Pseudobutyrivibrio xylanivorans (DSM 14809, ATCC BAA-455, Mz 5)

Name: Pseudobutyrivibrio xylanivorans (DSM 14809, ATCC BAA-455, Mz 5)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 6365

Type strain

Strain Designation Mz 5, Mz5

Culture col. no. DSM 14809 ATCC BAA-455 Mz 5 CIP 107891 Mz5

NCBI tax ID(s) 1123012 185007

Special Collections DSMZ CIP

History <- J. Kopecny, Czech Academy of Sciences, Prague, Czech Republic; Mz 5 <- M. Zorec {1997} 2003, M. Zorec, Domzale, Slovenia: strain Mz5 CIP <- 2003, M. Zorec, Domzale, Slovenia: strain Mz5

Links

Pseudobutyrivibrio xylanivorans Mz 5 is an anaerobe, thermophilic, Gram-negative prokaryote that was isolated from rumen fluid of cow.

Gram-negative rod-shaped anaerobe thermophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 100879

ATCC BAA-455,DSM 14809,CIP 107891

@ref 20215

Last LPSN update 2026-02-09 11:19:12

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Lachnospiraceae

Genus Pseudobutyrivibrio

Species Pseudobutyrivibrio xylanivorans

Full scientific name Pseudobutyrivibrio xylanivorans Kopecný et al. 2003

BacDive ID	Other strains from **Pseudobutyrivibrio xylanivorans** (2)	Type strain
6363	P. xylanivorans DSM 10296, NCFB 2397
6364	P. xylanivorans DSM 10317, NCFB 2399

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility
123997	negative	rod-shaped

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
5556	RUMEN BACTERIA MEDIUM (DSMZ Medium 330)	Medium recipe at MediaDive	Name: RUMEN BACTERIA MEDIUM (DSMZ Medium 330) Composition: Na2CO3 4.0 g/l Trypticase peptone 2.0 g/l D-Glucose 0.5 g/l Yeast extract 0.5 g/l Maltose 0.5 g/l Cellobiose 0.5 g/l Starch 0.5 g/l Glycerol 0.5 g/l NaCl 0.456 g/l K2HPO4 0.3 g/l L-Cysteine HCl x H2O 0.25 g/l Na2S x 9 H2O 0.25 g/l (NH4)2SO4 0.228 g/l KH2PO4 0.228 g/l MgSO4 x 7 H2O 0.095 g/l CaCl2 x 2 H2O 0.0608 g/l Hemin 0.001 g/l Sodium resazurin 0.0005 g/l NaOH None Distilled water
39960	MEDIUM 224 - for anaerobic bacteria TGV		Distilled water make up to (1000.000 ml);Glucose (10.000 g);Yeast extract (20.000 g);Resazurin (2.000 mg);Trypto casein soy broth (30.000 g);L-Cysteine (0.500 g);Hemin solution - M00149 (25.000 ml);Vitamins solution - M00850 (10.000 ml)
123997	CIP Medium 20	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
5556	positive	growth	40	thermophilic
39960	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
5556	anaerobe
125438	anaerobe	94.405
125439	anaerobe	96.3

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cellulose degradation	100	5 of 5
66794	dolichol and dolichyl phosphate biosynthesis	100	2 of 2
66794	gluconeogenesis	100	8 of 8
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	L-lactaldehyde degradation	100	3 of 3
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	suberin monomers biosynthesis	100	2 of 2
66794	starch degradation	100	10 of 10
66794	ppGpp biosynthesis	100	4 of 4
66794	adipate degradation	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	palmitate biosynthesis	90.91	20 of 22
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	Entner Doudoroff pathway	80	8 of 10
66794	glycogen metabolism	80	4 of 5
66794	threonine metabolism	80	8 of 10
66794	flavin biosynthesis	80	12 of 15
66794	peptidoglycan biosynthesis	80	12 of 15
66794	valine metabolism	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	acetate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	NAD metabolism	72.22	13 of 18
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	heme metabolism	71.43	10 of 14
66794	photosynthesis	71.43	10 of 14
66794	pyrimidine metabolism	71.11	32 of 45
66794	glycolysis	70.59	12 of 17
66794	vitamin B1 metabolism	69.23	9 of 13
66794	purine metabolism	69.15	65 of 94
66794	degradation of sugar alcohols	68.75	11 of 16
66794	vitamin B12 metabolism	67.65	23 of 34
66794	d-mannose degradation	66.67	6 of 9
66794	octane oxidation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	formaldehyde oxidation	66.67	2 of 3
66794	serine metabolism	66.67	6 of 9
66794	histidine metabolism	65.52	19 of 29
66794	d-xylose degradation	63.64	7 of 11
66794	ketogluconate metabolism	62.5	5 of 8
66794	alanine metabolism	62.07	18 of 29
66794	methionine metabolism	61.54	16 of 26
66794	lipid metabolism	61.29	19 of 31
66794	degradation of hexoses	61.11	11 of 18
66794	glutamate and glutamine metabolism	60.71	17 of 28
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	propionate fermentation	60	6 of 10
66794	glycine betaine biosynthesis	60	3 of 5
66794	hydrogen production	60	3 of 5
66794	methylglyoxal degradation	60	3 of 5
66794	oxidative phosphorylation	59.34	54 of 91
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	reductive acetyl coenzyme A pathway	57.14	4 of 7
66794	citric acid cycle	57.14	8 of 14
66794	polyamine pathway	56.52	13 of 23
66794	cysteine metabolism	55.56	10 of 18
66794	tryptophan metabolism	55.26	21 of 38
66794	metabolism of disaccharids	54.55	6 of 11
66794	leucine metabolism	53.85	7 of 13
66794	ethanol fermentation	50	1 of 2
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	50	4 of 8
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	biotin biosynthesis	50	2 of 4
66794	phenylmercury acetate degradation	50	1 of 2
66794	non-pathway related	50	19 of 38
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	sulfopterin metabolism	50	2 of 4
66794	butanoate fermentation	50	2 of 4
66794	urea cycle	46.15	6 of 13
66794	arginine metabolism	45.83	11 of 24
66794	proline metabolism	45.45	5 of 11
66794	lysine metabolism	45.24	19 of 42
66794	nitrate assimilation	44.44	4 of 9
66794	molybdenum cofactor biosynthesis	44.44	4 of 9
66794	degradation of pentoses	42.86	12 of 28
66794	propanol degradation	42.86	3 of 7
66794	ubiquinone biosynthesis	42.86	3 of 7
66794	isoprenoid biosynthesis	42.31	11 of 26
66794	arachidonate biosynthesis	40	2 of 5
66794	bacilysin biosynthesis	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	degradation of sugar acids	40	10 of 25
66794	sulfate reduction	38.46	5 of 13
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	vitamin B6 metabolism	36.36	4 of 11
66794	pentose phosphate pathway	36.36	4 of 11
66794	glutathione metabolism	35.71	5 of 14
66794	IAA biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	lipid A biosynthesis	33.33	3 of 9
66794	pantothenate biosynthesis	33.33	2 of 6
66794	cyanate degradation	33.33	1 of 3
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	enterobactin biosynthesis	33.33	1 of 3
66794	sulfoquinovose degradation	33.33	1 of 3
66794	3-phenylpropionate degradation	33.33	5 of 15
66794	myo-inositol biosynthesis	30	3 of 10
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	coenzyme M biosynthesis	30	3 of 10
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	tyrosine metabolism	28.57	4 of 14
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	cyclohexanol degradation	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	CMP-KDO biosynthesis	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	phenylpropanoid biosynthesis	23.08	3 of 13
66794	ascorbate metabolism	22.73	5 of 22
66794	arachidonic acid metabolism	22.22	4 of 18
66794	chlorophyll metabolism	22.22	4 of 18

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Mammals	#Bovinae (Cow, Cattle)
#Host Body-Site	#Organ	#Rumen
#Host Body Product	#Fluids	#Rumen fluid

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
5556	rumen fluid of cow	Donzale	Slovenia	SVN	Europe
123997	Animal, Cow, rumen fluid	Domzale	Slovenia	SVN	Europe

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
5556	1	Risk group (German classification) According to TRBA 466
123997	2	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	IMG-taxon 2585428087 annotated assembly for Pseudobutyrivibrio xylanivorans DSM 14809	scaffold	GCA_900141825	1123012.3	2585428087	1123012	65.24

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
5556	Pseudobutyrivibrio xylanovorans partial 16S rRNA gene, strain Mz 5	AJ428548	1442		185007

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pseudobutyrivibrio xylanivorans DSM 14809
NCBI: GCA_900141825

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	55.80	no
125439	motility	BacteriaNetⓘ	yes	57.30	no
125439	gram_stain	BacteriaNetⓘ	positive	76.10	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	96.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pseudobutyrivibrio xylanivorans DSM 14809 DSM 14809
NCBI: GCA_900141825.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	64.76	no
125438	anaerobic	anaerobicⓘ	yes	94.41	no
125438	aerobic	aerobicⓘ	no	96.58	yes
125438	spore-forming	spore-formingⓘ	no	51.68	no
125438	thermophilic	thermophileⓘ	no	90.51	no
125438	flagellated	motile2+ⓘ	yes	75.86	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Complete Genome Sequence of the Polysaccharide-Degrading Rumen Bacterium Pseudobutyrivibrio xylanivorans MA3014 Reveals an Incomplete Glycolytic Pathway.	Palevich N, Maclean PH, Kelly WJ, Leahy SC, Rakonjac J, Attwood GT.	Genome Biol Evol	10.1093/gbe/evaa165	2020
	Harnessing noncanonical crRNA for highly efficient genome editing.	Xun G, Zhu Z, Singh N, Lu J, Jain PK, Zhao H.	Nat Commun	10.1038/s41467-024-48012-x	2024
Genetics	Targeted Modification of Mammalian DNA by a Novel Type V Cas12a Endonuclease from Ruminococcus bromii.	Vasilev R, Gunitseva N, Shebanova R, Korzhenkov A, Vlaskina A, Evteeva M, Polushkina I, Nikitchina N, Toshchakov S, Kamenski P, Patrushev M, Mazunin I.	Int J Mol Sci	10.3390/ijms23169289	2022
Metabolism	The glycobiome of the rumen bacterium Butyrivibrio proteoclasticus B316(T) highlights adaptation to a polysaccharide-rich environment.	Kelly WJ, Leahy SC, Altermann E, Yeoman CJ, Dunne JC, Kong Z, Pacheco DM, Li D, Noel SJ, Moon CD, Cookson AL, Attwood GT.	PLoS One	10.1371/journal.pone.0011942	2010
Phylogeny	Youngiibacter fragilis gen. nov., sp. nov., isolated from natural gas production-water and reclassification of Acetivibrio multivorans as Youngiibacter multivorans comb. nov.	Lawson PA, Wawrik B, Allen TD, Johnson CN, Marks CR, Tanner RS, Harriman BH, Strapoc D, Callaghan AV.	Int J Syst Evol Microbiol	10.1099/ijs.0.053728-0	2014
Phylogeny	Prosthecate sphingomonads: proposal of Sphingomonas canadensis sp. nov.	Abraham WR, Estrela AB, Rohde M, Smit J, Vancanneyt M.	Int J Syst Evol Microbiol	10.1099/ijs.0.048678-0	2013
Phylogeny	Starkeya koreensis sp. nov., isolated from rice straw.	Im WT, Aslam Z, Lee M, Ten LN, Yang DC, Lee ST.	Int J Syst Evol Microbiol	10.1099/ijs.0.64093-0	2006
Phylogeny	Methanosaeta harundinacea sp. nov., a novel acetate-scavenging methanogen isolated from a UASB reactor.	Ma K, Liu X, Dong X.	Int J Syst Evol Microbiol	10.1099/ijs.0.63887-0	2006
Phylogeny	Butyrivibrio hungatei sp. nov. and Pseudobutyrivibrio xylanivorans sp. nov., butyrate-producing bacteria from the rumen.	Kopecny J, Zorec M, Mrazek J, Kobayashi Y, Marinsek-Logar R	Int J Syst Evol Microbiol	10.1099/ijs.0.02345-0	2003

References

#5556	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 14809
#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 )
#39960	; Curators of the CIP;
#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 )
#123997	Collection of Institut Pasteur ; Curators of the CIP; CIP 107891
#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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Pseudobutyrivibrio xylanivorans (DSM 14809, ATCC BAA-455, Mz 5)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900141825

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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