Name: Pseudobutyrivibrio ruminis A12-1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 6362

Type strain:

Species: Pseudobutyrivibrio ruminis

Strain Designation: A12-1

Culture col. no.: DSM 9787

Strain history: <- N. O. van Gylswyk, Swedish Univ. Agric. Sci., Uppsala, Sweden; A12-1

NCBI tax ID(s): 1123011 (strain), 46206 (species)

SI-ID 48708

DSM 9787

Section

Pseudobutyrivibrio ruminis A12-1 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from rumen of cow.

Gram-positive
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	*Pseudobutyrivibrio*
	Species	**Pseudobutyrivibrio ruminis**
	Full Scientific Name (LPSN)	Pseudobutyrivibrio ruminis van Gylswyk et al. 1996

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	positive Confidence in %100

Information on culture and growth conditions Culture and growth conditions

[Ref.: #3733]

Culture medium

PSEUDOBUTYRIVIBRIO MEDIUM (DSMZ Medium 712)

[Ref.: #3733]

Culture medium growth

[Ref.: #3733]

Culture medium link

Medium recipe at MediaDive

[Ref.: #3733]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #3733]			growth	37 °C

[Ref.: #3733]

Temperature range

mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #3733]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %99.998

[Ref.: #69480]

Ability of spore formation

no Confidence in %99.934

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	degradation of sugar alcohols	75	12 of 16
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	vitamin B12 metabolism	73.53	25 of 34
[Ref.: #66794]	peptidoglycan biosynthesis	73.33	11 of 15
[Ref.: #66794]	pentose phosphate pathway	72.73	8 of 11
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	tetrahydrofolate metabolism	71.43	10 of 14
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	threonine metabolism	70	7 of 10
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	pyrimidine metabolism	68.89	31 of 45
[Ref.: #66794]	purine metabolism	67.02	63 of 94
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	sulfoquinovose degradation	66.67	2 of 3
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	heme metabolism	64.29	9 of 14
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	histidine metabolism	62.07	18 of 29
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	oxidative phosphorylation	61.54	56 of 91
[Ref.: #66794]	methylglyoxal degradation	60	3 of 5
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	flavin biosynthesis	60	9 of 15
[Ref.: #66794]	Entner Doudoroff pathway	60	6 of 10
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	alanine metabolism	58.62	17 of 29
[Ref.: #66794]	degradation of hexoses	55.56	10 of 18
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	tryptophan metabolism	55.26	21 of 38
[Ref.: #66794]	metabolism of disaccharids	54.55	6 of 11
[Ref.: #66794]	leucine metabolism	53.85	7 of 13
[Ref.: #66794]	glutamate and glutamine metabolism	53.57	15 of 28
[Ref.: #66794]	citric acid cycle	50	7 of 14
[Ref.: #66794]	propionate fermentation	50	5 of 10
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	sulfopterin metabolism	50	2 of 4
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	urea cycle	46.15	6 of 13
[Ref.: #66794]	arginine metabolism	45.83	11 of 24
[Ref.: #66794]	proline metabolism	45.45	5 of 11
[Ref.: #66794]	non-pathway related	44.74	17 of 38
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	degradation of pentoses	42.86	12 of 28
[Ref.: #66794]	reductive acetyl coenzyme A pathway	42.86	3 of 7
[Ref.: #66794]	propanol degradation	42.86	3 of 7
[Ref.: #66794]	lysine metabolism	42.86	18 of 42
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	O-antigen biosynthesis	40	2 of 5
[Ref.: #66794]	4-hydroxyphenylacetate degradation	40	4 of 10
[Ref.: #66794]	lipid metabolism	38.71	12 of 31
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	37.5	3 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	37.5	3 of 8
[Ref.: #66794]	molybdenum cofactor biosynthesis	33.33	3 of 9
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	3-phenylpropionate degradation	33.33	5 of 15
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	glycine metabolism	30	3 of 10
[Ref.: #66794]	phenol degradation	30	6 of 20
[Ref.: #66794]	coenzyme M 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]	tyrosine metabolism	28.57	4 of 14
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	vitamin B6 metabolism	27.27	3 of 11
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	isoprenoid biosynthesis	23.08	6 of 26
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[Ref.: #66794]	ascorbate metabolism	22.73	5 of 22
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
[Ref.: #66794]	arachidonic acid metabolism	22.22	4 of 18
[Ref.: #66794]	polyamine pathway	21.74	5 of 23
[Ref.: #66794]	glutathione metabolism	21.43	3 of 14
		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.: #3733]	Sample type/isolated from	rumen of cow
* marker position based on {}

Isolation sources categories

#Host	#Mammals	#Bovinae (Cow, Cattle)
#Host Body-Site	#Organ	#Rumen
#Host Body-Site	#Gastrointestinal tract	#Stomach

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence X95893 (>99% sequence identity) for Pseudobutyrivibrio ruminis subclade from Microbeatlas

Aquatic Samples	3
Soil Samples	8
Animal Samples	1864
Plant Samples	65
Total Samples	1940

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

[Ref.: #3733]

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.: #3733]	P.ruminis 16S rRNA gene	X95893	1462	ENA	46206 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pseudobutyrivibrio ruminis DSM 9787	GCA_900218035	contig	GenBank	1123011 tax ID	*
[Ref.: #66792]	Pseudobutyrivibrio ruminis DSM 9787	1123011.4	wgs	PATRIC	1123011 tax ID	*
[Ref.: #66792]	Pseudobutyrivibrio ruminis DSM 9787	2596583532	draft	JGI IMG/M	1123011 tax ID	*

[Ref.: #3733]

GC-content

40.5 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: Pseudobutyrivibrio ruminis DSM 9787 PATRIC: 1123011.4
[Ref.: #69481]	spore-forming	no	74	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pseudobutyrivibrio ruminis DSM 9787 PATRIC: 1123011.4
[Ref.: #69480]	motile	yes	81.997	no
[Ref.: #69480]	flagellated	no	50	no
[Ref.: #69480]	gram-positive	yes	51.594	no
[Ref.: #69480]	anaerobic	yes	99.999	no
[Ref.: #69480]	aerobic	no	99.44	yes
[Ref.: #69480]	halophile	no	82.74	no
[Ref.: #69480]	spore-forming	no	53.782	no
[Ref.: #69480]	glucose-util	yes	83.953	no
[Ref.: #69480]	thermophile	no	94.354	yes
[Ref.: #69480]	glucose-ferment	yes	79.802	no

Availability in culture collections External links

[Ref.: #3733]

Culture collection no.

DSM 9787

[Ref.: #75835]

SI-ID 48708

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pararoseburia lenta gen. nov., sp. nov. isolated from human faeces.	Abdugheni R, Wang YJ, Li DH, Du MX, Liu C, Zhou N, Liu SJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.005371	2022	*

References

#3733

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 9787

#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 )

#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) .

#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 )

#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 )

#75835

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-ID48708.1 )

* These data were automatically processed and therefore are not curated

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Pseudobutyrivibrio ruminis DSM 9787

Pseudobutyrivibrio ruminis DSM 9787

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