Name: Anoxybacter fermentans DY22613
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 130818

Type strain:

Species: Anoxybacter fermentans

Strain Designation: DY22613

Culture col. no.: DSM 28033, JCM 19466, MCCC 1A06456

Strain history: X. Zeng DY22613.

NCBI tax ID(s): 1323375 (species)

SI-ID 404111

DSM 28033

Special Collections

DSMZ
JCM

Section

When using BacDive for research please cite our paper

Anoxybacter fermentans DY22613 is an anaerobe, thermophilic bacterium that was isolated from deep sea hydrothermal sulfide deposit, depth of 2891 m.

anaerobe
thermophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Bacillota*
	Class	*Clostridia*
	Order	*Halanaerobiales*
	Family	[Halanaerobiales, not assigned to family]
	Genus	*Anoxybacter*
	Species	**Anoxybacter fermentans**
	Full Scientific Name (LPSN)	Anoxybacter fermentans Zeng et al. 2015

Information on culture and growth conditions Culture and growth conditions

[Ref.: #22142]

Culture medium

MARINITOGA MEDIUM (DSMZ Medium 904)

[Ref.: #22142]

Culture medium growth

[Ref.: #22142]

Culture medium link

Medium recipe at MediaDive

[Ref.: #22142]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #22142]			growth	60 °C
[Ref.: #67770]			growth	60 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #22142]	Oxygen tolerance	anaerobe
[Ref.: #125439]	Oxygen tolerance	anaerobe Confidence in %99.1

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	hydrogen production	100	5 of 5
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	cyanate degradation	100	3 of 3
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	teichoic acid biosynthesis	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	95.45	21 of 22
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	pyrimidine metabolism	82.22	37 of 45
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	purine metabolism	77.66	73 of 94
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	urea cycle	76.92	10 of 13
[Ref.: #66794]	alanine metabolism	75.86	22 of 29
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	biotin biosynthesis	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	ppGpp biosynthesis	75	3 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	histidine metabolism	72.41	21 of 29
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	tetrahydrofolate metabolism	71.43	10 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	69.23	9 of 13
[Ref.: #66794]	vitamin B1 metabolism	69.23	9 of 13
[Ref.: #66794]	glutamate and glutamine metabolism	67.86	19 of 28
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	NAD metabolism	66.67	12 of 18
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	methionine metabolism	65.38	17 of 26
[Ref.: #66794]	heme metabolism	64.29	9 of 14
[Ref.: #66794]	gluconeogenesis	62.5	5 of 8
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	oxidative phosphorylation	60.44	55 of 91
[Ref.: #66794]	flavin biosynthesis	60	9 of 15
[Ref.: #66794]	myo-inositol biosynthesis	60	6 of 10
[Ref.: #66794]	glycolysis	58.82	10 of 17
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	degradation of hexoses	55.56	10 of 18
[Ref.: #66794]	lipid A biosynthesis	55.56	5 of 9
[Ref.: #66794]	degradation of pentoses	53.57	15 of 28
[Ref.: #66794]	non-pathway related	52.63	20 of 38
[Ref.: #66794]	tryptophan metabolism	50	19 of 38
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	propionate fermentation	50	5 of 10
[Ref.: #66794]	suberin monomers biosynthesis	50	1 of 2
[Ref.: #66794]	isoleucine metabolism	50	4 of 8
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	arginine metabolism	50	12 of 24
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	lipid metabolism	48.39	15 of 31
[Ref.: #66794]	lysine metabolism	47.62	20 of 42
[Ref.: #66794]	vitamin B12 metabolism	47.06	16 of 34
[Ref.: #66794]	leucine metabolism	46.15	6 of 13
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	4-hydroxyphenylacetate degradation	40	4 of 10
[Ref.: #66794]	Entner Doudoroff pathway	40	4 of 10
[Ref.: #66794]	methylglyoxal degradation	40	2 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	dTDPLrhamnose biosynthesis	37.5	3 of 8
[Ref.: #66794]	pentose phosphate pathway	36.36	4 of 11
[Ref.: #66794]	citric acid cycle	35.71	5 of 14
[Ref.: #66794]	polyamine pathway	34.78	8 of 23
[Ref.: #66794]	valine metabolism	33.33	3 of 9
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	glutathione metabolism	28.57	4 of 14
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	proline metabolism	27.27	3 of 11
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	degradation of sugar acids	24	6 of 25
[Ref.: #66794]	phenylpropanoid biosynthesis	23.08	3 of 13
[Ref.: #66794]	ascorbate metabolism	22.73	5 of 22
		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.: #22142]	Sample type/isolated from	deep sea hydrothermal sulfide deposit, depth of 2891 m
[Ref.: #22142]	Geographic location (country and/or sea, region)	East Pacific Rise
[Ref.: #22142]	Country	International waters
[Ref.: #22142]	Geographic location	-3.1000°/-102.6000°

[Ref.: #67770]	Sample type/isolated from	Deep-sea hydrothermal vent
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Condition	#Sulfuric	-
#Condition	#Thermophilic (>45°C)	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KC794015 (>99% sequence identity) for Anoxybacter fermentans subclade from Microbeatlas

Aquatic Samples	89
Soil Samples	10
Animal Samples	27
Plant Samples	3
Total Samples	129

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

[Ref.: #22142]

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.: #22142]	Anoxybacter fermentans strain DY22613 16S ribosomal RNA gene, partial sequence	KC794015	1500	GenBank ENA	1323375 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Anoxybacter fermentans DY22613	GCA_003991135	complete	GenBank ENA	1323375 tax ID	*
[Ref.: #66792]	Anoxybacter fermentans DY22613	2837169743	complete	JGI IMG/M	1323375 tax ID	*

[Ref.: #22142]	GC-content	36.7 mol%	sequence analysis
[Ref.: #67770]	GC-content	36.7 mol%	genome sequence analysis

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Anoxybacter fermentans DY22613 NCBI: GCA_003991135.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	73.013	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	yes	82.848	yes
[Ref.: #125438]	aerobic	aerobicⓘ	no	91.511	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	yes	62.947	no
[Ref.: #125438]	thermophile	thermophilicⓘ	yes	57.685	no
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	78.379	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Anoxybacter fermentans DY22613 NCBI: GCA_003991135
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	yes	78.1
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	67.2
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	positive	78.3
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	anaerobe	99.1

Availability in culture collections External links

[Ref.: #22142]

Culture collection no.

DSM 28033, JCM 19466, MCCC 1A06456

[Ref.: #89306]

SI-ID 404111

Literature:

Topic	Title	Authors	Journal	DOI	Year
Genetics	Complete genome sequence of Anoxybacter fermentans DY22613(T), a piezophilic dissimilatory Fe(III)-reducing bacterium isolated from East Pacific Rise hydrothermal sulfides.	Li X, Qiu D, Zeng X, Shao Z	Mar Genomics	10.1016/j.margen.2020.100755	2020	*
Phylogeny	Anoxybacter fermentans gen. nov., sp. nov., a piezophilic, thermophilic, anaerobic, fermentative bacterium isolated from a deep-sea hydrothermal vent.	Zeng X, Zhang Z, Li X, Zhang X, Cao J, Jebbar M, Alain K, Shao Z	Int J Syst Evol Microbiol	10.1099/ijs.0.068221-0	2014	*
	Extracellular electron transfer in fermentative bacterium Anoxybacter fermentans DY22613(T) isolated from deep-sea hydrothermal sulfides.	Li X, Zeng X, Qiu D, Zhang Z, Zhang X, Shao Z	Sci Total Environ	10.1016/j.scitotenv.2020.137723	2020	*

References

#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 )

#22142

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 28033

#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 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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 .

#89306

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-ID404111.1 )

#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 .

* These data were automatically processed and therefore are not curated

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