Name: Extibacter muris 40ccB-5824-ARE
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 131520

Type strain:

Species: Extibacter muris

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

Culture col. no.: DSM 28560, KCTC 15546

Strain history: <- Barbel Fosel, DSM

NCBI tax ID(s): 1796622 (species)

SI-ID 406499

DSM 28560

Other strains from Extibacter muris

E. muris SJ-24, DSM 28561

Section

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

rod-shaped
anaerobe
mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacillota*
	Class	*Clostridia*
	Order	*Eubacteriales*
	Family	*Lachnospiraceae*
	Genus	*Extibacter*
	Species	**Extibacter muris**
	Full Scientific Name (LPSN)	Extibacter muris Lagkouvardos et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #67771]	Gram stain	positive
[Ref.: #68367]	Gram stain	positive * from API 20A
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #67771]	Cell shape	rod-shaped
[Ref.: #68367]	Cell shape	rod-shaped * from API 20A

[Ref.: #22747]

Incubation period

1-2 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #22747]

Culture medium

WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339)

[Ref.: #22747]

Culture medium growth

[Ref.: #22747]

Culture medium link

Medium recipe at MediaDive

[Ref.: #22747]

Culture medium composition

expand / minimize

[Ref.: #22747]

Culture medium

CHOPPED MEAT MEDIUM (DSMZ Medium 78)

[Ref.: #22747]

Culture medium growth

[Ref.: #22747]

Culture medium link

Medium recipe at MediaDive

[Ref.: #22747]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #22747]			growth	37 °C
[Ref.: #67771]			growth	37 °C

[Ref.: #22747]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #22747]	Oxygen tolerance	anaerobe
[Ref.: #67771]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %100

[Ref.: #69481]	Ability of spore formation	no Confidence in %92
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.502

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68380]	arginine ChEBI	-	hydrolysis	* from API rID32A
[Ref.: #68367]	cellobiose ChEBI	-	builds acid from	* from API 20A
[Ref.: #68367]	D-glucose ChEBI	-	builds acid from	* from API 20A
[Ref.: #68367]	D-mannitol ChEBI	-	builds acid from	* from API 20A
[Ref.: #68367]	D-mannose ChEBI	-	builds acid from	* from API 20A
[Ref.: #68380]	D-mannose ChEBI	-	fermentation	* from API rID32A
[Ref.: #68367]	D-xylose ChEBI	-	builds acid from	* from API 20A
[Ref.: #68367]	esculin ChEBI	-	hydrolysis	* from API 20A
[Ref.: #68367]	gelatin ChEBI	-	hydrolysis	* from API 20A
[Ref.: #68367]	glycerol ChEBI	-	builds acid from	* from API 20A
[Ref.: #68367]	L-arabinose ChEBI	-	builds acid from	* from API 20A
[Ref.: #68380]	L-glutamate ChEBI	-	degradation	* from API rID32A
[Ref.: #68367]	L-rhamnose ChEBI	-	builds acid from	* from API 20A
[Ref.: #68367]	lactose ChEBI	-	builds acid from	* from API 20A
[Ref.: #68367]	maltose ChEBI	-	builds acid from	* from API 20A
[Ref.: #68367]	melezitose ChEBI	-	builds acid from	* from API 20A
[Ref.: #68380]	nitrate ChEBI	-	reduction	* from API rID32A
[Ref.: #68367]	raffinose ChEBI	-	builds acid from	* from API 20A
[Ref.: #68380]	raffinose ChEBI	-	fermentation	* from API rID32A
[Ref.: #68367]	salicin ChEBI	-	builds acid from	* from API 20A
[Ref.: #68367]	sorbitol ChEBI	-	builds acid from	* from API 20A
[Ref.: #68367]	sucrose ChEBI	-	builds acid from	* from API 20A
[Ref.: #68367]	trehalose ChEBI	-	builds acid from	* from API 20A
[Ref.: #68367]	tryptophan ChEBI	-	energy source	* from API 20A, API rID32A
[Ref.: #68367]	urea ChEBI	-	hydrolysis	* from API 20A, API rID32A
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #68367]		indole ChEBI	no	* from API 20A, API rID32A

	Physiological tests	Metabolite	Indole test
[Ref.: #68380]		indole ChEBI	-	* from API rID32A, API 20A

	Enzyme	Enzyme activity	EC number
[Ref.: #68380]	alanine arylamidase	-	3.4.11.2	* from API rID32A
[Ref.: #68380]	alkaline phosphatase	-	3.1.3.1	* from API rID32A
[Ref.: #68380]	alpha-arabinosidase	-	3.2.1.55	* from API rID32A
[Ref.: #68380]	alpha-fucosidase	-	3.2.1.51	* from API rID32A
[Ref.: #68380]	alpha-galactosidase	-	3.2.1.22	* from API rID32A
[Ref.: #68380]	alpha-glucosidase	-	3.2.1.20	* from API rID32A
[Ref.: #68380]	arginine dihydrolase	-	3.5.3.6	* from API rID32A
[Ref.: #68380]	beta-galactosidase	+	3.2.1.23	* from API rID32A
[Ref.: #68380]	beta-Galactosidase 6-phosphate	-		* from API rID32A
[Ref.: #68380]	beta-glucosidase	-	3.2.1.21	* from API rID32A, API 20A
[Ref.: #68380]	beta-glucuronidase	-	3.2.1.31	* from API rID32A
[Ref.: #68367]	catalase	-	1.11.1.6	* from API 20A
[Ref.: #68367]	gelatinase	-		* from API 20A
[Ref.: #68380]	glutamate decarboxylase	-	4.1.1.15	* from API rID32A
[Ref.: #68380]	glutamyl-glutamate arylamidase	-		* from API rID32A
[Ref.: #68380]	glycin arylamidase	-		* from API rID32A
[Ref.: #68380]	histidine arylamidase	-		* from API rID32A
[Ref.: #68380]	L-arginine arylamidase	-		* from API rID32A
[Ref.: #68380]	leucine arylamidase	-	3.4.11.1	* from API rID32A
[Ref.: #68380]	leucyl glycin arylamidase	-	3.4.11.1	* from API rID32A
[Ref.: #68380]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API rID32A
[Ref.: #68380]	phenylalanine arylamidase	-		* from API rID32A
[Ref.: #68380]	proline-arylamidase	+	3.4.11.5	* from API rID32A
[Ref.: #68380]	pyrrolidonyl arylamidase	-	3.4.19.3	* from API rID32A
[Ref.: #68380]	serine arylamidase	-		* from API rID32A
[Ref.: #68380]	tryptophan deaminase	-	4.1.99.1	* from API rID32A
[Ref.: #68380]	tyrosine arylamidase	-		* from API rID32A
[Ref.: #68380]	urease	-	3.5.1.5	* from API rID32A, API 20A
	Only first 10 entries are displayed. Click here to see all.

API® 20A:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Indole productionIND	Urease/urea hydrolysisURE	Acid from D-glucoseGLU	Acid from D-mannitolMAN	Acid from lactoseLAC	Acid from sucroseSAC	Acid from maltoseMAL	Acid from salicinSAL	Acid from D-xyloseXYL	Acid from L-arabinoseARA	Gelatinase/gelatin hydrolysisGEL	Esculin hydrolysis/beta-glucosidaseESC	Acid from glycerolGLY	Acid from cellobioseCEL	Acid from D-mannoseMNE	Acid from melezitoseMLZ	Acid from raffinoseRAF	Acid from sorbitolSOR	Acid from L-rhamnoseRHA	Acid from trehaloseTRE	CatalaseCAT	Spores presentSPOR	GramGRAM	Morphology coccus="+" rod="-"COCC
[Ref.: #22747]	2182	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	not determinedn.d.	+	-
[Ref.: #22747]	2126	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	not determinedn.d.	+	-

API® rID32A:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Urease/urea hydrolysisURE	Arginine dihydrolaseADH (Arg)	alpha-Galactosidasealpha GAL	beta-Galactosidasebeta GAL	beta-Galactosidase 6-phosphatebeta GP	alpha-Glucosidasealpha GLU	beta-Glucosidasebeta GLU	alpha-Arabinosidasealpha ARA	beta-Glucuronidasebeta GUR	beta-N-Acetyl-beta-glucosaminidasebeta NAG	Fermentation of D-mannoseMNE	Fermentation of raffinoseRAF	Glutamate decarboxylaseGDC	alpha-Fucosidasealpha FUC	Reduction of nitrateNIT	Indole productionIND	Alkaline phosphatasePAL	L-arginine arylamidaseArgA	Proline arylamidaseProA	Leucyl glycin arylamidaseLGA	Phenylalanine arylamidasePheA	Leucine arylamidaseLeuA	Pyrrolidonyl arylamidasePyrA	Tyrosine arylamidaseTyrA	Alanine arylamidaseAlaA	Glycin arylamidaseGlyA	Histidine arylamidaseHisA	Glutamyl-glutamate arylamidaseGGA	Serine arylamidaseSerA
[Ref.: #22747]	13095	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #22747]	Sample type/isolated from	caecal content; TNF^deltaARE/+ C57BL/6 mouse
[Ref.: #22747]	Geographic location (country and/or sea, region)	Freising
[Ref.: #22747]	Country	Germany
[Ref.: #22747]	Country ISO 3 Code	DEU
[Ref.: #22747]	Continent	Europe

[Ref.: #67771]	Sample type/isolated from	From caecal content, TNFdeltaARE/+ C57BL/6 mouse
[Ref.: #67771]	Geographic location (country and/or sea, region)	Freising
[Ref.: #67771]	Country	Germany
[Ref.: #67771]	Country ISO 3 Code	DEU
[Ref.: #67771]	Continent	Europe
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #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

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #22747]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #22747]	Extibacter muris strain 40cc-B-5824-ARE 16S ribosomal RNA gene, partial sequence	KR364761	1436	ENA	1796622 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Extibacter muris DSM 28560	GCA_004345005	contig	GenBank	1796622 tax ID	*
[Ref.: #66792]	Lachnospiraceae bacterium DSM 28560	1775269.3	wgs	PATRIC	1796622 tax ID	*
[Ref.: #66792]	Extibacter muris DSM 28560	2887369388	draft	JGI IMG/M	1796622 tax ID	*

[Ref.: #67771]

GC-content

47.9 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Lachnospiraceae bacterium DSM 28560 PATRIC: 1775269.3
[Ref.: #69481]	spore-forming	no	92	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Lachnospiraceae bacterium DSM 28560 PATRIC: 1775269.3
[Ref.: #69480]	motile	no	88.379	no
[Ref.: #69480]	gram-positive	yes	93.551	no
[Ref.: #69480]	anaerobic	yes	99.276	yes
[Ref.: #69480]	aerobic	no	98.558	no
[Ref.: #69480]	halophile	no	74.122	no
[Ref.: #69480]	spore-forming	no	51.718	no
[Ref.: #69480]	thermophile	no	98.601	yes
[Ref.: #69480]	glucose-util	yes	91.584	no
[Ref.: #69480]	flagellated	no	96.614	no
[Ref.: #69480]	glucose-ferment	yes	72.65	no

Availability in culture collections External links

[Ref.: #22747]

Culture collection no.

DSM 28560, KCTC 15546

[Ref.: #89934]

SI-ID 406499

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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#89934

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID406499.1 )

* These data were automatically processed and therefore are not curated

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Lachnospiraceae bacterium DSM 28560

Lachnospiraceae bacterium DSM 28560

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