Name: Ethanoligenens harbinense YUAN-3
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 17689

Type strain:

Species: Ethanoligenens harbinense

Strain Designation: YUAN-3

Culture col. no.: DSM 18485, CGMCC 1.5033, JCM 12961

Strain history: D. Xing et al. YUAN-3.

NCBI tax ID(s): 253239 (species)

SI-ID 290972

CGMCC 1.5033, JCM 12961, DSM 18485

Other strains from Ethanoligenens harbinense

E. harbinense JCM 12960, CGMCC 1151

Section

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

Gram-positive
motile
rod-shaped
anaerobe
mesophilic
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	*Eubacteriales*
	Family	*Oscillospiraceae*
	Genus	*Ethanoligenens*
	Species	**Ethanoligenens harbinense**
	Full Scientific Name (LPSN)	Ethanoligenens harbinense Xing et al. 2006

Information on morphological and physiological properties Morphology

[Ref.: #31627]	Gram stain	positive

[Ref.: #31627]	Cell length	1.5-8 µm

[Ref.: #31627]	Cell width	0.4-0.8 µm

[Ref.: #31627]	Cell shape	rod-shaped

[Ref.: #31627]	Motility	yes

[Ref.: #31627]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7556]

Culture medium

ETHANOLIGENES MEDIUM (DSMZ Medium 1057)

[Ref.: #7556]

Culture medium growth

[Ref.: #7556]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7556]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #7556]	growth	37 °C
[Ref.: #31627]	growth	20-44 °C
[Ref.: #31627]	optimum	35 °C
[Ref.: #67770]	growth	37 °C

[Ref.: #7556]	Temperature range	mesophilic
[Ref.: #31627]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31627]			optimum	4.5-5
[Ref.: #31627]			growth	3.5-9

Information on physiology and metabolism Physiology and metabolism

[Ref.: #7556]	Oxygen tolerance	anaerobe
[Ref.: #31627]	Oxygen tolerance	anaerobe

[Ref.: #31627]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31627]		NaCl		growth	0-2	%
[Ref.: #31627]		NaCl		optimum	0-2	%

[Ref.: #31627]

Observation

aggregates in chains

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31627]	cellobiose ChEBI	+	carbon source
[Ref.: #31627]	fructose ChEBI	+	carbon source
[Ref.: #31627]	galactose ChEBI	+	carbon source
[Ref.: #31627]	glucose ChEBI	+	carbon source
[Ref.: #31627]	lactose ChEBI	+	carbon source
[Ref.: #31627]	maltose ChEBI	+	carbon source
[Ref.: #31627]	mannose ChEBI	+	carbon source
[Ref.: #31627]	melibiose ChEBI	+	carbon source
[Ref.: #31627]	ribose ChEBI	+	carbon source
[Ref.: #31627]	sucrose ChEBI	+	carbon source

	Metabolite production	Metabolite	Production
[Ref.: #31627]		indole ChEBI	yes

	Physiological tests	Metabolite	Indole test
[Ref.: #31627]		indole ChEBI	+

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #31627]		urease	+	3.5.1.5

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #7556]	Sample type/isolated from	anaerobic sludge of molasses wastewater in a CSTR
[Ref.: #7556]	Geographic location (country and/or sea, region)	Harbin
[Ref.: #7556]	Country	China
[Ref.: #7556]	Country ISO 3 Code	CHN
[Ref.: #7556]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Anaerobic sludge of molasses wastewater
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #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

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

[Ref.: #7556]

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.: #7556]	Ethanoligenens harbinense strain YUAN-3 16S ribosomal RNA gene, partial sequence	AY295777	1499	ENA	663278 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Ethanoligenens harbinense YUAN-3	GCA_003020045	complete	GenBank	663278 tax ID	*
[Ref.: #66792]	Ethanoligenens harbinense YUAN-3	GCA_000178115	complete	GenBank	663278 tax ID	*
[Ref.: #66792]	Ethanoligenens harbinense YUAN-3	663278.4	complete	PATRIC	663278 tax ID	*
[Ref.: #66792]	Ethanoligenens harbinense YUAN-3T, DSM 18485	649633043	complete	JGI IMG/M	663278 tax ID	*

[Ref.: #7556]	GC-content	47.8-49.0 mol%
[Ref.: #31627]	GC-content	47.8 mol%
[Ref.: #67770]	GC-content	47.8 mol%	thermal denaturation, midpoint method (Tm)

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Ethanoligenens harbinense YUAN-3 YUAN-3 NCBI: GCA_003020045.1
[Ref.: #69480]	flagellated	no	54.388	no
[Ref.: #69480]	gram-positive	yes	85.895	yes
[Ref.: #69480]	anaerobic	yes	99.019	yes
[Ref.: #69480]	halophile	no	95.878	no
[Ref.: #69480]	spore-forming	no	69.832	yes
[Ref.: #69480]	glucose-util	yes	87.116	yes
[Ref.: #69480]	aerobic	no	97.057	yes
[Ref.: #69480]	thermophile	no	81.994	yes
[Ref.: #69480]	motile	yes	85.964	yes
[Ref.: #69480]	glucose-ferment	yes	70.86	no

Availability in culture collections External links

[Ref.: #7556]

Culture collection no.

DSM 18485, CGMCC 1.5033, JCM 12961

[Ref.: #86680]

SI-ID 290972

Literature:

Topic	Title	Authors	Journal	DOI	Year
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	*
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	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 )

#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 (see below)

#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 .

#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) .

#86680

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-ID290972.1 )

#27912

IJSEM 755 2006 ( DOI 10.1099/ijs.0.63926-0 , PubMed 16585689 )

* These data were automatically processed and therefore are not curated

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Ethanoligenens harbinense YUAN-3 YUAN-3

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