Anoxybacter fermentans (DSM 28033, JCM 19466, MCCC 1A06456)

Name: Anoxybacter fermentans (DSM 28033, JCM 19466, MCCC 1A06456)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 130818

Type strain

Strain Designation DY22613

Culture col. no. DSM 28033 JCM 19466 MCCC 1A06456 DY22613

NCBI tax ID(s) 1323375

Special Collections DSMZ JCM

History <- X. Zeng, Third Inst. Oceanography, State Oceanic Administration, Xiamen, China; DY22613 <- X. Zeng {2012} X. Zeng DY22613.

Links

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

anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 404111

JCM 19466,DSM 28033

@ref 20215

Last LPSN update 2026-02-09 11:31:19

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Halanaerobiales

Family [Halanaerobiales, not assigned to family]

Genus Anoxybacter

Species Anoxybacter fermentans

Full scientific name Anoxybacter fermentans Zeng et al. 2015

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
22142	MARINITOGA MEDIUM (DSMZ Medium 904)		Medium recipe at MediaDive	Name: MARINITOGA MEDIUM (DSMZ Medium 904) Composition: Sea Salt 30.0 g/l PIPES 6.0 g/l D-Glucose 2.5 g/l Tryptone 1.0 g/l Yeast extract 1.0 g/l Na2S x 9 H2O 0.5 g/l L-Cysteine HCl x H2O 0.5 g/l Sodium resazurin 0.0005 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
22142	positive	growth	60
67770	positive	growth	60

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
22142	anaerobe
125439	anaerobe	99.1

Pathway annotation

Computationally determined by

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

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Condition	#Sulfuric	-
#Condition	#Thermophilic (>45°C)	-

Isolation

@ref	Sample type	Geographic location	Country	Latitude	Longitude
22142	deep sea hydrothermal sulfide deposit, depth of 2891 m	East Pacific Rise	International waters	-3.1	-102.6 -3.1/-102.6
67770	Deep-sea hydrothermal vent

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
22142	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM399113v1 assembly for Anoxybacter fermentans DY22613	complete	GCA_003991135	1323375.3	2837169743	1323375	93.29

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
22142	Anoxybacter fermentans strain DY22613 16S ribosomal RNA gene, partial sequence	KC794015	1500		1323375

GC content

@ref	GC-content (mol%)	Method
22142	36.7	sequence analysis
67770	36.7	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Anoxybacter fermentans DY22613
NCBI: GCA_003991135

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	78.10	no
125439	motility	BacteriaNetⓘ	yes	67.20	no
125439	gram_stain	BacteriaNetⓘ	positive	78.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	99.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Anoxybacter fermentans DY22613
NCBI: GCA_003991135.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	73.01	no
125438	anaerobic	anaerobicⓘ	yes	82.85	yes
125438	aerobic	aerobicⓘ	no	91.51	yes
125438	spore-forming	spore-formingⓘ	yes	62.95	no
125438	thermophilic	thermophileⓘ	yes	57.69	no
125438	flagellated	motile2+ⓘ	yes	78.38	no

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
	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
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

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 .
#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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Anoxybacter fermentans (DSM 28033, JCM 19466, MCCC 1A06456)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003991135

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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