Name: Faecalibaculum rodentium DSM 103405
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 132424

Type strain:

Species: Faecalibaculum rodentium

Culture col. no.: DSM 103405, JCM 30274, KCTC 15484, ALO 17

Strain history: <- BC Kim, KRIBB

NCBI tax ID(s): 1702221 (species)

SI-ID 402765

DSM 103405

Special Collections

Other strains from Faecalibaculum rodentium

Section

Faecalibaculum rodentium DSM 103405 is an anaerobe, rod-shaped bacterium that was isolated from faeces, female C57BL/6 J mouse.

rod-shaped
anaerobe
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	*Erysipelotrichia*
	Order	*Erysipelotrichales*
	Family	*Erysipelotrichaceae*
	Genus	*Faecalibaculum*
	Species	**Faecalibaculum rodentium**
	Full Scientific Name (LPSN)	Faecalibaculum rodentium Chang et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #67771]	Gram stain	positive

[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #67771]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #24213]

Culture medium

PYG MEDIUM (MODIFIED) (DSMZ Medium 104)

[Ref.: #24213]

Culture medium growth

[Ref.: #24213]

Culture medium link

Medium recipe at MediaDive

[Ref.: #24213]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #24213]	growth	37 °C
[Ref.: #67770]	growth	37 °C
[Ref.: #67771]	growth	37 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #67771]

Oxygen tolerance

anaerobe

[Ref.: #67771]

Ability of spore formation

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	teichoic acid biosynthesis	100	1 of 1
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	peptidoglycan biosynthesis	93.33	14 of 15
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	starch degradation	80	8 of 10
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	palmitate biosynthesis	77.27	17 of 22
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	ppGpp biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	NAD metabolism	72.22	13 of 18
[Ref.: #66794]	glutamate and glutamine metabolism	71.43	20 of 28
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	pyrimidine metabolism	68.89	31 of 45
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	purine metabolism	64.89	61 of 94
[Ref.: #66794]	metabolism of disaccharids	63.64	7 of 11
[Ref.: #66794]	pentose phosphate pathway	63.64	7 of 11
[Ref.: #66794]	gluconeogenesis	62.5	5 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	factor 420 biosynthesis	60	3 of 5
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	CO2 fixation in Crenarchaeota	55.56	5 of 9
[Ref.: #66794]	tryptophan metabolism	55.26	21 of 38
[Ref.: #66794]	histidine metabolism	55.17	16 of 29
[Ref.: #66794]	alanine metabolism	55.17	16 of 29
[Ref.: #66794]	oxidative phosphorylation	54.95	50 of 91
[Ref.: #66794]	degradation of hexoses	50	9 of 18
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	heme metabolism	50	7 of 14
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	tetrahydrofolate metabolism	50	7 of 14
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	arginine metabolism	50	12 of 24
[Ref.: #66794]	isoprenoid biosynthesis	50	13 of 26
[Ref.: #66794]	methionine metabolism	50	13 of 26
[Ref.: #66794]	leucine metabolism	46.15	6 of 13
[Ref.: #66794]	vitamin B1 metabolism	46.15	6 of 13
[Ref.: #66794]	proline metabolism	45.45	5 of 11
[Ref.: #66794]	lysine metabolism	45.24	19 of 42
[Ref.: #66794]	cysteine metabolism	44.44	8 of 18
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	glutathione metabolism	42.86	6 of 14
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	flavin biosynthesis	40	6 of 15
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	degradation of pentoses	39.29	11 of 28
[Ref.: #66794]	lipid metabolism	38.71	12 of 31
[Ref.: #66794]	urea cycle	38.46	5 of 13
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	non-pathway related	36.84	14 of 38
[Ref.: #66794]	d-xylose degradation	36.36	4 of 11
[Ref.: #66794]	degradation of sugar acids	36	9 of 25
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	33.33	3 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	30.77	4 of 13
[Ref.: #66794]	phenol degradation	30	6 of 20
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	myo-inositol biosynthesis	30	3 of 10
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	29.41	5 of 17
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	25	2 of 8
[Ref.: #66794]	ascorbate metabolism	22.73	5 of 22
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #24213]	Sample type/isolated from	faeces, female C57BL/6 J mouse
[Ref.: #24213]	Country	Republic of Korea
[Ref.: #24213]	Country ISO 3 Code	KOR
[Ref.: #24213]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Mouse faeces

[Ref.: #67771]	Sample type/isolated from	From mouse faeces, 36-weeks(=9 month)-old female C57BL/6 J mouse
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host	#Mammals	#Muridae (Mouse/Rat)
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KP881689 (>99% sequence identity) for Faecalibaculum rodentium subclade from Microbeatlas

Aquatic Samples	1524
Soil Samples	1546
Animal Samples	70176
Plant Samples	500
Total Samples	73746

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

[Ref.: #24213]

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.: #24213]	Faecalibaculum rodentium strain ALO17 16S ribosomal RNA gene, partial sequence	KP881689	1487	GenBank ENA	1702221 tax ID
[Ref.: #124043]	Bacillus subtilis strain KFP-17 16S ribosomal RNA gene, partial sequence.	KT380827	1487	GenBank ENA	1702221 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Faecalibaculum rodentium ALO17	GCA_001564455	complete	GenBank ENA	1702221 tax ID

[Ref.: #24213]	GC-content	52.3 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67771]	GC-content	52.3 mol%

Availability in culture collections External links

[Ref.: #24213]

Culture collection no.

DSM 103405, JCM 30274, KCTC 15484, ALO 17

[Ref.: #90764]

SI-ID 402765

Literature:

Topic	Title	Authors	Journal	DOI	Year
Genetics	Whole genome sequencing of "Faecalibaculum rodentium" ALO17, isolated from C57BL/6J laboratory mouse feces.	Lim S, Chang DH, Ahn S, Kim BC	Gut Pathog	10.1186/s13099-016-0087-3	2016	*
Phylogeny	Faecalibaculum rodentium gen. nov., sp. nov., isolated from the faeces of a laboratory mouse.	Chang DH, Rhee MS, Ahn S, Bang BH, Oh JE, Lee HK, Kim BC	Antonie Van Leeuwenhoek	10.1007/s10482-015-0583-3	2015	*

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 )

#24213

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 103405

#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;
#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 .

#90764

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-ID402765.1 )

#124043

Dr. Isabel Schober, Dr. Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .

* These data were automatically processed and therefore are not curated

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