Name: Anoxybacter fermentans DY22613
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/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

Section

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

motile
spore-forming
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	*Halanaerobiales*
	Family	[Halanaerobiales, not assigned to family]
	Genus	*Anoxybacter*
	Species	**Anoxybacter fermentans**
	Full Scientific Name (LPSN)	Anoxybacter fermentans Zeng et al. 2015

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Motility	yes Confidence in %96.895

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

[Ref.: #22142]	Temperature range	thermophilic
[Ref.: #67770]	Temperature range	thermophilic
[Ref.: #69480]	Temperature range	thermophilic Confidence in %99.999

Information on physiology and metabolism Physiology and metabolism

[Ref.: #22142]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %99.998

[Ref.: #69480]

Ability of spore formation

yes Confidence in %99.551

	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	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	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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Anoxybacter fermentans DY22613 NCBI: GCA_003991135.1
[Ref.: #69481]	spore-forming	yes	52	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Anoxybacter fermentans DY22613 NCBI: GCA_003991135.1
[Ref.: #69480]	motile	yes	87.011	no
[Ref.: #69480]	flagellated	no	74.017	no
[Ref.: #69480]	gram-positive	no	84.584	no
[Ref.: #69480]	anaerobic	yes	99.048	yes
[Ref.: #69480]	aerobic	no	97.407	yes
[Ref.: #69480]	halophile	no	87.935	no
[Ref.: #69480]	spore-forming	yes	69.766	no
[Ref.: #69480]	thermophile	yes	99.999	yes
[Ref.: #69480]	glucose-util	yes	86.794	no
[Ref.: #69480]	glucose-ferment	no	66.053	no

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 .

#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 )

#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 )

* These data were automatically processed and therefore are not curated

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