Breznakibacter xylanolyticus (DSM 6779, ATCC 51429, KCTC 15201)

Name: Breznakibacter xylanolyticus (DSM 6779, ATCC 51429, KCTC 15201)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 3772

Type strain

Strain Designation XM3

Culture col. no. DSM 6779 ATCC 51429 KCTC 15201 XM3

NCBI tax ID(s) 990

Special Collections DSMZ KCTC

Links

Breznakibacter xylanolyticus XM3 is an anaerobe, mesophilic, motile prokaryote that was isolated from freshwater sediment.

motile rod-shaped anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 7705

LMG 13153,DSM 6779,KCTC 15201,ATCC 51429

@ref 20215

Last LPSN update 2025-12-16 09:47:38

Domain Pseudomonadati

Phylum Bacteroidota

Class Bacteroidia

Order Bacteroidales

Family Marinilabiliaceae

Genus Breznakibacter

Species Breznakibacter xylanolyticus

Full scientific name Breznakibacter xylanolyticus (Haack and Breznak 1993) García-López et al. 2020

Synonyms (1)

Cytophaga xylanolytica

Morphology

Cell morphology

@ref	Cell shape	Flagellum arrangement
67771	rod-shaped	gliding
67771
125439

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
2813	ANAEROBIC FRESHWATER (FWM) MEDIUM (DSMZ Medium 503)		Medium recipe at MediaDive	Name: ANAEROBIC FRESHWATER (FWM) MEDIUM (DSMZ Medium 503; with strain-specific modifications) Composition: D-Xylose 1.99402 g/l Na2CO3 1.49551 g/l NaCl 0.997008 g/l KCl 0.498505 g/l MgCl2 x 6 H2O 0.398803 g/l Na2S x 9 H2O 0.299103 g/l NH4Cl 0.249252 g/l KH2PO4 0.199402 g/l CaCl2 x 2 H2O 0.149552 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l Sodium resazurin 0.000498505 g/l NaOH 0.000498504 g/l Pyridoxine hydrochloride 0.000299103 g/l Nicotinic acid 0.000199402 g/l Thiamine-HCl x 2 H2O 0.000199402 g/l CoCl2 x 6 H2O 0.000189432 g/l Calcium pantothenate 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l Vitamin B12 9.97009e-05 g/l p-Aminobenzoic acid 7.97607e-05 g/l ZnCl2 6.97906e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l D-(+)-biotin 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
2813	positive	growth	30	mesophilic
67771	positive	growth	30	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
2813	anaerobe
67771	anaerobe
125439	anaerobe

Spore formation

@ref	Spore formation	Confidence
125439		99.6

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cellulose degradation	100	5 of 5
66794	coenzyme A metabolism	100	4 of 4
66794	biotin biosynthesis	100	4 of 4
66794	adipate degradation	100	2 of 2
66794	L-lactaldehyde degradation	100	3 of 3
66794	starch degradation	100	10 of 10
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CMP-KDO biosynthesis	100	4 of 4
66794	sulfopterin metabolism	100	4 of 4
66794	ppGpp biosynthesis	100	4 of 4
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	tetrahydrofolate metabolism	100	14 of 14
66794	glycogen metabolism	100	5 of 5
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	lipoate biosynthesis	100	5 of 5
66794	palmitate biosynthesis	95.45	21 of 22
66794	lipid A biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	propanol degradation	85.71	6 of 7
66794	NAD metabolism	83.33	15 of 18
66794	peptidoglycan biosynthesis	80	12 of 15
66794	Entner Doudoroff pathway	80	8 of 10
66794	hydrogen production	80	4 of 5
66794	methylglyoxal degradation	80	4 of 5
66794	propionate fermentation	80	8 of 10
66794	vitamin K metabolism	80	4 of 5
66794	photosynthesis	78.57	11 of 14
66794	heme metabolism	78.57	11 of 14
66794	valine metabolism	77.78	7 of 9
66794	pyrimidine metabolism	77.78	35 of 45
66794	d-mannose degradation	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	vitamin B1 metabolism	76.92	10 of 13
66794	vitamin B12 metabolism	76.47	26 of 34
66794	purine metabolism	75.53	71 of 94
66794	isoleucine metabolism	75	6 of 8
66794	gluconeogenesis	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	flavin biosynthesis	73.33	11 of 15
66794	pentose phosphate pathway	72.73	8 of 11
66794	vitamin B6 metabolism	72.73	8 of 11
66794	citric acid cycle	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	threonine metabolism	70	7 of 10
66794	enterobactin biosynthesis	66.67	2 of 3
66794	degradation of hexoses	66.67	12 of 18
66794	octane oxidation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	formaldehyde oxidation	66.67	2 of 3
66794	methionine metabolism	65.38	17 of 26
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	glutamate and glutamine metabolism	64.29	18 of 28
66794	d-xylose degradation	63.64	7 of 11
66794	leucine metabolism	61.54	8 of 13
66794	sulfate reduction	61.54	8 of 13
66794	degradation of pentoses	60.71	17 of 28
66794	non-pathway related	60.53	23 of 38
66794	glycine betaine biosynthesis	60	3 of 5
66794	coenzyme M biosynthesis	60	6 of 10
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	histidine metabolism	58.62	17 of 29
66794	alanine metabolism	58.62	17 of 29
66794	lipid metabolism	58.06	18 of 31
66794	tryptophan metabolism	57.89	22 of 38
66794	reductive acetyl coenzyme A pathway	57.14	4 of 7
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	CO2 fixation in Crenarchaeota	55.56	5 of 9
66794	cysteine metabolism	55.56	10 of 18
66794	proline metabolism	54.55	6 of 11
66794	metabolism of disaccharids	54.55	6 of 11
66794	degradation of sugar acids	52	13 of 25
66794	kanosamine biosynthesis II	50	1 of 2
66794	tyrosine metabolism	50	7 of 14
66794	butanoate fermentation	50	2 of 4
66794	ketogluconate metabolism	50	4 of 8
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	selenocysteine biosynthesis	50	3 of 6
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	lysine metabolism	50	21 of 42
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	arginine metabolism	45.83	11 of 24
66794	polyamine pathway	43.48	10 of 23
66794	factor 420 biosynthesis	40	2 of 5
66794	phenylacetate degradation (aerobic)	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	degradation of sugar alcohols	37.5	6 of 16
66794	oxidative phosphorylation	37.36	34 of 91
66794	phenol degradation	35	7 of 20
66794	molybdenum cofactor biosynthesis	33.33	3 of 9
66794	cyanate degradation	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	nitrate assimilation	33.33	3 of 9
66794	IAA biosynthesis	33.33	1 of 3
66794	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	1,4-dihydroxy-6-naphthoate biosynthesis	33.33	2 of 6
66794	sphingosine metabolism	33.33	2 of 6
66794	ascorbate metabolism	31.82	7 of 22
66794	urea cycle	30.77	4 of 13
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	myo-inositol biosynthesis	30	3 of 10
66794	mevalonate metabolism	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	3-phenylpropionate degradation	26.67	4 of 15
66794	carnitine metabolism	25	2 of 8
66794	lactate fermentation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	4-hydroxymandelate degradation	22.22	2 of 9
66794	allantoin degradation	22.22	2 of 9
66794	glutathione metabolism	21.43	3 of 14

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Sediment
#Environmental	#Aquatic	#Freshwater

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
2813	freshwater sediment	Germany	DEU	Europe
67771	From freshwater sediment	Germany	DEU	Europe

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
2813	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67771	ASM325427v1 assembly for Breznakibacter xylanolyticus DSM 6779	scaffold	GCA_003254275	990.3	2593339275	990	52.47

Genome browser: GCA_003254275

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
2813	Cytophaga xylanolytica partial 16S rRNA gene, type strain DSM6779T	FR733683	1507		990

GC content

@ref	GC-content (mol%)
2813	45.5
67771	46.6
67771	45.5

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Breznakibacter xylanolyticus DSM 6779
NCBI: GCA_003254275

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.60	no
125439	motility	BacteriaNetⓘ	no	71.30	no
125439	gram_stain	BacteriaNetⓘ	negative	97.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	97.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Cytophaga xylanolytica strain DSM 6779
PATRIC: 990.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	88.07	yes
125438	anaerobic	anaerobicⓘ	yes	70.35	yes
125438	aerobic	aerobicⓘ	no	83.52	no
125438	spore-forming	spore-formingⓘ	no	88.63	no
125438	thermophilic	thermophileⓘ	no	93.06	yes
125438	flagellated	motile2+ⓘ	no	83.53	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes.	Garcia-Lopez M, Meier-Kolthoff JP, Tindall BJ, Gronow S, Woyke T, Kyrpides NC, Hahnke RL, Goker M.	Front Microbiol	10.3389/fmicb.2019.02083	2019

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 )
#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 .
#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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Breznakibacter xylanolyticus (DSM 6779, ATCC 51429, KCTC 15201)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003254275

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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