Name: Pseudobutyrivibrio xylanivorans Mz 5
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 6365

Type strain:

Species: Pseudobutyrivibrio xylanivorans

Strain Designation: Mz 5, Mz5

Culture col. no.: DSM 14809, ATCC BAA-455, CIP 107891

Strain history: CIP <- 2003, M. Zorec, Domzale, Slovenia: strain Mz5

NCBI tax ID(s): 1123012 (strain), 185007 (species)

SI-ID 100879

ATCC BAA-455, DSM 14809, CIP 107891

Other strains from Pseudobutyrivibrio xylanivorans

P. xylanivorans DSM 10296, NCFB 2397
P. xylanivorans DSM 10317, NCFB 2399

Section

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

Gram-negative
rod-shaped
anaerobe
thermophilic
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 xylanivorans**
	Full Scientific Name (LPSN)	Pseudobutyrivibrio xylanivorans Kopecný et al. 2003

Information on morphological and physiological properties Morphology

[Ref.: #123997]	Gram stain	negative

[Ref.: #123997]	Cell shape	rod-shaped

[Ref.: #123997]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #5556]

Culture medium

RUMEN BACTERIA MEDIUM (DSMZ Medium 330)

[Ref.: #5556]

Culture medium growth

[Ref.: #5556]

Culture medium link

Medium recipe at MediaDive

[Ref.: #5556]

Culture medium composition

expand / minimize

[Ref.: #39960]

Culture medium

MEDIUM 224 - for anaerobic bacteria TGV

[Ref.: #39960]

Culture medium growth

[Ref.: #39960]

Culture medium composition

expand / minimize

[Ref.: #123997]

Culture medium

CIP Medium 20

[Ref.: #123997]

Culture medium growth

[Ref.: #123997]

Culture medium link

Medium recipe provided by DSMZ

	Temperatures	Kind of temperature		Temperature
[Ref.: #5556]			growth	40 °C
[Ref.: #39960]			growth	37 °C

[Ref.: #5556]	Temperature range	thermophilic
[Ref.: #39960]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #5556]

Oxygen tolerance

anaerobe

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	100	2 of 2
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	palmitate biosynthesis	90.91	20 of 22
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	NAD metabolism	72.22	13 of 18
[Ref.: #66794]	tetrahydrofolate metabolism	71.43	10 of 14
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	heme metabolism	71.43	10 of 14
[Ref.: #66794]	photosynthesis	71.43	10 of 14
[Ref.: #66794]	pyrimidine metabolism	71.11	32 of 45
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	vitamin B1 metabolism	69.23	9 of 13
[Ref.: #66794]	purine metabolism	69.15	65 of 94
[Ref.: #66794]	degradation of sugar alcohols	68.75	11 of 16
[Ref.: #66794]	vitamin B12 metabolism	67.65	23 of 34
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	histidine metabolism	65.52	19 of 29
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	alanine metabolism	62.07	18 of 29
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	lipid metabolism	61.29	19 of 31
[Ref.: #66794]	degradation of hexoses	61.11	11 of 18
[Ref.: #66794]	glutamate and glutamine metabolism	60.71	17 of 28
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	propionate fermentation	60	6 of 10
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	methylglyoxal degradation	60	3 of 5
[Ref.: #66794]	oxidative phosphorylation	59.34	54 of 91
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
[Ref.: #66794]	reductive acetyl coenzyme A pathway	57.14	4 of 7
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	polyamine pathway	56.52	13 of 23
[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]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	50	4 of 8
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	non-pathway related	50	19 of 38
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	sulfopterin metabolism	50	2 of 4
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[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]	lysine metabolism	45.24	19 of 42
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	44.44	4 of 9
[Ref.: #66794]	degradation of pentoses	42.86	12 of 28
[Ref.: #66794]	propanol degradation	42.86	3 of 7
[Ref.: #66794]	ubiquinone biosynthesis	42.86	3 of 7
[Ref.: #66794]	isoprenoid biosynthesis	42.31	11 of 26
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	bacilysin biosynthesis	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	degradation of sugar acids	40	10 of 25
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	vitamin B6 metabolism	36.36	4 of 11
[Ref.: #66794]	pentose phosphate pathway	36.36	4 of 11
[Ref.: #66794]	glutathione metabolism	35.71	5 of 14
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	3-phenylpropionate degradation	33.33	5 of 15
[Ref.: #66794]	myo-inositol biosynthesis	30	3 of 10
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	tyrosine metabolism	28.57	4 of 14
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	phenylpropanoid biosynthesis	23.08	3 of 13
[Ref.: #66794]	ascorbate metabolism	22.73	5 of 22
[Ref.: #66794]	arachidonic acid metabolism	22.22	4 of 18
[Ref.: #66794]	chlorophyll metabolism	22.22	4 of 18
		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.: #5556]	Sample type/isolated from	rumen fluid of cow
[Ref.: #5556]	Geographic location (country and/or sea, region)	Donzale
[Ref.: #5556]	Country	Slovenia
[Ref.: #5556]	Country ISO 3 Code	SVN
[Ref.: #5556]	Continent	Europe

[Ref.: #123997]	Sample type/isolated from	Animal, Cow, rumen fluid
[Ref.: #123997]	Geographic location (country and/or sea, region)	Domzale
[Ref.: #123997]	Country	Slovenia
[Ref.: #123997]	Country ISO 3 Code	SVN
[Ref.: #123997]	Continent	Europe
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

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

[Ref.: #5556]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #123997]	Biosafety level	2	Risk group (French classification)

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.: #5556]	Pseudobutyrivibrio xylanovorans partial 16S rRNA gene, strain Mz 5	AJ428548	1442	ENA	185007 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pseudobutyrivibrio xylanivorans DSM 14809	GCA_900141825	scaffold	GenBank	1123012 tax ID	*
[Ref.: #66792]	Pseudobutyrivibrio xylanivorans DSM 14809	1123012.3	wgs	PATRIC	1123012 tax ID	*
[Ref.: #66792]	Pseudobutyrivibrio xylanivorans DSM 14809	2585428087	draft	JGI IMG/M	1123012 tax ID	*

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pseudobutyrivibrio xylanivorans DSM 14809 DSM 14809 NCBI: GCA_900141825.1
[Ref.: #69480]	motile	yes	78.746	no
[Ref.: #69480]	flagellated	no	55.568	no
[Ref.: #69480]	gram-positive	yes	56.427	no
[Ref.: #69480]	anaerobic	yes	99.545	yes
[Ref.: #69480]	aerobic	no	98.949	yes
[Ref.: #69480]	halophile	no	92.107	no
[Ref.: #69480]	spore-forming	yes	63.712	no
[Ref.: #69480]	thermophile	no	90.724	no
[Ref.: #69480]	glucose-util	yes	88.769	no
[Ref.: #69480]	glucose-ferment	yes	78.611	no

Availability in culture collections External links

[Ref.: #5556]

Culture collection no.

DSM 14809, ATCC BAA-455, CIP 107891

[Ref.: #75838]

SI-ID 100879

Literature:

Topic	Title	Authors	Journal	DOI	Year
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 )

#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) .

#75838

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-ID100879.1 )

#123997 Collection of Institut Pasteur ; Curators of the CIP; CIP 107891
* These data were automatically processed and therefore are not curated

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Pseudobutyrivibrio xylanivorans DSM 14809 DSM 14809

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