Paraprevotella clara (DSM 19731, JCM 14859, YIT 11840)

Name: Paraprevotella clara (DSM 19731, JCM 14859, YIT 11840)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 12569

Type strain

Culture col. no. DSM 19731 JCM 14859 YIT 11840

NCBI tax ID(s) 762968 454154

Special Collections DSMZ JCM Literature strains

History DSMZ <- H. Sakon, Yakult Central Inst. Microbiol. Res., Kunitachi-shi, Japan <- F. Nagai and M. Morotomi; YIT 11840 JCM <-- M. Morotomi A7 (=YIT 11840).

Links

Paraprevotella clara DSM 19731 is an anaerobe, Gram-negative, rod-shaped bacterium that was isolated from faecal sample from healthy Japanese male.

Gram-negative rod-shaped anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 401674

JCM 14859,DSM 19731

@ref 20215

Last LPSN update 2026-05-29 08:27:50

Domain Bacteria

Phylum Bacteroidota

Class Bacteroidia

Order Bacteroidales

Family Prevotellaceae

Genus Paraprevotella

Species Paraprevotella clara

Full scientific name Paraprevotella clara Morotomi et al. 2009

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
29184	negative	1.45 µm	0.85 µm	rod-shaped
125438					90.095
125438	negative				96.623

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
8270	CHOPPED MEAT MEDIUM (DSMZ Medium 78)		Medium recipe at MediaDive	Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
8270	positive	growth	37
67770	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
8270	anaerobe
29184	anaerobe
125439	obligate anaerobe	99.617

Spore formation

@ref	Spore formation	Confidence
29184
125438		93.497
125439		99.743

Observation

67770

Observationquinones: MK-10, MK-11

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29184	30089 ChEBI	acetate	+	carbon source
29184	22599 ChEBI	arabinose	+	carbon source
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
68380	16024 ChEBI	D-mannose	-	fermentation	from API rID32A
29184	17234 ChEBI	glucose	+	carbon source
29184	29987 ChEBI	glutamate	+	carbon source
68380	29985 ChEBI	L-glutamate	-	degradation	from API rID32A
29184	17716 ChEBI	lactose	+	carbon source
29184	17306 ChEBI	maltose	+	carbon source
29184	37684 ChEBI	mannose	+	carbon source
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
29184	16634 ChEBI	raffinose	+	carbon source
68380	16634 ChEBI	raffinose	-	fermentation	from API rID32A
29184	30031 ChEBI	succinate	+	carbon source
68380	27897 ChEBI	tryptophan	-	energy source	from API rID32A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A
29184	18222 ChEBI	xylose	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68380	35581 ChEBI	indole		from API rID32A

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68380	35581 ChEBI	indole	-	from API rID32A

Enzymes

@ref	Value	Activity	Ec
29184	acid phosphatase	+	3.1.3.2
68380	alanine arylamidase	+	3.4.11.2	from API rID32A
29184	alkaline phosphatase	+	3.1.3.1
68380	alkaline phosphatase	+	3.1.3.1	from API rID32A
68380	alpha-arabinosidase	+	3.2.1.55	from API rID32A
68380	alpha-fucosidase	-	3.2.1.51	from API rID32A
29184	alpha-galactosidase	+	3.2.1.22
68380	alpha-galactosidase	+	3.2.1.22	from API rID32A
68380	alpha-glucosidase	-	3.2.1.20	from API rID32A
68380	arginine dihydrolase	-	3.5.3.6	from API rID32A
68380	beta-galactosidase	+	3.2.1.23	from API rID32A
68380	beta-Galactosidase 6-phosphate	-		from API rID32A
68380	beta-glucosidase	-	3.2.1.21	from API rID32A
68380	beta-glucuronidase	-	3.2.1.31	from API rID32A
68380	glutamate decarboxylase	-	4.1.1.15	from API rID32A
68380	glutamyl-glutamate arylamidase	+		from API rID32A
68380	glycin arylamidase	-		from API rID32A
68380	histidine arylamidase	-		from API rID32A
68380	L-arginine arylamidase	-		from API rID32A
68380	leucine arylamidase	-	3.4.11.1	from API rID32A
68380	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API rID32A
68380	phenylalanine arylamidase	-		from API rID32A
68380	proline-arylamidase	-	3.4.11.5	from API rID32A
68380	pyrrolidonyl arylamidase	-	3.4.19.3	from API rID32A
68380	serine arylamidase	-		from API rID32A
68380	tryptophan deaminase	-	4.1.99.1	from API rID32A
68380	tyrosine arylamidase	-		from API rID32A
68380	urease	-	3.5.1.5	from API rID32A

API rID32A

@ref	URE	ADH (Arg)	alpha GAL	beta GAL	beta-Galactosidase 6-phosphatebeta GP	alpha GLU	beta GLU	alpha ARA	beta GUR	beta-N-Acetyl-beta-glucosaminidasebeta NAG	MNE	RAF	GDC	alpha FUC	Reduction of nitrateNIT	IND	PAL	L-arginine arylamidaseArgA	ProA	LGA	Phenylalanine arylamidasePheA	Leucine arylamidaseLeuA	PyrA	Tyrosine arylamidaseTyrA	Alanine arylamidaseAlaA	Glycin arylamidaseGlyA	Histidine arylamidaseHisA	Glutamyl-glutamate arylamidaseGGA	Serine arylamidaseSerA
8270	-	-	+	+	-	-	-	+	-	-	-	-	-	-	-	-	+	-	-	+/-	-	-	-	-	+	-	-	+	-

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Host species
8270	faecal sample from healthy Japanese male	Tokyo	Japan	JPN	Asia
67770	Human feces					Homo sapiens

Taxonmaps

69479

Global distribution of 16S sequence AB547651 (>99% sequence identity) for Paraprevotella from Microbeatlas

Aquatic Samples	10
Soil Samples	3
Animal Samples	3533
Plant Samples	2
Total Samples	3548

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
8270	1	Risk group (German 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	ASM23395v1 assembly for Paraprevotella clara YIT 11840	scaffold	GCA_000233955	762968.3	2513237390	762968	31.36

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Paraprevotella clara gene for 16S ribosomal RNA, partial sequence, strain: JCM 14859	AB547651	1480		454154
8270	Paraprevotella clara gene for 16S ribosomal RNA, partial sequence	AB331896	1483		762968

GC content

@ref	GC-content (mol%)	Method
8270	48.1	high performance liquid chromatography (HPLC)
29184	48.1

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM23395v1 assembly for Paraprevotella clara YIT 11840
NCBI: GCA_000233955

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	99.62	no
125439	gram_stain	BacteriaNetⓘ	negative	88.42	no
125439	spore_formation	BacteriaNetⓘ	no	99.74	no
125439	motility	BacteriaNetⓘ	no	81.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paraprevotella clara YIT 11840 YIT 11840
NCBI: GCA_000233955.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.62	yes
125438	anaerobic	anaerobicⓘ	yes	87.81	yes
125438	aerobic	aerobicⓘ	no	93.04	yes
125438	spore-forming	spore-formingⓘ	no	93.50	yes
125438	thermophilic	thermophileⓘ	no	92.71	yes
125438	flagellated	motile2+ⓘ	no	90.10	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
	Oligosaccharides with different glycosidic bonds regulate gut microbiota: differential modulation of bacterial and fungal communities and their metabolism in vitro.	Lu X, Zou J, Feng X, Han G, Zhu L, Chen Y, Yang Y, Jin J, Ji X, Zhao L.	Food Res Int	10.1016/j.foodres.2025.117481	2025
	Intake of neutral core human milk oligosaccharides (HMOs) during early life improves long-term bone quality.	Bonnet N, Schmidt FN, Baruchet M, Migliavacca E, Ramos-Nieves M, Favre L, Brassart D, Mletzko K, Busse B, Koopmans SJ, Horcajada MN.	J Nutr Biochem	10.1016/j.jnutbio.2025.109968	2025
	Exploring bacterial metabolites in microbe-human host dialogue and their therapeutic potential in Alzheimer's diseases.	Singh SD, Bharali P, Nagamani S.	Mol Divers	10.1007/s11030-024-11028-y	2025
	The molecular mechanisms of steroid hormone effects on cognitive function.	Nguyen HD, Vu GH, Kim WK.	Arch Gerontol Geriatr	10.1016/j.archger.2024.105684	2025
	A consortium of Hordeum vulgare and gut microbiota against non-alcoholic fatty liver disease via data-driven analysis.	Lee SB, Gupta H, Min BH, Ganesan R, Sharma SP, Won SM, Jeong JJ, Cha MG, Kwon GH, Jeong MK, Hyun JY, Eom JA, Park HJ, Yoon SJ, Lee SY, Choi MR, Kim DJ, Oh KK, Suk KT.	Artif Cells Nanomed Biotechnol	10.1080/21691401.2024.2347380	2024
	The causal association between gut microbiota and postpartum depression: a two-sample Mendelian randomization study.	Jin W, Li B, Wang L, Zhu L, Chai S, Hou R.	Front Microbiol	10.3389/fmicb.2024.1415237	2024
	Association between gut microbiota composition and physical functioning in patients with knee osteoarthritis: a machine learning study.	de Sire A, Mancuso E, Marotta N, Massimino M, Zito R, Averta C, Bartalotta I, Palummo A, Cerantonio A, Citrigno L, Soverini M, Castagnetti A, Mannino GC, Ammendolia A, Andreozzi F.	Sci Rep	10.1038/s41598-025-24500-y	2025
Genetics	Influence of the Gut Microbiota on Acute Ischemic Stroke Functional Outcomes at Three Months.	Lledos M, Prats-Sanchez L, Muino E, Cullell N, Llucia-Carol L, Carcel-Marquez J, Gallego-Fabrega C, Martin-Campos JM, Marin R, Aguilera-Simon A, Guasch-Jimenez M, Ezcurra-Diaz G, Camps-Renom P, Del Mar Freijo M, Marti-Fabregas J, Fernandez-Cadenas I.	Eur J Neurol	10.1111/ene.70265	2025
	Fecal Proteolytic Bacteria and Staphylococcal Superantigens Are Associated With Abdominal Pain Severity in Irritable Bowel Syndrome.	Quan R, Decraecker L, Appeltans I, Cuende-Estevez M, Van Remoortel S, Aguilera-Lizarraga J, Wang Z, Hicks G, Wykosky J, McLean P, Denadai-Souza A, Hussein H, Boeckxstaens GE.	Am J Gastroenterol	10.14309/ajg.0000000000003042	2025
	Exploring the causal associations of the gut microbiota and plasma metabolites with ovarian cancer: an approach of mendelian randomization analysis combined with network pharmacology and molecular docking.	Guo J, Wang C, Li H, Ding C.	J Ovarian Res	10.1186/s13048-025-01610-9	2025
	Multi-omics analysis reveals the key factors involved in the severity of the Alzheimer's disease.	Meng L, Jin H, Yulug B, Altay O, Li X, Hanoglu L, Cankaya S, Coskun E, Idil E, Nogaylar R, Ozsimsek A, Shoaie S, Turkez H, Nielsen J, Zhang C, Boren J, Uhlen M, Mardinoglu A.	Alzheimers Res Ther	10.1186/s13195-024-01578-6	2024
Genetics	Diet-Gut Microbiota Relations: Critical Appraisal of Evidence From Studies Using Metagenomics.	Lotankar M, Houttu N, Mokkala K, Laitinen K.	Nutr Rev	10.1093/nutrit/nuae192	2025
Phylogeny	16S rDNA-based detection technology: use in lambs infected with Nematodirus oiratianus to analyze changes in intestinal flora.	Li SY, Hou B, Wuyun Q, Eerdeni Z, Zang D, Hasi S.	Parasite	10.1051/parasite/2025052	2025
	Maternal oral sodium propionate supplementation restores gut integrity and mitigates stress-induced metabolic and behavioral outcomes in offspring.	Bagaev A, Sur D, Agranyoni O, Pe'er N, Savita BK, Rocha BGS, Thanos PK, Navon-Venezia S, Pinhasov A.	Transl Psychiatry	10.1038/s41398-025-03436-x	2025
	Fecal short-chain fatty acids vary by sex and amyloid status.	Kuehn JF, Zhang Q, Heston MB, Kang JW, Harding SJ, Davenport-Sis NJ, Peter DC, Kerby RL, Vemuganti V, Schiffmann EC, Tallon MM, Harpt J, Hajra A, Wheeler JL, Shankar S, Mickol A, Zemberi J, Chow H, Zhang E, Clements E, Noughani H, Forst A, Everitt G, Kollmorgen G, Quijano-Rubio C, Christian BT, Carlsson CM, Johnson SC, Asthana S, Zetterberg H, Blennow K, Ulland TK, Rey FE, Bendlin BB.	Alzheimers Dement	10.1002/alz.70877	2025
	Knowledge graph-derived feed efficiency analysis via pig gut microbiota.	Zhang J, Jiang Q, Du Z, Geng Y, Hu Y, Tong Q, Song Y, Zhang HY, Yan X, Feng Z.	Sci Rep	10.1038/s41598-024-64835-6	2024
Metabolism	Gut microbiota-mediated modulation of host amino acid availability and metabolism.	Han Z, Zhao L, Hu Q, Hung I, Liu C, Liu S, Mei X, Zeng X, Bin P, Wang J.	Gut Microbes	10.1080/19490976.2025.2552345	2025
	Carotenoids from Halophilic Archaea: A Novel Approach to Improve Egg Quality and Cecal Microbiota in Laying Hens.	Dou X, Zhang G, Tang H, Chen X, Chen B, Mei Y, Jiao H, Ren M.	Animals (Basel)	10.3390/ani14233470	2024
	The radioprotective role of human Alistipes onderdonkii identified by multi-omic analysis in patients with prostate cancer.	Yu Y, Park S, Jeon J, Lee SH, Kim H, Seo D, Park M, Park E, Kim JY, Cho SJ, Jo S, Park G, Yang JY.	Discov Oncol	10.1007/s12672-025-02992-4	2025
	Effects of Tiaopi Xiezhuo decoction on constipation and gut dysbiosis in patients with peritoneal dialysis.	Peng Y, Zeng Y, Zheng T, Xie X, Wu J, Fu L, Lu F, Zhang, Chen Y, Liu X, Wang L.	Pharm Biol	10.1080/13880209.2023.2193595	2023
	Baseline intestinal microbiota composition influences response to a real-world dietary fiber intervention.	Hoffmann Sarda FA, Giuntini EB, Oliveira A, Souza GS, Prado SBR, Taddei CR, Tadini CC, Bittinger K, Bushman FD, Menezes EW, Hoffmann C.	NPJ Biofilms Microbiomes	10.1038/s41522-025-00817-4	2025
	Symbiotic microbial population composition of Apolygus lucorum under temperature and pesticide pressures.	Ma M, Xue H, Zhu X, Wang L, Niu L, Luo J, Cui J, Gao X.	Front Microbiol	10.3389/fmicb.2024.1485708	2024
Pathogenicity	3-O-Acetyl-11-Keto-beta-Boswellic Acid Suppresses Colitis-Associated Colorectal Cancer by Inhibiting the NF-Kb Signaling Pathway and Remodeling Gut Microbiota.	Xu F, Li W, Zheng XJ, Hao Y, Yang YH, Yang H, Zhang S, Cao WX, Li XX, Zhang X, Du GH, Ji TF, Wang JH.	Oncol Res	10.32604/or.2025.062386	2025
	Investigating Plasma Metabolomics and Gut Microbiota Changes Associated With Parkinson Disease: A Focus on Caffeine Metabolism.	Chen CC, Chiu JY, Tan AH, Toh TS, Lim SY, Tan EK, Pettersson S, Hsu CC, Liou JM, Wu MS, Hsu CL, Lin CH.	Neurology	10.1212/wnl.0000000000213592	2025
	Gut commensal bacterium Bacteroides vulgatus exacerbates helminth-induced cardiac fibrosis through succinate accumulation.	Wang J, Yin J, Liu X, Liu Y, Jin X.	PLoS Pathog	10.1371/journal.ppat.1013069	2025
Genetics	Investigating the association between gut microbiome and aortic aneurysm diseases: a bidirectional two-sample Mendelian randomization analysis.	Sun Y, Dong H, Sun C, Du D, Gao R, Voevoda M, Knyazev R, Wu N.	Front Cell Infect Microbiol	10.3389/fcimb.2024.1406845	2024
	Vancomycin relieves tacrolimus-induced hyperglycemia by eliminating gut bacterial beta-glucuronidase enzyme activity.	Li P, Zhang R, Zhou J, Guo P, Liu Y, Shi S.	Gut Microbes	10.1080/19490976.2024.2310277	2024
Metabolism	Probio-X Relieves Symptoms of Hyperlipidemia by Regulating Patients' Gut Microbiome, Blood Lipid Metabolism, and Lifestyle Habits.	Wang H, Ma C, Li Y, Zhang L, A L, Yang C, Zhao F, Han H, Shang D, Yang F, Zhang Y, Zhang H, Sun Z, Guo R.	Microbiol Spectr	10.1128/spectrum.04440-22	2023
	Effects of Lacticaseibacillus paracasei K56 on perceived stress among pregraduate students: a double-blind, randomized, placebo-controlled trial.	Guan Y, Zhu R, Zhao W, Wang L, You L, Zeng Z, Jiang Q, Zhu Z, Gou J, Zhang Q, Guo J, Li K, Zhao L, Li Y, Wang P, Fang B, Hung W, He J, Zhang L, Wang R, He J.	Front Nutr	10.3389/fnut.2025.1544713	2025
Genetics	Genomic Insights into the Distribution of Peptidases and Proteolytic Capacity among Prevotella and Paraprevotella Species.	Patra AK, Yu Z.	Microbiol Spectr	10.1128/spectrum.02185-21	2022
Metabolism	Identification of gut microbes associated with feed efficiency by daily-phase feeding strategy in growing-finishing pigs.	Jiang Q, Xie C, Chen L, Xiao H, Xie Z, Zhu X, Ma L, Yan X.	Anim Nutr	10.1016/j.aninu.2022.09.005	2023
Metabolism	Multi-omic profiling reveals associations between the gut microbiome, host genome and transcriptome in patients with colorectal cancer.	Zou S, Yang C, Zhang J, Zhong D, Meng M, Zhang L, Chen H, Fang L.	J Transl Med	10.1186/s12967-024-04984-4	2024
	A molecular conveyor belt-associated protein controls the rotational direction of the bacterial type 9 secretion system.	Trivedi A, Miratsky JA, Henderson EC, Singharoy A, Shrivastava A.	mBio	10.1128/mbio.01125-25	2025
	Longitudinal big biological data in the AI era.	Mardinoglu A, Turkez H, Shong M, Srinivasulu VP, Nielsen J, Palsson BO, Hood L, Uhlen M.	Mol Syst Biol	10.1038/s44320-025-00134-0	2025
	Short-chain fatty acids play a key role in antibody response to SARS-CoV-2 infection in people living with HIV.	Pan J, Zhang X, Shi D, Tian X, Xu L, Lu X, Dong M, Yao P, Pan Z, Ling Z, Wu N, Yao H.	Sci Rep	10.1038/s41598-024-82596-0	2024
	Gut microbiome is linked to functions of peripheral immune cells in transition cows during excessive lipolysis.	Gu F, Zhu S, Tang Y, Liu X, Jia M, Malmuthuge N, Valencak TG, McFadden JW, Liu JX, Sun HZ.	Microbiome	10.1186/s40168-023-01492-3	2023
Genetics	Gut microbiome in endometriosis: a cohort study on 1000 individuals.	Perez-Prieto I, Vargas E, Salas-Espejo E, Lull K, Canha-Gouveia A, Perez LA, Fontes J, Salumets A, Andreson R, Aasmets O, Estonian Biobank research team, Whiteson K, Org E, Altmae S.	BMC Med	10.1186/s12916-024-03503-y	2024
Genetics	Comparative Metagenomics and Metabolomes Reveals Abnormal Metabolism Activity Is Associated with Gut Microbiota in Alzheimer's Disease Mice.	Sun P, Zhu H, Li X, Shi W, Guo Y, Du X, Zhang L, Su L, Qin C.	Int J Mol Sci	10.3390/ijms231911560	2022
Enzymology	Alterations and correlations of the gut microbiome, metabolism and immunity in patients with primary biliary cirrhosis.	Lv LX, Fang DQ, Shi D, Chen DY, Yan R, Zhu YX, Chen YF, Shao L, Guo FF, Wu WR, Li A, Shi HY, Jiang XW, Jiang HY, Xiao YH, Zheng SS, Li LJ.	Environ Microbiol	10.1111/1462-2920.13401	2016
	Multi-omics of the gut microbial ecosystem in patients with microsatellite-instability-high gastrointestinal cancer resistant to immunotherapy.	Cheng S, Han Z, Dai D, Li F, Zhang X, Lu M, Lu Z, Wang X, Zhou J, Li J, Guo X, Song P, Qiu C, Shen W, Zhang Q, Zhu N, Wang X, Tan Y, Kou Y, Yin X, Shen L, Peng Z.	Cell Rep Med	10.1016/j.xcrm.2023.101355	2024
	Functional host-specific adaptation of the intestinal microbiome in hominids.	Ruhlemann MC, Bang C, Gogarten JF, Hermes BM, Groussin M, Waschina S, Poyet M, Ulrich M, Akoua-Koffi C, Deschner T, Muyembe-Tamfum JJ, Robbins MM, Surbeck M, Wittig RM, Zuberbuhler K, Baines JF, Leendertz FH, Franke A.	Nat Commun	10.1038/s41467-023-44636-7	2024
Pathogenicity	Commensal microbiota-derived metabolite agmatine triggers inflammation to promote colorectal tumorigenesis.	Lu Y, Cui A, Zhang X.	Gut Microbes	10.1080/19490976.2024.2348441	2024
Genetics	Gut microbiota associated with cryptococcal meningitis and dysbiosis caused by anti-fungal treatment.	Li H, Zhang L, Zhang K, Huang Y, Liu Y, Lu X, Liao W, Liu X, Zhang Q, Pan W.	Front Microbiol	10.3389/fmicb.2022.1086239	2022
	Prenatal Lead Exposure Is Associated with Reduced Abundance of Beneficial Gut Microbial Cliques in Late Childhood: An Investigation Using Microbial Co-Occurrence Analysis (MiCA).	Midya V, Lane JM, Gennings C, Torres-Olascoaga LA, Gregory JK, Wright RO, Arora M, Tellez-Rojo MM, Eggers S.	Environ Sci Technol	10.1021/acs.est.3c04346	2023
Genetics	Species- and subspecies-level characterization of health-associated bacterial consortia that colonize the human gut during infancy.	Minot SS, Mayer-Blackwell K, Fiore-Gartland A, Johnson A, Self S, Bhatti P, Yao L, Liu L, Sun X, Jinfa Y, Kublin J.	Gut Microbes	10.1080/19490976.2024.2414975	2024
	Association between gut microbiota and gastrointestinal cancer: a two-sample bi-directional Mendelian randomization study.	Su Q, Jin C, Bo Z, Yang Y, Wang J, Wang J, Zhou J, Chen Y, Zeng H, Chen G, Wang Y.	Front Microbiol	10.3389/fmicb.2023.1181328	2023
	Deep metagenomic characterization of gut microbial community and function in preeclampsia.	Lv LJ, Li SH, Wen JY, Wang GY, Li H, He TW, Lv QB, Xiao MC, Duan HL, Chen MC, Yi ZT, Yan QL, Yin AH.	Front Cell Infect Microbiol	10.3389/fcimb.2022.933523	2022
Genetics	Correlation of the gut microbiome and immune-related adverse events in gastrointestinal cancer patients treated with immune checkpoint inhibitors.	Zhang Y, Cheng S, Zou H, Han Z, Xie T, Zhang B, Dai D, Yin X, Liang Y, Kou Y, Tan Y, Shen L, Peng Z.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1099063	2023
	Altered gut microbiome composition in patients with Vogt-Koyanagi-Harada disease.	Ye Z, Wu C, Zhang N, Du L, Cao Q, Huang X, Tang J, Wang Q, Li F, Zhou C, Xu Q, Xiong X, Kijlstra A, Qin N, Yang P.	Gut Microbes	10.1080/19490976.2019.1700754	2020
Pathogenicity	Phenotyping of Fecal Microbiota of Winnie, a Rodent Model of Spontaneous Chronic Colitis, Reveals Specific Metabolic, Genotoxic, and Pro-inflammatory Properties.	Tala A, Guerra F, Resta SC, Calcagnile M, Barca A, Tredici SM, De Donno MD, Vacca M, Liso M, Chieppa M, De Angelis M, Verri T, Bozzetti MG, Bucci C, Alifano P.	Inflammation	10.1007/s10753-022-01706-0	2022
	Dysbiosis Triggers ACF Development in Genetically Predisposed Subjects.	De Santis S, Liso M, Vacca M, Verna G, Cavalcanti E, Coletta S, Calabrese FM, Eri R, Lippolis A, Armentano R, Mastronardi M, De Angelis M, Chieppa M.	Cancers (Basel)	10.3390/cancers13020283	2021
	Microbial Proteins in Stomach Biopsies Associated with Gastritis, Ulcer, and Gastric Cancer.	Aziz S, Rasheed F, Akhter TS, Zahra R, Konig S.	Molecules	10.3390/molecules27175410	2022
	Identifying Gut Microbiota associated with Gastrointestinal Symptoms upon Roux-en-Y Gastric Bypass.	Wijdeveld M, van Olst N, van der Vossen EWJ, de Brauw M, Acherman YIZ, de Goffau MC, Gerdes VEA, Nieuwdorp M.	Obes Surg	10.1007/s11695-023-06610-6	2023
Genetics	Alterations in Gut Microbiome Composition and Function in Irritable Bowel Syndrome and Increased Probiotic Abundance with Daily Supplementation.	Phan J, Nair D, Jain S, Montagne T, Flores DV, Nguyen A, Dietsche S, Gombar S, Cotter P.	mSystems	10.1128/msystems.01215-21	2021
Metabolism	A Novel Family of RNA-Binding Proteins Regulate Polysaccharide Metabolism in Bacteroides thetaiotaomicron.	Adams AND, Azam MS, Costliow ZA, Ma X, Degnan PH, Vanderpool CK.	J Bacteriol	10.1128/jb.00217-21	2021
	Differences in Gut Microbiome in Hospitalized Immunocompetent vs. Immunocompromised Children, Including Those With Sickle Cell Disease.	Mohandas S, Soma VL, Tran TDB, Sodergren E, Ambooken T, Goldman DL, Weinstock G, Herold BC.	Front Pediatr	10.3389/fped.2020.583446	2020
Genetics	A Metagenome-Wide Association Study of the Gut Microbiome and Metabolic Syndrome.	Qin Q, Yan S, Yang Y, Chen J, Li T, Gao X, Yan H, Wang Y, Wang J, Wang S, Ding S.	Front Microbiol	10.3389/fmicb.2021.682721	2021
	Insight into gut dysbiosis of patients with inflammatory bowel disease and ischemic colitis.	Dahal RH, Kim S, Kim YK, Kim ES, Kim J.	Front Microbiol	10.3389/fmicb.2023.1174832	2023
Phylogeny	Diversity and abundance of the bacterial 16S rRNA gene sequences in forestomach of alpacas (Lama pacos) and sheep (Ovis aries).	Pei CX, Liu Q, Dong CS, Li H, Jiang JB, Gao WJ.	Anaerobe	10.1016/j.anaerobe.2010.06.004	2010
Transcriptome	The fecal microbiota of patients with primary biliary cholangitis (PBC) causes PBC-like liver lesions in mice and exacerbates liver damage in a mouse model of PBC.	Jiang H, Yu Y, Hu X, Du B, Shao Y, Wang F, Chen L, Yan R, Li L, Lv L.	Gut Microbes	10.1080/19490976.2024.2383353	2024
	Holstein and Jersey Steers Differ in Rumen Microbiota and Enteric Methane Emissions Even Fed the Same Total Mixed Ration.	Islam M, Kim SH, Ramos SC, Mamuad LL, Son AR, Yu Z, Lee SS, Cho YI, Lee SS.	Front Microbiol	10.3389/fmicb.2021.601061	2021
	Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices.	Huang KD, Amend L, Galvez EJC, Lesker TR, de Oliveira R, Bielecka A, Blanco-Miguez A, Valles-Colomer M, Ruf I, Pasolli E, Buer J, Segata N, Esser S, Strowig T, Kehrmann J.	Cell Rep Med	10.1016/j.xcrm.2024.101426	2024
	Hypergravity disrupts murine intestinal microbiota.	Alauzet C, Cunat L, Wack M, Lozniewski A, Busby H, Agrinier N, Cailliez-Grimal C, Frippiat JP.	Sci Rep	10.1038/s41598-019-45153-8	2019
	The Effects of Moderate Alcohol Consumption on Circulating Metabolites and Gut Microbiota in Patients With Coronary Artery Disease.	Zhao X, Zhou R, Li H, Fan Y, Sun Y, Hu X, Zhang S.	Front Cardiovasc Med	10.3389/fcvm.2021.767692	2021
Pathogenicity	Associations of dietary diversity with the gut microbiome, fecal metabolites, and host metabolism: results from 2 prospective Chinese cohorts.	Xiao C, Wang JT, Su C, Miao Z, Tang J, Ouyang Y, Yan Y, Jiang Z, Fu Y, Shuai M, Gou W, Xu F, Yu EY, Liang Y, Liang X, Tian Y, Wang J, Huang F, Zhang B, Wang H, Chen YM, Zheng JS.	Am J Clin Nutr	10.1093/ajcn/nqac178	2022
	Metagenomic analysis reveals crosstalk between gut microbiota and glucose-lowering drugs targeting the gastrointestinal tract in Chinese patients with type 2 diabetes: a 6 month, two-arm randomised trial.	Zhang X, Ren H, Zhao C, Shi Z, Qiu L, Yang F, Zhou X, Han X, Wu K, Zhong H, Li Y, Li J, Ji L.	Diabetologia	10.1007/s00125-022-05768-5	2022
	Co-fermented defatted rice bran alters gut microbiota and improves growth performance, antioxidant capacity, immune status and intestinal permeability of finishing pigs.	Su W, Jiang Z, Wang C, Zhang Y, Gong T, Wang F, Jin M, Wang Y, Lu Z.	Anim Nutr	10.1016/j.aninu.2022.07.008	2022
Genetics	Positive Synergistic Effects of Quercetin and Rice Bran on Human Gut Microbiota Reduces Enterobacteriaceae Family Abundance and Elevates Propionate in a Bioreactor Model.	Ghimire S, Wongkuna S, Sankaranarayanan R, Ryan EP, Bhat GJ, Scaria J.	Front Microbiol	10.3389/fmicb.2021.751225	2021
	Human gut bacteria contain acquired interbacterial defence systems.	Ross BD, Verster AJ, Radey MC, Schmidtke DT, Pope CE, Hoffman LR, Hajjar AM, Peterson SB, Borenstein E, Mougous JD.	Nature	10.1038/s41586-019-1708-z	2019
Genetics	Composition and Functions of the Gut Microbiome in Pediatric Obesity: Relationships with Markers of Insulin Resistance.	Orsso CE, Peng Y, Deehan EC, Tan Q, Field CJ, Madsen KL, Walter J, Prado CM, Tun HM, Haqq AM.	Microorganisms	10.3390/microorganisms9071490	2021
	Long-Term Lactulose Administration Improves Dysbiosis Induced by Antibiotic and C. difficile in the PathoGut^TM SHIME Model.	Calatayud M, Duysburgh C, Van den Abbeele P, Franckenstein D, Kuchina-Koch A, Marzorati M.	Antibiotics (Basel)	10.3390/antibiotics11111464	2022
Phenotype	Moving beyond microbiome-wide associations to causal microbe identification.	Surana NK, Kasper DL.	Nature	10.1038/nature25019	2017
	Glucose-lowering effects of a synbiotic combination containing Pediococcus acidilactici in C. elegans and mice.	Yavorov-Dayliev D, Milagro FI, Ayo J, Oneca M, Goyache I, Lopez-Yoldi M, Aranaz P.	Diabetologia	10.1007/s00125-023-05981-w	2023
	Ileal immune tonus is a prognosis marker of proximal colon cancer in mice and patients.	Picard M, Yonekura S, Slowicka K, Petta I, Rauber C, Routy B, Richard C, Iebba V, Tidjani Alou M, Becharef S, Ly P, Pizzato E, Lehmann CHK, Amon L, Klein C, Opolon P, Gomperts Boneca I, Scoazec JY, Hollebecque A, Malka D, Ghiringhelli F, Dudziak D, Berx G, Vereecke L, van Loo G, Kroemer G, Zitvogel L, Roberti MP.	Cell Death Differ	10.1038/s41418-020-00684-w	2021
	A powerful machine learning approach to identify interactions of differentially abundant gut microbial subsets in patients with metastatic and non-metastatic pancreatic cancer.	Villani A, Fontana A, Panebianco C, Ferro C, Copetti M, Pavlovic R, Drago D, Fiorentini C, Terracciano F, Bazzocchi F, Canistro G, Pisati F, Maiello E, Latiano TP, Perri F, Pazienza V.	Gut Microbes	10.1080/19490976.2024.2375483	2024
	Plant-Based Diet Index and Metabolic Risk in Men: Exploring the Role of the Gut Microbiome.	Li Y, Wang DD, Satija A, Ivey KL, Li J, Wilkinson JE, Li R, Baden M, Chan AT, Huttenhower C, Rimm EB, Hu FB, Sun Q.	J Nutr	10.1093/jn/nxab175	2021
Genetics	Revealing the developmental characterization of rumen microbiome and its host in newly received cattle during receiving period contributes to formulating precise nutritional strategies.	Li Y, Mao K, Zang Y, Lu G, Qiu Q, Ouyang K, Zhao X, Song X, Xu L, Liang H, Qu M.	Microbiome	10.1186/s40168-023-01682-z	2023
	The Immune Barrier of Porcine Uterine Mucosa Differs Dramatically at Proliferative and Secretory Phases and Could Be Positively Modulated by Colonizing Microbiota.	Han D, Sun P, Hu Y, Wang J, Hua G, Chen J, Shao C, Tian F, Darwish HYA, Tai Y, Yang X, Chang J, Ma Y.	Front Immunol	10.3389/fimmu.2021.750808	2021
Transcriptome	Diet Transition from High-Forage to High-Concentrate Alters Rumen Bacterial Community Composition, Epithelial Transcriptomes and Ruminal Fermentation Parameters in Dairy Cows.	Ramos SC, Jeong CD, Mamuad LL, Kim SH, Kang SH, Kim ET, Cho YI, Lee SS, Lee SS.	Animals (Basel)	10.3390/ani11030838	2021
Genetics	Breast-Milk Microbiota Linked to Celiac Disease Development in Children: A Pilot Study From the PreventCD Cohort.	Benitez-Paez A, Olivares M, Szajewska H, Piescik-Lech M, Polanco I, Castillejo G, Nunez M, Ribes-Koninckx C, Korponay-Szabo IR, Koletzko S, Meijer CR, Mearin ML, Sanz Y.	Front Microbiol	10.3389/fmicb.2020.01335	2020
Pathogenicity	Obesity-associated inflammation countered by a Mediterranean diet: the role of gut-derived metabolites.	Florkowski M, Abiona E, Frank KM, Brichacek AL.	Front Nutr	10.3389/fnut.2024.1392666	2024
	Drivers and determinants of strain dynamics following fecal microbiota transplantation.	Schmidt TSB, Li SS, Maistrenko OM, Akanni W, Coelho LP, Dolai S, Fullam A, Glazek AM, Hercog R, Herrema H, Jung F, Kandels S, Orakov A, Thielemann R, von Stetten M, Van Rossum T, Benes V, Borody TJ, de Vos WM, Ponsioen CY, Nieuwdorp M, Bork P.	Nat Med	10.1038/s41591-022-01913-0	2022
	Vaginal Microbiome Composition in Early Pregnancy and Risk of Spontaneous Preterm and Early Term Birth Among African American Women.	Dunlop AL, Satten GA, Hu YJ, Knight AK, Hill CC, Wright ML, Smith AK, Read TD, Pearce BD, Corwin EJ.	Front Cell Infect Microbiol	10.3389/fcimb.2021.641005	2021
	Bifidobacterium longum R0175 Protects Rats against d-Galactosamine-Induced Acute Liver Failure.	Wang K, Lv L, Yan R, Wang Q, Jiang H, Wu W, Li Y, Ye J, Wu J, Yang L, Bian X, Jiang X, Lu Y, Xie J, Wang Q, Shen J, Li L.	mSphere	10.1128/msphere.00791-19	2020
	The Role of the Microbiome on the Pathogenesis and Treatment of Colorectal Cancer.	Yu I, Wu R, Tokumaru Y, Terracina KP, Takabe K.	Cancers (Basel)	10.3390/cancers14225685	2022
	Effects of Diet-Modulated Autologous Fecal Microbiota Transplantation on Weight Regain.	Rinott E, Youngster I, Yaskolka Meir A, Tsaban G, Zelicha H, Kaplan A, Knights D, Tuohy K, Fava F, Scholz MU, Ziv O, Rubin E, Tirosh A, Rudich A, Bluher M, Stumvoll M, Ceglarek U, Clement K, Koren O, Wang DD, Hu FB, Stampfer MJ, Shai I.	Gastroenterology	10.1053/j.gastro.2020.08.041	2021
	Elucidating the gut microbiota composition and the bioactivity of immunostimulatory commensals for the optimization of immune checkpoint inhibitors.	Daillere R, Routy B, Goubet AG, Cogdill A, Ferrere G, Alves-Costa Silva C, Fluckiger A, Ly P, Haddad Y, Pizzato E, Thelemaque C, Fidelle M, Mazzenga M, Roberti MP, Melenotte C, Liu P, Terrisse S, Kepp O, Kroemer G, Zitvogel L, Derosa L.	Oncoimmunology	10.1080/2162402x.2020.1794423	2020
	The Intestinal Microbiota in the Development of Chronic Liver Disease: Current Status.	Stojic J, Kukla M, Grgurevic I.	Diagnostics (Basel)	10.3390/diagnostics13182960	2023
	Metagenomic analysis of bacterial community structure and diversity of lignocellulolytic bacteria in Vietnamese native goat rumen.	Do TH, Dao TK, Nguyen KHV, Le NG, Nguyen TMP, Le TL, Phung TN, van Straalen NM, Roelofs D, Truong NH.	Asian-Australas J Anim Sci	10.5713/ajas.17.0174	2018
	Responses of Intestinal Mucosal Barrier Functions of Rats to Simulated Weightlessness.	Jin M, Zhang H, Zhao K, Xu C, Shao D, Huang Q, Shi J, Yang H.	Front Physiol	10.3389/fphys.2018.00729	2018
	Artificial intelligence-driven multi-omics approaches in Alzheimer's disease: Progress, challenges, and future directions.	Ren F, Wei J, Chen Q, Hu M, Yu L, Mi J, Zhou X, Qin D, Wu J, Wu A.	Acta Pharm Sin B	10.1016/j.apsb.2025.07.030	2025
	Carbohydrate Staple Food Modulates Gut Microbiota of Mongolians in China.	Li J, Hou Q, Zhang J, Xu H, Sun Z, Menghe B, Zhang H.	Front Microbiol	10.3389/fmicb.2017.00484	2017
Genetics	CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes.	Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW.	Genome Res	10.1101/gr.186072.114	2015
	Ginsenosides Rb3 and Rd reduce polyps formation while reinstate the dysbiotic gut microbiota and the intestinal microenvironment in Apc^Min/+ mice.	Huang G, Khan I, Li X, Chen L, Leong W, Ho LT, Hsiao WLW.	Sci Rep	10.1038/s41598-017-12644-5	2017
	The application of rumen simulation technique (RUSITEC) for studying dynamics of the bacterial community and metabolome in rumen fluid and the effects of a challenge with Clostridium perfringens.	Wetzels SU, Eger M, Burmester M, Kreienbrock L, Abdulmawjood A, Pinior B, Wagner M, Breves G, Mann E.	PLoS One	10.1371/journal.pone.0192256	2018
	Changes to the gut microbiota induced by losartan contributes to its antihypertensive effects.	Robles-Vera I, Toral M, de la Visitacion N, Sanchez M, Gomez-Guzman M, Munoz R, Algieri F, Vezza T, Jimenez R, Galvez J, Romero M, Redondo JM, Duarte J.	Br J Pharmacol	10.1111/bph.14965	2020
Phylogeny	Prior Dietary Practices and Connections to a Human Gut Microbial Metacommunity Alter Responses to Diet Interventions.	Griffin NW, Ahern PP, Cheng J, Heath AC, Ilkayeva O, Newgard CB, Fontana L, Gordon JI.	Cell Host Microbe	10.1016/j.chom.2016.12.006	2017
	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
Metabolism	l-Galactose metabolism in Bacteroides vulgatus from the human gut microbiota.	Hobbs ME, Williams HJ, Hillerich B, Almo SC, Raushel FM.	Biochemistry	10.1021/bi500656m	2014
Phylogeny	Molecular diversity of rumen bacterial communities from tannin-rich and fiber-rich forage fed domestic Sika deer (Cervus nippon) in China.	Li ZP, Liu HL, Li GY, Bao K, Wang KY, Xu C, Yang YF, Yang FH, Wright AD.	BMC Microbiol	10.1186/1471-2180-13-151	2013
Metabolism	Pseudoprevotella muciniphila gen. nov., sp. nov., a mucin-degrading bacterium attached to the bovine rumen epithelium.	Na SW, Chun BH, Beak SH, Khan SA, Haque MN, Lee JS, Jeon CO, Lee SS, Baik M.	PLoS One	10.1371/journal.pone.0251791	2021
Genetics	Butyricimonas phoceensis sp. nov., a new anaerobic species isolated from the human gut microbiota of a French morbidly obese patient.	Togo AH, Diop A, Dubourg G, Nguyen TT, Andrieu C, Caputo A, Couderc C, Fournier PE, Maraninchi M, Valero R, Raoult D, Million M.	New Microbes New Infect	10.1016/j.nmni.2016.07.010	2016
Phylogeny	Paraprevotella clara gen. nov., sp. nov. and Paraprevotella xylaniphila sp. nov., members of the family 'Prevotellaceae' isolated from human faeces.	Morotomi M, Nagai F, Sakon H, Tanaka R	Int J Syst Evol Microbiol	10.1099/ijs.0.008169-0	2009

References

#8270	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19731
#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 )
#25608	IJSEM 1895 2009 ( DOI 10.1099/ijs.0.008169-0 , PubMed 19567577 )
#29184	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #25608
#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;
#68380	Automatically annotated from API rID32A .
#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 .
#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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Paraprevotella clara (DSM 19731, JCM 14859, YIT 11840)

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