Name: Breznakibacter xylanolyticus XM3
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 3772

Type strain:

Species: Breznakibacter xylanolyticus

Strain Designation: XM3

Culture col. no.: DSM 6779, ATCC 51429, KCTC 15201

Strain history: <- DSM <- JA Breznak, Center for Microbial Ecology, Michigan State Univ., USA, XM3

NCBI tax ID(s): 990 (species)

SI-ID 7705

LMG 13153, DSM 6779, ATCC 51429

Special Collections

DSMZ
KCTC

Section

Breznakibacter xylanolyticus XM3 is an anaerobe, motile, rod-shaped bacterium that was isolated from freshwater sediment.

motile
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	*Bacteroidota*
	Class	*Bacteroidia*
	Order	*Bacteroidales*
	Family	*Marinilabiliaceae*
	Genus	*Breznakibacter*
	Species	**Breznakibacter xylanolyticus**
	Full Scientific Name (LPSN)	Breznakibacter xylanolyticus (Haack and Breznak 1993) García-López et al. 2020

Synonym

Cytophaga xylanolytica

Information on morphological and physiological properties Morphology

[Ref.: #67771]	Gram stain	negative

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

[Ref.: #67771]	Motility	yes

[Ref.: #67771]	Flagellum arrangement	gliding

Information on culture and growth conditions Culture and growth conditions

[Ref.: #2813]

Culture medium

ANAEROBIC FRESHWATER (FWM) MEDIUM (DSMZ Medium 503)

[Ref.: #2813]

Culture medium growth

[Ref.: #2813]

Culture medium link

Medium recipe at MediaDive

[Ref.: #2813]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #2813]			growth	30 °C
[Ref.: #67771]			growth	30 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #2813]	Oxygen tolerance	anaerobe
[Ref.: #67771]	Oxygen tolerance	anaerobe

[Ref.: #69481]

Ability of spore formation

no Confidence in %100

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	tetrahydrofolate metabolism	100	14 of 14
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	lipoate biosynthesis	100	5 of 5
[Ref.: #66794]	palmitate biosynthesis	95.45	21 of 22
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	methylglyoxal degradation	80	4 of 5
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	vitamin K metabolism	80	4 of 5
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	pyrimidine metabolism	77.78	35 of 45
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	vitamin B12 metabolism	76.47	26 of 34
[Ref.: #66794]	purine metabolism	75.53	71 of 94
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	pentose phosphate pathway	72.73	8 of 11
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	threonine metabolism	70	7 of 10
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	degradation of hexoses	66.67	12 of 18
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	methionine metabolism	65.38	17 of 26
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	glutamate and glutamine metabolism	64.29	18 of 28
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	leucine metabolism	61.54	8 of 13
[Ref.: #66794]	sulfate reduction	61.54	8 of 13
[Ref.: #66794]	degradation of pentoses	60.71	17 of 28
[Ref.: #66794]	non-pathway related	60.53	23 of 38
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	coenzyme M biosynthesis	60	6 of 10
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	histidine metabolism	58.62	17 of 29
[Ref.: #66794]	alanine metabolism	58.62	17 of 29
[Ref.: #66794]	lipid metabolism	58.06	18 of 31
[Ref.: #66794]	tryptophan metabolism	57.89	22 of 38
[Ref.: #66794]	reductive acetyl coenzyme A pathway	57.14	4 of 7
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	CO2 fixation in Crenarchaeota	55.56	5 of 9
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	proline metabolism	54.55	6 of 11
[Ref.: #66794]	metabolism of disaccharids	54.55	6 of 11
[Ref.: #66794]	degradation of sugar acids	52	13 of 25
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	lysine metabolism	50	21 of 42
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	46.15	6 of 13
[Ref.: #66794]	arginine metabolism	45.83	11 of 24
[Ref.: #66794]	polyamine pathway	43.48	10 of 23
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	degradation of sugar alcohols	37.5	6 of 16
[Ref.: #66794]	oxidative phosphorylation	37.36	34 of 91
[Ref.: #66794]	phenol degradation	35	7 of 20
[Ref.: #66794]	molybdenum cofactor biosynthesis	33.33	3 of 9
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
[Ref.: #66794]	glycolate and glyoxylate degradation	33.33	2 of 6
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	33.33	2 of 6
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	ascorbate metabolism	31.82	7 of 22
[Ref.: #66794]	urea cycle	30.77	4 of 13
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	myo-inositol biosynthesis	30	3 of 10
[Ref.: #66794]	mevalonate metabolism	28.57	2 of 7
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	3-phenylpropionate degradation	26.67	4 of 15
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
[Ref.: #66794]	allantoin degradation	22.22	2 of 9
[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.: #2813]	Sample type/isolated from	freshwater sediment
[Ref.: #2813]	Country	Germany
[Ref.: #2813]	Country ISO 3 Code	DEU
[Ref.: #2813]	Continent	Europe

[Ref.: #67771]	Sample type/isolated from	From freshwater sediment
[Ref.: #67771]	Country	Germany
[Ref.: #67771]	Country ISO 3 Code	DEU
[Ref.: #67771]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Sediment
#Environmental	#Aquatic	#Freshwater

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence FR733683 (>99% sequence identity) for Breznakibacter xylanolyticus subclade from Microbeatlas

Aquatic Samples	2284
Soil Samples	147
Animal Samples	322
Plant Samples	82
Total Samples	2835

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

[Ref.: #2813]

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.: #2813]	Cytophaga xylanolytica partial 16S rRNA gene, type strain DSM6779T	FR733683	1507	GenBank ENA	990 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67771]	Breznakibacter xylanolyticus DSM 6779	GCA_003254275	scaffold	GenBank ENA	990 tax ID
[Ref.: #66792]	Cytophaga xylanolytica strain DSM 6779	990.3	wgs	PATRIC	990 tax ID	*
[Ref.: #66792]	Cytophaga xylanolytica DSM 6779	2593339275	draft	JGI IMG/M	990 tax ID	*

[Ref.: #2813]	GC-content	45.5 mol%
[Ref.: #67771]	GC-content	46.6 mol%	genome sequence analysis
[Ref.: #67771]	GC-content	45.5 mol%	Buoyant density centrifugation (BD)

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Breznakibacter xylanolyticus DSM 6779 NCBI: GCA_003254275.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Cytophaga xylanolytica strain DSM 6779 PATRIC: 990.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	88.072	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	yes	70.354	yes
[Ref.: #69480]	aerobic	aerobicⓘ	no	83.515	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	88.633	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	93.059	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	83.534	yes

Availability in culture collections External links

[Ref.: #2813]

Culture collection no.

DSM 6779, ATCC 51429, KCTC 15201

[Ref.: #73284]

SI-ID 7705

References

#2813

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 6779

#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 )

#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 .

#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 )

#73284

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-ID7705.1 )

* These data were automatically processed and therefore are not curated

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Breznakibacter xylanolyticus DSM 6779

Cytophaga xylanolytica strain DSM 6779

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