Ethanoligenens harbinense (DSM 18485, CGMCC 1.5033, JCM 12961)

Name: Ethanoligenens harbinense (DSM 18485, CGMCC 1.5033, JCM 12961)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17689

Type strain

Strain Designation YUAN-3

Culture col. no. DSM 18485 CGMCC 1.5033 JCM 12961 YUAN-3

NCBI tax ID(s) 253239

Special Collections DSMZ JCM Literature strains

History <- JCM; JCM 12961 <- D. Xing, Harbin Institute of Technology, Harbin, China; YUAN-3 D. Xing et al. YUAN-3.

Links

Ethanoligenens harbinense YUAN-3 is an anaerobe, mesophilic, Gram-positive prokaryote that was isolated from anaerobic sludge of molasses wastewater in a CSTR.

Gram-positive motile rod-shaped anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 290972

CGMCC 1.5033,JCM 12961,DSM 18485

@ref 20215

Last LPSN update 2026-02-09 11:22:17

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Oscillospiraceae

Genus Ethanoligenens

Species Ethanoligenens harbinense

Full scientific name Ethanoligenens harbinense Xing et al. 2006

BacDive ID	Other strains from **Ethanoligenens harbinense** (1)	Type strain
161289	E. harbinense JCM 12960, CGMCC 1151

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
31627	positive	1.5-8 µm	0.4-0.8 µm	rod-shaped
125439	negative					94.5

Pigmentation

31627

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
7556	ETHANOLIGENES MEDIUM (DSMZ Medium 1057)		Medium recipe at MediaDive	Name: ETHANOLIGENES MEDIUM (DSMZ Medium 1057) Composition: D-Glucose 9.98004 g/l Tryptone 3.99202 g/l Beef extract 1.99601 g/l K2HPO4 1.49701 g/l Yeast extract 0.998004 g/l L-Cysteine HCl x H2O 0.499002 g/l MgCl2 x 6 H2O 0.199601 g/l FeSO4 x 7 H2O 0.0998004 g/l Nitrilotriacetic acid 0.0127745 g/l FeCl2 x 4 H2O 0.000998004 g/l NaCl 0.000998004 g/l Sodium resazurin 0.000499002 g/l MnCl2 x 4 H2O 9.98004e-05 g/l ZnCl2 9.98004e-05 g/l NiCl2 x 6 H2O 9.98004e-05 g/l CaCl2 x 2 H2O 9.98004e-05 g/l Pyridoxine hydrochloride 9.98004e-05 g/l p-Aminobenzoic acid 4.99002e-05 g/l Calcium D-(+)-pantothenate 4.99002e-05 g/l (DL)-alpha-Lipoic acid 4.99002e-05 g/l Nicotinic acid 4.99002e-05 g/l Riboflavin 4.99002e-05 g/l Thiamine HCl 4.99002e-05 g/l Na2WO4 x 2 H2O 3.99202e-05 g/l CoCl2 x 6 H2O 2.99401e-05 g/l Na2MoO4 x 2 H2O 2.99401e-05 g/l Na2SeO3 x 5 H2O 2.99401e-05 g/l Folic acid 1.99601e-05 g/l Biotin 1.99601e-05 g/l CuCl2 1.99601e-05 g/l H3BO3 9.98004e-06 g/l Vitamin B12 9.98004e-07 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
7556	positive	growth	37	mesophilic
31627	positive	growth	20-44
31627	positive	optimum	35	mesophilic
67770	positive	growth	37	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
31627	positive	optimum	4.5-5
31627	positive	growth	3.5-9	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
7556	anaerobe
31627	anaerobe
125438	anaerobe	94.406
125439	obligate anaerobe	94.8

Spore formation

@ref	Spore formation	Confidence
31627
125439		96

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31627	NaCl	positive	growth	0-2 %
31627	NaCl	positive	optimum	0-2 %

Observation

31627

Observationaggregates in chains

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31627	17057 ChEBI	cellobiose	+	carbon source
31627	28757 ChEBI	fructose	+	carbon source
31627	28260 ChEBI	galactose	+	carbon source
31627	17234 ChEBI	glucose	+	carbon source
31627	17716 ChEBI	lactose	+	carbon source
31627	17306 ChEBI	maltose	+	carbon source
31627	37684 ChEBI	mannose	+	carbon source
31627	28053 ChEBI	melibiose	+	carbon source
31627	33942 ChEBI	ribose	+	carbon source
31627	17992 ChEBI	sucrose	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
31627	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
31627	35581 ChEBI	indole	+

Enzymes

@ref	Value	Activity	Ec
31627	urease	+	3.5.1.5

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Industrial	-
#Engineered	#Waste	#Industrial wastewater
#Environmental	#Terrestrial	#Mud (Sludge)
#Condition	#Anoxic (anaerobic)	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
7556	anaerobic sludge of molasses wastewater in a CSTR	Harbin	China	CHN	Asia
67770	Anaerobic sludge of molasses wastewater

Taxonmaps

69479

Global distribution of 16S sequence AY295777 (>99% sequence identity) for Ethanoligenens harbinense subclade from Microbeatlas

Aquatic Samples	416
Soil Samples	285
Animal Samples	938
Plant Samples	38
Total Samples	1677

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7556	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
66792	ASM302004v1 assembly for Ethanoligenens harbinense YUAN-3	complete	GCA_003020045			663278	99.18
66792	ASM17811v2 assembly for Ethanoligenens harbinense YUAN-3	complete	GCA_000178115	663278.4	649633043	663278	98.84

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7556	Ethanoligenens harbinense strain YUAN-3 16S ribosomal RNA gene, partial sequence	AY295777	1499		663278

GC content

@ref	GC-content (mol%)	Method
7556	47.8-49.0
31627	47.8
67770	47.8	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Ethanoligenens harbinense YUAN-3
NCBI: GCA_003020045

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	96.00	no
125439	motility	BacteriaNetⓘ	yes	50.10	no
125439	gram_stain	BacteriaNetⓘ	negative	94.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	94.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Ethanoligenens harbinense YUAN-3 YUAN-3
NCBI: GCA_003020045.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	70.19	yes
125438	anaerobic	anaerobicⓘ	yes	94.41	yes
125438	aerobic	aerobicⓘ	no	96.94	no
125438	spore-forming	spore-formingⓘ	no	51.64	yes
125438	thermophilic	thermophileⓘ	no	75.79	no
125438	flagellated	motile2+ⓘ	yes	66.76	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Functional Comparison of Bacteria from the Human Gut and Closely Related Non-Gut Bacteria Reveals the Importance of Conjugation and a Paucity of Motility and Chemotaxis Functions in the Gut Environment.	Dobrijevic D, Abraham AL, Jamet A, Maguin E, van de Guchte M.	PLoS One	10.1371/journal.pone.0159030	2016
Metabolism	Linking genome content to biofuel production yields: a meta-analysis of major catabolic pathways among select H2 and ethanol-producing bacteria.	Carere CR, Rydzak T, Verbeke TJ, Cicek N, Levin DB, Sparling R.	BMC Microbiol	10.1186/1471-2180-12-295	2012
Metabolism	Quantitative proteomic analysis reveals the ethanologenic metabolism regulation of Ethanoligenens harbinense by exogenous ethanol addition.	Li H, Mei X, Liu B, Xie G, Ren N, Xing D	Biotechnol Biofuels	10.1186/s13068-019-1511-y	2019
Metabolism	Insights on acetate-ethanol fermentation by hydrogen-producing Ethanoligenens under acetic acid accumulation based on quantitative proteomics.	Li H, Mei X, Liu B, Li Z, Wang B, Ren N, Xing D	Environ Int	10.1016/j.envint.2019.05.013	2019
Metabolism	Composition of extracellular polymeric substances influences the autoaggregation capability of hydrogen-producing bacterium Ethanoligenens harbinense.	Ren N, Xie T, Xing D	Bioresour Technol	10.1016/j.biortech.2009.05.021	2009
Phylogeny	Caproiciproducens galactitolivorans gen. nov., sp. nov., a bacterium capable of producing caproic acid from galactitol, isolated from a wastewater treatment plant.	Kim BC, Seung Jeon B, Kim S, Kim H, Um Y, Sang BI	Int J Syst Evol Microbiol	10.1099/ijsem.0.000665	2015
Phylogeny	Ethanoligenens harbinense gen. nov., sp. nov., isolated from molasses wastewater.	Xing D, Ren N, Li Q, Lin M, Wang A, Zhao L	Int J Syst Evol Microbiol	10.1099/ijs.0.63926-0	2006

References

#7556	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18485
#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 )
#27912	IJSEM 755 2006 ( DOI 10.1099/ijs.0.63926-0 , PubMed 16585689 )
#31627	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #27912
#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) .
#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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Ethanoligenens harbinense (DSM 18485, CGMCC 1.5033, JCM 12961)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003020045

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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