Parabacteroides distasonis (CIP 104284, DSM 20701, ATCC 8503)

Name: Parabacteroides distasonis (CIP 104284, DSM 20701, ATCC 8503)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 12497

Type strain

Strain Designation 10159

Culture col. no. CIP 104284 DSM 20701 ATCC 8503 CCUG 4941 JCM 5825 2 more

NCBI tax ID(s) 435591 823

Special Collections DSMZ CCUG JCM CIP

History DSMZ <- NCTC; NCTC 11152 <- ATCC; ATCC 8503 <- A. H. Eggerth; JCM <-- ATCC 8503 <-- A. H. Eggerth. CIP <- 1994, J.P. Carlier, Inst. Pasteur, Paris, France: strain 10159 <- NCTC <- ATCC <- A.H. Eggerth

Links

Parabacteroides distasonis 10159 is an anaerobe, Gram-negative, rod-shaped bacterium that was isolated from Human feces.

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

Name and taxonomic classification

SI-ID 34972

ATCC 8503,NCTC 11152,CCUG 4941,CIP 104284,DSM 20701,JCM 5825,KCTC 5133,VTT E-062943,CNCTC 5420,LMG 28899

@ref 20215

Last LPSN update 2026-05-29 08:27:49

Domain Bacteria

Phylum Bacteroidota

Class Bacteroidia

Order Bacteroidales

Family Tannerellaceae

Genus Parabacteroides

Species Parabacteroides distasonis

Full scientific name Parabacteroides distasonis (Eggerth and Gagnon 1933) Sakamoto and Benno 2006

Synonyms (1)

Bacteroides distasonis

BacDive ID	Other strains from **Parabacteroides distasonis** (17)	Type strain
130882	P. distasonis SAB-131-CoC-3, DSM 29491
152089	P. distasonis CCUG 45716
156806	P. distasonis CCUG 65470
156930	P. distasonis CCUG 67118
157009	P. distasonis CCUG 68616
158876	P. distasonis WCA3-693-APC-2H, DSM 106899
158877	P. distasonis H6_9, DSM 108211
158878	P. distasonis H1_7, DSM 108218
159982	P. distasonis APCS2/PD, DSM 112022
161283	P. distasonis JCM 1294
161351	P. distasonis JCM 13400
161352	P. distasonis JCM 13401
161353	P. distasonis JCM 13402
161354	P. distasonis JCM 13403
161355	P. distasonis JCM 13404
169198	P. distasonis 31/2, DSM 24965, BEI HM-169
169199	P. distasonis Cla-AP-4, DSM 111137

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility	Confidence
118948	negative	rod-shaped
125438	negative			91.202

Colony morphology

8779

Incubation period1-2 days

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
8779	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
8779	FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a)	Medium recipe at MediaDive	Name: FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a) Composition: Fastidious Anaerobe Basal Broth 35.4 g/l Distilled water
8779	CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)	Medium recipe at MediaDive	Name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l K2HPO4 5.0 g/l Yeast extract 5.0 g/l D-Glucose 4.0 g/l Starch 1.0 g/l Maltose 1.0 g/l Cellobiose 1.0 g/l L-Cysteine HCl 0.5 g/l Ethanol 0.19 g/l Vitamin K3 0.05 g/l Hemin 0.005 g/l Sodium resazurin 0.0005 g/l Vitamin K1 NaOH Distilled water
41097	MEDIUM 20 - for Anaerobic bacteria		Agar (15.000 g);Glucose (5.000 g);Yeast extract (20.000 g);Tryptone (30.000 g);Cysteine hydrochloride (0.500 g);distilled water (1000.000 ml);Hemin solution -M00149 (25.000 ml)
118948	CIP Medium 20	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
8779	positive	growth	37
41097	positive	growth	37
44811	positive	growth	37
67770	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
8779	anaerobe
44811	anaerobe
118948	anaerobe
125439	anaerobe	92.757

Spore formation

@ref	Spore formation	Confidence
125438		90.141
125439		90.594

Compound production

@ref	Compound
8779	catalase
8779	superoxide dismutase

Observation

67770

Observationquinones: MK-9, MK-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
68380	16024 ChEBI	D-mannose	+	fermentation	from API rID32A
68380	29985 ChEBI	L-glutamate	+	degradation	from API rID32A
118948	17632 ChEBI	nitrate	-	reduction
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
118948	16301 ChEBI	nitrite	-	reduction
68380	27897 ChEBI	tryptophan	-	energy source	from API rID32A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68380	35581 ChEBI	indole		from API rID32A
118948	35581 ChEBI	indole

Metabolite tests

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

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
68380	alanine arylamidase	+	3.4.11.2	from API rID32A
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68380	alkaline phosphatase	+	3.1.3.1	from API rID32A
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68380	alpha-fucosidase	-	3.2.1.51	from API rID32A
68382	alpha-galactosidase	+	3.2.1.22	from API zym
68380	alpha-galactosidase	+	3.2.1.22	from API rID32A
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68380	alpha-glucosidase	+	3.2.1.20	from API rID32A
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68380	arginine dihydrolase	-	3.5.3.6	from API rID32A
68382	beta-galactosidase	+	3.2.1.23	from API zym
68380	beta-galactosidase	+	3.2.1.23	from API rID32A
68382	beta-glucosidase	+	3.2.1.21	from API zym
68380	beta-glucosidase	+	3.2.1.21	from API rID32A
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68380	beta-glucuronidase	-	3.2.1.31	from API rID32A
67770	catalase		1.11.1.6
118948	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
68380	glutamate decarboxylase	+	4.1.1.15	from API rID32A
68380	glycin arylamidase	+		from API rID32A
68380	L-arginine arylamidase	+		from API rID32A
68382	leucine arylamidase	+	3.4.11.1	from API zym
68380	leucine arylamidase	+	3.4.11.1	from API rID32A
68380	leucyl glycin arylamidase	+	3.4.11.1	from API rID32A
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68380	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API rID32A
68382	naphthol-AS-BI-phosphohydrolase	-		from API zym
118948	oxidase	-
67770	superoxide dismutase		1.15.1.1
68382	trypsin	-	3.4.21.4	from API zym
68380	tryptophan deaminase	-	4.1.99.1	from API rID32A
118948	urease	-	3.5.1.5
68380	urease	-	3.5.1.5	from API rID32A
68382	valine arylamidase	-		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	lipoate biosynthesis	100	5 of 5
66794	formaldehyde oxidation	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	kanosamine biosynthesis II	100	2 of 2
66794	glycogen metabolism	100	5 of 5
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	cardiolipin biosynthesis	100	7 of 7
66794	acetate fermentation	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	methylglyoxal degradation	100	5 of 5
66794	biotin biosynthesis	100	4 of 4
66794	gluconeogenesis	100	8 of 8
66794	coenzyme A metabolism	100	4 of 4
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	sulfopterin metabolism	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	teichoic acid biosynthesis	100	1 of 1
66794	vitamin B6 metabolism	90.91	10 of 11
66794	starch degradation	90	9 of 10
66794	Entner Doudoroff pathway	90	9 of 10
66794	d-mannose degradation	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	propanol degradation	85.71	6 of 7
66794	phenylalanine metabolism	84.62	11 of 13
66794	pyrimidine metabolism	84.44	38 of 45
66794	purine metabolism	81.91	77 of 94
66794	pentose phosphate pathway	81.82	9 of 11
66794	hydrogen production	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	propionate fermentation	80	8 of 10
66794	threonine metabolism	80	8 of 10
66794	vitamin K metabolism	80	4 of 5
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	vitamin B12 metabolism	79.41	27 of 34
66794	photosynthesis	78.57	11 of 14
66794	NAD metabolism	77.78	14 of 18
66794	vitamin B1 metabolism	76.92	10 of 13
66794	glycolysis	76.47	13 of 17
66794	alanine metabolism	75.86	22 of 29
66794	CMP-KDO biosynthesis	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	ppGpp biosynthesis	75	3 of 4
66794	glutamate and glutamine metabolism	75	21 of 28
66794	butanoate fermentation	75	3 of 4
66794	flavin biosynthesis	73.33	11 of 15
66794	proline metabolism	72.73	8 of 11
66794	d-xylose degradation	72.73	8 of 11
66794	citric acid cycle	71.43	10 of 14
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	histidine metabolism	68.97	20 of 29
66794	degradation of sugar alcohols	68.75	11 of 16
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	octane oxidation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	UDP-GlcNAc biosynthesis	66.67	2 of 3
66794	non-pathway related	65.79	25 of 38
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	methionine metabolism	65.38	17 of 26
66794	lysine metabolism	64.29	27 of 42
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	leucine metabolism	61.54	8 of 13
66794	glycine betaine biosynthesis	60	3 of 5
66794	cellulose degradation	60	3 of 5
66794	myo-inositol biosynthesis	60	6 of 10
66794	cysteine metabolism	55.56	10 of 18
66794	degradation of hexoses	55.56	10 of 18
66794	tryptophan metabolism	55.26	21 of 38
66794	metabolism of disaccharids	54.55	6 of 11
66794	arginine metabolism	54.17	13 of 24
66794	lipid metabolism	51.61	16 of 31
66794	oxidative phosphorylation	50.55	46 of 91
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	ketogluconate metabolism	50	4 of 8
66794	degradation of pentoses	50	14 of 28
66794	tyrosine metabolism	50	7 of 14
66794	selenocysteine biosynthesis	50	3 of 6
66794	quinate degradation	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	toluene degradation	50	2 of 4
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	degradation of sugar acids	48	12 of 25
66794	urea cycle	46.15	6 of 13
66794	ascorbate metabolism	45.45	10 of 22
66794	polyamine pathway	43.48	10 of 23
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	heme metabolism	42.86	6 of 14
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	arachidonate biosynthesis	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	O-antigen biosynthesis	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	nitrate assimilation	33.33	3 of 9
66794	enterobactin biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	cyanate degradation	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	molybdenum cofactor biosynthesis	33.33	3 of 9
66794	sulfate reduction	30.77	4 of 13
66794	glutathione metabolism	28.57	4 of 14
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	cyclohexanol degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4

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
118948	-	+	-	+	-	+	-	-	-	-	+	-	+	+	-	+	+	+	-	-

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
8779	-	-	+	+	-	+	+	+	-	+	+	+	+	-	-	-	+	+	+/-	+	+	+	+	+	+	+	+	+	-
8779	-	-	+	+	-	+	+	-	-	+	+	-	+	-	-	-	+	+	-	+	+	+	+	+/-	+	+	+	+	-
8779	-	-	+	+	-	+	+	+	-	+	+	+	+	-	-	-	+	+	-	+	-	+	-	-	+	+	-	+	-
8779	-	-	+	+	-	+	+	+	-	+	+	+	+	-	-	-	+	+	-	+	+	+	+	+	+	+	+	+	-
8779	-	-	+	+	+	+	+	+	-	+	+	+	+	-	-	-	+	+	-	+	+	+	+	+	+	+	+	+	+/-
8779	-	-	+	+	-	+	+	+	-	+	+	-	+	-	-	-	+	+	-	+	+	+	+/-	+/-	+	+	+	+/-	-

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Host species	Isolation date
44811	Human feces	Homo sapiens
67770	Human feces	Homo sapiens
118948			1942

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
8779	2	Risk group (German classification) According to TRBA 466
118948	2	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	Parabacteroides distasonis strain FDAARGOS_1565	complete		823.3784		823	99.8
124043	ASM2073594v1 assembly for Parabacteroides distasonis FDAARGOS_1565	complete	GCA_020735945	823.3764		823	99.16
66792	ASM1284v1 assembly for Parabacteroides distasonis ATCC 8503	complete	GCA_000012845	435591.13	640753039	435591	99.08
66792	Parabacteroides distasonis 82G9 assembly for Parabacteroides distasonis ATCC 8503	complete	GCA_900683725	435591.48	2841273300	435591	98.48
67770	50681_F01 assembly for Parabacteroides distasonis NCTC11152	contig	GCA_900445525	823.244	2870967820	823	78.24

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Parabacteroides distasonis gene for 16S ribosomal RNA, partial sequence, strain: JCM 5825	AB238922	1488	823
20218	Bacteroides distasonis 16S-23S rDNA intergenic spacer region	AF176689	411	435591
20218	Bacteroides distasonis strain ATCC 8503 16S-23S ribosomal RNA intergenic spacer, partial sequence	AY546490	519	435591
20218	Parabacteroides distasonis strain JCM5825 16S ribosomal RNA gene, partial sequence	EU136681	1911	823
20218	Parabacteroides distasonis culture-collection DSM:20701 16S ribosomal RNA gene, partial sequence	HQ131775	933	823
20218	Bacteroides distasonis 16S ribosomal RNA	M86695	1539	823
8779	Parabacteroides distasonis strain JCM 5825 16S ribosomal RNA, partial sequence	NR_041342	1488	823

GC content

@ref	GC-content (mol%)	Method
8779	44.0
8779	45.1	sequence analysis
67770	44	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Parabacteroides distasonis strain FDAARGOS_1565
BV-BRC: 823.3784

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	92.76	no
125439	motility	BacteriaNetⓘ	no	72.95	no
125439	gram_stain	BacteriaNetⓘ	negative	83.05	no
125439	spore_formation	BacteriaNetⓘ	no	90.59	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Parabacteroides distasonis ATCC 8503 ATCC 8503
NCBI: GCA_000012845.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	91.20	no
125438	anaerobic	anaerobicⓘ	yes	86.22	yes
125438	aerobic	aerobicⓘ	no	90.38	yes
125438	spore-forming	spore-formingⓘ	no	90.14	no
125438	thermophilic	thermophileⓘ	no	92.45	yes
125438	flagellated	motile2+ⓘ	no	88.10	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Therapeutic potential of Parabacteroides distasonis in gastrointestinal and hepatic disease.	Duan J, Li Q, Cheng Y, Zhu W, Liu H, Li F.	MedComm (2020)	10.1002/mco2.70017	2024
	Parabacteroides as a promising target for disease intervention: current stage and pending issues.	Liu J, Qiu H, Zhao J, Shao N, Chen C, He Z, Zhao X, Zhao J, Zhou Y, Xu L.	NPJ Biofilms Microbiomes	10.1038/s41522-025-00772-0	2025
Phylogeny	Berberine alters gut microbial function through modulation of bile acids.	Wolf PG, Devendran S, Doden HL, Ly LK, Moore T, Takei H, Nittono H, Murai T, Kurosawa T, Chlipala GE, Green SJ, Kakiyama G, Kashyap P, McCracken VJ, Gaskins HR, Gillevet PM, Ridlon JM.	BMC Microbiol	10.1186/s12866-020-02020-1	2021
Metabolism	Sulfonolipids as novel metabolite markers of Alistipes and Odoribacter affected by high-fat diets.	Walker A, Pfitzner B, Harir M, Schaubeck M, Calasan J, Heinzmann SS, Turaev D, Rattei T, Endesfelder D, Castell WZ, Haller D, Schmid M, Hartmann A, Schmitt-Kopplin P.	Sci Rep	10.1038/s41598-017-10369-z	2017
	Administration of Bovine Milk Oligosaccharide to Weaning Gnotobiotic Mice Inoculated with a Simplified Infant Type Microbiota.	Jakobsen LMA, Sundekilde UK, Andersen HJ, Kot W, Mejia JLC, Nielsen DS, Hansen AK, Bertram HC.	Microorganisms	10.3390/microorganisms9051003	2021
Metabolism	Microbial short-chain fatty acids modulate CD8⁺ T cell responses and improve adoptive immunotherapy for cancer.	Luu M, Riester Z, Baldrich A, Reichardt N, Yuille S, Busetti A, Klein M, Wempe A, Leister H, Raifer H, Picard F, Muhammad K, Ohl K, Romero R, Fischer F, Bauer CA, Huber M, Gress TM, Lauth M, Danhof S, Bopp T, Nerreter T, Mulder IE, Steinhoff U, Hudecek M, Visekruna A.	Nat Commun	10.1038/s41467-021-24331-1	2021
Metabolism	SIMMER employs similarity algorithms to accurately identify human gut microbiome species and enzymes capable of known chemical transformations.	Bustion AE, Nayak RR, Agrawal A, Turnbaugh PJ, Pollard KS.	Elife	10.7554/elife.82401	2023
	Developing standards for the microbiome field.	Amos GCA, Logan A, Anwar S, Fritzsche M, Mate R, Bleazard T, Rijpkema S.	Microbiome	10.1186/s40168-020-00856-3	2020
Metabolism	Methotrexate impacts conserved pathways in diverse human gut bacteria leading to decreased host immune activation.	Nayak RR, Alexander M, Deshpande I, Stapleton-Gray K, Rimal B, Patterson AD, Ubeda C, Scher JU, Turnbaugh PJ.	Cell Host Microbe	10.1016/j.chom.2020.12.008	2021
	Development of an in vitro Model of Human Gut Microbiota for Screening the Reciprocal Interactions With Antibiotics, Drugs, and Xenobiotics.	El Houari A, Ecale F, Mercier A, Crapart S, Laparre J, Soulard B, Ramnath M, Berjeaud JM, Rodier MH, Crepin A.	Front Microbiol	10.3389/fmicb.2022.828359	2022
	Temporal development of the infant gut microbiota in immunoglobulin E-sensitized and nonsensitized children determined by the GA-map infant array.	Vebo HC, Sekelja M, Nestestog R, Storro O, Johnsen R, Oien T, Rudi K.	Clin Vaccine Immunol	10.1128/cvi.00062-11	2011
Genetics	Draft genome sequence of Parabacteroides distasonis SZCHProba001, isolated from feces of a 6-year-old boy.	Zhu Z, Zhang C, Liao Z, Guan J, Xie X, Li Z, Lin B, Chen H, Zhuang Z, Meng S, Zou Y, Li W, Luo M, Dai D.	Microbiol Resour Announc	10.1128/mra.00422-25	2025
Pathogenicity	The potential effect of gut microbiota on the secretion of selected cytokines by human cells in vitro.	Kopa-Stojak PN, Kleniewska P, Hoffmann A, Pawliczak R.	Sci Rep	10.1038/s41598-025-01581-3	2025
	One-pot Enzymatic Synthesis of Sophorose from Sucrose and Glucose.	Tatebe Y, Yamamoto Y, Isono N.	J Appl Glycosci (1999)	10.5458/jag.7201201	2025
	Parabacteroides distasonis regulates the infectivity and pathogenicity of SVCV at different water temperatures.	Zhang Y, Gao Y, Li C, Zhang YA, Lu Y, Ye J, Liu X.	Microbiome	10.1186/s40168-024-01799-9	2024
	The potential immunomodulatory role of the gut microbiota in the pathogenesis of asthma: an in vitro study.	Kleniewska P, Kopa-Stojak PN, Hoffmann A, Pawliczak R.	Sci Rep	10.1038/s41598-023-47003-0	2023
	Parabacteroides distasonis promotes liver regeneration by increasing beta-hydroxybutyric acid (BHB) production and BHB-driven STAT3 signals.	Guo M, Jiang X, Ouyang H, Zhang X, Zhang S, Wang P, Bi G, Wu T, Zhou W, Liang F, Yang X, Fan S, Fang JH, Chen P, Bi H.	Acta Pharm Sin B	10.1016/j.apsb.2025.01.024	2025
Phylogeny	Classification of Parabacteroides distasonis and other Bacteroidetes using O- antigen virulence gene: RfbA-Typing and hypothesis for pathogenic vs. probiotic strain differentiation.	Bank NC, Singh V, Rodriguez-Palacios A.	Gut Microbes	10.1080/19490976.2021.1997293	2022
	Lessons from the model gut Bacteroidales Bacteroides fragilis and Bacteroides thetaiotaomicron and future opportunities.	Comstock LE.	J Bacteriol	10.1128/jb.00346-25	2025
	Parabacteroides distasonis-Derived Outer Membrane Vesicles Enhance Antitumor Immunity Against Colon Tumors by Modulating CXCL10 and CD8⁺ T Cells.	Liang R, Li P, Yang N, Xiao X, Gong J, Zhang X, Bai Y, Chen Y, Xie Z, Liao Q.	Drug Des Devel Ther	10.2147/dddt.s457338	2024
	A Porphyromonas gingivalis hypothetical protein controlled by the type I-C CRISPR-Cas system is a novel adhesin important in virulence.	Irfan M, Solbiati J, Duran-Pinedo A, Rocha FG, Gibson FC, Frias-Lopez J.	mSystems	10.1128/msystems.01231-23	2024
	Protection against fibrosis by a bacterial consortium in metabolic dysfunction-associated steatohepatitis and the role of amino acid metabolism.	Kwan SY, Gonzales KA, Jamal MA, Stevenson HL, Tan L, Lorenzi PL, Futreal PA, Hawk ET, McCormick JB, Fisher-Hoch SP, Jenq RR, Beretta L.	Gut Microbes	10.1080/19490976.2024.2399260	2024
	Complete Genome Sequence of a Parabacteroides distasonis Strain (CavFT hAR46) Isolated from a Gut Wall-Cavitating Microlesion in a Patient with Severe Crohn's Disease.	Yang F, Kumar A, Davenport KW, Kelliher JM, Ezeji JC, Good CE, Jacobs MR, Conger M, West G, Fiocchi C, Cominelli F, Dichosa AEK, Rodriguez-Palacios A.	Microbiol Resour Announc	10.1128/mra.00585-19	2019
	Production of deoxycholic acid by low-abundant microbial species is associated with impaired glucose metabolism.	Wahlstrom A, Brumbaugh A, Sjoland W, Olsson L, Wu H, Henricsson M, Lundqvist A, Makki K, Hazen SL, Bergstrom G, Marschall HU, Fischbach MA, Backhed F.	Nat Commun	10.1038/s41467-024-48543-3	2024
	Gut microbiota-bile acid crosstalk contributes to the rebound weight gain after calorie restriction in mice.	Li M, Wang S, Li Y, Zhao M, Kuang J, Liang D, Wang J, Wei M, Rajani C, Ma X, Tang Y, Ren Z, Chen T, Zhao A, Hu C, Shen C, Jia W, Liu P, Zheng X, Jia W.	Nat Commun	10.1038/s41467-022-29589-7	2022
	Characterization of Two Parabacteroides distasonis Candidate Strains as New Live Biotherapeutics against Obesity.	Cuffaro B, Boutillier D, Desramaut J, Jablaoui A, Werkmeister E, Trottein F, Waligora-Dupriet AJ, Rhimi M, Maguin E, Grangette C.	Cells	10.3390/cells12091260	2023
	Coarse-grained model of serial dilution dynamics in synthetic human gut microbiome.	Mahajan T, Maslov S.	PLoS Comput Biol	10.1371/journal.pcbi.1013222	2025
Pathogenicity	Parabacteroides distasonis: intriguing aerotolerant gut anaerobe with emerging antimicrobial resistance and pathogenic and probiotic roles in human health.	Ezeji JC, Sarikonda DK, Hopperton A, Erkkila HL, Cohen DE, Martinez SP, Cominelli F, Kuwahara T, Dichosa AEK, Good CE, Jacobs MR, Khoretonenko M, Veloo A, Rodriguez-Palacios A.	Gut Microbes	10.1080/19490976.2021.1922241	2021
Pathogenicity	Visceral adiposity in postmenopausal women is associated with a pro-inflammatory gut microbiome and immunogenic metabolic endotoxemia.	Gaber M, Wilson AS, Millen AE, Hovey KM, LaMonte MJ, Wactawski-Wende J, Ochs-Balcom HM, Cook KL.	Microbiome	10.1186/s40168-024-01901-1	2024
	Metabolic Effects of Bovine Milk Oligosaccharides on Selected Commensals of the Infant Microbiome-Commensalism and Postbiotic Effects.	Jakobsen LMA, Maldonado-Gomez MX, Sundekilde UK, Andersen HJ, Nielsen DS, Bertram HC.	Metabolites	10.3390/metabo10040167	2020
	Fusobacterium nucleatum promotes tumor progression in KRAS p.G12D-mutant colorectal cancer by binding to DHX15.	Zhu H, Li M, Bi D, Yang H, Gao Y, Song F, Zheng J, Xie R, Zhang Y, Liu H, Yan X, Kong C, Zhu Y, Xu Q, Wei Q, Qin H.	Nat Commun	10.1038/s41467-024-45572-w	2024
Genetics	Antigenic operon fragmentation and diversification mechanism in Bacteroidota impacts gut metagenomics and pathobionts in Crohn's disease microlesions.	Bank NC, Singh V, McCourt B, Burberry A, Roberts KD, Grubb B, Rodriguez-Palacios A.	Gut Microbes	10.1080/19490976.2024.2350150	2024
	Indoleacrylic acid produced by Parabacteroides distasonis alleviates type 2 diabetes via activation of AhR to repair intestinal barrier.	Liu D, Zhang S, Li S, Zhang Q, Cai Y, Li P, Li H, Shen B, Liao Q, Hong Y, Xie Z.	BMC Biol	10.1186/s12915-023-01578-2	2023
	Ruminococcus gnavus and Limosilactobacillus reuteri Regulate Reg3gamma Expression through Multiple Pathways.	Ramirez ZE, Surana NK.	Immunohorizons	10.4049/immunohorizons.2200096	2023
Metabolism	The impact of progressive chronic kidney disease on hepatic drug metabolism.	Hartjes ED, Lim YJ, Velenosi TJ, Al KF, Macklaim JM, Kucey AS, Reid G, Burton JP, Gloor GB, Urquhart BL.	Drug Metab Dispos	10.1016/j.dmd.2025.100085	2025
	Influence of the densities and nutritional components of bacterial colonies on the culture-enriched gut bacterial community structure.	Gu Y, Yan D, Wu M, Li M, Li P, Wang J, Chang Y, Yang F, Di S, Ni S, Yang M, Liu J.	AMB Express	10.1186/s13568-021-01240-6	2021
Genetics	Discovery of antimicrobial peptides in the global microbiome with machine learning.	Santos-Junior CD, Torres MDT, Duan Y, Rodriguez Del Rio A, Schmidt TSB, Chong H, Fullam A, Kuhn M, Zhu C, Houseman A, Somborski J, Vines A, Zhao XM, Bork P, Huerta-Cepas J, de la Fuente-Nunez C, Coelho LP.	Cell	10.1016/j.cell.2024.05.013	2024
Genetics	Comparative Analysis and Data Provenance for 1,113 Bacterial Genome Assemblies.	Yarmosh DA, Lopera JG, Puthuveetil NP, Combs PF, Reese AL, Tabron C, Pierola AE, Duncan J, Greenfield SR, Marlow R, King S, Riojas MA, Bagnoli J, Benton B, Jacobs JL.	mSphere	10.1128/msphere.00077-22	2022
	Gut Microbiota and B Cell Receptor (BCR) Inhibitors for the Treatment of Chronic Lymphocytic Leukemia: Is Biodiversity Correlated with Clinical Response or Immune-Related Adverse Event Occurrence? A Cross-Sectional Study.	Zuccaro V, Petazzoni G, Mileto I, Corbella M, Asperges E, Sacchi P, Rattotti S, Varettoni M, Defrancesco I, Cambieri P, Baldanti F, Arcaini L, Bruno R.	Microorganisms	10.3390/microorganisms11051305	2023
	High Diversity but Monodominance of Multidrug-Resistant Bacteria in Immunocompromised Pediatric Patients with Acute Lymphoblastic Leukemia Developing GVHD Are Not Associated with Changes in Gut Mycobiome.	Sardzikova S, Andrijkova K, Svec P, Beke G, Klucar L, Minarik G, Bielik V, Kolenova A, Soltys K.	Antibiotics (Basel)	10.3390/antibiotics12121667	2023
	Gut-Thyroid axis: How gut microbial dysbiosis associated with euthyroid thyroid cancer.	Ishaq HM, Mohammad IS, Hussain R, Parveen R, Shirazi JH, Fan Y, Shahzad M, Hayat K, Li H, Ihsan A, Muhammad KS, Usman M, Zhang S, Yuan L, Ullah S, Paiva-Santos AC, Xu J.	J Cancer	10.7150/jca.66816	2022
Pathogenicity	Oral Supplements of Combined Bacillus licheniformis Zhengchangsheng® and Xylooligosaccharides Improve High-Fat Diet-Induced Obesity and Modulate the Gut Microbiota in Rats.	Li Y, Liu M, Liu H, Wei X, Su X, Li M, Yuan J.	Biomed Res Int	10.1155/2020/9067821	2020
Metabolism	Strain-level fitness in the gut microbiome is an emergent property of glycans and a single metabolite.	Park SY, Rao C, Coyte KZ, Kuziel GA, Zhang Y, Huang W, Franzosa EA, Weng JK, Huttenhower C, Rakoff-Nahoum S.	Cell	10.1016/j.cell.2022.01.002	2022
Genetics	Genome Evolution and Nitrogen Fixation in Bacterial Ectosymbionts of a Protist Inhabiting Wood-Feeding Cockroaches.	Tai V, Carpenter KJ, Weber PK, Nalepa CA, Perlman SJ, Keeling PJ.	Appl Environ Microbiol	10.1128/aem.00611-16	2016
Enzymology	Mammalian-like type II glutaminyl cyclases in Porphyromonas gingivalis and other oral pathogenic bacteria as targets for treatment of periodontitis.	Taudte N, Linnert M, Rahfeld JU, Piechotta A, Ramsbeck D, Buchholz M, Kolenko P, Parthier C, Houston JA, Veillard F, Eick S, Potempa J, Schilling S, Demuth HU, Stubbs MT.	J Biol Chem	10.1016/j.jbc.2021.100263	2021
Genetics	Allelic Variation in a Single Genomic Region Alters the Microbiome of the Snail Biomphalaria glabrata.	Allan ERO, Tennessen JA, Sharpton TJ, Blouin MS.	J Hered	10.1093/jhered/esy014	2018
	Crystal structure and metal binding properties of the periplasmic iron component EfeM from Pseudomonas syringae EfeUOB/M iron-transport system.	Rajasekaran MB, Hussain R, Siligardi G, Andrews SC, Watson KA.	Biometals	10.1007/s10534-022-00389-2	2022
Genetics	Strand-specific community RNA-seq reveals prevalent and dynamic antisense transcription in human gut microbiota.	Bao G, Wang M, Doak TG, Ye Y.	Front Microbiol	10.3389/fmicb.2015.00896	2015
Genetics	Investigation of potential targets of Porphyromonas CRISPRs among the genomes of Porphyromonas species.	Watanabe T, Shibasaki M, Maruyama F, Sekizaki T, Nakagawa I.	PLoS One	10.1371/journal.pone.0183752	2017
Phylogeny	Genome sequence of the marine bacterium Marinilabilia salmonicolor JCM 21150T.	Kumar S, Subramanian S, Raghava GP, Pinnaka AK.	J Bacteriol	10.1128/jb.00649-12	2012
Phylogeny	Gilbert's Syndrome and the Gut Microbiota - Insights From the Case-Control BILIHEALTH Study.	Zohrer PA, Hana CA, Seyed Khoei N, Molzer C, Hormann-Wallner M, Tosevska A, Doberer D, Marculescu R, Bulmer AC, Herbold CW, Berry D, Wagner KH.	Front Cell Infect Microbiol	10.3389/fcimb.2021.701109	2021
	Interbacterial warfare in the human gut: insights from Bacteroidales' perspective.	Jiang K, Pang X, Li W, Xu X, Yang Y, Shang C, Gao X.	Gut Microbes	10.1080/19490976.2025.2473522	2025
	Structural and Biochemical Characterization of a Nonbinding SusD-Like Protein Involved in Xylooligosaccharide Utilization by an Uncultured Human Gut Bacteroides Strain.	Tauzin AS, Wang Z, Cioci G, Li X, Labourel A, Machado B, Lippens G, Potocki-Veronese G.	mSphere	10.1128/msphere.00244-22	2022
Metabolism	C-Glycoside metabolism in the gut and in nature: Identification, characterization, structural analyses and distribution of C-C bond-cleaving enzymes.	Mori T, Kumano T, He H, Watanabe S, Senda M, Moriya T, Adachi N, Hori S, Terashita Y, Kawasaki M, Hashimoto Y, Awakawa T, Senda T, Abe I, Kobayashi M.	Nat Commun	10.1038/s41467-021-26585-1	2021
	Gut microbial taxa elevated by dietary sugar disrupt memory function.	Noble EE, Olson CA, Davis E, Tsan L, Chen YW, Schade R, Liu C, Suarez A, Jones RB, de La Serre C, Yang X, Hsiao EY, Kanoski SE.	Transl Psychiatry	10.1038/s41398-021-01309-7	2021
Pathogenicity	Compositional changes to the ileal microbiome precede the onset of spontaneous ileitis in SHIP deficient mice.	Dobranowski PA, Tang C, Sauve JP, Menzies SC, Sly LM.	Gut Microbes	10.1080/19490976.2018.1560767	2019
Metabolism	Buried chloride stereochemistry in the Protein Data Bank.	Carugo O.	BMC Struct Biol	10.1186/s12900-014-0019-8	2014
Metabolism	Involvement of the microbiota-gut-brain axis in chronic restraint stress: disturbances of the kynurenine metabolic pathway in both the gut and brain.	Deng Y, Zhou M, Wang J, Yao J, Yu J, Liu W, Wu L, Wang J, Gao R.	Gut Microbes	10.1080/19490976.2020.1869501	2021
Proteome	Structures of single-layer beta-sheet proteins evolved from beta-hairpin repeats.	Xu Q, Biancalana M, Grant JC, Chiu HJ, Jaroszewski L, Knuth MW, Lesley SA, Godzik A, Elsliger MA, Deacon AM, Wilson IA.	Protein Sci	10.1002/pro.3683	2019
Genetics	Reconstruction of Bacterial and Viral Genomes from Multiple Metagenomes.	Gupta A, Kumar S, Prasoodanan VP, Harish K, Sharma AK, Sharma VK.	Front Microbiol	10.3389/fmicb.2016.00469	2016
Enzymology	High occurrence of Fusobacterium nucleatum and Clostridium difficile in the intestinal microbiota of colorectal carcinoma patients.	Fukugaiti MH, Ignacio A, Fernandes MR, Ribeiro Junior U, Nakano V, Avila-Campos MJ.	Braz J Microbiol	10.1590/s1517-838246420140665	2015
	Molecular Alteration Analysis of Human Gut Microbial Composition in Graves' disease Patients.	Ishaq HM, Mohammad IS, Shahzad M, Ma C, Raza MA, Wu X, Guo H, Shi P, Xu J.	Int J Biol Sci	10.7150/ijbs.24151	2018
Metabolism	A Commensal Dipeptidyl Aminopeptidase with Specificity for N-Terminal Glycine Degrades Human-Produced Antimicrobial Peptides in Vitro.	Xu JH, Jiang Z, Solania A, Chatterjee S, Suzuki B, Lietz CB, Hook VYH, O'Donoghue AJ, Wolan DW.	ACS Chem Biol	10.1021/acschembio.8b00420	2018
	Pglyrp-Regulated Gut Microflora Prevotella falsenii, Parabacteroides distasonis and Bacteroides eggerthii Enhance and Alistipes finegoldii Attenuates Colitis in Mice.	Dziarski R, Park SY, Kashyap DR, Dowd SE, Gupta D.	PLoS One	10.1371/journal.pone.0146162	2016
	Multicenter Performance Evaluation of the Simplexa Bordetella Direct Kit in Nasopharyngeal Swab Specimens.	Chow SK, Arbefeville S, Boyanton BL, Dault EM, Dunn J, Ferrieri P, Greene W, Pence MA, Otiso J, Richter S, Schutzbank TE.	J Clin Microbiol	10.1128/jcm.01041-20	2020
	Proanthocyanidin-enriched cranberry extract induces resilient bacterial community dynamics in a gnotobiotic mouse model.	Neto CC, Mortzfeld BM, Turbitt JR, Bhattarai SK, Yeliseyev V, DiBenedetto N, Bry L, Bucci V.	Microb Cell	10.15698/mic2021.06.752	2021
	Type VI secretion systems of human gut Bacteroidales segregate into three genetic architectures, two of which are contained on mobile genetic elements.	Coyne MJ, Roelofs KG, Comstock LE.	BMC Genomics	10.1186/s12864-016-2377-z	2016
	Deep-learning-enabled antibiotic discovery through molecular de-extinction.	Wan F, Torres MDT, Peng J, de la Fuente-Nunez C.	Nat Biomed Eng	10.1038/s41551-024-01201-x	2024
	Insights from Bacteroides Species in Children with Type 1 Diabetes.	Matos J, Matos I, Calha M, Santos P, Duarte I, Cardoso Y, Faleiro ML.	Microorganisms	10.3390/microorganisms9071436	2021
Metabolism	Resistant starch, microbiome, and precision modulation.	Dobranowski PA, Stintzi A.	Gut Microbes	10.1080/19490976.2021.1926842	2021
Genetics	Enterotoxigenic and non-enterotoxigenic Bacteroides fragilis from fecal microbiota of children.	Ignacio A, Fernandes MR, Avila-Campos MJ, Nakano V.	Braz J Microbiol	10.1590/s1517-838246420140728	2015
Pathogenicity	In vitro antimicrobial activity of razupenem (SMP-601, PTZ601) against anaerobic bacteria.	Tran CM, Tanaka K, Yamagishi Y, Goto T, Mikamo H, Watanabe K.	Antimicrob Agents Chemother	10.1128/aac.01038-10	2011
	Design, construction, and in vivo augmentation of a complex gut microbiome.	Cheng AG, Ho PY, Aranda-Diaz A, Jain S, Yu FB, Meng X, Wang M, Iakiviak M, Nagashima K, Zhao A, Murugkar P, Patil A, Atabakhsh K, Weakley A, Yan J, Brumbaugh AR, Higginbottom S, Dimas A, Shiver AL, Deutschbauer A, Neff N, Sonnenburg JL, Huang KC, Fischbach MA.	Cell	10.1016/j.cell.2022.08.003	2022
	Intracellular Fusobacterium nucleatum infection attenuates antitumor immunity in esophageal squamous cell carcinoma.	Li Y, Xing S, Chen F, Li Q, Dou S, Huang Y, An J, Liu W, Zhang G.	Nat Commun	10.1038/s41467-023-40987-3	2023
	Salmonella Typhimurium utilizes a T6SS-mediated antibacterial weapon to establish in the host gut.	Sana TG, Flaugnatti N, Lugo KA, Lam LH, Jacobson A, Baylot V, Durand E, Journet L, Cascales E, Monack DM.	Proc Natl Acad Sci U S A	10.1073/pnas.1608858113	2016
Enzymology	A distinctive 'microbial signature' in celiac pediatric patients.	Schippa S, Iebba V, Barbato M, Di Nardo G, Totino V, Checchi MP, Longhi C, Maiella G, Cucchiara S, Conte MP.	BMC Microbiol	10.1186/1471-2180-10-175	2010
Metabolism	Characterization of an invertase with pH tolerance and truncation of its N-terminal to shift optimum activity toward neutral pH.	Du L, Pang H, Wang Z, Lu J, Wei Y, Huang R.	PLoS One	10.1371/journal.pone.0062306	2013
	Eukaryote to gut bacteria transfer of a glycoside hydrolase gene essential for starch breakdown in plants.	Arias MC, Danchin EG, Coutinho P, Henrissat B, Ball S.	Mob Genet Elements	10.4161/mge.20375	2012
Metabolism	Strain dropouts reveal interactions that govern the metabolic output of the gut microbiome.	Wang M, Osborn LJ, Jain S, Meng X, Weakley A, Yan J, Massey WJ, Varadharajan V, Horak A, Banerjee R, Allende DS, Chan ER, Hajjar AM, Wang Z, Dimas A, Zhao A, Nagashima K, Cheng AG, Higginbottom S, Hazen SL, Brown JM, Fischbach MA.	Cell	10.1016/j.cell.2023.05.037	2023
Pathogenicity	The Use of Defined Microbial Communities To Model Host-Microbe Interactions in the Human Gut.	Elzinga J, van der Oost J, de Vos WM, Smidt H.	Microbiol Mol Biol Rev	10.1128/mmbr.00054-18	2019
Genetics	To assemble or not to resemble-A validated Comparative Metatranscriptomics Workflow (CoMW).	Anwar MZ, Lanzen A, Bang-Andreasen T, Jacobsen CS.	Gigascience	10.1093/gigascience/giz096	2019
Pathogenicity	In vitro activity of tomopenem (CS-023/RO4908463) against anaerobic bacteria.	Tanaka K, Mikamo H, Nakao K, Ichiishi T, Goto T, Yamagishi Y, Watanabe K.	Antimicrob Agents Chemother	10.1128/aac.00595-08	2009
Pathogenicity	Fish oil enhances recovery of intestinal microbiota and epithelial integrity in chronic rejection of intestinal transplant.	Li Q, Zhang Q, Wang C, Tang C, Zhang Y, Li N, Li J.	PLoS One	10.1371/journal.pone.0020460	2011
Pathogenicity	Acceptive Immunity: The Role of Fucosylated Glycans in Human Host-Microbiome Interactions.	Kononova S, Litvinova E, Vakhitov T, Skalinskaya M, Sitkin S.	Int J Mol Sci	10.3390/ijms22083854	2021
Metabolism	A bacterial bile acid metabolite modulates T_reg activity through the nuclear hormone receptor NR4A1.	Li W, Hang S, Fang Y, Bae S, Zhang Y, Zhang M, Wang G, McCurry MD, Bae M, Paik D, Franzosa EA, Rastinejad F, Huttenhower C, Yao L, Devlin AS, Huh JR.	Cell Host Microbe	10.1016/j.chom.2021.07.013	2021
Metabolism	Slimy partners: the mucus barrier and gut microbiome in ulcerative colitis.	Fang J, Wang H, Zhou Y, Zhang H, Zhou H, Zhang X.	Exp Mol Med	10.1038/s12276-021-00617-8	2021
	Evolution of endonuclease IV protein family: an in silico analysis.	Kanchan S, Sharma P, Chowdhury S.	3 Biotech	10.1007/s13205-019-1696-6	2019
Metabolism	A metabolomics pipeline for the mechanistic interrogation of the gut microbiome.	Han S, Van Treuren W, Fischer CR, Merrill BD, DeFelice BC, Sanchez JM, Higginbottom SK, Guthrie L, Fall LA, Dodd D, Fischbach MA, Sonnenburg JL.	Nature	10.1038/s41586-021-03707-9	2021
Metabolism	An ecological network of polysaccharide utilization among human intestinal symbionts.	Rakoff-Nahoum S, Coyne MJ, Comstock LE.	Curr Biol	10.1016/j.cub.2013.10.077	2014
Genetics	Metagenomic sequencing of marine periphyton: taxonomic and functional insights into biofilm communities.	Sanli K, Bengtsson-Palme J, Nilsson RH, Kristiansson E, Alm Rosenblad M, Blanck H, Eriksson KM.	Front Microbiol	10.3389/fmicb.2015.01192	2015
Genetics	Distilled single-cell genome sequencing and de novo assembly for sparse microbial communities.	Taghavi Z, Movahedi NS, Draghici S, Chitsaz H.	Bioinformatics	10.1093/bioinformatics/btt420	2013
	The human gut virome: inter-individual variation and dynamic response to diet.	Minot S, Sinha R, Chen J, Li H, Keilbaugh SA, Wu GD, Lewis JD, Bushman FD.	Genome Res	10.1101/gr.122705.111	2011
Metabolism	Proteomic analysis of a noninvasive human model of acute inflammation and its resolution: the twenty-one day gingivitis model.	Grant MM, Creese AJ, Barr G, Ling MR, Scott AE, Matthews JB, Griffiths HR, Cooper HJ, Chapple IL.	J Proteome Res	10.1021/pr100446f	2010
Enzymology	Structural bases for N-glycan processing by mannoside phosphorylase.	Ladeveze S, Cioci G, Roblin P, Mourey L, Tranier S, Potocki-Veronese G.	Acta Crystallogr D Biol Crystallogr	10.1107/s1399004715006604	2015
	Dynamic Modulation of the Gut Microbiota and Metabolome by Bacteriophages in a Mouse Model.	Hsu BB, Gibson TE, Yeliseyev V, Liu Q, Lyon L, Bry L, Silver PA, Gerber GK.	Cell Host Microbe	10.1016/j.chom.2019.05.001	2019
Genetics	Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing.	Ranjan R, Rani A, Metwally A, Metwally A, McGee HS, Perkins DL.	Biochem Biophys Res Commun	10.1016/j.bbrc.2015.12.083	2016
Pathogenicity	Reprofiled anthelmintics abate hypervirulent stationary-phase Clostridium difficile.	Gooyit M, Janda KD.	Sci Rep	10.1038/srep33642	2016
	Comparing the similarity of different groups of bacteria to the human proteome.	Trost B, Pajon R, Jayaprakash T, Kusalik A.	PLoS One	10.1371/journal.pone.0034007	2012
Enzymology	Molecular cloning, expression, and characterization of four novel thermo-alkaliphilic enzymes retrieved from a metagenomic library.	Maruthamuthu M, van Elsas JD.	Biotechnol Biofuels	10.1186/s13068-017-0808-y	2017
	Evolution of symbiotic bacteria in the distal human intestine.	Xu J, Mahowald MA, Ley RE, Lozupone CA, Hamady M, Martens EC, Henrissat B, Coutinho PM, Minx P, Latreille P, Cordum H, Van Brunt A, Kim K, Fulton RS, Fulton LA, Clifton SW, Wilson RK, Knight RD, Gordon JI.	PLoS Biol	10.1371/journal.pbio.0050156	2007
	Rapid PCR Detection of Mycoplasma hominis, Ureaplasma urealyticum, and Ureaplasma parvum.	Cunningham SA, Mandrekar JN, Rosenblatt JE, Patel R.	Int J Bacteriol	10.1155/2013/168742	2013
	Presence of Segmented Filamentous Bacteria in Human Children and Its Potential Role in the Modulation of Human Gut Immunity.	Chen B, Chen H, Shu X, Yin Y, Li J, Qin J, Chen L, Peng K, Xu F, Gu W, Zhao H, Jiang L, Li L, Song J, Elitsur Y, Yu HD, Jiang M, Wang X, Xiang C.	Front Microbiol	10.3389/fmicb.2018.01403	2018
Metabolism	A gut bacterial pathway metabolizes aromatic amino acids into nine circulating metabolites.	Dodd D, Spitzer MH, Van Treuren W, Merrill BD, Hryckowian AJ, Higginbottom SK, Le A, Cowan TM, Nolan GP, Fischbach MA, Sonnenburg JL.	Nature	10.1038/nature24661	2017
	Glycobiology Aspects of the Periodontal Pathogen Tannerella forsythia.	Posch G, Sekot G, Friedrich V, Megson ZA, Koerdt A, Messner P, Schaffer C.	Biomolecules	10.3390/biom2040467	2012
Metabolism	Role of glycoside phosphorylases in mannose foraging by human gut bacteria.	Ladeveze S, Tarquis L, Cecchini DA, Bercovici J, Andre I, Topham CM, Morel S, Laville E, Monsan P, Lombard V, Henrissat B, Potocki-Veronese G.	J Biol Chem	10.1074/jbc.m113.483628	2013
Metabolism	Characterization and scope of S-layer protein O-glycosylation in Tannerella forsythia.	Posch G, Pabst M, Brecker L, Altmann F, Messner P, Schaffer C.	J Biol Chem	10.1074/jbc.m111.284893	2011
Enzymology	Structural characterization of a conserved, calcium-dependent periplasmic protease from Legionella pneumophila.	Chatterjee D, Boyd CD, O'Toole GA, Sondermann H.	J Bacteriol	10.1128/jb.00640-12	2012
Phenotype	Moving beyond microbiome-wide associations to causal microbe identification.	Surana NK, Kasper DL.	Nature	10.1038/nature25019	2017
Genetics	Microbiome of fungus-growing termites: a new reservoir for lignocellulase genes.	Liu N, Yan X, Zhang M, Xie L, Wang Q, Huang Y, Zhou X, Wang S, Zhou Z.	Appl Environ Microbiol	10.1128/aem.01521-10	2011
Metabolism	The uroS and yifB Genes Conserved among Tetrapyrrole Synthesizing-Deficient Bacteroidales Are Involved in Bacteroides fragilis Heme Assimilation and Survival in Experimental Intra-abdominal Infection and Intestinal Colonization.	Parker AC, Bergonia HA, Seals NL, Baccanale CL, Rocha ER.	Infect Immun	10.1128/iai.00103-20	2020
	Bioprospecting metagenomics of decaying wood: mining for new glycoside hydrolases.	Li LL, Taghavi S, McCorkle SM, Zhang YB, Blewitt MG, Brunecky R, Adney WS, Himmel ME, Brumm P, Drinkwater C, Mead DA, Tringe SG, Lelie Dv.	Biotechnol Biofuels	10.1186/1754-6834-4-23	2011
	Environmental and gut bacteroidetes: the food connection.	Thomas F, Hehemann JH, Rebuffet E, Czjzek M, Michel G.	Front Microbiol	10.3389/fmicb.2011.00093	2011
Metabolism	An in vitro model of the horse gut microbiome enables identification of lactate-utilizing bacteria that differentially respond to starch induction.	Biddle AS, Black SJ, Blanchard JL.	PLoS One	10.1371/journal.pone.0077599	2013
Transcriptome	Alignment-free Transcriptomic and Metatranscriptomic Comparison Using Sequencing Signatures with Variable Length Markov Chains.	Liao W, Ren J, Wang K, Wang S, Zeng F, Wang Y, Sun F.	Sci Rep	10.1038/srep37243	2016
Genetics	Ensemble analysis of adaptive compressed genome sequencing strategies.	Taghavi Z.	BMC Bioinformatics	10.1186/1471-2105-15-s9-s13	2014
	The Gut Microbiota Mediates the Anti-Seizure Effects of the Ketogenic Diet.	Olson CA, Vuong HE, Yano JM, Liang QY, Nusbaum DJ, Hsiao EY.	Cell	10.1016/j.cell.2018.04.027	2018
Genetics	Pre_GI: a global map of ontological links between horizontally transferred genomic islands in bacterial and archaeal genomes.	Pierneef R, Cronje L, Bezuidt O, Reva ON.	Database (Oxford)	10.1093/database/bav058	2015
	MetaTrans: an open-source pipeline for metatranscriptomics.	Martinez X, Pozuelo M, Pascal V, Campos D, Gut I, Gut M, Azpiroz F, Guarner F, Manichanh C.	Sci Rep	10.1038/srep26447	2016
	A novel diphospho-P,P'-diester from Methanobacterium thermoautotrophicum.	Seely RJ, Fahrney DE.	J Biol Chem	10.1016/s0021-9258(17)44350-x	1983
Metabolism	Ferritin-like family proteins in the anaerobe Bacteroides fragilis: when an oxygen storm is coming, take your iron to the shelter.	Rocha ER, Smith CJ.	Biometals	10.1007/s10534-013-9650-2	2013
Genetics	Protein languages differ depending on microorganism lifestyle.	Grzymski JJ, Marsh AG.	PLoS One	10.1371/journal.pone.0096910	2014
Metabolism	Metabolic mechanism of mannan in a ruminal bacterium, Ruminococcus albus, involving two mannoside phosphorylases and cellobiose 2-epimerase: discovery of a new carbohydrate phosphorylase, beta-1,4-mannooligosaccharide phosphorylase.	Kawahara R, Saburi W, Odaka R, Taguchi H, Ito S, Mori H, Matsui H.	J Biol Chem	10.1074/jbc.m112.390336	2012
Metabolism	Distribution analysis of hydrogenases in surface waters of marine and freshwater environments.	Barz M, Beimgraben C, Staller T, Germer F, Opitz F, Marquardt C, Schwarz C, Gutekunst K, Vanselow KH, Schmitz R, LaRoche J, Schulz R, Appel J.	PLoS One	10.1371/journal.pone.0013846	2010
Metabolism	Phylum-wide general protein O-glycosylation system of the Bacteroidetes.	Coyne MJ, Fletcher CM, Chatzidaki-Livanis M, Posch G, Schaffer C, Comstock LE.	Mol Microbiol	10.1111/mmi.12220	2013
	Spatial organization of a model 15-member human gut microbiota established in gnotobiotic mice.	Mark Welch JL, Hasegawa Y, McNulty NP, Gordon JI, Borisy GG.	Proc Natl Acad Sci U S A	10.1073/pnas.1711596114	2017
Enzymology	Rapid stool-based diagnosis of Clostridium difficile infection by real-time PCR in a children's hospital.	Luna RA, Boyanton BL, Mehta S, Courtney EM, Webb CR, Revell PA, Versalovic J.	J Clin Microbiol	10.1128/jcm.01983-10	2011
Metabolism	A selective gut bacterial bile salt hydrolase alters host metabolism.	Yao L, Seaton SC, Ndousse-Fetter S, Adhikari AA, DiBenedetto N, Mina AI, Banks AS, Bry L, Devlin AS.	Elife	10.7554/elife.37182	2018
Phylogeny	New degenerate Cytophaga-Flexibacter-Bacteroides-specific 16S ribosomal DNA-targeted oligonucleotide probes reveal high bacterial diversity in River Taff epilithon.	O'Sullivan LA, Weightman AJ, Fry JC.	Appl Environ Microbiol	10.1128/aem.68.1.201-210.2002	2002
Genetics	Information theoretic perspective on genome clustering.	Veluchamy A, Mehta P, Srividhya KV, Vikram H, Govind MK, Gupta R, Aziz Bin Dukhyil A, Abdullah Alharbi R, Abdullah Aloyuni S, Hassan MM, Krishnaswamy S.	Saudi J Biol Sci	10.1016/j.sjbs.2020.12.039	2021
Metabolism	The effects of micronutrient deficiencies on bacterial species from the human gut microbiota.	Hibberd MC, Wu M, Rodionov DA, Li X, Cheng J, Griffin NW, Barratt MJ, Giannone RJ, Hettich RL, Osterman AL, Gordon JI.	Sci Transl Med	10.1126/scitranslmed.aal4069	2017
Metabolism	Structural and sequence analysis of imelysin-like proteins implicated in bacterial iron uptake.	Xu Q, Rawlings ND, Farr CL, Chiu HJ, Grant JC, Jaroszewski L, Klock HE, Knuth MW, Miller MD, Weekes D, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA.	PLoS One	10.1371/journal.pone.0021875	2011
Phylogeny	Diet-induced metabolic improvements in a hamster model of hypercholesterolemia are strongly linked to alterations of the gut microbiota.	Martinez I, Wallace G, Zhang C, Legge R, Benson AK, Carr TP, Moriyama EN, Walter J.	Appl Environ Microbiol	10.1128/aem.00380-09	2009
	Annotation of Protein Domains Reveals Remarkable Conservation in the Functional Make up of Proteomes Across Superkingdoms.	Nasir A, Naeem A, Khan MJ, Nicora HD, Caetano-Anolles G.	Genes (Basel)	10.3390/genes2040869	2011
	Resistance of Capnocytophaga canimorsus to killing by human complement and polymorphonuclear leukocytes.	Shin H, Mally M, Meyer S, Fiechter C, Paroz C, Zaehringer U, Cornelis GR.	Infect Immun	10.1128/iai.01324-08	2009
	The complete genome sequence of the pathogenic intestinal spirochete Brachyspira pilosicoli and comparison with other Brachyspira genomes.	Wanchanthuek P, Bellgard MI, La T, Ryan K, Moolhuijzen P, Chapman B, Black M, Schibeci D, Hunter A, Barrero R, Phillips ND, Hampson DJ.	PLoS One	10.1371/journal.pone.0011455	2010
Metabolism	Evolutionary primacy of sodium bioenergetics.	Mulkidjanian AY, Galperin MY, Makarova KS, Wolf YI, Koonin EV.	Biol Direct	10.1186/1745-6150-3-13	2008
Metabolism	Evolution and multiplicity of arginine decarboxylases in polyamine biosynthesis and essential role in Bacillus subtilis biofilm formation.	Burrell M, Hanfrey CC, Murray EJ, Stanley-Wall NR, Michael AJ.	J Biol Chem	10.1074/jbc.m110.163154	2010
	Noncellulosomal cohesin- and dockerin-like modules in the three domains of life.	Peer A, Smith SP, Bayer EA, Lamed R, Borovok I.	FEMS Microbiol Lett	10.1111/j.1574-6968.2008.01420.x	2009
	Metabolic network model of a human oral pathogen.	Mazumdar V, Snitkin ES, Amar S, Segre D.	J Bacteriol	10.1128/jb.01123-08	2009
	Evolution of the oligopeptide transporter family.	Gomolplitinant KM, Saier MH.	J Membr Biol	10.1007/s00232-011-9347-9	2011
	Development of culture methods capable of culturing a wide range of predominant species of intestinal bacteria.	Hirano R, Nishita I, Nakai R, Bito A, Sasabe R, Kurihara S.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1056866	2023
	Carotenoid productivity in human intestinal bacteria Eubacterium limosum and Leuconostoc mesenteroides with functional analysis of their carotenoid biosynthesis genes.	Matsumoto W, Takemura M, Nanaura H, Ami Y, Maoka T, Shindo K, Kurihara S, Misawa N.	Eng Microbiol	10.1016/j.engmic.2024.100147	2024
	Combined oral intake of short and long fructans alters the gut microbiota in food allergy model mice and contributes to food allergy prevention.	Takahashi H, Fujii T, Yamakawa S, Yamada C, Fujiki K, Kondo N, Funasaka K, Hirooka Y, Tochio T.	BMC Microbiol	10.1186/s12866-023-03021-6	2023
Genetics	Kelpie: generating full-length 'amplicons' from whole-metagenome datasets.	Greenfield P, Tran-Dinh N, Midgley D.	PeerJ	10.7717/peerj.6174	2019
Phylogeny	Age-related changes in gut microbiota composition from newborn to centenarian: a cross-sectional study.	Odamaki T, Kato K, Sugahara H, Hashikura N, Takahashi S, Xiao JZ, Abe F, Osawa R.	BMC Microbiol	10.1186/s12866-016-0708-5	2016
	In Vitro Utilization Characteristics of Maltobionic Acid and Its Effects on Bowel Movements in Healthy Subjects.	Fukami K, Suehiro D, Ohnishi M.	J Appl Glycosci (1999)	10.5458/jag.jag.jag-2019_0013	2020
	Next-generation prebiotic promotes selective growth of bifidobacteria, suppressing Clostridioides difficile.	Hirano R, Sakanaka M, Yoshimi K, Sugimoto N, Eguchi S, Yamauchi Y, Nara M, Maeda S, Ami Y, Gotoh A, Katayama T, Iida N, Kato T, Ohno H, Fukiya S, Yokota A, Nishimoto M, Kitaoka M, Nakai H, Kurihara S.	Gut Microbes	10.1080/19490976.2021.1973835	2021
Genetics	Loss of sex and age driven differences in the gut microbiome characterize arthritis-susceptible 0401 mice but not arthritis-resistant 0402 mice.	Gomez A, Luckey D, Yeoman CJ, Marietta EV, Berg Miller ME, Murray JA, White BA, Taneja V.	PLoS One	10.1371/journal.pone.0036095	2012
Metabolism	Gut microbial carbohydrate metabolism contributes to insulin resistance.	Takeuchi T, Kubota T, Nakanishi Y, Tsugawa H, Suda W, Kwon AT, Yazaki J, Ikeda K, Nemoto S, Mochizuki Y, Kitami T, Yugi K, Mizuno Y, Yamamichi N, Yamazaki T, Takamoto I, Kubota N, Kadowaki T, Arner E, Carninci P, Ohara O, Arita M, Hattori M, Koyasu S, Ohno H.	Nature	10.1038/s41586-023-06466-x	2023
Metabolism	The 'in vivo lifestyle' of bile acid 7alpha-dehydroxylating bacteria: comparative genomics, metatranscriptomic, and bile acid metabolomics analysis of a defined microbial community in gnotobiotic mice.	Ridlon JM, Devendran S, Alves JM, Doden H, Wolf PG, Pereira GV, Ly L, Volland A, Takei H, Nittono H, Murai T, Kurosawa T, Chlipala GE, Green SJ, Hernandez AG, Fields CJ, Wright CL, Kakiyama G, Cann I, Kashyap P, McCracken V, Gaskins HR	Gut Microbes	10.1080/19490976.2019.1618173	2019
Enzymology	Identification and characterization of a novel fumarase gene by metagenome expression cloning from marine microorganisms.	Jiang C, Wu LL, Zhao GC, Shen PH, Jin K, Hao ZY, Li SX, Ma GF, Luo FF, Hu GQ, Kang WL, Qin XM, Bi YL, Tang XL, Wu B	Microb Cell Fact	10.1186/1475-2859-9-91	2010
Phylogeny	Reclassification of Bacteroides distasonis, Bacteroides goldsteinii and Bacteroides merdae as Parabacteroides distasonis gen. nov., comb. nov., Parabacteroides goldsteinii comb. nov. and Parabacteroides merdae comb. nov.	Sakamoto M, Benno Y	Int J Syst Evol Microbiol	10.1099/ijs.0.64192-0	2006
Pathogenicity	Growth inhibition of intestinal bacteria and mutagenicity of 2-, 3-, 4-aminobiphenyls, benzidine, and biphenyl.	Chung KT, Adris P	Toxicol In Vitro	10.1016/s0887-2333(02)00131-5	2003
Cultivation	Effect of heme on Bacteroides distasonis catalase and aerotolerance.	Gregory EM, Fanning DD	J Bacteriol	10.1128/jb.156.3.1012-1018.1983	1983
Metabolism	Production and some properties of catalase and superoxide dismutase from the anaerobe Bacteroides distasonis.	Gregory EM, Kowalski JB, Holdeman LV	J Bacteriol	10.1128/jb.129.3.1298-1302.1977	1977
	Characterization and description of Gabonibacter chumensis sp. nov., isolated from feces of a patient with non-small cell lung cancer treated with immunotherapy.	Diop K, Pidgeon R, Diop A, Benlaifaoui M, Belkaid W, Malo J, Bernet E, Veyrier F, Jacq M, Brun Y, Elkrief A, Castagner B, Routy B, Richard C.	Arch Microbiol	10.1007/s00203-023-03671-0	2023
Phylogeny	Parabacteroides acidifaciens sp. nov., isolated from human faeces.	Wang YJ, Xu XJ, Zhou N, Sun Y, Liu C, Liu SJ, You X	Int J Syst Evol Microbiol	10.1099/ijsem.0.003230	2019

References

#8779	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 20701
#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 )
#41097	; Curators of the CIP;
#44811	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 4941
#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) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68380	Automatically annotated from API rID32A .
#68382	Automatically annotated from API zym .
#118948	Collection of Institut Pasteur ; Curators of the CIP; CIP 104284
#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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Parabacteroides distasonis (CIP 104284, DSM 20701, ATCC 8503)

Name and taxonomic classification

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Genome browser: GCA_020735945

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