porcine reproductive and respiratory syndrome and other viral co-infections.	Zhao G, Zhang L, Li C, Zhao J, Liu N, Li Y, Wang J, Liu L.	Microb Pathog	10.1016/j.micpath.2020.104385	2020
Genetics	M1CR0B1AL1Z3R-a user-friendly web server for the analysis of large-scale microbial genomics data.	Avram O, Rapoport D, Portugez S, Pupko T.	Nucleic Acids Res	10.1093/nar/gkz423	2019
	Fungal Community Investigation from Propolis Natural Products: Diversity and Antibacterial Activities Evaluation.	Sallemi S, Lekired A, Korbi N, Saadouli I, Cherif A, Zidi I, Klibi N, Ouzari HI, Mosbah A.	Evid Based Complement Alternat Med	10.1155/2022/7151655	2022
	Analysis of BlaEC family class C beta-lactamase.	Schmidt J, Zdarska V, Kolar M, Mlynarcik P.	FEMS Microbiol Lett	10.1093/femsle/fnad097	2023
	Genital Inflammation Is Not Associated With Decreased Vaginal Tenofovir Concentrations in Women Taking Oral PrEP.	Morris S, Cottrell M, Rawlings SA, Peterson S, Karris M, Pacheco D, Chaillon A, Kay A, Chow K, Anderson PL, Gianella S, Blumenthal J.	J Acquir Immune Defic Syndr	10.1097/qai.0000000000002884	2022
Genetics	Genome-scale metabolic network reconstructions of diverse Escherichia strains reveal strain-specific adaptations.	Monk JM.	Philos Trans R Soc Lond B Biol Sci	10.1098/rstb.2021.0236	2022
	Questioning the source of identified non-foodborne pathogens from food-contact wooden surfaces used in Hong Kong's urban wet markets.	Rao S, Ngan WY, Chan LC, Sekoai PT, Fung AHY, Pu Y, Yao Y, Habimana O.	One Health	10.1016/j.onehlt.2021.100300	2021
	Contaminated drinking water facilitates Escherichia coli strain-sharing within households in urban informal settlements.	Kim DD, Swarthout JM, Worby CJ, Chieng B, Mboya J, Earl AM, Njenga SM, Pickering AJ.	Nat Microbiol	10.1038/s41564-025-01986-w	2025
	Microbiotal characteristics colonized in intestinal mucosa of mice with diarrhoea and repeated stress.	Zhang C, Shao H, Peng X, Liu T, Tan Z.	3 Biotech	10.1007/s13205-020-02368-1	2020
Pathogenicity	Responses in ileal and cecal bacteria to low and high amylose/amylopectin ratio diets in growing pigs.	Luo YH, Yang C, Wright AD, He J, Chen DW.	Appl Microbiol Biotechnol	10.1007/s00253-015-6917-2	2015
Genetics	The origin and evolution of IncF33 plasmids based on large-scale data sets.	Gao G, He W, Jiao Y, Cai Z, Lv L, Liu J-H.	mSystems	10.1128/msystems.00508-23	2023
	Microbial species and intraspecies units exist and are maintained by ecological cohesiveness coupled to high homologous recombination.	Conrad RE, Brink CE, Viver T, Rodriguez-R LM, Aldeguer-Riquelme B, Hatt JK, Venter SN, Rossello-Mora R, Amann R, Konstantinidis KT.	Nat Commun	10.1038/s41467-024-53787-0	2024
Genetics	Breaking the Cycle: A Yeast Mannan-Rich Fraction Beneficially Modulates Egg Quality and the Antimicrobial Resistome Associated with Layer Hen Caecal Microbiomes under Commercial Conditions.	Corrigan A, McCooey P, Taylor-Pickard J, Stockdale S, Murphy R.	Microorganisms	10.3390/microorganisms12081562	2024
	Resistance and Co-Resistance of Metallo-Beta-Lactamase Genes in Diarrheal and Urinary-Tract Pathogens in Bangladesh.	Shanta AS, Islam N, Al Asad M, Akter K, Habib MB, Hossain MJ, Nahar S, Godman B, Islam S.	Microorganisms	10.3390/microorganisms12081589	2024
Genetics	Escherichia coli from six European countries reveals differences in profile and distribution of critical antimicrobial resistance determinants within One Health compartments, 2013 to 2020.	Kaspersen HP, Brouwer MS, Nunez-Garcia J, Cardenas-Rey I, AbuOun M, Duggett N, Ellaby N, Delgado-Blas J, Hammerl JA, Getino M, Serna C, Naas T, Veldman KT, Bossers A, Sunde M, Mo SS, Jorgensen SB, Ellington M, Gonzalez-Zorn B, La Ragione R, Glaser P, Anjum MF.	Euro Surveill	10.2807/1560-7917.es.2024.29.47.2400295	2024
	One Health compartment analysis of ESBL-producing Escherichia coli reveals multiple transmission events in a rural area of Madagascar.	Gay N, Rabenandrasana MAN, Panandiniaina HP, Rakotoninidrina MF, Ramahatafandry IT, Enouf V, Roger F, Collard JM, Cardinale E, Rieux A, Loire E.	J Antimicrob Chemother	10.1093/jac/dkad125	2023
Genetics	16S-FASAS: an integrated pipeline for synthetic full-length 16S rRNA gene sequencing data analysis.	Zhang K, Lin R, Chang Y, Zhou Q, Zhang Z.	PeerJ	10.7717/peerj.14043	2022
	Secondary metabolites from the Aspergillus sp. in the rhizosphere soil of Phoenix dactylifera (Palm tree).	Orfali R, Perveen S.	BMC Chem	10.1186/s13065-019-0624-5	2019
Phylogeny	plASgraph2: using graph neural networks to detect plasmid contigs from an assembly graph.	Sielemann J, Sielemann K, Brejova B, Vinar T, Chauve C.	Front Microbiol	10.3389/fmicb.2023.1267695	2023
	Evidence of interspecies O antigen gene cluster transfer between Shigella boydii 15 and Escherichia fergusonii.	Azmuda N, Rahman MZ, Sultana M, Jenssen EL, Khan SI, Birkeland NK.	APMIS	10.1111/j.1600-0463.2012.02926.x	2012
	Changes in Metabolic Regulation and the Microbiota Composition after Supplementation with Different Fatty Acids in db/db Mice.	Martinez-Carrillo BE, Mondragon-Velasquez T, Ramirez-Duran N, Aguirre-Garrido JF, Valdes-Ramos R, Guadarrama-Lopez AL, Castillo-Cardiel A.	Int J Food Sci	10.1155/2022/3336941	2022
	IS26 drives the dissemination of bla _CTX-M genes in an Ecuadorian community.	Salinas L, Cardenas P, Graham JP, Trueba G.	Microbiol Spectr	10.1128/spectrum.02504-23	2024
	Bacterial isolation from internal organs of rats (Rattus rattus) captured in Baghdad city of Iraq.	Ayyal NM, Abbas ZA, Karim AJ, Abbas ZM, Al-Salihi KA, Khalaf JM, Mahmood DD, Mohammed EA, Jumaa RS, Abdul-Majeed DI.	Vet World	10.14202/vetworld.2019.119-125	2019
	Characterizing the chicken gut colonization ability of a diverse group of bacteria.	Poudel B, Shterzer N, Sbehat Y, Ben-Porat N, Rakover M, Tovy-Sharon R, Wolicki D, Rahamim S, Bar-Shira E, Mills E.	Poult Sci	10.1016/j.psj.2022.102136	2022
	Molecular Identification and Selection of Probiotic Strains Able to Reduce the Serum TMAO Level in Mice Challenged with Choline.	Ramireddy L, Tsen HY, Chiang YC, Hung CY, Wu SR, Young SL, Lin JS, Huang CH, Chiu SH, Chen CC, Chen CC.	Foods	10.3390/foods10122931	2021
Phylogeny	Isolation and epidemiological characterization of heat-labile enterotoxin-producing Escherichia fergusonii from healthy chickens.	Oh JY, Kang MS, An BK, Shin EG, Kim MJ, Kwon JH, Kwon YK.	Vet Microbiol	10.1016/j.vetmic.2012.05.020	2012
Metabolism	Evaluation of the Feasibility of In Vitro Metabolic Interruption of Trimethylamine with Resveratrol Butyrate Esters and Its Purified Monomers.	Huang PH, Chen DQ, Chen YW, Shih MK, Lee BH, Tain YL, Hsieh CW, Hou CY.	Molecules	10.3390/molecules29020429	2024
Metabolism	Identification of commensal gut bacterial strains with lipogenic effects contributing to NAFLD in children.	Wei J, Luo J, Yang F, Dai W, Pan X, Luo M.	iScience	10.1016/j.isci.2024.108861	2024
	Antimicrobial Susceptibility Profile of Pathogenic and Commensal Bacteria Recovered from Cattle and Goat Farms.	Mukuna W, Aniume T, Pokharel B, Khwatenge C, Basnet A, Kilonzo-Nthenge A.	Antibiotics (Basel)	10.3390/antibiotics12020420	2023
Pathogenicity	Metformin alleviates choline diet-induced TMAO elevation in C57BL/6J mice by influencing gut-microbiota composition and functionality.	Su C, Li X, Yang Y, Du Y, Zhang X, Wang L, Hong B.	Nutr Diabetes	10.1038/s41387-021-00169-w	2021
	Enteritis and Septicemia in a Horse Associated With Infection by Escherichia fergusonii	Weiss ATA, LA 1/4bke-Becker A, Krenz M, van der Grinten E.	J Equine Vet Sci	10.1016/j.jevs.2011.01.005	2011
Genetics	Metagenomic and Culturomics Analysis of Microbial Communities within Surface Sediments and the Prevalence of Antibiotic Resistance Genes in a Pristine River: The Zaqu River in the Lancang River Source Region, China.	Yan Y, Xu J, Huang W, Fan Y, Li Z, Tian M, Ma J, Lu X, Liang J.	Microorganisms	10.3390/microorganisms12050911	2024
	Gut Microbiome Interactions with Oxidative Stress: Mechanisms and Consequences for Health.	Semenova N, Garashchenko N, Kolesnikov S, Darenskaya M, Kolesnikova L.	Pathophysiology	10.3390/pathophysiology31030023	2024
Metabolism	Novel lipopeptide biosurfactant produced by hydrocarbon degrading and heavy metal tolerant bacterium Escherichia fergusonii KLU01 as a potential tool for bioremediation.	Sriram MI, Gayathiri S, Gnanaselvi U, Jenifer PS, Mohan Raj S, Gurunathan S.	Bioresour Technol	10.1016/j.biortech.2011.06.094	2011
	Experimental models of fatty liver diseases: Status and appraisal.	Wang H, Shen H, Seo W, Hwang S.	Hepatol Commun	10.1097/hc9.0000000000000200	2023
Enzymology	Haemophilus influenzae and SARS-CoV-2: Is there a role for investigation?	Borkakoty B, Bali NK.	Indian J Med Microbiol	10.1016/j.ijmmb.2021.03.008	2021
Genetics	Completion of draft bacterial genomes by long-read sequencing of synthetic genomic pools.	Derakhshani H, Bernier SP, Marko VA, Surette MG.	BMC Genomics	10.1186/s12864-020-06910-6	2020
Pathogenicity	Curcumin Modulation of the Gut-Brain Axis for Neuroinflammation and Metabolic Disorders Prevention and Treatment.	Cerullo M, Armeli F, Mengoni B, Menin M, Crudeli ML, Businaro R.	Nutrients	10.3390/nu17091430	2025
	Antimicrobial Resistance (AMR) of Bacteria Isolated from Dogs with Canine Parvovirus (CPV) Infection: The Need for a Rational Use of Antibiotics in Companion Animal Health.	Schiro G, Gambino D, Mira F, Vitale M, Guercio A, Purpari G, Antoci F, Licitra F, Chiaramonte G, La Giglia M, Randazzo V, Vicari D.	Antibiotics (Basel)	10.3390/antibiotics11020142	2022
	Escherichia fergusonii Associated with Pneumonia in a Beef Cow.	Rimoldi GM, Moeller RB.	J Vet Med	10.1155/2013/829532	2013
	Genomic analysis of Escherichia coli circulating in the Brazilian poultry sector.	da Silva CR, do Valle Barroso M, Gozi KS, Fontana H, Nogueira MCL, Lincopan N, Casella T.	Braz J Microbiol	10.1007/s42770-022-00799-x	2022
	Antimicrobial Activity of Dihydroisocoumarin Isolated from Wadi Lajab Sediment-Derived Fungus Penicillium chrysogenum: In Vitro and In Silico Study.	Orfali R, Perveen S, AlAjmI MF, Ghaffar S, Rehman MT, AlanzI AR, Gamea SB, Essa Khwayri M.	Molecules	10.3390/molecules27113630	2022
	Fabrication of Biohybrid Nanofibers by the Green Electrospinning Technique and Their Antibacterial Activity.	Thamer BM, Al-Sabri AE, Almansob A, El-Newehy MH.	ACS Omega	10.1021/acsomega.1c07141	2022
	The Vaginal Community State Types Microbiome-Immune Network as Key Factor for Bacterial Vaginosis and Aerobic Vaginitis.	De Seta F, Campisciano G, Zanotta N, Ricci G, Comar M.	Front Microbiol	10.3389/fmicb.2019.02451	2019
	The highly diverse plasmid population found in Escherichia coli colonizing travellers to Laos and its role in antimicrobial resistance gene carriage.	Snaith AE, Dunn SJ, Moran RA, Newton PN, Dance DAB, Davong V, Kuenzli E, Kantele A, Corander J, McNally A.	Microb Genom	10.1099/mgen.0.001000	2023
	Th17 cells in primary Sjögren's syndrome negatively correlate with increased Roseburia and Coprococcus.	Xin X, Wang Q, Qing J, Song W, Gui Y, Li X, Li Y.	Front Immunol	10.3389/fimmu.2022.974648	2022
	Mesenteric Adipose Tissue-Derived Klebsiella variicola Disrupts Intestinal Barrier and Promotes Colitis by Type VI Secretion System.	Gong J, Yu J, Yin S, Ke J, Wu J, Liu C, Luo Z, Cheng WM, Xie Y, Chen Y, He Z, Lan P.	Adv Sci (Weinh)	10.1002/advs.202205272	2023
Genetics	Escherichia albertii as a Potential Enteropathogen in the Light of Epidemiological and Genomic Studies.	Leszczynska K, Swiecicka I, Daniluk T, Lebensztejn D, Chmielewska-Deptula S, Leszczynska D, Gawor J, Kliber M.	Genes (Basel)	10.3390/genes14071384	2023
	Lifestyle Interventions for Non-Obese Patients Both with, and at Risk, of Non-Alcoholic Fatty Liver Disease.	Zhang XL, Wang TY, Targher G, Byrne CD, Zheng MH.	Diabetes Metab J	10.4093/dmj.2022.0048	2022
	In-Vitro Characterization of Growth Inhibition against the Gut Pathogen of Potentially Probiotic Lactic Acid Bacteria Strains Isolated from Fermented Products.	Jung JY, Han SS, Kim ZH, Kim MH, Kang HK, Jin HM, Lee MH.	Microorganisms	10.3390/microorganisms9102141	2021
	Antibacterial and Antifungal Sesquiterpenoids from Aerial Parts of Anvillea garcinii.	Perveen S, Alqahtani J, Orfali R, Aati HY, Al-Taweel AM, Ibrahim TA, Khan A, Yusufoglu HS, Abdel-Kader MS, Taglialatela-Scafati O.	Molecules	10.3390/molecules25071730	2020
Metabolism	Isolation, identification and characterization of human intestinal bacteria with the ability to utilize chloramphenicol as the sole source of carbon and energy.	Xin Z, Fengwei T, Gang W, Xiaoming L, Qiuxiang Z, Hao Z, Wei C.	FEMS Microbiol Ecol	10.1111/j.1574-6941.2012.01440.x	2012
Phylogeny	Use of citrate adonitol agar as a selective medium for the isolation of Escherichia fergusonii from a captive reindeer herd.	Foster G, Evans J, Tryland M, Hollamby S, MacArthur I, Gordon E, Harley J, Voigt K.	Vet Microbiol	10.1016/j.vetmic.2010.01.014	2010
	Endophytic microorganisms from coffee tissues as plant growth promoters and biocontrol agents of coffee leaf rust	Silva HSA, Tozzi JPL, Terrasan CRF, Bettiol W.	Biol Control	10.1016/j.biocontrol.2012.06.005	2012
	Assessing the Bacterial Community Composition of Bivalve Mollusks Collected in Aquaculture Farms and Respective Susceptibility to Antibiotics.	Salgueiro V, Reis L, Ferreira E, Botelho MJ, Manageiro V, Canica M.	Antibiotics (Basel)	10.3390/antibiotics10091135	2021
	Enhanced production of N-acetyl-glucosaminidase by marine Aeromonas caviae CHZ306 in bioreactor.	Cardozo FA, Feitosa V, Mendonca CMN, da Silva FVS, Converti A, de Souza Oliveira RP, Pessoa A.	Braz J Microbiol	10.1007/s42770-023-01088-x	2023
Genetics	Fecal Microbiota Composition, Their Interactions, and Metagenome Function in US Adults with Type 2 Diabetes According to Enterotypes.	Park S, Zhang T, Kang S.	Int J Mol Sci	10.3390/ijms24119533	2023
	At-hatch administration of probiotic to chickens can introduce beneficial changes in gut microbiota.	Baldwin S, Hughes RJ, Hao Van TT, Moore RJ, Stanley D.	PLoS One	10.1371/journal.pone.0194825	2018
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
	Characterisation of Variants of Cyclic di-GMP Turnover Proteins Associated with Semi-Constitutive rdar Morphotype Expression in Commensal and Uropathogenic Escherichia coli Strains.	Cimdins-Ahne A, Naemi AO, Li F, Simm R, Romling U.	Microorganisms	10.3390/microorganisms11082048	2023
	Environmental determinants and demographic influences on global urban microbiomes, antimicrobial resistance and pathogenicity.	Chen Y, Fu X, Ou Z, Li J, Lin S, Wu Y, Wang X, Deng Y, Sun Y.	NPJ Biofilms Microbiomes	10.1038/s41522-023-00459-4	2023
Pathogenicity	Padina boryana mediated green synthesis of crystalline palladium nanoparticles as potential nanodrug against multidrug resistant bacteria and cancer cells.	Sonbol H, Ameen F, AlYahya S, Almansob A, Alwakeel S.	Sci Rep	10.1038/s41598-021-84794-6	2021
	Headspace solid-phase microextraction method for extracting volatile constituents from the different parts of Saudi Anethum graveolens L. and their antimicrobial activity.	Aati HY, Perveen S, Aati S, Orfali R, Alqahtani JH, Al-Taweel AM, Wanner J, Aati AY.	Heliyon	10.1016/j.heliyon.2022.e09051	2022
	Molecular Epidemiology of mcr-1-Positive Escherichia coli and Klebsiella pneumoniae Isolates: Results from Russian Sentinel Surveillance (2013-2018).	Shapovalova V, Shaidullina E, Azizov I, Sheck E, Martinovich A, Dyachkova M, Matsvay A, Savochkina Y, Khafizov K, Kozlov R, Shipulin G, Edelstein M.	Microorganisms	10.3390/microorganisms10102034	2022
Phylogeny	Study of the Vaginal Microbiota in Healthy Women of Reproductive Age.	Alonzo Martinez MC, Cazorla E, Canovas E, Martinez-Blanch JF, Martinez-Blanch JF, Chenoll E, Climent E, Navarro-Lopez V.	Microorganisms	10.3390/microorganisms9051069	2021
	Diversity and phage sensitivity to phages of porcine enterotoxigenic Escherichia coli.	Gambino M, Kushwaha SK, Wu Y, van Haastrecht P, Klein-Sousa V, Lutz VT, Bejaoui S, Jensen CMC, Bojer MS, Song W, Xiao M, Taylor NMI, Nobrega FL, Brondsted L.	Appl Environ Microbiol	10.1128/aem.00807-24	2024
Genetics	Characterizations of the multi-kingdom gut microbiota in Chinese patients with gouty arthritis.	Chen C, Zhang Y, Yao X, Yan Q, Li S, Zhong Q, Liu Z, Tang F, Liu C, Li H, Zhu D, Lan W, Ling Y, Lu D, Xu H, Ning Q, Wang Y, Jiang Z, Zhang Q, Gu G, Sun L, Wang N, Wang G, Zhang A, Ullah H, Sun W, Ma W.	BMC Microbiol	10.1186/s12866-023-03097-0	2023
	Antibiotic resistance in conjunctival and enteric bacterial flora in raptors housed in a zoological garden.	Sala A, Taddei S, Santospirito D, Sandri C, Magnone W, Cabassi CS.	Vet Med Sci	10.1002/vms3.38	2016
	First isolation of verocytotoxin-producing Escherichia coli O157:H7 from sports animals in Southern Thailand.	Songsri J, Mala W, Wisessombat S, Siritham K, Cheha S, Noisa N, Wongtawan T, Klangbud WK.	Vet World	10.14202/vetworld.2022.2275-2284	2022
	Ginger essential oil and citral ameliorates atherosclerosis in ApoE^-/- mice by modulating trimethylamine-N-oxide and gut microbiota.	Panyod S, Wu WK, Peng SY, Tseng YJ, Hsieh YC, Chen RA, Huang HS, Chen YH, Chuang HL, Hsu CC, Shen TD, Yang KC, Ho CT, Wu MS, Sheen LY.	NPJ Sci Food	10.1038/s41538-023-00196-0	2023
Enzymology	Escherichia fergusonii bacteremia in a diabetic patient with pancreatic cancer.	Lai CC, Cheng A, Huang YT, Chung KP, Lee MR, Liao CH, Hsueh PR.	J Clin Microbiol	10.1128/jcm.05355-11	2011
	Genomic Characteristics and Molecular Epidemiology of Multidrug-Resistant Klebsiella pneumoniae Strains Carried by Wild Birds.	Wang X, Zhao J, Ji F, Wang M, Wu B, Qin J, Dong G, Zhao R, Wang C.	Microbiol Spectr	10.1128/spectrum.02691-22	2023
	Transposition mechanism of ISApl1-the determinant of colistin resistance dissemination.	Li W, He Z, Di W, Xu W, Li Y, Sun B.	Antimicrob Agents Chemother	10.1128/aac.01231-23	2024
	Dysbiosis in intestinal microbiome linked to fecal blood determined by direct hybridization.	Cafiero C, Re A, Pisconti S, Trombetti M, Perri M, Colosimo M, D'Amato G, Gallelli L, Cannataro R, Molinario C, Fazio A, Caroleo MC, Cione E.	3 Biotech	10.1007/s13205-020-02351-w	2020
Pathogenicity	The diarrheal mechanism of mice with a high-fat diet in a fatigued state is associated with intestinal mucosa microbiota.	Liu J, Qiao B, Deng N, Wu Y, Li D, Tan Z.	3 Biotech	10.1007/s13205-023-03491-5	2023
	Changes in Lolium perenne L. rhizosphere microbiome during phytoremediation of Cd- and Hg-contaminated soils.	Saldarriaga JF, Lopez JE, Diaz-Garcia L, Montoya-Ruiz C.	Environ Sci Pollut Res Int	10.1007/s11356-023-25501-y	2023
	Biosynthesis and Characterization of Zinc Oxide Nanoparticles and Their Impact on the Composition of Gut Microbiota in Healthy and Attention-Deficit Hyperactivity Disorder Children.	Zhou G, Yu R, Ahmed T, Jiang H, Zhang M, Lv L, Alhumaydhi FA, Allemailem KS, Li B.	Front Microbiol	10.3389/fmicb.2021.700707	2021
	Gut virome-wide association analysis identifies cross-population viral signatures for inflammatory bowel disease.	Tian X, Li S, Wang C, Zhang Y, Feng X, Yan Q, Guo R, Wu F, Wu C, Wang Y, Huo X, Ma X.	Microbiome	10.1186/s40168-024-01832-x	2024
Pathogenicity	Sex differences in colonization of gut microbiota from a man with short-term vegetarian and inulin-supplemented diet in germ-free mice.	Wang JJ, Wang J, Pang XY, Zhao LP, Tian L, Wang XP.	Sci Rep	10.1038/srep36137	2016
	Escherichia Coli: What Is and Which Are?	Cobo-Simon M, Hart R, Ochman H.	Mol Biol Evol	10.1093/molbev/msac273	2023
	Promotion of Deoxycholic Acid Effect on Colonic Cancer Cell Lines In Vitro by Altering the Mucosal Microbiota.	Ma Y, Zhang Y, Qu R, Zhou X, Sun L, Wang K, Jiang C, Zhang Z, Fu W.	Microorganisms	10.3390/microorganisms10122486	2022
	Tumor bacterial markers diagnose the initiation and four stages of colorectal cancer.	Cai P, Xiong J, Sha H, Dai X, Lu J.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1123544	2023
Genetics	Metagenomic engineering of the mammalian gut microbiome in situ.	Ronda C, Chen SP, Cabral V, Yaung SJ, Wang HH.	Nat Methods	10.1038/s41592-018-0301-y	2019
	Occurrence and Characteristics of ESBL- and Carbapenemase- Producing Escherichia coli from Wild and Feral Birds in Greece.	Athanasakopoulou Z, Diezel C, Braun SD, Sofia M, Giannakopoulos A, Monecke S, Gary D, Krahmer D, Chatzopoulos DC, Touloudi A, Birtsas P, Palli M, Georgakopoulos G, Spyrou V, Petinaki E, Ehricht R, Billinis C.	Microorganisms	10.3390/microorganisms10061217	2022
Phylogeny	icaR and icaT are Ancient Chromosome Genes Encoding Substrates of the Type III Secretion Apparatus in Shigella flexneri.	Silue N, Campbell-Valois FX.	mSphere	10.1128/msphere.00115-22	2022
	Substantial viral and bacterial diversity at the bat-tick interface.	Ortiz-Baez AS, Jaenson TGT, Holmes EC, Pettersson JH, Wilhelmsson P.	Microb Genom	10.1099/mgen.0.000942	2023
	Gastrointestinal Microbiome Disruption and Antibiotic-Associated Diarrhea in Children Receiving Antibiotic Therapy for Community-Acquired Pneumonia.	Kwon J, Kong Y, Wade M, Williams DJ, Creech CB, Evans S, Walter EB, Martin JM, Gerber JS, Newland JG, Hofto ME, Staat MA, Chambers HF, Fowler VG, Huskins WC, Pettigrew MM.	J Infect Dis	10.1093/infdis/jiac082	2022
	Characterisation of Escherichia fergusonii isolates from farm animals using an Escherichia coli virulence gene array and tissue culture adherence assays.	Wragg P, La Ragione RM, Best A, Reichel R, Anjum MF, Mafura M, Woodward MJ.	Res Vet Sci	10.1016/j.rvsc.2008.05.014	2009
	Ability of three DNA-based assays to identify presumptive Escherichia coli colonies isolated from water by the culture-based mFC agar method.	Maheux AF, Berube E, Boudreau DK, Cantin P, Boissinot M, Bissonnette L, Rodrigue L, Bergeron MG.	Water Res	10.1016/j.watres.2011.02.021	2011
Transcriptome	Magnetic chitin beads (MCB) coated with Vibrio cholerae reveals transcriptome dynamics in adult mice with a complex gut microbiota.	Qin ZX, Chen GZ, Bao W, Ma Y, Yang XM, Yi CR, Luo M, Hu J, Liu Z.	Gut Microbes	10.1080/19490976.2023.2274125	2023
Pathogenicity	Characterization of genes expressed in response to cadmium exposure in the earthworm Eisenia fetida using DDRT-PCR.	Wang X, Chang L, Sun Z, Ma H.	Ecotoxicol Environ Saf	10.1016/j.ecoenv.2010.07.015	2010
	The meconium microbiota shares more features with the amniotic fluid microbiota than the maternal fecal and vaginal microbiota.	He Q, Kwok LY, Xi X, Zhong Z, Ma T, Xu H, Meng H, Zhao F, Zhang H.	Gut Microbes	10.1080/19490976.2020.1794266	2020
Genetics	Benchmarking taxonomic classifiers with Illumina and Nanopore sequence data for clinical metagenomic diagnostic applications.	Govender KN, Eyre DW.	Microb Genom	10.1099/mgen.0.000886	2022
	Atherosclerosis amelioration by allicin in raw garlic through gut microbiota and trimethylamine-N-oxide modulation.	Panyod S, Wu WK, Chen PC, Chong KV, Yang YT, Chuang HL, Chen CC, Chen RA, Liu PY, Chung CH, Huang HS, Lin AY, Shen TD, Yang KC, Huang TF, Hsu CC, Ho CT, Kao HL, Orekhov AN, Wu MS, Sheen LY.	NPJ Biofilms Microbiomes	10.1038/s41522-022-00266-3	2022
Phylogeny	Microbial community composition and function in an urban waterway with combined sewer overflows before and after implementation of a stormwater storage pipe.	Matsui K, Miki T.	PeerJ	10.7717/peerj.14684	2023
	Cultivated Enterococcus faecium B6 from children with obesity promotes nonalcoholic fatty liver disease by the bioactive metabolite tyramine.	Wei J, Luo J, Yang F, Feng X, Zeng M, Dai W, Pan X, Yang Y, Li Y, Duan Y, Xiao X, Ye P, Yao Z, Liu Y, Huang Z, Zhang J, Zhong Y, Xu N, Luo M.	Gut Microbes	10.1080/19490976.2024.2351620	2024
Metabolism	Identification and characterization of novel phosphate regulon genes, ecs0540-ecs0544, in Escherichia coli O157:H7.	Yoshida Y, Sugiyama S, Oyamada T, Yokoyama K, Makino K.	Mol Genet Genomics	10.1007/s00438-010-0559-y	2010
	Increasing resistance in community-acquired urinary tract infections in Latin America, five years after the implementation of national therapeutic guidelines.	Bours PH, Polak R, Hoepelman AI, Delgado E, Jarquin A, Matute AJ.	Int J Infect Dis	10.1016/j.ijid.2010.02.2264	2010
Phylogeny	Identification of Staphylococcus species isolated from preputium of Aceh cattle based on 16S rRNA gene sequences analysis.	Hambal M, Admi M, Safika S, Sari WE, Ferasyi TR, Dasrul D, Balqis U, Darmawi D.	Vet World	10.14202/vetworld.2019.1540-1545	2019
Phylogeny	Design and application of an efficient cellulose-degrading microbial consortium and carboxymethyl cellulase production optimization.	Zhang G, Dong Y.	Front Microbiol	10.3389/fmicb.2022.957444	2022
Phylogeny	First description of an extended-spectrum-beta-lactamase-producing multidrug-resistant Escherichia fergusonii strain in a patient with cystitis.	Lagace-Wiens PR, Baudry PJ, Pang P, Hammond G.	J Clin Microbiol	10.1128/jcm.00364-10	2010
	In situ targeted base editing of bacteria in the mouse gut.	Brodel AK, Charpenay LH, Galtier M, Fuche FJ, Terrasse R, Poquet C, Havranek J, Pignotti S, Krawczyk A, Arraou M, Prevot G, Spadoni D, Yarnall MTN, Hessel EM, Fernandez-Rodriguez J, Duportet X, Bikard D.	Nature	10.1038/s41586-024-07681-w	2024
	Lectin-Seq: A method to profile lectin-microbe interactions in native communities.	McPherson RL, Isabella CR, Walker RL, Sergio D, Bae S, Gaca T, Raman S, Nguyen LTT, Wesener DA, Halim M, Wuo MG, Dugan A, Kerby R, Ghosh S, Rey FE, Dhennezel C, Pishchany G, Lensch V, Vlamakis H, Alm EJ, Xavier RJ, Kiessling LL.	Sci Adv	10.1126/sciadv.add8766	2023
	Naturally competent bacteria and their genetic parasites-a battle for control over horizontal gene transfer?	Vesel N, Stare E, Stefanic P, Floccari VA, Mandic-Mulec I, Dragos A.	FEMS Microbiol Rev	10.1093/femsre/fuaf035	2025
Enzymology	Analytical comparison of nine PCR primer sets designed to detect the presence of Escherichia coli/Shigella in water samples.	Maheux AF, Picard FJ, Boissinot M, Bissonnette L, Paradis S, Bergeron MG.	Water Res	10.1016/j.watres.2009.04.017	2009
Phylogeny	Compositional and Functional Characteristics of Swine Slurry Microbes through 16S rRNA Metagenomic Sequencing Approach.	Kumar H, Jang YN, Kim K, Park J, Jung MW, Park JE.	Animals (Basel)	10.3390/ani10081372	2020
	Retrospective Screening and Analysis of mcr-1 and bla _NDM in Gram-Negative Bacteria in China, 2010-2019.	Fan R, Li C, Duan R, Qin S, Liang J, Xiao M, Lv D, Jing H, Wang X.	Front Microbiol	10.3389/fmicb.2020.00121	2020
	Impact of gut microbiome on dyslipidemia in japanese adults: Assessment of the Shika-machi super preventive health examination results for causal inference.	Miyajima Y, Karashima S, Ogai K, Taniguchi K, Ogura K, Kawakami M, Nambo H, Kometani M, Aono D, Demura M, Yoneda T, Tsujiguchi H, Hara A, Nakamura H, Okamoto S.	Front Cell Infect Microbiol	10.3389/fcimb.2022.908997	2022
Metabolism	The impact of iron and heme availability on the healthy human gut microbiome in vivo and in vitro.	Celis AI, Relman DA, Huang KC.	Cell Chem Biol	10.1016/j.chembiol.2022.12.001	2023
Genetics	Genome-wide analysis of selective constraints on high stability regions of mRNA reveals multiple compensatory mutations in Escherichia coli.	Mao Y, Li Q, Zhang Y, Zhang J, Wei G, Tao S.	PLoS One	10.1371/journal.pone.0073299	2013
Phylogeny	Functional eubacteria species along with trans-domain gut inhabitants favour dysgenic diversity in oxalate stone disease.	Suryavanshi MV, Bhute SS, Gune RP, Shouche YS.	Sci Rep	10.1038/s41598-018-33773-5	2018
	Network-guided genomic and metagenomic analysis of the faecal microbiota of the critically endangered kakapo.	Waite DW, Dsouza M, Sekiguchi Y, Hugenholtz P, Taylor MW.	Sci Rep	10.1038/s41598-018-26484-4	2018
	Antibacterial activity and cytotoxicity of a novel bacteriocin isolated from Pseudomonas sp. strain 166.	Wang Y, Haqmal MA, Liang YD, Muhammad I, Zhao XO, Elken EM, Gao YH, Jia Y, He CG, Wang YM, Kong LC, Ma HX.	Microb Biotechnol	10.1111/1751-7915.14096	2022
	A comprehensive review on the medicinally valuable endosymbiotic fungi Penicillium chrysogenum.	Shaaban R, Elnaggar MS, Khalil N, Singab ANB.	Arch Microbiol	10.1007/s00203-023-03580-2	2023
	Silver Nanoparticles of Artemisia sieberi Extracts: Chemical Composition and Antimicrobial Activities.	Al-Otibi F, Alshammry NA, Alharbi RI, Bin-Jumah MN, AlSubaie MM.	Plants (Basel)	10.3390/plants12112093	2023
Genetics	Comprehensive Genomic Investigation of Tigecycline Resistance Gene tet(X4)-Bearing Strains Expanding among Different Settings.	Li R, Li Y, Peng K, Yin Y, Liu Y, He T, Bai L, Wang Z.	Microbiol Spectr	10.1128/spectrum.01633-21	2021
	Fibrino-necrotic typhlitis caused by Escherichia fergusonii in ostriches (Struthio camelus).	Herraez P, Rodriguez AF, Espinosa de los Monteros A, Acosta AB, Jaber JR, Castellano J, Castroa A.	Avian Dis	10.1637/7221-061104r	2005
Phylogeny	Phylum barrier and Escherichia coli intra-species phylogeny drive the acquisition of antibiotic-resistance genes.	Petitjean M, Condamine B, Burdet C, Denamur E, Ruppe E, Ruppe E.	Microb Genom	10.1099/mgen.0.000489	2021
	Diverse Durham collection phages demonstrate complex BREX defense responses.	Kelly A, Went SC, Mariano G, Shaw LP, Picton DM, Duffner SJ, Coates I, Herdman-Grant R, Gordeeva J, Drobiazko A, Isaev A, Lee YJ, Luyten Y, Morgan RD, Weigele P, Severinov K, Wenner N, Hinton JCD, Blower TR.	Appl Environ Microbiol	10.1128/aem.00623-23	2023
	Biosynthesized Gold, Silver, Palladium, Platinum, Copper, and Other Transition Metal Nanoparticles.	Roszczenko P, Szewczyk OK, Czarnomysy R, Bielawski K, Bielawska A.	Pharmaceutics	10.3390/pharmaceutics14112286	2022
	Fine-Scale Reconstruction of the Evolution of FII-33 Multidrug Resistance Plasmids Enables High-Resolution Genomic Surveillance.	Hu Y, Moran RA, Blackwell GA, McNally A, Zong Z.	mSystems	10.1128/msystems.00831-21	2022
	Emergence and Spread of Cephalosporinases in Wildlife: A Review.	Palmeira JD, Cunha MV, Carvalho J, Ferreira H, Fonseca C, Torres RT.	Animals (Basel)	10.3390/ani11061765	2021
Pathogenicity	Editing of a Specific Strain of Escherichia coli in the Mouse Gut Using Native Phages.	Ping L, Zhuoya L, Pei J, Jingchao C, Yi L, Guosheng L, Hailei W.	Microbiol Spectr	10.1128/spectrum.01804-22	2022
	Analysis of a poultry slaughter process: Influence of process stages on the microbiological contamination of broiler carcasses.	Althaus D, Zweifel C, Stephan R.	Ital J Food Saf	10.4081/ijfs.2017.7097	2017
	Plant-Derived Nutraceuticals in Mental Health and Brain Function: Mechanisms of Action and Therapeutic Potential.	Borrego-Ruiz A, Borrego JJ.	Int J Mol Sci	10.3390/ijms26188849	2025
	Overcoming donor variability and risks associated with fecal microbiota transplants through bacteriophage-mediated treatments.	Rasmussen TS, Mao X, Forster S, Larsen SB, Von Munchow A, Tranaes KD, Brunse A, Larsen F, Mejia JLC, Adamberg S, Hansen AK, Adamberg K, Hansen CHF, Nielsen DS.	Microbiome	10.1186/s40168-024-01820-1	2024
Phylogeny	Genomic diversity of Escherichia coli isolates from non-human primates in the Gambia.	Foster-Nyarko E, Alikhan NF, Ravi A, Thilliez G, Thomson NM, Baker D, Kay G, Cramer JD, O'Grady J, Antonio M, Pallen MJ.	Microb Genom	10.1099/mgen.0.000428	2020
	Massive annotation of bacterial L-asparaginases reveals their puzzling distribution and frequent gene transfer events.	Zielezinski A, Loch JI, Karlowski WM, Jaskolski M.	Sci Rep	10.1038/s41598-022-19689-1	2022
	Development of Decellularized Fish Skin Scaffold Decorated with Biosynthesized Silver Nanoparticles for Accelerated Burn Wound Healing.	Adhikari SP, Paudel A, Sharma A, Thapa B, Khanal N, Shastri N, Rai S, Adhikari R.	Int J Biomater	10.1155/2023/8541621	2023
	Escherichia vulneris: an unusual cause of complicated diarrhoea and sepsis in an infant. A case report and review of literature.	Jain S, Nagarjuna D, Gaind R, Chopra S, Debata PK, Dawar R, Sardana R, Yadav M.	New Microbes New Infect	10.1016/j.nmni.2016.07.002	2016
Pathogenicity	Current knowledge and perspectives of potential impacts of Salmonella enterica on the profile of the gut microbiota.	Aljahdali NH, Sanad YM, Han J, Foley SL.	BMC Microbiol	10.1186/s12866-020-02008-x	2020
Pathogenicity	Multidrug-resistant Escherichia fergusonii: a case of acute cystitis.	Savini V, Catavitello C, Talia M, Manna A, Pompetti F, Favaro M, Fontana C, Febbo F, Balbinot A, Di Berardino F, Di Bonaventura G, Di Zacomo S, Esattore F, D'Antonio D.	J Clin Microbiol	10.1128/jcm.01210-07	2008
Pathogenicity	Plasmid typing and resistance profiling of Escherichia fergusonii and other Enterobacteriaceae isolates from South Korean farm animals.	Rayamajhi N, Cha SB, Shin SW, Jung BY, Lim SK, Yoo HS.	Appl Environ Microbiol	10.1128/aem.02188-10	2011
Metabolism	Microbiome-metabolomics reveals gut microbiota associated with glycine-conjugated metabolites and polyamine metabolism in chronic kidney disease.	Feng YL, Cao G, Chen DQ, Vaziri ND, Chen L, Zhang J, Wang M, Guo Y, Zhao YY.	Cell Mol Life Sci	10.1007/s00018-019-03155-9	2019
Pathogenicity	Role of Gut Microbiome in Atherosclerosis: Molecular and Therapeutic Aspects.	Salazar J, Morillo V, Suarez MK, Castro A, Ramirez P, Rojas M, Anez R, D'Marco L, Chacin-Gonzalez M, Bermudez V.	Curr Cardiol Rev	10.2174/1573403x19666230202164524	2023
	Comprehensive Analysis of the Effect of Probiotic Intake by the Mother on Human Breast Milk and Infant Fecal Microbiota.	Shin DY, Park J, Yi DY.	J Korean Med Sci	10.3346/jkms.2021.36.e58	2021
	Characterization of antimicrobial resistance in chicken-source phylogroup F Escherichia coli: similar populations and resistance spectrums between E. coli recovered from chicken colibacillosis tissues and retail raw meats in Eastern China.	Wang M, Jiang M, Wang Z, Chen R, Zhuge X, Dai J.	Poult Sci	10.1016/j.psj.2021.101370	2021
	A comparative assessment of conventional and molecular methods, including MinION nanopore sequencing, for surveying water quality.	Acharya K, Khanal S, Pantha K, Amatya N, Davenport RJ, Werner D.	Sci Rep	10.1038/s41598-019-51997-x	2019
Enzymology	Survey of pathogens in threatened wild red-tailed Amazon parrot (Amazona brasiliensis) nestlings in Rasa Island, Brazil.	Vaz FF, Serafini PP, Locatelli-Dittrich R, Meurer R, Durigon EL, de Araujo J, Thomazelli LM, Ometto T, Sipinski EAB, Sezerban RM, Abbud MC, Raso TF.	Braz J Microbiol	10.1016/j.bjm.2017.03.004	2017
	Bacterial enteropathogens associated with diarrhea in a rural population of Haiti.	Jackson JC, Farone AL, Farone MB.	Res Rep Trop Med	10.2147/rrtm.s23426	2011
	Novel WYL domain-containing transcriptional activator acts in response to genotoxic stress in rapidly growing mycobacteria.	Keller LML, Flattich K, Weber-Ban E.	Commun Biol	10.1038/s42003-023-05592-6	2023
	Effect of Fermented Medicinal Plants as Dietary Additives on Food Preference and Fecal Microbial Quality in Dogs.	Park DH, Kothari D, Niu KM, Han SG, Yoon JE, Lee HG, Kim SK.	Animals (Basel)	10.3390/ani9090690	2019
Genetics	Prevalence and molecular characteristics of polymyxin-resistant Enterobacterales in a Chinese tertiary teaching hospital.	Xiao C, Li X, Huang L, Cao H, Han L, Ni Y, Xia H, Yang Z.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1118122	2023
Genetics	Assessment of plasmids for relating the 2020 Salmonella enterica serovar Newport onion outbreak to farms implicated by the outbreak investigation.	Commichaux S, Rand H, Javkar K, Molloy EK, Pettengill JB, Pightling A, Hoffmann M, Pop M, Jayeola V, Foley S, Luo Y.	BMC Genomics	10.1186/s12864-023-09245-0	2023
	ESBL-Producing, Carbapenem- and Ciprofloxacin-Resistant Escherichia coli in Belgian and Dutch Broiler and Pig Farms: A Cross-Sectional and Cross-Border Study.	De Koster S, Ringenier M, Lammens C, Stegeman A, Tobias T, Velkers F, Vernooij H, Kluytmans-van den Bergh M, Kluytmans J, Dewulf J, Goossens H, On Behalf Of The I-Health Study Group.	Antibiotics (Basel)	10.3390/antibiotics10080945	2021
Phylogeny	Microbial dysbiosis in pediatric patients with Crohn's disease.	Kaakoush NO, Day AS, Huinao KD, Leach ST, Lemberg DA, Dowd SE, Mitchell HM.	J Clin Microbiol	10.1128/jcm.01396-12	2012
	Emergence of plasmid-mediated mcr genes from Gram-negative bacteria at the human-animal interface.	Javed H, Saleem S, Zafar A, Ghafoor A, Shahzad AB, Ejaz H, Junaid K, Jahan S.	Gut Pathog	10.1186/s13099-020-00392-3	2020
Genetics	BMScan: using whole genome similarity to rapidly and accurately identify bacterial meningitis causing species.	Topaz N, Boxrud D, Retchless AC, Nichols M, Chang HY, Hu F, Wang X.	BMC Infect Dis	10.1186/s12879-018-3324-1	2018
Phylogeny	A Longitudinal Characterization of the Seminal Microbiota and Antibiotic Resistance in Yearling Beef Bulls Subjected to Different Rates of Gain.	Webb EM, Holman DB, Schmidt KN, Crouse MS, Dahlen CR, Cushman RA, Snider AP, McCarthy KL, Amat S.	Microbiol Spectr	10.1128/spectrum.05180-22	2023
Metabolism	Gut bacterial metabolites modulate endoplasmic reticulum stress.	Ke X, You K, Pichaud M, Haiser HJ, Graham DB, Vlamakis H, Porter JA, Xavier RJ.	Genome Biol	10.1186/s13059-021-02496-8	2021
Enzymology	Identification of a chromosome-borne class C beta-lactamase from Erwinia rhapontici.	Naas T, Aubert D, Vimont S, Nordmann P.	J Antimicrob Chemother	10.1093/jac/dkh446	2004
Phylogeny	Improved Species-Level Clinical Identification of Enterobacteriaceae through Broad-Range dnaJ PCR and Sequencing.	McLean K, Rosenthal CA, Sengupta D, Owens J, Cookson BT, Hoffman NG, Salipante SJ.	J Clin Microbiol	10.1128/jcm.00986-19	2019
Metabolism	Retinal artery occlusion is associated with compositional and functional shifts in the gut microbiome and altered trimethylamine-N-oxide levels.	Zysset-Burri DC, Keller I, Berger LE, Neyer PJ, Steuer C, Wolf S, Zinkernagel MS.	Sci Rep	10.1038/s41598-019-51698-5	2019
Metabolism	Colicins produced by the Escherichia fergusonii strains closely resemble colicins encoded by Escherichia coli.	Smajs D, Karpathy SE, Smarda J, Weinstock GM.	FEMS Microbiol Lett	10.1111/j.1574-6968.2002.tb11091.x	2002
	Higher Prevalence of Extended-Spectrum Cephalosporin-Resistant Enterobacterales in Dogs Attended for Enteric Viruses in Brazil Before and After Treatment with Cephalosporins.	Salgado-Caxito M, Moreno-Switt AI, Paes AC, Shiva C, Munita JM, Rivas L, Benavides JA.	Antibiotics (Basel)	10.3390/antibiotics10020122	2021
Metabolism	The Escherichia fergusonii iucABCD iutA genes are located within a larger chromosomal region similar to pathogenicity Islands.	Smajs D, Smarda J, Weinstock GM.	Folia Microbiol (Praha)	10.1007/bf02930946	2003
Metabolism	Extended-Spectrum-Beta-Lactamase- and Plasmid-Encoded Cephamycinase-Producing Enterobacteria in the Broiler Hatchery as a Potential Mode of Pseudo-Vertical Transmission.	Projahn M, Daehre K, Roesler U, Friese A.	Appl Environ Microbiol	10.1128/aem.02364-16	2017
Metabolism	Combining amplicon sequencing and metabolomics in cirrhotic patients highlights distinctive microbiota features involved in bacterial translocation, systemic inflammation and hepatic encephalopathy.	Iebba V, Guerrieri F, Di Gregorio V, Levrero M, Gagliardi A, Santangelo F, Sobolev AP, Circi S, Giannelli V, Mannina L, Schippa S, Merli M.	Sci Rep	10.1038/s41598-018-26509-y	2018
	Cloning and sequencing of the beta-lactamase gene and surrounding DNA sequences of Citrobacter braakii, Citrobacter murliniae, Citrobacter werkmanii, Escherichia fergusonii and Enterobacter cancerogenus.	Naas T, Aubert D, Fortineau N, Nordmann P.	FEMS Microbiol Lett	10.1111/j.1574-6968.2002.tb11374.x	2002
	Multimodal interactions of drugs, natural compounds and pollutants with the gut microbiota.	Lindell AE, Zimmermann-Kogadeeva M, Patil KR.	Nat Rev Microbiol	10.1038/s41579-022-00681-5	2022
	Antimicrobial resistance and population genomics of multidrug-resistant Escherichia coli in pig farms in mainland China.	Peng Z, Hu Z, Li Z, Zhang X, Jia C, Li T, Dai M, Tan C, Xu Z, Wu B, Chen H, Wang X.	Nat Commun	10.1038/s41467-022-28750-6	2022
Genetics	Gut Microbial and Metabolic Responses to Salmonella enterica Serovar Typhimurium and Candida albicans.	Bratburd JR, Keller C, Vivas E, Gemperline E, Li L, Rey FE, Currie CR.	mBio	10.1128/mbio.02032-18	2018
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Phylogeny	Reanalysis of the Mars500 experiment reveals common gut microbiome alterations in astronauts induced by long-duration confinement.	Brereton NJB, Pitre FE, Gonzalez E.	Comput Struct Biotechnol J	10.1016/j.csbj.2021.03.040	2021
Enzymology	Isolation of Escherichia fergusonii from the feces and internal organs of a goat with diarrhea.	Hariharan H, Lopez A, Conboy G, Coles M, Muirhead T.	Can Vet J		2007
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Metabolism	Conversion of Rutin, a Prevalent Dietary Flavonol, by the Human Gut Microbiota.	Riva A, Kolimar D, Spittler A, Wisgrill L, Herbold CW, Abranko L, Berry D.	Front Microbiol	10.3389/fmicb.2020.585428	2020
Phylogeny	Population structure analysis and laboratory monitoring of Shigella by core-genome multilocus sequence typing.	Yassine I, Lefevre S, Hansen EE, Ruckly C, Carle I, Lejay-Collin M, Fabre L, Rafei R, Clermont D, de la Gandara MP, Dabboussi F, Thomson NR, Weill FX.	Nat Commun	10.1038/s41467-022-28121-1	2022
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Enzymology	Impact of rapid identification of positive blood cultures using the Verigene system on antibiotic prescriptions: A prospective study of community-onset bacteremia in a tertiary hospital in Japan.	Hayakawa K, Mezaki K, Kobayakawa M, Yamamoto K, Mutoh Y, Tsuboi M, Hasimoto T, Nagamatsu M, Kutsuna S, Takeshita N, Katanami Y, Ishikane M, Ohmagari N.	PLoS One	10.1371/journal.pone.0181548	2017
	Novel strain-level resolution of Crohn's disease mucosa-associated microbiota via an ex vivo combination of microbe culture and metagenomic sequencing.	Teh JJ, Berendsen EM, Hoedt EC, Kang S, Zhang J, Zhang F, Liu Q, Hamilton AL, Wilson-O'Brien A, Ching J, Sung JJY, Yu J, Ng SC, Kamm MA, Morrison M.	ISME J	10.1038/s41396-021-00991-1	2021
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Genetics	Deciphering chloramphenicol biotransformation mechanisms and microbial interactions via integrated multi-omics and cultivation-dependent approaches.	Zhang J, Li X, Klumper U, Lei H, Berendonk TU, Guo F, Yu K, Yang C, Li B.	Microbiome	10.1186/s40168-022-01361-5	2022
	Microbiota in mesenteric adipose tissue from Crohn's disease promote colitis in mice.	He Z, Wu J, Gong J, Ke J, Ding T, Zhao W, Cheng WM, Luo Z, He Q, Zeng W, Yu J, Jiao N, Liu Y, Zheng B, Dai L, Zhi M, Wu X, Jobin C, Lan P.	Microbiome	10.1186/s40168-021-01178-8	2021
Phylogeny	Geography, seasonality, and host-associated population structure influence the fecal microbiome of a genetically depauparate Arctic mammal.	Bird S, Prewer E, Kutz S, Leclerc LM, Vilaca ST, Kyle CJ.	Ecol Evol	10.1002/ece3.5768	2019
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Enzymology	Improvement of detection of bacterial pathogens in normally sterile body sites with a focus on orthopedic samples by use of a commercial 16S rRNA broad-range PCR and sequence analysis.	Grif K, Heller I, Prodinger WM, Lechleitner K, Lass-Florl C, Orth D.	J Clin Microbiol	10.1128/jcm.00362-12	2012
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Genetics	Market Chickens as a Source of Antibiotic-Resistant Escherichia coli in a Peri-Urban Community in Lima, Peru.	Murray M, Salvatierra G, Davila-Barclay A, Ayzanoa B, Castillo-Vilcahuaman C, Huang M, Pajuelo MJ, Lescano AG, Cabrera L, Calderon M, Berg DE, Gilman RH, Tsukayama P.	Front Microbiol	10.3389/fmicb.2021.635871	2021
	Identification and characterization of the WYL BrxR protein and its gene as separable regulatory elements of a BREX phage restriction system.	Luyten YA, Hausman DE, Young JC, Doyle LA, Higashi KM, Ubilla-Rodriguez NC, Lambert AR, Arroyo CS, Forsberg KJ, Morgan RD, Stoddard BL, Kaiser BK.	Nucleic Acids Res	10.1093/nar/gkac311	2022
	Metaproteomic Insights Into the Microbial Community in Pozol.	Rizo J, Guillen D, Diaz-Ruiz G, Wacher C, Encarnacion S, Sanchez S, Rodriguez-Sanoja R.	Front Nutr	10.3389/fnut.2021.714814	2021
Metabolism	Degradation of raw or film-incorporated beta-cyclodextrin by enzymes and colonic bacteria.	Fetzner A, Bohm S, Schreder S, Schubert R.	Eur J Pharm Biopharm	10.1016/j.ejpb.2004.02.001	2004
	Alterations in the airborne bacterial community during Asian dust events occurring between February and March 2015 in South Korea.	Cha S, Lee D, Jang JH, Lim S, Yang D, Seo T.	Sci Rep	10.1038/srep37271	2016
	Emergence of an Auxin Sensing Domain in Plant-Associated Bacteria.	Gavira JA, Rico-Jimenez M, Ortega A, Petukhova NV, Bug DS, Castellvi A, Porozov YB, Zhulin IB, Krell T, Matilla MA.	mBio	10.1128/mbio.03363-22	2023
Metabolism	Characterisation of the bacterial microbiota of the vagina of dairy cows and isolation of pediocin-producing Pediococcus acidilactici.	Wang Y, Ametaj BN, Ambrose DJ, Ganzle MG.	BMC Microbiol	10.1186/1471-2180-13-19	2013
Pathogenicity	The CIAMIB: a Large and Metabolically Diverse Collection of Inflammation-Associated Bacteria from the Murine Gut.	Wong EO, Brownlie EJE, Ng KM, Kathirgamanathan S, Yu FB, Merrill BD, Huang KC, Martin A, Tropini C, Navarre WW.	mBio	10.1128/mbio.02949-21	2022
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Phylogeny	Conventional culture methods with commercially available media unveil the presence of novel culturable bacteria.	Ito T, Sekizuka T, Kishi N, Yamashita A, Kuroda M.	Gut Microbes	10.1080/19490976.2018.1491265	2019
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Enzymology	Oligonucleotide probe for the visualization of Escherichia coli/Escherichia fergusonii cells by in situ hybridization: specificity and potential applications.	Regnault B, Martin-Delautre S, Lejay-Collin M, Lefevre M, Grimont PA.	Res Microbiol	10.1016/s0923-2508(00)00222-9	2000
	Microbiomes of air dust collected during the ground-based closed bioregenerative life support experiment "Lunar Palace 365".	Yang J, Fu Y, Liu H.	Environ Microbiome	10.1186/s40793-022-00399-0	2022
	Beneficial Effects of Essential Oils from the Mediterranean Diet on Gut Microbiota and Their Metabolites in Ischemic Heart Disease and Type-2 Diabetes Mellitus.	Sanchez-Quintero MJ, Delgado J, Medina-Vera D, Becerra-Munoz VM, Queipo-Ortuno MI, Estevez M, Plaza-Andrades I, Rodriguez-Capitan J, Sanchez PL, Crespo-Leiro MG, Jimenez-Navarro MF, Pavon-Moron FJ.	Nutrients	10.3390/nu14214650	2022
	An ArcA-Modulated Small RNA in Pathogenic Escherichia coli K1.	Sun H, Song Y, Chen F, Zhou C, Liu P, Fan Y, Zheng Y, Wan X, Feng L.	Front Microbiol	10.3389/fmicb.2020.574833	2020
	Oncogenic Virome Benefits from the Different Vaginal Microbiome-Immune Axes.	Campisciano G, Gheit T, De Seta F, Cason C, Zanotta N, Delbue S, Ricci G, Ferrante P, Tommasino M, Comar M.	Microorganisms	10.3390/microorganisms7100414	2019
	Gut microbiota in regulatory T cell generation and function: mechanisms and health implications.	Sharma A, Sharma G, Im SH.	Gut Microbes	10.1080/19490976.2025.2516702	2025
Metabolism	Electro-fermentation triggering population selection in mixed-culture glycerol fermentation.	Moscoviz R, Trably E, Bernet N.	Microb Biotechnol	10.1111/1751-7915.12747	2018
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Phylogeny	Reads2Type: a web application for rapid microbial taxonomy identification.	Saputra D, Rasmussen S, Larsen MV, Haddad N, Sperotto MM, Aarestrup FM, Lund O, Sicheritz-Ponten T.	BMC Bioinformatics	10.1186/s12859-015-0829-0	2015
	Dynamic Changes in Fecal Microbial Communities of Neonatal Dairy Calves by Aging and Diarrhea.	Kim ET, Lee SJ, Kim TY, Lee HG, Atikur RM, Gu BH, Kim DH, Park BY, Son JK, Kim MH.	Animals (Basel)	10.3390/ani11041113	2021
Phylogeny	Co-occurrence of pederin-producing and Wolbachia endobacteria in Paederus fuscipes Curtis, 1840 (Coleoptera: Staphilinidae) and its evolutionary consequences.	Maleki-Ravasan N, Akhavan N, Raz A, Jafari M, Zakeri S, Dinparast Djadid N.	Microbiologyopen	10.1002/mbo3.777	2019
Metabolism	Nanoscale zero-valent iron/persulfate enhanced upflow anaerobic sludge blanket reactor for dye removal: Insight into microbial metabolism and microbial community.	Pan F, Zhong X, Xia D, Yin X, Li F, Zhao D, Ji H, Liu W.	Sci Rep	10.1038/srep44626	2017
	Structural Variations of Vaginal and Endometrial Microbiota: Hints on Female Infertility.	Riganelli L, Iebba V, Piccioni M, Illuminati I, Bonfiglio G, Neroni B, Calvo L, Gagliardi A, Levrero M, Merlino L, Mariani M, Capri O, Pietrangeli D, Schippa S, Guerrieri F.	Front Cell Infect Microbiol	10.3389/fcimb.2020.00350	2020
Phylogeny	Decreasing prevalence of contamination with extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E) in retail chicken meat in the Netherlands.	Huizinga P, Kluytmans-van den Bergh M, Rossen JW, Willemsen I, Verhulst C, Savelkoul PHM, Friedrich AW, Garcia-Cobos S, Kluytmans J.	PLoS One	10.1371/journal.pone.0226828	2019
	Optimization of the 16S rRNA sequencing analysis pipeline for studying in vitro communities of gut commensals.	Celis AI, Aranda-Diaz A, Culver R, Xue K, Relman D, Shi H, Huang KC.	iScience	10.1016/j.isci.2022.103907	2022
	Microbial succession during wheat bran fermentation and colonisation by human faecal microbiota as a result of niche diversification.	De Paepe K, Verspreet J, Courtin CM, Van de Wiele T.	ISME J	10.1038/s41396-019-0550-5	2020
	Evaluating the contribution of gut microbiome to the variance of porcine serum glucose and lipid concentration.	Huang X, Fang S, Yang H, Gao J, He M, Ke S, Zhao Y, Chen C, Huang L.	Sci Rep	10.1038/s41598-017-15044-x	2017
Enzymology	Development of selected bacterial groups of the rectal microbiota of healthy calves during the first week postpartum.	Schwaiger K, Storch J, Bauer C, Bauer J.	J Appl Microbiol	10.1111/jam.14484	2020
	A prospective evaluation of serum methionine-related metabolites in relation to pancreatic cancer risk in two prospective cohort studies.	Huang JY, Luu HN, Butler LM, Midttun O, Ulvik A, Wang R, Jin A, Gao YT, Tan Y, Ueland PM, Koh WP, Yuan JM.	Int J Cancer	10.1002/ijc.32994	2020
Genetics	Metabolic and genetic basis for auxotrophies in Gram-negative species.	Seif Y, Choudhary KS, Hefner Y, Anand A, Yang L, Palsson BO.	Proc Natl Acad Sci U S A	10.1073/pnas.1910499117	2020
	A 3' UTR-derived small RNA connecting nitrogen and carbon metabolism in enteric bacteria.	Walling LR, Kouse AB, Shabalina SA, Zhang H, Storz G.	Nucleic Acids Res	10.1093/nar/gkac748	2022
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	Evolution and Sequence Diversity of FhuA in Salmonella and Escherichia.	Wang Y, Chen X, Hu Y, Zhu G, White AP, Koster W.	Infect Immun	10.1128/iai.00573-18	2018
Genetics	Merging Metagenomics and Spatial Epidemiology To Understand the Distribution of Antimicrobial Resistance Genes from Enterobacteriaceae in Wild Owls.	Miller EA, Ponder JB, Willette M, Johnson TJ, VanderWaal KL.	Appl Environ Microbiol	10.1128/aem.00571-20	2020
	Modulation of Circulating Trimethylamine N-Oxide Concentrations by Dietary Supplements and Pharmacological Agents: A Systematic Review.	Kalagi NA, Abbott KA, Alburikan KA, Alkofide HA, Stojanovski E, Garg ML.	Adv Nutr	10.1093/advances/nmz012	2019
	The Prevalence and Evolutionary Conservation of Inverted Repeats in Proteobacteria.	Lavi B, Levy Karin E, Pupko T, Hazkani-Covo E.	Genome Biol Evol	10.1093/gbe/evy044	2018
	Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae.	Shaw LP, Chau KK, Kavanagh J, AbuOun M, Stubberfield E, Gweon HS, Barker L, Rodger G, Bowes MJ, Hubbard ATM, Pickford H, Swann J, Gilson D, Smith RP, Hoosdally SJ, Sebra R, Brett H, Peto TEA, Bailey MJ, Crook DW, Read DS, Anjum MF, Walker AS, Stoesser N, REHAB consortium.	Sci Adv	10.1126/sciadv.abe3868	2021
Phylogeny	Heavy metal and microbial safety assessment of raw and cooked pumpkin and Amaranthus viridis leaves grown in Abakaliki, Nigeria.	Azi F, Odo MO, Okorie PA, Njoku HA, Nwobasi VN, David E, Onu TC.	Food Sci Nutr	10.1002/fsn3.739	2018
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Genetics	O-antigen biosynthesis gene clusters of Escherichia albertii: their diversity and similarity to Escherichia coli gene clusters and the development of an O-genotyping method.	Ooka T, Seto K, Ogura Y, Nakamura K, Iguchi A, Gotoh Y, Honda M, Etoh Y, Ikeda T, Sugitani W, Konno T, Kawano K, Imuta N, Yoshiie K, Hara-Kudo Y, Murakami K, Hayashi T, Nishi J.	Microb Genom	10.1099/mgen.0.000314	2019
Biotechnology	Soleris®Enterobacteriaceae for the Detection of Enterobacteriaceae in Select Foods: AOAC Performance Tested MethodSM 121901.	Alles S, Roman B, Betts G, Jordan S, Everis L, Montei C, Biswas P, Mozola M, Donofrio R.	J AOAC Int	10.1093/jaoacint/qsaa001	2020
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Phylogeny	Genomic diversity of Escherichia coli isolates from backyard chickens and guinea fowl in the Gambia.	Foster-Nyarko E, Alikhan NF, Ravi A, Thomson NM, Jarju S, Kwambana-Adams BA, Secka A, O'Grady J, Antonio M, Pallen MJ.	Microb Genom	10.1099/mgen.0.000484	2021
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Genetics	An Approximate Bayesian Computation Approach for Modeling Genome Rearrangements.	Moshe A, Wygoda E, Ecker N, Loewenthal G, Avram O, Israeli O, Hazkani-Covo E, Pe'er I, Pupko T.	Mol Biol Evol	10.1093/molbev/msac231	2022
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	CRISPR Content Correlates with the Pathogenic Potential of Escherichia coli.	Garcia-Gutierrez E, Almendros C, Mojica FJ, Guzman NM, Garcia-Martinez J, Garcia-Martinez J.	PLoS One	10.1371/journal.pone.0131935	2015
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	Dysbiosis and compositional alterations with aging in the gut microbiota of patients with heart failure.	Kamo T, Akazawa H, Suda W, Saga-Kamo A, Shimizu Y, Yagi H, Liu Q, Nomura S, Naito AT, Takeda N, Harada M, Toko H, Kumagai H, Ikeda Y, Takimoto E, Suzuki JI, Honda K, Morita H, Hattori M, Komuro I.	PLoS One	10.1371/journal.pone.0174099	2017
Phylogeny	Comparative genomic analysis of the secondary flagellar (flag-2) system in the order Enterobacterales.	De Maayer P, Pillay T, Coutinho TA.	BMC Genomics	10.1186/s12864-020-6529-9	2020
Enzymology	Impact of investigational microbiota therapeutic RBX2660 on the gut microbiome and resistome revealed by a placebo-controlled clinical trial.	Kwak S, Choi J, Hink T, Reske KA, Blount K, Jones C, Bost MH, Sun X, Burnham CD, Dubberke ER, Dantas G, CDC Prevention Epicenter Program.	Microbiome	10.1186/s40168-020-00907-9	2020
	Organic acid production from potato starch waste fermentation by rumen microbial communities from Dutch and Thai dairy cows.	Palakawong Na Ayudthaya S, van de Weijer AHP, van Gelder AH, Stams AJM, de Vos WM, Plugge CM.	Biotechnol Biofuels	10.1186/s13068-018-1012-4	2018
Genetics	Defining the Genome Features of Escherichia albertii, an Emerging Enteropathogen Closely Related to Escherichia coli.	Ooka T, Ogura Y, Katsura K, Seto K, Kobayashi H, Kawano K, Tokuoka E, Furukawa M, Harada S, Yoshino S, Seto J, Ikeda T, Yamaguchi K, Murase K, Gotoh Y, Imuta N, Nishi J, Gomes TA, Beutin L, Hayashi T.	Genome Biol Evol	10.1093/gbe/evv211	2015
Enzymology	High prevalence of Salmonella and IMP-4-producing Enterobacteriaceae in the silver gull on Five Islands, Australia.	Dolejska M, Masarikova M, Dobiasova H, Jamborova I, Karpiskova R, Havlicek M, Carlile N, Priddel D, Cizek A, Literak I.	J Antimicrob Chemother	10.1093/jac/dkv306	2016
	Resistance determinants and their genetic context in enterobacteria from a longitudinal study of pigs reared under various husbandry conditions.	Poulin-Laprade D, Brouard JS, Gagnon N, Turcotte A, Langlois A, Matte JJ, Carrillo CD, Zaheer R, McAllister T, Topp E, Talbot G.	Appl Environ Microbiol	10.1128/aem.02612-20	2021
Metabolism	Genomic epidemiology and carbon metabolism of Escherichia coli serogroup O145 reflect contrasting phylogenies.	Collis RM, Biggs PJ, Midwinter AC, Browne AS, Wilkinson DA, Irshad H, French NP, Brightwell G, Cookson AL.	PLoS One	10.1371/journal.pone.0235066	2020
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Enzymology	Temperature gradient gel electrophoresis of fecal 16S rRNA reveals active Escherichia coli in the microbiota of patients with ulcerative colitis.	Sokol H, Lepage P, Seksik P, Dore J, Marteau P.	J Clin Microbiol	10.1128/jcm.02600-05	2006
	Bacterial persistence promotes the evolution of antibiotic resistance by increasing survival and mutation rates.	Windels EM, Michiels JE, Fauvart M, Wenseleers T, Van den Bergh B, Michiels J.	ISME J	10.1038/s41396-019-0344-9	2019
Metabolism	Non-lethal Inhibition of Gut Microbial Trimethylamine Production for the Treatment of Atherosclerosis.	Wang Z, Roberts AB, Buffa JA, Levison BS, Zhu W, Org E, Org E, Gu X, Huang Y, Zamanian-Daryoush M, Culley MK, DiDonato AJ, Fu X, Hazen JE, Krajcik D, DiDonato JA, Lusis AJ, Hazen SL.	Cell	10.1016/j.cell.2015.11.055	2015
Genetics	Hierarchical sets: analyzing pangenome structure through scalable set visualizations.	Pedersen TL.	Bioinformatics	10.1093/bioinformatics/btx034	2017
Phenotype	Study of the Aminoglycoside Subsistence Phenotype of Bacteria Residing in the Gut of Humans and Zoo Animals.	Bello Gonzalez Tde J, Zuidema T, Bor G, Smidt H, van Passel MW.	Front Microbiol	10.3389/fmicb.2015.01550	2015
Phylogeny	Ultrahigh-Throughput Multiplexing and Sequencing of >500-Base-Pair Amplicon Regions on the Illumina HiSeq 2500 Platform.	Holm JB, Humphrys MS, Robinson CK, Settles ML, Ott S, Fu L, Yang H, Gajer P, He X, McComb E, Gravitt PE, Ghanem KG, Brotman RM, Ravel J.	mSystems	10.1128/msystems.00029-19	2019
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Metabolism	Bacteriocinogeny in experimental pigs treated with indomethacin and Escherichia coli Nissle.	Bures J, Smajs D, Kvetina J, Forstl M, Smarda J, Kohoutova D, Kunes M, Cyrany J, Tacheci I, Rejchrt S, Lesna J, Vorisek V, Kopacova M.	World J Gastroenterol	10.3748/wjg.v17.i5.609	2011
	The Arginine Deiminase Operon Is Responsible for a Fitness Trade-Off in Extended-Spectrum-beta-Lactamase-Producing Strains of Escherichia coli.	Billard-Pomares T, Clermont O, Castellanos M, Magdoud F, Royer G, Condamine B, Fouteau S, Barbe V, Roche D, Cruveiller S, Medigue C, Pognard D, Glodt J, Dion S, Rigal O, Picard B, Denamur E, Branger C.	Antimicrob Agents Chemother	10.1128/aac.00635-19	2019
Genetics	The global distribution and spread of the mobilized colistin resistance gene mcr-1.	Wang R, van Dorp L, Shaw LP, Bradley P, Wang Q, Wang X, Jin L, Zhang Q, Liu Y, Rieux A, Dorai-Schneiders T, Weinert LA, Iqbal Z, Didelot X, Wang H, Balloux F.	Nat Commun	10.1038/s41467-018-03205-z	2018
Phylogeny	New Insights Into DAEC and EAEC Pathogenesis and Phylogeny.	Meza-Segura M, Zaidi MB, Vera-Ponce de Leon A, Moran-Garcia N, Martinez-Romero E, Nataro JP, Estrada-Garcia T.	Front Cell Infect Microbiol	10.3389/fcimb.2020.572951	2020
	Serine Utilization as a Potential Competition Mechanism Between Salmonella and a Chicken Cecal Bacterium.	Ha SD, Ricke SC, Nisbet DJ, Corrier DE, Deloach JR.	J Food Prot	10.4315/0362-028x-57.12.1074	1994
	Commensal Escherichia coli Aggravates Acute Necrotizing Pancreatitis through Targeting of Intestinal Epithelial Cells.	Zheng J, Lou L, Fan J, Huang C, Mei Q, Wu J, Guo Y, Lu Y, Wang X, Zeng Y.	Appl Environ Microbiol	10.1128/aem.00059-19	2019
	Plant-Mediated Zinc Oxide Nanoparticles: Advances in the New Millennium towards Understanding Their Therapeutic Role in Biomedical Applications.	Murali M, Kalegowda N, Gowtham HG, Ansari MA, Alomary MN, Alghamdi S, Shilpa N, Singh SB, Thriveni MC, Aiyaz M, Angaswamy N, Lakshmidevi N, Adil SF, Hatshan MR, Amruthesh KN.	Pharmaceutics	10.3390/pharmaceutics13101662	2021
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Metabolism	Chemoreceptor gene loss and acquisition via horizontal gene transfer in Escherichia coli.	Borziak K, Fleetwood AD, Zhulin IB.	J Bacteriol	10.1128/jb.00421-13	2013
	Antibacterial Efficacy of Silver Nanoparticles on Endometritis Caused by Prevotella melaninogenica and Arcanobacterum pyogenes in Dairy Cattle.	Gurunathan S, Choi YJ, Kim JH.	Int J Mol Sci	10.3390/ijms19041210	2018
Pathogenicity	Cleaning and disinfection programs against Campylobacter jejuni for broiler chickens: productive performance, microbiological assessment and characterization.	de Castro Burbarelli MF, do Valle Polycarpo G, Deliberali Lelis K, Granghelli CA, Carao de Pinho AC, Ribeiro Almeida Queiroz S, Fernandes AM, Moro de Souza RL, Gaglianone Moro ME, de Andrade Bordin R, de Albuquerque R.	Poult Sci	10.3382/ps/pex153	2017
	Automated pangenomic analysis in target selection for PCR detection and identification of bacteria by use of ssGeneFinder Webserver and its application to Salmonella enterica serovar Typhi.	Ho CC, Wu AK, Tse CW, Yuen KY, Lau SK, Woo PC.	J Clin Microbiol	10.1128/jcm.06843-11	2012
	Immunomodulatory and Prebiotic Effects of 2'-Fucosyllactose in Suckling Rats.	Azagra-Boronat I, Massot-Cladera M, Mayneris-Perxachs J, Knipping K, Van't Land B, Tims S, Stahl B, Garssen J, Franch A, Castell M, Rodriguez-Lagunas MJ, Perez-Cano FJ.	Front Immunol	10.3389/fimmu.2019.01773	2019
	Bacterial diversity in meconium of preterm neonates and evolution of their fecal microbiota during the first month of life.	Moles L, Gomez M, Heilig H, Bustos G, Fuentes S, de Vos W, Fernandez L, Rodriguez JM, Jimenez E.	PLoS One	10.1371/journal.pone.0066986	2013
Pathogenicity	The Prevalence of Extended-Spectrum Beta-Lactamase-Producing Multidrug-Resistant Escherichia Coli in Poultry Chickens and Variation According to Farming Practices in Punjab, India.	Brower CH, Mandal S, Hayer S, Sran M, Zehra A, Patel SJ, Kaur R, Chatterjee L, Mishra S, Das BR, Singh P, Singh R, Gill JPS, Laxminarayan R.	Environ Health Perspect	10.1289/ehp292	2017
Enzymology	Examination of equine glandular stomach lesions for bacteria, including Helicobacter spp by fluorescence in situ hybridisation.	Husted L, Jensen TK, Olsen SN, Molbak L.	BMC Microbiol	10.1186/1471-2180-10-84	2010
Genetics	The landscape of bacterial presence in tumor and adjacent normal tissue across 9 major cancer types using TCGA exome sequencing.	Rodriguez RM, Hernandez BY, Menor M, Deng Y, Khadka VS.	Comput Struct Biotechnol J	10.1016/j.csbj.2020.03.003	2020
Metabolism	Prevalence of plasmid-mediated quinolone resistance and its association with extended-spectrum beta-lactamase and AmpC beta-lactamase in Enterobacteriaceae.	Jeong HS, Bae IK, Shin JH, Jung HJ, Kim SH, Lee JY, Oh SH, Kim HR, Chang CL, Kho WG, Lee JN.	Korean J Lab Med	10.3343/kjlm.2011.31.4.257	2011
Enzymology	Molecular identification of clinical "difficult-to-identify" microbes from sequencing 16S ribosomal DNA and internal transcribed spacer 2.	Cheng C, Sun J, Zheng F, Wu K, Rui Y.	Ann Clin Microbiol Antimicrob	10.1186/1476-0711-13-1	2014
Phylogeny	Whole-genome sequencing of uropathogenic Escherichia coli reveals long evolutionary history of diversity and virulence.	Lo Y, Zhang L, Foxman B, Zollner S.	Infect Genet Evol	10.1016/j.meegid.2015.06.023	2015
	The role of the microbiome in NAFLD and NASH.	Kolodziejczyk AA, Zheng D, Shibolet O, Elinav E.	EMBO Mol Med	10.15252/emmm.201809302	2019
Pathogenicity	Associations among Antibiotic and Phage Resistance Phenotypes in Natural and Clinical Escherichia coli Isolates.	Allen RC, Pfrunder-Cardozo KR, Meinel D, Egli A, Hall AR.	mBio	10.1128/mbio.01341-17	2017
	Uncovering the composition of microbial community structure and metagenomics among three gut locations in pigs with distinct fatness.	Yang H, Huang X, Fang S, Xin W, Huang L, Chen C.	Sci Rep	10.1038/srep27427	2016
	A Colorimetric DNA Hybridization Method for the Detection of Escherichia coli in Foods.	Hsu HY, Chan SW, Sobell DI, Halbert DN, Groody EP.	J Food Prot	10.4315/0362-028x-54.4.249	1991
	Microbiome analysis reveals the abundance of bacterial pathogens in Rousettus leschenaultii guano.	Banskar S, Bhute SS, Suryavanshi MV, Punekar S, Shouche YS.	Sci Rep	10.1038/srep36948	2016
Phylogeny	Development of a novel genus-specific real-time PCR assay for detection and differentiation of Bartonella species and genotypes.	Diaz MH, Bai Y, Malania L, Winchell JM, Kosoy MY.	J Clin Microbiol	10.1128/jcm.06621-11	2012
Genetics	Comparative genomics analysis of pKF3-94 in Klebsiella pneumoniae reveals plasmid compatibility and horizontal gene transfer.	Ying J, Wu S, Zhang K, Wang Z, Zhu W, Zhu M, Zhang Y, Cheng C, Wang H, Tou H, Zhu C, Li P, Ying J, Xu T, Yi H, Li J, Ni L, Xu Z, Bao Q, Lu J.	Front Microbiol	10.3389/fmicb.2015.00831	2015
Genetics	To kill or to be killed: pangenome analysis of Escherichia coli strains reveals a tailocin specific for pandemic ST131.	Tantoso E, Eisenhaber B, Kirsch M, Shitov V, Zhao Z, Eisenhaber F.	BMC Biol	10.1186/s12915-022-01347-7	2022
Genetics	Whole-Genome Analysis of Antimicrobial-Resistant and Extraintestinal Pathogenic Escherichia coli in River Water.	Gomi R, Matsuda T, Matsumura Y, Yamamoto M, Tanaka M, Ichiyama S, Yoneda M.	Appl Environ Microbiol	10.1128/aem.02703-16	2017
Genetics	imGLAD: accurate detection and quantification of target organisms in metagenomes.	Castro JC, Rodriguez-R LM, Harvey WT, Weigand MR, Hatt JK, Carter MQ, Konstantinidis KT.	PeerJ	10.7717/peerj.5882	2018
Phylogeny	Illumina-based analysis of microbial community diversity.	Degnan PH, Ochman H.	ISME J	10.1038/ismej.2011.74	2012
	Characterization of Biosurfactant Produced during Degradation of Hydrocarbons Using Crude Oil As Sole Source of Carbon.	Patowary K, Patowary R, Kalita MC, Deka S.	Front Microbiol	10.3389/fmicb.2017.00279	2017
Metabolism	Marinobacter sp. from marine sediments produce highly stable surface-active agents for combatting marine oil spills.	Raddadi N, Giacomucci L, Totaro G, Fava F.	Microb Cell Fact	10.1186/s12934-017-0797-3	2017
	Extended-spectrum beta-lactamase-encoding genes are spreading on a wide range of Escherichia coli plasmids existing prior to the use of third-generation cephalosporins.	Branger C, Ledda A, Billard-Pomares T, Doublet B, Fouteau S, Barbe V, Roche D, Cruveiller S, Medigue C, Castellanos M, Decre D, Drieux-Rouze L, Clermont O, Glodt J, Tenaillon O, Cloeckaert A, Arlet G, Denamur E.	Microb Genom	10.1099/mgen.0.000203	2018
Enzymology	A survey of the aerobic bacteria in the feces of captive raptors.	Bangert RL, Ward AC, Stauber EH, Cho BR, Widders PR.	Avian Dis	10.2307/1590948	1988
Genetics	Composition, taxonomy and functional diversity of the oropharynx microbiome in individuals with schizophrenia and controls.	Castro-Nallar E, Bendall ML, Perez-Losada M, Sabuncyan S, Severance EG, Dickerson FB, Schroeder JR, Yolken RH, Crandall KA.	PeerJ	10.7717/peerj.1140	2015
Metabolism	16S rRNA gene profiling and genome reconstruction reveal community metabolic interactions and prebiotic potential of medicinal herbs used in neurodegenerative disease and as nootropics.	Peterson CT, Sharma V, Iablokov SN, Albayrak L, Khanipov K, Uchitel S, Chopra D, Mills PJ, Fofanov Y, Rodionov DA, Peterson SN.	PLoS One	10.1371/journal.pone.0213869	2019
Metabolism	l-Carnitine in omnivorous diets induces an atherogenic gut microbial pathway in humans.	Koeth RA, Lam-Galvez BR, Kirsop J, Wang Z, Levison BS, Gu X, Copeland MF, Bartlett D, Cody DB, Dai HJ, Culley MK, Li XS, Fu X, Wu Y, Li L, DiDonato JA, Tang WHW, Garcia-Garcia JC, Hazen SL.	J Clin Invest	10.1172/jci94601	2019
Enzymology	Mechanistic insights into the allosteric regulation of bacterial ADP-glucose pyrophosphorylases.	Comino N, Cifuente JO, Marina A, Orrantia A, Eguskiza A, Guerin ME.	J Biol Chem	10.1074/jbc.m116.773408	2017
Metabolism	Microbial and Genetic Resources for Cobalamin (Vitamin B12) Biosynthesis: From Ecosystems to Industrial Biotechnology.	Balabanova L, Averianova L, Marchenok M, Son O, Tekutyeva L.	Int J Mol Sci	10.3390/ijms22094522	2021
Phylogeny	Quantitative analysis of commensal Escherichia coli populations reveals host-specific enterotypes at the intra-species level.	Smati M, Clermont O, Bleibtreu A, Fourreau F, David A, Daubie AS, Hignard C, Loison O, Picard B, Denamur E.	Microbiologyopen	10.1002/mbo3.266	2015
	The effect of dietary supplementation with spent cider yeast on the Swine distal gut microbiome.	Upadrasta A, O'Sullivan L, O'Sullivan O, Sexton N, Lawlor PG, Hill C, Fitzgerald GF, Stanton C, Ross RP.	PLoS One	10.1371/journal.pone.0075714	2013
Metabolism	Identification of a third osmoprotectant transport system, the osmU system, in Salmonella enterica.	Frossard SM, Khan AA, Warrick EC, Gately JM, Hanson AD, Oldham ML, Sanders DA, Csonka LN.	J Bacteriol	10.1128/jb.00495-12	2012
	Using Amplicon Sequencing To Characterize and Monitor Bacterial Diversity in Drinking Water Distribution Systems.	Shaw JL, Monis P, Weyrich LS, Sawade E, Drikas M, Cooper AJ.	Appl Environ Microbiol	10.1128/aem.01297-15	2015
Genetics	Protective role of the vulture facial skin and gut microbiomes aid adaptation to scavenging.	Zepeda Mendoza ML, Roggenbuck M, Manzano Vargas K, Hansen LH, Brunak S, Gilbert MTP, Sicheritz-Ponten T.	Acta Vet Scand	10.1186/s13028-018-0415-3	2018
Phylogeny	Cryptic lineages of the genus Escherichia.	Walk ST, Alm EW, Gordon DM, Ram JL, Toranzos GA, Tiedje JM, Whittam TS.	Appl Environ Microbiol	10.1128/aem.01262-09	2009
Genetics	Sequencing a piece of history: complete genome sequence of the original Escherichia coli strain.	Dunne KA, Chaudhuri RR, Rossiter AE, Beriotto I, Browning DF, Squire D, Cunningham AF, Cole JA, Loman N, Henderson IR.	Microb Genom	10.1099/mgen.0.000106	2017
Pathogenicity	A population genomics approach to exploiting the accessory 'resistome' of Escherichia coli.	Goldstone RJ, Smith DGE.	Microb Genom	10.1099/mgen.0.000108	2017
Enzymology	A Novel Triculture System (CC3) for Simultaneous Enzyme Production and Hydrolysis of Common Grasses through Submerged Fermentation.	Leo VV, Passari AK, Joshi JB, Mishra VK, Uthandi S, Ramesh N, Gupta VK, Saikia R, Sonawane VC, Singh BP.	Front Microbiol	10.3389/fmicb.2016.00447	2016
Phylogeny	Matrix-assisted laser desorption ionization-time of flight mass spectrometry for the discrimination of food-borne microorganisms.	Mazzeo MF, Sorrentino A, Gaita M, Cacace G, Di Stasio M, Facchiano A, Comi G, Malorni A, Siciliano RA.	Appl Environ Microbiol	10.1128/aem.72.2.1180-1189.2006	2006
Phylogeny	Evaluating the occurrence of Escherichia albertii in chicken carcass rinses by PCR, Vitek analysis, and sequencing of the rpoB gene.	Lindsey RL, Fedorka-Cray PJ, Abley M, Turpin JB, Meinersmann RJ.	Appl Environ Microbiol	10.1128/aem.03681-14	2015
Enzymology	Evaluation of high-throughput PCR and microarray-based assay in conjunction with automated DNA extraction instruments for diagnosis of sepsis.	Laakso S, Kirveskari J, Tissari P, Maki M.	PLoS One	10.1371/journal.pone.0026655	2011
Phylogeny	Multilaboratory validation of rapid spot tests for identification of Escherichia coli.	York MK, Baron EJ, Clarridge JE, Thomson RB, Weinstein MP.	J Clin Microbiol	10.1128/jcm.38.9.3394-3398.2000	2000
Phylogeny	No evidence for a bovine mastitis Escherichia coli pathotype.	Leimbach A, Poehlein A, Vollmers J, Gorlich D, Daniel R, Dobrindt U.	BMC Genomics	10.1186/s12864-017-3739-x	2017
Phylogeny	Virulence genotypes and phylogenetic background of Escherichia coli serogroup O6 isolates from humans, dogs, and cats.	Johnson JR, Johnston B, Clabots CR, Kuskowski MA, Roberts E, DebRoy C.	J Clin Microbiol	10.1128/jcm.00674-07	2008
Pathogenicity	Quantitative analysis of persister fractions suggests different mechanisms of formation among environmental isolates of E. coli.	Hofsteenge N, van Nimwegen E, Silander OK.	BMC Microbiol	10.1186/1471-2180-13-25	2013
Metabolism	Natural transformation facilitates transfer of transposons, integrons and gene cassettes between bacterial species.	Domingues S, Harms K, Fricke WF, Johnsen PJ, da Silva GJ, Nielsen KM.	PLoS Pathog	10.1371/journal.ppat.1002837	2012
	Benchmarking of methods for genomic taxonomy.	Larsen MV, Cosentino S, Lukjancenko O, Saputra D, Rasmussen S, Hasman H, Sicheritz-Ponten T, Aarestrup FM, Ussery DW, Lund O.	J Clin Microbiol	10.1128/jcm.02981-13	2014
Metabolism	Confirmational identification of Escherichia coli, a comparison of genotypic and phenotypic assays for glutamate decarboxylase and beta-D-glucuronidase.	McDaniels AE, Rice EW, Reyes AL, Johnson CH, Haugland RA, Stelma GN.	Appl Environ Microbiol	10.1128/aem.62.9.3350-3354.1996	1996
Metabolism	Gut Microbial Metabolite TMAO Enhances Platelet Hyperreactivity and Thrombosis Risk.	Zhu W, Gregory JC, Org E, Org E, Buffa JA, Gupta N, Wang Z, Li L, Fu X, Wu Y, Mehrabian M, Sartor RB, McIntyre TM, Silverstein RL, Tang WHW, DiDonato JA, Brown JM, Lusis AJ, Hazen SL.	Cell	10.1016/j.cell.2016.02.011	2016
	A Bioinformatic Analysis of Integrative Mobile Genetic Elements Highlights Their Role in Bacterial Adaptation.	Durrant MG, Li MM, Siranosian BA, Montgomery SB, Bhatt AS.	Cell Host Microbe	10.1016/j.chom.2019.10.022	2020
	Within-species lateral genetic transfer and the evolution of transcriptional regulation in Escherichia coli and Shigella.	Skippington E, Ragan MA.	BMC Genomics	10.1186/1471-2164-12-532	2011
	CRISPR distribution within the Escherichia coli species is not suggestive of immunity-associated diversifying selection.	Touchon M, Charpentier S, Clermont O, Rocha EP, Denamur E, Branger C.	J Bacteriol	10.1128/jb.01307-10	2011
Metabolism	Complex transcriptional and post-transcriptional regulation of an enzyme for lipopolysaccharide modification.	Moon K, Six DA, Lee HJ, Raetz CR, Gottesman S.	Mol Microbiol	10.1111/mmi.12257	2013
Genetics	Phylogenetic incongruence in E. coli O104: understanding the evolutionary relationships of emerging pathogens in the face of homologous recombination.	Hao W, Allen VG, Jamieson FB, Low DE, Alexander DC.	PLoS One	10.1371/journal.pone.0033971	2012
Phylogeny	Extraintestinal pathogenic Escherichia coli strains of avian and human origin: link between phylogenetic relationships and common virulence patterns.	Moulin-Schouleur M, Reperant M, Laurent S, Bree A, Mignon-Grasteau S, Germon P, Rasschaert D, Schouler C.	J Clin Microbiol	10.1128/jcm.00037-07	2007
Pathogenicity	Cross-sectional and longitudinal comparisons of the predominant fecal microbiota compositions of a group of pediatric patients with cystic fibrosis and their healthy siblings.	Duytschaever G, Huys G, Huys G, Bekaert M, Boulanger L, De Boeck K, Vandamme P.	Appl Environ Microbiol	10.1128/aem.05933-11	2011
	A null model for microbial diversification.	Straub TJ, Zhaxybayeva O.	Proc Natl Acad Sci U S A	10.1073/pnas.1619993114	2017
Metabolism	Characterization of two UDP-Gal:GalNAc-diphosphate-lipid beta1,3-galactosyltransferases WbwC from Escherichia coli serotypes O104 and O5.	Wang S, Czuchry D, Liu B, Vinnikova AN, Gao Y, Vlahakis JZ, Szarek WA, Wang L, Feng L, Brockhausen I.	J Bacteriol	10.1128/jb.01698-14	2014
	Escherichia albertii in wild and domestic birds.	Oaks JL, Besser TE, Walk ST, Gordon DM, Beckmen KB, Burek KA, Haldorson GJ, Bradway DS, Ouellette L, Rurangirwa FR, Davis MA, Dobbin G, Whittam TS.	Emerg Infect Dis	10.3201/eid1604.090695	2010
	Phylogeny Reconstruction with Alignment-Free Method That Corrects for Horizontal Gene Transfer.	Bromberg R, Grishin NV, Otwinowski Z.	PLoS Comput Biol	10.1371/journal.pcbi.1004985	2016
Pathogenicity	Ganoderma lucidum reduces obesity in mice by modulating the composition of the gut microbiota.	Chang CJ, Lin CS, Lu CC, Martel J, Ko YF, Ojcius DM, Tseng SF, Wu TR, Chen YY, Young JD, Lai HC.	Nat Commun	10.1038/ncomms8489	2015
	Escherichia coli YafP protein modulates DNA damaging property of the nitroaromatic compounds.	Gutierrez A, Elez M, Clermont O, Denamur E, Matic I.	Nucleic Acids Res	10.1093/nar/gkr050	2011
	The microbiome of uncontacted Amerindians.	Clemente JC, Pehrsson EC, Blaser MJ, Sandhu K, Gao Z, Wang B, Magris M, Hidalgo G, Contreras M, Noya-Alarcon O, Lander O, McDonald J, Cox M, Walter J, Oh PL, Ruiz JF, Rodriguez S, Shen N, Song SJ, Metcalf J, Knight R, Dantas G, Dominguez-Bello MG.	Sci Adv	10.1126/sciadv.1500183	2015
Metabolism	PhoB activates Escherichia coli O157:H7 virulence factors in response to inorganic phosphate limitation.	Chekabab SM, Jubelin G, Dozois CM, Harel J.	PLoS One	10.1371/journal.pone.0094285	2014
Phylogeny	Whole-genome phylogeny of Escherichia coli/Shigella group by feature frequency profiles (FFPs).	Sims GE, Kim SH.	Proc Natl Acad Sci U S A	10.1073/pnas.1105168108	2011
Pathogenicity	Dietary iron depletion at weaning imprints low microbiome diversity and this is not recovered with oral Nano Fe(III).	Pereira DI, Aslam MF, Frazer DM, Schmidt A, Walton GE, McCartney AL, Gibson GR, Anderson GJ, Powell JJ.	Microbiologyopen	10.1002/mbo3.213	2015
Metabolism	Expression of Shigella flexneri gluQ-rs gene is linked to dksA and controlled by a transcriptional terminator.	Caballero VC, Toledo VP, Maturana C, Fisher CR, Payne SM, Salazar JC.	BMC Microbiol	10.1186/1471-2180-12-226	2012
Metabolism	Core and panmetabolism in Escherichia coli.	Vieira G, Sabarly V, Bourguignon PY, Durot M, Le Fevre F, Mornico D, Vallenet D, Bouvet O, Denamur E, Schachter V, Medigue C.	J Bacteriol	10.1128/jb.01192-10	2011
	Histo-blood group antigen-like substances of human enteric bacteria as specific adsorbents for human noroviruses.	Miura T, Sano D, Suenaga A, Yoshimura T, Fuzawa M, Nakagomi T, Nakagomi O, Okabe S.	J Virol	10.1128/jvi.01060-13	2013
Metabolism	A commensal gone bad: complete genome sequence of the prototypical enterotoxigenic Escherichia coli strain H10407.	Crossman LC, Chaudhuri RR, Beatson SA, Wells TJ, Desvaux M, Cunningham AF, Petty NK, Mahon V, Brinkley C, Hobman JL, Savarino SJ, Turner SM, Pallen MJ, Penn CW, Parkhill J, Turner AK, Johnson TJ, Thomson NR, Smith SG, Henderson IR.	J Bacteriol	10.1128/jb.00710-10	2010
Phylogeny	The Changing Face of the Family Enterobacteriaceae (Order: "Enterobacterales"): New Members, Taxonomic Issues, Geographic Expansion, and New Diseases and Disease Syndromes.	Janda JM, Abbott SL.	Clin Microbiol Rev	10.1128/cmr.00174-20	2021
Metabolism	Using comparative genomics to uncover new kinds of protein-based metabolic organelles in bacteria.	Jorda J, Lopez D, Wheatley NM, Yeates TO.	Protein Sci	10.1002/pro.2196	2013
Phylogeny	A very early-branching Staphylococcus aureus lineage lacking the carotenoid pigment staphyloxanthin.	Holt DC, Holden MT, Tong SY, Castillo-Ramirez S, Clarke L, Quail MA, Currie BJ, Parkhill J, Bentley SD, Feil EJ, Giffard PM.	Genome Biol Evol	10.1093/gbe/evr078	2011
	Homologs of the small RNA SgrS are broadly distributed in enteric bacteria but have diverged in size and sequence.	Horler RS, Vanderpool CK.	Nucleic Acids Res	10.1093/nar/gkp501	2009
Phylogeny	A comparative genomic analysis of diverse clonal types of enterotoxigenic Escherichia coli reveals pathovar-specific conservation.	Sahl JW, Steinsland H, Redman JC, Angiuoli SV, Nataro JP, Sommerfelt H, Rasko DA.	Infect Immun	10.1128/iai.00932-10	2011
Metabolism	Structuring the bacterial genome: Y1-transposases associated with REP-BIME sequences.	Ton-Hoang B, Siguier P, Quentin Y, Onillon S, Marty B, Fichant G, Chandler M.	Nucleic Acids Res	10.1093/nar/gkr1198	2012
Enzymology	Structural explanation for allolactose (lac operon inducer) synthesis by lacZ beta-galactosidase and the evolutionary relationship between allolactose synthesis and the lac repressor.	Wheatley RW, Lo S, Jancewicz LJ, Dugdale ML, Huber RE.	J Biol Chem	10.1074/jbc.m113.455436	2013
	Phylogenetic comparisons reveal multiple acquisitions of the toxin genes by enterotoxigenic Escherichia coli strains of different evolutionary lineages.	Turner SM, Chaudhuri RR, Jiang ZD, DuPont H, Gyles C, Penn CW, Pallen MJ, Henderson IR.	J Clin Microbiol	10.1128/jcm.01474-06	2006
Phylogeny	Single-nucleotide polymorphism phylotyping of Escherichia coli.	Hommais F, Pereira S, Acquaviva C, Escobar-Paramo P, Denamur E.	Appl Environ Microbiol	10.1128/aem.71.8.4784-4792.2005	2005
	The tip of the tail needle affects the rate of DNA delivery by bacteriophage P22.	Leavitt JC, Gogokhia L, Gilcrease EB, Bhardwaj A, Cingolani G, Casjens SR.	PLoS One	10.1371/journal.pone.0070936	2013
Genetics	Complete genome sequence and comparative metabolic profiling of the prototypical enteroaggregative Escherichia coli strain 042.	Chaudhuri RR, Sebaihia M, Hobman JL, Webber MA, Leyton DL, Goldberg MD, Cunningham AF, Scott-Tucker A, Ferguson PR, Thomas CM, Frankel G, Tang CM, Dudley EG, Roberts IS, Rasko DA, Pallen MJ, Parkhill J, Nataro JP, Thomson NR, Henderson IR.	PLoS One	10.1371/journal.pone.0008801	2010
	Molecular analysis of asymptomatic bacteriuria Escherichia coli strain VR50 reveals adaptation to the urinary tract by gene acquisition.	Beatson SA, Ben Zakour NL, Totsika M, Forde BM, Watts RE, Mabbett AN, Szubert JM, Sarkar S, Phan MD, Peters KM, Petty NK, Alikhan NF, Sullivan MJ, Sullivan MJ, Gawthorne JA, Stanton-Cook M, Nhu NT, Chong TM, Yin WF, Chan KG, Hancock V, Ussery DW, Ulett GC, Schembri MA.	Infect Immun	10.1128/iai.02810-14	2015
	Effect of antimicrobial growth promoter administration on the intestinal microbiota of beef cattle.	Reti KL, Thomas MC, Yanke LJ, Selinger LB, Inglis GD.	Gut Pathog	10.1186/1757-4749-5-8	2013
Genetics	Small variable segments constitute a major type of diversity of bacterial genomes at the species level.	Touzain F, Denamur E, Medigue C, Barbe V, El Karoui M, Petit MA.	Genome Biol	10.1186/gb-2010-11-4-r45	2010
Genetics	Insights from 20 years of bacterial genome sequencing.	Land M, Hauser L, Jun SR, Nookaew I, Leuze MR, Ahn TH, Karpinets T, Lund O, Kora G, Wassenaar T, Poudel S, Ussery DW.	Funct Integr Genomics	10.1007/s10142-015-0433-4	2015
	Diversification of the Salmonella fimbriae: a model of macro- and microevolution.	Yue M, Rankin SC, Blanchet RT, Nulton JD, Edwards RA, Schifferli DM.	PLoS One	10.1371/journal.pone.0038596	2012
	Selection-driven transcriptome polymorphism in Escherichia coli/Shigella species.	Le Gall T, Darlu P, Escobar-Paramo P, Picard B, Denamur E.	Genome Res	10.1101/gr.2405905	2005
	Molecular keys to speciation: DNA polymorphism and the control of genetic exchange in enterobacteria.	Vulic M, Dionisio F, Taddei F, Radman M.	Proc Natl Acad Sci U S A	10.1073/pnas.94.18.9763	1997
Metabolism	Identification of a regulated alkaline phosphatase, a cell surface-associated lipoprotein, in Mycobacterium smegmatis.	Kriakov J, Lee Sh, Jacobs WR.	J Bacteriol	10.1128/jb.185.16.4983-4991.2003	2003
Metabolism	Identification and characterization of Cronobacter iron acquisition systems.	Grim CJ, Kothary MH, Gopinath G, Jarvis KG, Beaubrun JJ, McClelland M, Tall BD, Franco AA.	Appl Environ Microbiol	10.1128/aem.01457-12	2012
Metabolism	Genomic comparison of Escherichia coli O104:H4 isolates from 2009 and 2011 reveals plasmid, and prophage heterogeneity, including shiga toxin encoding phage stx2.	Ahmed SA, Awosika J, Baldwin C, Bishop-Lilly KA, Biswas B, Broomall S, Chain PS, Chertkov O, Chokoshvili O, Coyne S, Davenport K, Detter JC, Dorman W, Erkkila TH, Folster JP, Frey KG, George M, Gleasner C, Henry M, Hill KK, Hubbard K, Insalaco J, Johnson S, Kitzmiller A, Krepps M, Lo CC, Luu T, McNew LA, Minogue T, Munk CA, Osborne B, Patel M, Reitenga KG, Rosenzweig CN, Shea A, Shen X, Strockbine N, Tarr C, Teshima H, van Gieson E, Verratti K, Wolcott M, Xie G, Sozhamannan S, Gibbons HS, Threat Characterization Consortium.	PLoS One	10.1371/journal.pone.0048228	2012
Pathogenicity	A weak adaptive response to alkylation damage in Salmonella typhimurium.	Vaughan P, Sedgwick B.	J Bacteriol	10.1128/jb.173.12.3656-3662.1991	1991
	A novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and DNA viral systems.	Zhang D, Iyer LM, Aravind L.	Nucleic Acids Res	10.1093/nar/gkr036	2011
Genetics	Comparison of the Escherichia coli K-12 genome with sampled genomes of a Klebsiella pneumoniae and three salmonella enterica serovars, Typhimurium, Typhi and Paratyphi.	McClelland M, Florea L, Sanderson K, Clifton SW, Parkhill J, Churcher C, Dougan G, Wilson RK, Miller W.	Nucleic Acids Res	10.1093/nar/28.24.4974	2000
Phylogeny	Multiplex polymerase chain reaction for identification of Escherichia coli, Escherichia albertii and Escherichia fergusonii.	Lindsey RL, Garcia-Toledo L, Fasulo D, Gladney LM, Strockbine N	J Microbiol Methods	10.1016/j.mimet.2017.06.005	2017
Metabolism	Degradation of curcuminoids by in vitro pure culture fermentation.	Tan S, Rupasinghe TW, Tull DL, Boughton B, Oliver C, McSweeny C, Gras SL, Augustin MA	J Agric Food Chem	10.1021/jf5031168	2014
Phylogeny	Pathogenic and multidrug-resistant Escherichia fergusonii from broiler chicken.	Forgetta V, Rempel H, Malouin F, Vaillancourt R Jr, Topp E, Dewar K, Diarra MS	Poult Sci	10.3382/ps.2011-01738	2012
Phylogeny	Escherichia fergusonii and Enterobacter taylorae, two new species of Enterobacteriaceae isolated from clinical specimens.	Farmer JJ 3rd, Fanning GR, Davis BR, O'Hara CM, Riddle C, Hickman-Brenner FW, Asbury MA, Lowery VA 3rd, Brenner DJ	J Clin Microbiol	10.1128/jcm.21.1.77-81.1985	1985
	Crystal structure of the BREX phage defence protein BrxA.	Beck IN, Picton DM, Blower TR	Curr Res Struct Biol	10.1016/j.crstbi.2022.06.001	2022
Phylogeny	Escherichia ruysiae sp. nov., a novel Gram-stain-negative bacterium, isolated from a faecal sample of an international traveller.	van der Putten BCL, Matamoros S, Mende DR, Scholl ER, Consortium C, Schultsz C.	Int J Syst Evol Microbiol	10.1099/ijsem.0.004609	2021
Phylogeny	The new species Enterobacter oryziphilus sp. nov. and Enterobacter oryzendophyticus sp. nov. are key inhabitants of the endosphere of rice.	Hardoim PR, Nazir R, Sessitsch A, Elhottova D, Korenblum E, van Overbeek LS, van Elsas JD.	BMC Microbiol	10.1186/1471-2180-13-164	2013
Phylogeny	Intestinirhabdus alba gen. nov., sp. nov., a novel genus of the family Enterobacteriaceae, isolated from the gut of plastic-eating larvae of the Coleoptera insect Zophobas atratus.	Xu Z, Xia M, Huo YX, Yang Y	Int J Syst Evol Microbiol	10.1099/ijsem.0.004364	2020
Phylogeny	Escherichia marmotae sp. nov., isolated from faeces of Marmota himalayana.	Liu S, Jin D, Lan R, Wang Y, Meng Q, Dai H, Lu S, Hu S, Xu J	Int J Syst Evol Microbiol	10.1099/ijs.0.000228	2015

References

#5121	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 13698
#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 )
#39147	; Curators of the CIP;
#46882	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 18766
#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;
#68371	Automatically annotated from API 50CH acid .
#68382	Automatically annotated from API zym .
#69479	João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .
#119305	Collection of Institut Pasteur ; Curators of the CIP; CIP 104947
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Escherichia fergusonii (DSM 13698, ATCC 35469, CDC 0568-73)

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