Archive BacDiveID:10.13145/bacdive17689.20230509.8.1

Strain identifier

BacDive ID: 17689

Type strain:

Species: Ethanoligenens harbinense

Strain Designation: YUAN-3

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

NCBI tax ID(s): 253239 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.

General

@ref: 7556

BacDive-ID: 17689

DSM-Number: 18485

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive, motile, rod-shaped

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

NCBI tax id

NCBI tax id: 253239
Matching level: species

strain history

@ref	history
7556	<- JCM <- D. Xing, Harbin Institute of Technology, Harbin, China; YUAN-3
67770	D. Xing et al. YUAN-3.

doi: 10.13145/bacdive17689.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/bacillota
domain: Bacteria
phylum: Bacillota
class: Clostridia
order: Eubacteriales
family: Oscillospiraceae
genus: Ethanoligenens
species: Ethanoligenens harbinense
full scientific name: Ethanoligenens harbinense Xing et al. 2006

@ref: 7556

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Oscillospiraceae

genus: Ethanoligenens

species: Ethanoligenens harbinense

full scientific name: Ethanoligenens harbinense Xing et al. 2006

strain designation: YUAN-3

type strain: yes

Morphology

cell morphology

@ref: 31627
gram stain: positive
cell length: 1.5-8 µm
cell width: 0.4-0.8 µm
cell shape: rod-shaped
motility: yes

pigmentation

@ref: 31627
production: yes

Culture and growth conditions

culture medium

@ref: 7556
name: ETHANOLIGENES MEDIUM (DSMZ Medium 1057)
growth: yes
link: https://mediadive.dsmz.de/medium/1057
composition: 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	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	growth	3.5-9	alkaliphile
31627	positive	optimum	4.5-5

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance
7556	anaerobe
31627	anaerobe

spore formation

@ref: 31627
spore formation: no

halophily

@ref	salt	growth	tested relation	concentration
31627	NaCl	positive	growth	0-2 %
31627	NaCl	positive	optimum	0-2 %

observation

@ref: 31627
observation: aggregates in chains

metabolite utilization

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

metabolite production

@ref: 31627
Chebi-ID: 35581
metabolite: indole
production: yes

metabolite tests

@ref: 31627
Chebi-ID: 35581
metabolite: indole
indole test: +

enzymes

@ref: 31627
value: urease
activity: +
ec: 3.5.1.5

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent
7556	anaerobic sludge of molasses wastewater in a CSTR	Harbin	China	CHN	Asia
67770	Anaerobic sludge of molasses wastewater

isolation source categories

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

taxonmaps

@ref: 69479
File name: preview.99_3335.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15828;96_1741;97_2082;98_2558;99_3335&stattab=map
Last taxonomy: Ethanoligenens harbinense subclade
16S sequence: AY295777
Sequence Identity:
Total samples: 1677
soil counts: 285
aquatic counts: 416
animal counts: 938
plant counts: 38

Safety information

risk assessment

@ref: 7556
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 7556
description: Ethanoligenens harbinense strain YUAN-3 16S ribosomal RNA gene, partial sequence
accession: AY295777
length: 1499
database: ena
NCBI tax ID: 663278

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Ethanoligenens harbinense YUAN-3	GCA_003020045	complete	ncbi	663278
66792	Ethanoligenens harbinense YUAN-3	GCA_000178115	complete	ncbi	663278
66792	Ethanoligenens harbinense YUAN-3	663278.4	complete	patric	663278
66792	Ethanoligenens harbinense YUAN-3T, DSM 18485	649633043	complete	img	663278

GC content

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

Genome-based predictions

predictions

trait	prediction	confidence	training_data
flagellated	no	54.388	no
gram-positive	yes	85.895	yes
anaerobic	yes	99.019	yes
halophile	no	95.878	no
spore-forming	no	69.832	yes
glucose-util	yes	87.116	yes
aerobic	no	97.057	yes
thermophile	no	81.994	yes
motile	yes	85.964	yes
glucose-ferment	yes	70.86	no

External links

@ref: 7556

culture collection no.: DSM 18485, CGMCC 1.5033, JCM 12961

straininfo link

@ref: 86680
straininfo: 290972

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	16585689	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	Anaerobiosis, Gram-Positive Bacteria/classification/isolation & purification/physiology, Molasses/microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/analysis/genetics, Water Microbiology	Genetics
Metabolism	19502053	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	Biopolymers/chemistry, Cation Exchange Resins/chemistry, Extracellular Space/chemistry, Gram-Positive Bacteria/cytology/growth & development, Hydrogen/metabolism, Time Factors
Phylogeny	26474980	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	Bacterial Typing Techniques, Base Composition, Caproates/metabolism, Clostridiales/classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Galactitol/metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Waste Water/*microbiology	Metabolism
Metabolism	31085357	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	Acetic Acid/metabolism, Bacterial Proteins/analysis, Clostridiales/metabolism, Ethanol/metabolism, Fermentation, Proteome/*analysis, Stress, Physiological	Proteome
Metabolism	31297154	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

Reference

@id	authors	catalogue	doi/url	title	ID_cross_reference	pubmed
7556	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18485)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-18485
20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.		10.1099/ijsem.0.004332	List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
31627	Barberan A, Caceres Velazquez H, Jones S, Fierer N.		10.1128/mSphere.00237-17	Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information	27912	28776041
66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770	Curators of the JCM		https://jcm.brc.riken.jp/en/
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.		https://microbeatlas.org/	MicrobeAtlas 1.0 beta
86680	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID290972.1	StrainInfo: A central database for resolving microbial strain identifiers