Bacteroides fragilis (CIP 104785, ATCC 51477, JCM 11017)

Name: Bacteroides fragilis (CIP 104785, ATCC 51477, JCM 11017)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 134478

Type strain

Strain Designation HSP 40

Culture col. no. CIP 104785 ATCC 51477 JCM 11017 HSP 40

NCBI tax ID(s) 1235816 817

Special Collections JCM CIP

Links

Bacteroides fragilis HSP 40 is an anaerobe, mesophilic, Gram-negative prokaryote of the family Bacteroidaceae.

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

Name and taxonomic classification

SI-ID 43008

ATCC 51477,CIP 104785,JCM 11017

@ref 20215

Last LPSN update 2025-12-16 10:02:03

Domain Pseudomonadati

Phylum Bacteroidota

Class Bacteroidia

Order Bacteroidales

Family Bacteroidaceae

Genus Bacteroides

Species Bacteroides fragilis

Full scientific name Bacteroides fragilis (Veillon and Zuber 1898) Castellani and Chalmers 1919 (Approved Lists 1980)

Synonyms (3)

"Bacteroides hominis"
"Bacillus fragilis"
Bacteroides hominis

BacDive ID	Other strains from **Bacteroides fragilis** (28)	Type strain
1585	B. fragilis EN-2, Onslow, DSM 2151, ATCC 25285, JCM 11019, ... (type strain)
1584	B. fragilis LRA 048 07 85, CCUG 25931, DSM 1396, ATCC ...
1586	B. fragilis mprl 1839, MPRL 1839/MH3, DSM 9668
1587	B. fragilis mprl 1842, DSM 9669
1589	B. fragilis mprl 1843, DSM 9671
136722	B. fragilis CIP pIP417
136849	B. fragilis CIP pIP419
136850	B. fragilis CIP pIP421
136938	B. fragilis 638R, CIP 108284
137572	B. fragilis BF8, CIP 108277
138258	B. fragilis 10010, CIP 105891, ATCC 43858
138259	B. fragilis CIP 105892, ATCC 43859
147853	B. fragilis CCUG 34384
147901	B. fragilis CCUG 34457
148540	B. fragilis CCUG 35615
148584	B. fragilis CCUG 35671
149129	B. fragilis CCUG 36902
149142	B. fragilis CCUG 36926
149442	B. fragilis CCUG 37758
153390	B. fragilis CCUG 49424
154543	B. fragilis CCUG 54315
158881	B. fragilis COR2-248-WT-1, DSM 103087
159983	B. fragilis 638R/pIP417(nimA), DSM 103646
159984	B. fragilis BF8, DSM 103647
162044	B. fragilis JCM 17585
162045	B. fragilis JCM 17586
162046	B. fragilis JCM 17587
174360	B. fragilis HM-216, 2/1/56, DSM 24895

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
125438	negative		90.359
125439	negative		99.1
32824	negative	rod-shaped

Colony morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Composition	Medium link
32824	MEDIUM 6 - Columbia agar with 10 % horse blood		Distilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
32824	CIP Medium 6			Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
32824	positive	growth	37	mesophilic
67770	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
32824	anaerobe
125439	obligate anaerobe	98.9

Spore formation

@ref	Spore formation	Confidence
125439		99.8

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32824	17057 ChEBI	cellobiose	-	degradation
32824	15824 ChEBI	D-fructose	+	degradation
32824	17634 ChEBI	D-glucose	+	degradation
32824	65327 ChEBI	D-xylose	+	degradation
32824	4853 ChEBI	esculin	+	hydrolysis
32824	17716 ChEBI	lactose	+	degradation
32824	17306 ChEBI	maltose	+	degradation
32824	17632 ChEBI	nitrate	-	reduction
32824	17632 ChEBI	nitrate	+	respiration
32824	16301 ChEBI	nitrite	-	reduction
32824	17814 ChEBI	salicin	-	degradation
32824	17992 ChEBI	sucrose	+	degradation

Antibiotic resistance

@ref	ChEBI	Metabolite	Is antibiotic	Is sensitive	Is resistant
32824	6909	metronidazole

Metabolite production

@ref	Chebi-ID	Metabolite	Production
32824	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	+	3.2.1.51	from API zym
68382	alpha-galactosidase	+	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68382	alpha-mannosidase	+	3.2.1.24	from API zym
32824	amylase	-
68382	beta-galactosidase	+	3.2.1.23	from API zym
32824	beta-galactosidase	+	3.2.1.23
68382	beta-glucosidase	+	3.2.1.21	from API zym
68382	beta-glucuronidase	+	3.2.1.31	from API zym
32824	caseinase	+	3.4.21.50
32824	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
32824	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
32824	gelatinase	-
32824	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
32824	lipase	-
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
32824	oxidase	-
32824	protease	-
68382	trypsin	-	3.4.21.4	from API zym
32824	tween esterase	-
32824	urease	-	3.5.1.5
68382	valine arylamidase	-		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
32824	-	+	+	+	-	+	-	-	-	-	+	+	+	+	+	+	+	+	+	+

Isolation, sampling and environmental information

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
32824		Barcelona	Spain	ESP	Europe
32824	Human, Peritoneal exudate	Barcelona	Spain	ESP	Europe

Taxonmaps

69479

Global distribution of 16S sequence AB542764 (>99% sequence identity) for Bacteroides fragilis subclade from Microbeatlas

Aquatic Samples	7159
Soil Samples	2825
Animal Samples	211201
Plant Samples	810
Total Samples	221995

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
32824	2	Risk group (French classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM61342v1 assembly for Bacteroides fragilis JCM 11017	contig	GCA_000613425	1235816.3	2585427861	1235816	12.43

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
67770	Bacteroides fragilis gene for 16S ribosomal RNA, partial sequence, strain: JCM 11017	AB542764	1490		817

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Bacteroides fragilis JCM 11017
NCBI: GCA_000613425

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	98.90	no
125439	gram_stain	BacteriaNetⓘ	negative	99.10	no
125439	motility	BacteriaNetⓘ	no	79.30	no
125439	spore_formation	BacteriaNetⓘ	no	99.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Bacteroides fragilis JCM 11017
PATRIC: 1235816.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	90.36	no
125438	anaerobic	anaerobicⓘ	yes	77.91	yes
125438	spore-forming	spore-formingⓘ	no	87.96	no
125438	aerobic	aerobicⓘ	no	87.51	yes
125438	thermophilic	thermophileⓘ	no	97.11	no
125438	flagellated	motile2+ⓘ	no	88.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Learning ecosystem-scale dynamics from microbiome data with MDSINE2.	Gibson TE, Kim Y, Acharya S, Kaplan DE, DiBenedetto N, Lavin R, Berger B, Allegretti JR, Bry L, Gerber GK.	Nat Microbiol	10.1038/s41564-025-02112-6	2025
Genetics	Complete genome sequence of Croceibacter bacteriophage P2559S.	Kang I, Kang D, Cho JC.	J Virol	10.1128/jvi.01396-12	2012
Enzymology	Determination of crAssphage in water samples and applicability for tracking human faecal pollution.	Garcia-Aljaro C, Balleste E, Muniesa M, Jofre J.	Microb Biotechnol	10.1111/1751-7915.12841	2017
	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
Enzymology	Diversity of bacteroides fragilis strains in their capacity to recover phages from human and animal wastes and from fecally polluted wastewater.	Puig A, Queralt N, Jofre J, Araujo R.	Appl Environ Microbiol	10.1128/aem.65.4.1772-1776.1999	1999
Stress	Survival of bacterial indicator species and bacteriophages after thermal treatment of sludge and sewage.	Moce-Llivina L, Muniesa M, Pimenta-Vale H, Lucena F, Jofre J.	Appl Environ Microbiol	10.1128/aem.69.3.1452-1456.2003	2003
	Sunlight inactivation of fecal bacteriophages and bacteria in sewage-polluted seawater.	Sinton LW, Finlay RK, Lynch PA.	Appl Environ Microbiol	10.1128/aem.65.8.3605-3613.1999	1999
Pathogenicity	Genome Sequencing of the Antibiotic-Resistant Leucobacter sp. HNU-1 and Its Developmental Toxicity in Caenorhabditis elegans.	Ju J, Lu X, Gao Z, Yin H, Xu S, Li H.	Int J Mol Sci	10.3390/ijms26083673	2025
	CRISPR-Cas Systems in Bacteroides fragilis, an Important Pathobiont in the Human Gut Microbiome.	Tajkarimi M, Wexler HM.	Front Microbiol	10.3389/fmicb.2017.02234	2017
Genetics	A simple method that enhances minority species detection in the microbiota: 16S metagenome-DRIP (Deeper Resolution using an Inhibitory Primer).	Nakajima A, Yoshida K, Gotoh A, Katoh T, Ojima MN, Sakanaka M, Xiao JZ, Odamaki T, Katayama T.	Microbiome Res Rep	10.20517/mrr.2022.08	2022
	Properties of Plant Extracts from Adriatic Maritime Zone for Innovative Food and Packaging Applications: Insights into Bioactive Profiles, Protective Effects, Antioxidant Potentials and Antimicrobial Activity	Babic P, Cvetnic T, Canak I, Dujmovic M, Semencic M, Supljika F, Vranjes Z, Debeaufort F, Benbettaieb N, Descours E, Kurek M.	Antioxidants (Basel)		2025
Metabolism	Identification of a TLR2-stimulating lipoprotein in Bacteroides fragilis JCM 11019 (NCTC 9343).	Hashimoto M, Eguchi H, Tawaratsumida K, Kirikae T, Suda Y.	Innate Immun	10.1177/1753425912454179	2013
Enzymology	Use of a genetically-engineered Escherichia coli strain as a sample process control for quantification of the host-specific bacterial genetic markers.	Kobayashi A, Sano D, Taniuchi A, Ishii S, Okabe S.	Appl Microbiol Biotechnol	10.1007/s00253-013-5188-z	2013
	Gut commensals-derived succinate impels colonic inflammation in ulcerative colitis.	Dalal R, Sadhu S, Batra A, Goswami S, Dandotiya J, K V V, Yadav R, Singh V, Chaturvedi K, Kannan R, Kumar S, Kumar Y, Rathore DK, Salunke DB, Ahuja V, Awasthi A.	NPJ Biofilms Microbiomes	10.1038/s41522-025-00672-3	2025
	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
	Intestinal Bacteria as Powerful Trapping Lifeforms for the Elimination of Radioactive Cesium.	Saito K, Kuroda K, Suzuki R, Kino Y, Sekine T, Shinoda H, Yamashiro H, Fukuda T, Kobayashi J, Abe Y, Nishimura J, Urushihara Y, Yoneyama H, Fukumoto M, Isogai E.	Front Vet Sci	10.3389/fvets.2019.00070	2019
Phylogeny	Distribution of different species of the Bacteroides fragilis group in individuals with Japanese cedar pollinosis.	Odamaki T, Xiao JZ, Sakamoto M, Kondo S, Yaeshima T, Iwatsuki K, Togashi H, Enomoto T, Benno Y.	Appl Environ Microbiol	10.1128/aem.01106-08	2008
Pathogenicity	Human LYPD8 protein inhibits motility of flagellated bacteria.	Hsu CC, Okumura R, Takeda K.	Inflamm Regen	10.1186/s41232-017-0056-3	2017
Metabolism	Hydrogen peroxide-forming NADH oxidase belonging to the peroxiredoxin oxidoreductase family: existence and physiological role in bacteria.	Nishiyama Y, Massey V, Takeda K, Kawasaki S, Sato J, Watanabe T, Niimura Y.	J Bacteriol	10.1128/jb.183.8.2431-2438.2001	2001
Pathogenicity	The capability of non-native strains of Bacteroides bacteria to detect bacteriophages as faecal indicators in a tropical area.	Sirikanchana K, Wangkahad B, Mongkolsuk S	J Appl Microbiol	10.1111/jam.12646	2014
Genetics	Genome sequence of the Bacteroides fragilis phage ATCC 51477-B1.	Hawkins SA, Layton AC, Ripp S, Williams D, Sayler GS	Virol J	10.1186/1743-422X-5-97	2008
Enzymology	Leucobacter humi sp. nov., Isolated from Forest Soil.	Her J, Lee SS.	Curr Microbiol	10.1007/s00284-015-0820-z	2015
Phylogeny	Haloplanus salinus sp. nov., an extremely halophilic archaeon from a Chinese marine solar saltern.	Qiu XX, Zhao ML, Han D, Zhang WJ, Cui HL.	Arch Microbiol	10.1007/s00203-013-0929-z	2013
Phylogeny	Haloplanus aerogenes sp. nov., an extremely halophilic archaeon from a marine solar saltern.	Cui HL, Gao X, Yang X, Xu XW.	Int J Syst Evol Microbiol	10.1099/ijs.0.025023-0	2011
Phylogeny	Bifidobacterium stercoris sp. nov., isolated from human faeces.	Kim MS, Roh SW, Bae JW.	Int J Syst Evol Microbiol	10.1099/ijs.0.019943-0	2010

References

#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 )
#32824	Collection of Institut Pasteur ; Curators of the CIP; CIP 104785
#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;
#68382	Automatically annotated from API zym .
#69479	João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .
#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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Bacteroides fragilis (CIP 104785, ATCC 51477, JCM 11017)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Antibiotic resistance

Metabolite production

Enzymes

API zym

Isolation, sampling and environmental information

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000613425

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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