Bacteroides caecimuris (DSM 26085, KCTC 15547, I48)

Name: Bacteroides caecimuris (DSM 26085, KCTC 15547, I48)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 131518

Type strain

Strain Designation I48

Culture col. no. DSM 26085 KCTC 15547 I48

NCBI tax ID(s) 1796613

Special Collections DSMZ KCTC Mouse DZIF

Links

Bacteroides caecimuris I48 is an anaerobe, mesophilic, rod-shaped prokaryote that was isolated from intestinal content; wildtype C57BL/6 mouse.

rod-shaped anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 402793

KCTC 15547,DSM 26085

@ref 20215

Last LPSN update 2025-12-16 10:01:16

Domain Pseudomonadati

Phylum Bacteroidota

Class Bacteroidia

Order Bacteroidales

Family Bacteroidaceae

Genus Bacteroides

Species Bacteroides caecimuris

Full scientific name Bacteroides caecimuris Lagkouvardos et al. 2016

Morphology

Cell morphology

@ref	Cell shape
67771	rod-shaped
67771
125439
125438

Colony morphology

22745

Incubation period1-2 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
22745	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
22745	COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)		Medium recipe at MediaDive	Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
22745	positive	growth	37	mesophilic
67771	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
22745	anaerobe
67771	anaerobe
125439	anaerobe

Spore formation

@ref	Spore formation	Confidence
125439		96.8

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
68380	29985 ChEBI	L-glutamate	-	degradation	from API rID32A
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
68380	16634 ChEBI	raffinose	+	fermentation	from API rID32A
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

Metabolite tests

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

Enzymes

@ref	Value	Activity	Ec
68380	alanine arylamidase	+	3.4.11.2	from API rID32A
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
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	glutamate decarboxylase	-	4.1.1.15	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	leucyl glycin 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
22745	-	-	+	+	-	+	+	+	-	+	+	+	-	+	-	-	+	-	-	+	-	-	-	-	+	-	-	+	-
22745	-	-	+	+	-	+	+	+	-	+	+	+	-	+	-	-	+	-	-	+	-	-	-	-	+	-	-	+	-
22745	-	-	+	+	-	+	+	+	-	+	-	+	-	+	-	-	+	-	-	+	-	-	-	-	+	-	-	-	-
22745	not determinedn.d.	-	+	+	-	+	+/-	+	+/-	+	-	+	-	+	-	-	+	-	-	+	-	-	-	-	+	-	-	+/-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Mammals	#Muridae (Mouse/Rat)
#Host Body-Site	#Gastrointestinal tract	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
22745	intestinal content; wildtype C57BL/6 mouse	Zurich	Switzerland	CHE	Europe
67771	From intestinal content, wildtype C57BL/6 mouse	Zurich	Eswatini	SWZ	Africa

Taxonmaps

69479

Global distribution of 16S sequence KR364741 (>99% sequence identity) for Bacteroides caecimuris subclade from Microbeatlas

Aquatic Samples	825
Soil Samples	555
Animal Samples	43540
Plant Samples	273
Total Samples	45193

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
22745	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM168872v2 assembly for Bacteroides caecimuris I48	complete	GCA_001688725	1796613.40	2718217776	1796613	99.58
66792	ASM1669712v1 assembly for Bacteroides caecimuris I48	chromosome	GCA_016697125	1796613.25	8005047353	1796613	85.72
66792	ASM2327790v1 assembly for Bacteroides caecimuris I48	chromosome	GCA_023277905	1796613.31	8119473618	1796613	85.69
66792	ASM222166v1 assembly for Bacteroides caecimuris I48	contig	GCA_002221665	1796613.10	2773857902	1796613	75.54

Genome browser: GCA_001688725

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
22745	Bacteroides caecimuris strain I48 16S ribosomal RNA gene, partial sequence	KR364741	1517		1796613

GC content

@ref	GC-content (mol%)	Method
22745	42.6	sequence analysis
67771	42.6	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Bacteroides caecimuris I48
NCBI: GCA_001688725

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	96.80	no
125439	motility	BacteriaNetⓘ	no	72.90	no
125439	gram_stain	BacteriaNetⓘ	negative	98.10	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	91.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Bacteroides caecimuris I48
NCBI: GCA_001688725.2

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	93.81	yes
125438	anaerobic	anaerobicⓘ	yes	88.08	yes
125438	aerobic	aerobicⓘ	no	94.17	no
125438	spore-forming	spore-formingⓘ	no	88.96	no
125438	thermophilic	thermophileⓘ	no	92.90	yes
125438	flagellated	motile2+ⓘ	no	89.50	no

Literature

Title	Authors	Journal	DOI	Year
Nutritional and host environments determine community ecology and keystone species in a synthetic gut bacterial community.	Weiss AS, Niedermeier LS, von Strempel A, Burrichter AG, Ring D, Meng C, Kleigrewe K, Lincetto C, Hubner J, Stecher B.	Nat Commun	10.1038/s41467-023-40372-0	2023
In vitro and in vivo selection and cost of bacteriophage resistance on natural Escherichia coli.	Cardoso LL, Gaissmaier MS, von Strempel A, Keys T, Matchado MS, Salvado Silva M, Ring D, Slack E, Stecher B.	Microlife	10.1093/femsml/uqaf017	2025
The gut bacterium Extibacter muris produces secondary bile acids and influences liver physiology in gnotobiotic mice.	Streidl T, Karkossa I, Segura Munoz RR, Eberl C, Zaufel A, Plagge J, Schmaltz R, Schubert K, Basic M, Schneider KM, Afify M, Trautwein C, Tolba R, Stecher B, Doden HL, Ridlon JM, Ecker J, Moustafa T, von Bergen M, Ramer-Tait AE, Clavel T.	Gut Microbes	10.1080/19490976.2020.1854008	2021
Reproducible Colonization of Germ-Free Mice With the Oligo-Mouse-Microbiota in Different Animal Facilities.	Eberl C, Ring D, Munch PC, Beutler M, Basic M, Slack EC, Schwarzer M, Srutkova D, Lange A, Frick JS, Bleich A, Stecher B.	Front Microbiol	10.3389/fmicb.2019.02999	2019
The human intestinal bacterium Eggerthella lenta influences gut metabolomes in gnotobiotic mice	Viehof A, Haange S, Streidl T, Schubert K, Engelmann B, Haller D, Rolle-Kampczyk U, von Bergen M, Clavel T.	Microbiome Res Rep		2024
Bacteriophages targeting protective commensals impair resistance against Salmonella Typhimurium infection in gnotobiotic mice.	von Strempel A, Weiss AS, Wittmann J, Salvado Silva M, Ring D, Wortmann E, Clavel T, Debarbieux L, Kleigrewe K, Stecher B.	PLoS Pathog	10.1371/journal.ppat.1011600	2023
In vitro and in vivo characterization of Clostridium scindens bile acid transformations.	Marion S, Studer N, Desharnais L, Menin L, Escrig S, Meibom A, Hapfelmeier S, Bernier-Latmani R.	Gut Microbes	10.1080/19490976.2018.1549420	2019
Functional Intestinal Bile Acid 7alpha-Dehydroxylation by Clostridium scindens Associated with Protection from Clostridium difficile Infection in a Gnotobiotic Mouse Model.	Studer N, Desharnais L, Beutler M, Brugiroux S, Terrazos MA, Menin L, Schurch CM, McCoy KD, Kuehne SA, Minton NP, Stecher B, Bernier-Latmani R, Hapfelmeier S.	Front Cell Infect Microbiol	10.3389/fcimb.2016.00191	2016

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 )
#22745	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 26085
#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) .
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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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Bacteroides caecimuris (DSM 26085, KCTC 15547, I48)

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

Metabolite production

Metabolite tests

Enzymes

API rID32A

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001688725

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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