Extibacter muris (DSM 28560, KCTC 15546, 40ccB-5824-ARE)

Name: Extibacter muris (DSM 28560, KCTC 15546, 40ccB-5824-ARE)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 131520

Type strain

Strain Designation 40ccB-5824-ARE, JM-40

Culture col. no. DSM 28560 KCTC 15546 40ccB-5824-ARE JM-40

NCBI tax ID(s) 1796622

Special Collections DSMZ KCTC Mouse DZIF

Links

Extibacter muris 40ccB-5824-ARE is an anaerobe, mesophilic, rod-shaped prokaryote that was isolated from caecal content; TNF^deltaARE/+ C57BL/6 mouse.

rod-shaped anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 406499

KCTC 15546,DSM 28560

@ref 20215

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

Domain Bacillati

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Lachnospiraceae

Genus Extibacter

Species Extibacter muris

Full scientific name Extibacter muris Lagkouvardos et al. 2017

BacDive ID	Other strains from **Extibacter muris** (1)	Type strain
131521	E. muris SJ-24, DSM 28561

Morphology

Cell morphology

@ref	Cell shape
68367	rod-shaped	from API 20A
68367		from API 20A
67771	rod-shaped
67771

Colony morphology

22747

Incubation period1-2 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
22747	WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339)		Medium recipe at MediaDive	Name: WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339) Composition: dehydrated Wilkins-Chalgren medium 33.0 g/l L-Cysteine HCl 0.3 g/l Sodium resazurin 0.0005 g/l Distilled water
22747	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)	Range
22747	positive	growth	37	mesophilic
67771	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
22747	anaerobe
67771	anaerobe
125439	anaerobe

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
68367	17057 ChEBI	cellobiose	-	builds acid from	from API 20A
68367	17634 ChEBI	D-glucose	-	builds acid from	from API 20A
68367	16899 ChEBI	D-mannitol	-	builds acid from	from API 20A
68380	16024 ChEBI	D-mannose	-	fermentation	from API rID32A
68367	16024 ChEBI	D-mannose	-	builds acid from	from API 20A
68367	65327 ChEBI	D-xylose	-	builds acid from	from API 20A
68367	4853 ChEBI	esculin	-	hydrolysis	from API 20A
68367	5291 ChEBI	gelatin	-	hydrolysis	from API 20A
68367	17754 ChEBI	glycerol	-	builds acid from	from API 20A
68367	30849 ChEBI	L-arabinose	-	builds acid from	from API 20A
68380	29985 ChEBI	L-glutamate	-	degradation	from API rID32A
68367	62345 ChEBI	L-rhamnose	-	builds acid from	from API 20A
68367	17716 ChEBI	lactose	-	builds acid from	from API 20A
68367	17306 ChEBI	maltose	-	builds acid from	from API 20A
68367	6731 ChEBI	melezitose	-	builds acid from	from API 20A
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
68380	16634 ChEBI	raffinose	-	fermentation	from API rID32A
68367	16634 ChEBI	raffinose	-	builds acid from	from API 20A
68367	17814 ChEBI	salicin	-	builds acid from	from API 20A
68367	30911 ChEBI	sorbitol	-	builds acid from	from API 20A
68367	17992 ChEBI	sucrose	-	builds acid from	from API 20A
68367	27082 ChEBI	trehalose	-	builds acid from	from API 20A
68380	27897 ChEBI	tryptophan	-	energy source	from API rID32A
68367	27897 ChEBI	tryptophan	-	energy source	from API 20A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A
68367	16199 ChEBI	urea	-	hydrolysis	from API 20A

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68380	35581 ChEBI	indole		from API rID32A
68367	35581 ChEBI	indole		from API 20A

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68380	35581 ChEBI	indole	-	from API rID32A
68367	35581 ChEBI	indole	-	from API 20A

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	beta-glucosidase	-	3.2.1.21	from API rID32A
68367	beta-glucosidase	-	3.2.1.21	from API 20A
68380	beta-glucuronidase	-	3.2.1.31	from API rID32A
68367	catalase	-	1.11.1.6	from API 20A
68367	gelatinase	-		from API 20A
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	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
68367	urease	-	3.5.1.5	from API 20A

API 20A

@ref	IND	URE	GLU	MAN	LAC	SAC	MAL	SAL	XYL	ARA	GEL	ESC	GLY	CEL	MNE	MLZ	RAF	SOR	RHA	TRE	CAT	Spores presentSPOR	GramGRAM	Morphology coccus="+" rod="-"COCC
22747	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	not determinedn.d.	+	-
22747	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	not determinedn.d.	+	-

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
22747	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Mammals	#Muridae (Mouse/Rat)
#Host Body-Site	#Gastrointestinal tract	#Large intestine
#Host Body Product	#Gastrointestinal tract	#Caecal content

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
22747	caecal content; TNF^deltaARE/+ C57BL/6 mouse	Freising	Germany	DEU	Europe
67771	From caecal content, TNFdeltaARE/+ C57BL/6 mouse	Freising	Germany	DEU	Europe

Taxonmaps

69479

Global distribution of 16S sequence KR364761 (>99% sequence identity) for Extibacter muris subclade from Microbeatlas

Aquatic Samples	6
Soil Samples
Animal Samples	515
Plant Samples	1
Total Samples	522

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
22747	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	ASM434500v1 assembly for Extibacter muris DSM 28560	contig	GCA_004345005	1775269.3	2887369388	1796622	56.36

Genome browser: GCA_004345005

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
22747	Extibacter muris strain 40cc-B-5824-ARE 16S ribosomal RNA gene, partial sequence	KR364761	1436		1796622

GC content

67771

GC-content (mol%)47.9

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Extibacter muris DSM 28560
NCBI: GCA_004345005

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	74.60	no
125439	motility	BacteriaNetⓘ	yes	78.30	no
125439	gram_stain	BacteriaNetⓘ	variable	65.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	99.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Lachnospiraceae bacterium DSM 28560
PATRIC: 1775269.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	76.51	yes
125438	anaerobic	anaerobicⓘ	yes	88.06	no
125438	spore-forming	spore-formingⓘ	yes	52.49	no
125438	aerobic	aerobicⓘ	no	92.80	no
125438	thermophilic	thermophileⓘ	no	91.28	yes
125438	flagellated	motile2+ⓘ	no	83.90	no

Literature

Title	Authors	Journal	DOI	Year
Strain-dependent induction of primary bile acid 7-dehydroxylation by cholic acid.	Vico-Oton E, Volet C, Jacquemin N, Dong Y, Hapfelmeier S, Meibom KL, Bernier-Latmani R.	BMC Microbiol	10.1186/s12866-024-03433-y	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
Occurrence of vanHAX and Related Genes beyond the Actinobacteria Phylum.	Yushchuk O, Binda E, Fedorenko V, Marinelli F.	Genes (Basel)	10.3390/genes13111960	2022
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

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 )
#22747	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 28560
#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;
#68367	Automatically annotated from API 20A .
#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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Extibacter muris (DSM 28560, KCTC 15546, 40ccB-5824-ARE)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20A

API rID32A

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_004345005

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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