Acetobacteroides hydrogenigenes (DSM 24657, CGMCC 1.5173, JCM 17603)

Name: Acetobacteroides hydrogenigenes (DSM 24657, CGMCC 1.5173, JCM 17603)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 131580

Type strain

Strain Designation RL-C

Culture col. no. DSM 24657 CGMCC 1.5173 JCM 17603 RL-C

NCBI tax ID(s) 979970

Special Collections DSMZ JCM

History <- Y.-L. Qiu, Qingdao Institute of Bioenergy & Bioprocess Technology, Chinese Academy of Sciences (CAS), Qingdao; RL-C Y.-L. Qiu and Y. Sekiguchi strain RL-C.

Links

Acetobacteroides hydrogenigenes RL-C is a bacterium that was isolated from reed swamp.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 405703

JCM 17603,DSM 24657

@ref 20215

Last LPSN update 2026-02-09 11:31:30

Domain Bacteria

Phylum Bacteroidota

Class Bacteroidia

Order Bacteroidales

Family Williamwhitmaniaceae

Genus Acetobacteroides

Species Acetobacteroides hydrogenigenes

Full scientific name Acetobacteroides hydrogenigenes Su et al. 2014

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	99.7

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
23376	ACETOBACTEROIDES MEDIUM (DSMZ Medium 1647)		Medium recipe at MediaDive	Name: ACETOBACTEROIDES MEDIUM (DSMZ Medium 1647) Composition: NaHCO3 2.5 g/l NH4Cl 0.824796 g/l Na2S x 9 H2O 0.3 g/l L-Cysteine HCl x H2O 0.3 g/l MgCl2 x 6 H2O 0.2 g/l Yeast extract 0.2 g/l Glucose 0.18 g/l KH2PO4 0.14 g/l Nitrilotriacetic acid 0.0128 g/l Resazurin 0.001 g/l NaCl 0.001 g/l FeCl2 x 4 H2O 0.001 g/l NiCl2 x 6 H2O 0.0001 g/l ZnCl2 0.0001 g/l MnCl2 x 4 H2O 0.0001 g/l CaCl2 x 2 H2O 0.0001 g/l Na2WO4 x 2 H2O 4e-05 g/l CoCl2 x 6 H2O 3e-05 g/l Na2SeO3 x 5 H2O 3e-05 g/l Na2MoO4 x 2 H2O 3e-05 g/l CuCl2 2e-05 g/l Pyridoxine hydrochloride 1e-05 g/l H3BO3 1e-05 g/l p-Aminobenzoic acid 5e-06 g/l Thiamine-HCl x 2 H2O 5e-06 g/l Riboflavin 5e-06 g/l Lipoic acid 5e-06 g/l Nicotinic acid 5e-06 g/l D-Calcium pantothenate 5e-06 g/l Na2SeO3 4e-06 g/l Na2WO4 4e-06 g/l Folic acid 2e-06 g/l Biotin 2e-06 g/l Vitamin B12 1e-07 g/l Distilled water
23376	TREPONEMA SACCHAROPHILUM MEDIUM (DSMZ Medium 323)		Medium recipe at MediaDive	Name: TREPONEMA SACCHAROPHILUM MEDIUM (DSMZ Medium 323) Composition: Agar 12.0 g/l Na2CO3 2.5 g/l D-Glucose 2.0 g/l Trypticase peptone 2.0 g/l Yeast extract 2.0 g/l L-Cysteine HCl x H2O 1.0 g/l (NH4)2SO4 0.9 g/l NaCl 0.9 g/l KH2PO4 0.45 g/l K2HPO4 0.45 g/l MgSO4 x 7 H2O 0.19 g/l CaCl2 x 2 H2O 0.12 g/l Sodium resazurin 0.0005 g/l n-Butyric acid iso-Butyric acid DL-2-Methylbutyric acid n-Valeric acid iso-Valeric acid Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
23376	positive	growth	37
67770	positive	growth	37

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125439		99.9

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	gluconeogenesis	100	8 of 8
66794	lipoate biosynthesis	100	5 of 5
66794	coenzyme A metabolism	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	methylglyoxal degradation	100	5 of 5
66794	glycogen metabolism	100	5 of 5
66794	starch degradation	100	10 of 10
66794	biotin biosynthesis	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	sulfopterin metabolism	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	ppGpp biosynthesis	100	4 of 4
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	vitamin B6 metabolism	90.91	10 of 11
66794	threonine metabolism	90	9 of 10
66794	Entner Doudoroff pathway	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	photosynthesis	85.71	12 of 14
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	propanol degradation	85.71	6 of 7
66794	peptidoglycan biosynthesis	80	12 of 15
66794	hydrogen production	80	4 of 5
66794	cellulose degradation	80	4 of 5
66794	flavin biosynthesis	80	12 of 15
66794	glycine betaine biosynthesis	80	4 of 5
66794	vitamin K metabolism	80	4 of 5
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	pyrimidine metabolism	77.78	35 of 45
66794	d-mannose degradation	77.78	7 of 9
66794	lipid A biosynthesis	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	alanine metabolism	75.86	22 of 29
66794	butanoate fermentation	75	3 of 4
66794	glutamate and glutamine metabolism	75	21 of 28
66794	acetate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	histidine metabolism	72.41	21 of 29
66794	citric acid cycle	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	vitamin B12 metabolism	70.59	24 of 34
66794	glycolysis	70.59	12 of 17
66794	purine metabolism	70.21	66 of 94
66794	propionate fermentation	70	7 of 10
66794	NAD metabolism	66.67	12 of 18
66794	acetoin degradation	66.67	2 of 3
66794	formaldehyde oxidation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	enterobactin biosynthesis	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	serine metabolism	66.67	6 of 9
66794	methionine metabolism	65.38	17 of 26
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	lipid metabolism	64.52	20 of 31
66794	proline metabolism	63.64	7 of 11
66794	d-xylose degradation	63.64	7 of 11
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	non-pathway related	60.53	23 of 38
66794	coenzyme M biosynthesis	60	6 of 10
66794	reductive acetyl coenzyme A pathway	57.14	4 of 7
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	heme metabolism	57.14	8 of 14
66794	degradation of sugar acids	56	14 of 25
66794	CO2 fixation in Crenarchaeota	55.56	5 of 9
66794	tryptophan metabolism	55.26	21 of 38
66794	lysine metabolism	54.76	23 of 42
66794	pentose phosphate pathway	54.55	6 of 11
66794	arginine metabolism	54.17	13 of 24
66794	leucine metabolism	53.85	7 of 13
66794	urea cycle	53.85	7 of 13
66794	pantothenate biosynthesis	50	3 of 6
66794	ethanol fermentation	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	degradation of hexoses	50	9 of 18
66794	adipate degradation	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	kanosamine biosynthesis II	50	1 of 2
66794	toluene degradation	50	2 of 4
66794	cysteine metabolism	50	9 of 18
66794	vitamin B1 metabolism	46.15	6 of 13
66794	degradation of sugar alcohols	43.75	7 of 16
66794	tyrosine metabolism	42.86	6 of 14
66794	degradation of pentoses	42.86	12 of 28
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	phenylacetate degradation (aerobic)	40	2 of 5
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	factor 420 biosynthesis	40	2 of 5
66794	polyamine pathway	39.13	9 of 23
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	ketogluconate metabolism	37.5	3 of 8
66794	metabolism of disaccharids	36.36	4 of 11
66794	oxidative phosphorylation	35.16	32 of 91
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	molybdenum cofactor biosynthesis	33.33	3 of 9
66794	IAA biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	ascorbate metabolism	31.82	7 of 22
66794	phosphatidylethanolamine bioynthesis	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	vitamin E metabolism	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	sulfate reduction	23.08	3 of 13
66794	carotenoid biosynthesis	22.73	5 of 22
66794	arachidonic acid metabolism	22.22	4 of 18
66794	4-hydroxymandelate 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	#Terrestrial	#Wetland (Swamp)
#Host	#Plants	#Herbaceous plants (Grass,Crops)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
23376	reed swamp	Shandong Province, Qingdao (36° 00' 00'' N 120° 00' 00'' E)	China	CHN	Asia	36	120 36/120
67770	Reed swamp in Qingdao	Shandong Province	China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB611036 (>99% sequence identity) for Acetobacteroides hydrogenigenes subclade from Microbeatlas

Aquatic Samples	431
Soil Samples	16
Animal Samples	9
Plant Samples	13
Total Samples	469

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
23376	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	ASM434020v1 assembly for Acetobacteroides hydrogenigenes RL-C	scaffold	GCA_004340205	979970.3	2731639222	979970	64.72

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
23376	Acetobacteroides hydrogenigenes gene for 16S rRNA, partial sequence	AB611036	1440		979970

GC content

@ref	GC-content (mol%)	Method
23376	51.2	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Acetobacteroides hydrogenigenes RL-C
NCBI: GCA_004340205

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.90	no
125439	motility	BacteriaNetⓘ	no	60.00	no
125439	gram_stain	BacteriaNetⓘ	negative	99.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	89.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Acetobacteroides hydrogenigenes RL-C
NCBI: GCA_004340205.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	89.73	no
125438	anaerobic	anaerobicⓘ	yes	69.93	no
125438	aerobic	aerobicⓘ	no	84.61	no
125438	spore-forming	spore-formingⓘ	no	86.77	no
125438	thermophilic	thermophileⓘ	no	92.05	no
125438	flagellated	motile2+ⓘ	no	81.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Identification and cultivation of anaerobic bacterial scavengers of dead cells.	Hirakata Y, Mei R, Morinaga K, Katayama T, Tamaki H, Meng XY, Watari T, Yamaguchi T, Hatamoto M, Nobu MK.	ISME J	10.1038/s41396-023-01538-2	2023
Phylogeny	Acetobacteroides hydrogenigenes gen. nov., sp. nov., an anaerobic hydrogen-producing bacterium in the family Rikenellaceae isolated from a reed swamp.	Su XL, Tian Q, Zhang J, Yuan XZ, Shi XS, Guo RB, Qiu YL	Int J Syst Evol Microbiol	10.1099/ijs.0.063917-0	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 )
#23376	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24657
#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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Acetobacteroides hydrogenigenes (DSM 24657, CGMCC 1.5173, JCM 17603)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

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_004340205

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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