Strain identifier

BacDive ID: 17689

Type strain: Yes

Species: Ethanoligenens harbinense

Strain Designation: YUAN-3

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

NCBI tax ID(s): 253239 (species)

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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

@refhistory
7556<- JCM; JCM 12961 <- D. Xing, Harbin Institute of Technology, Harbin, China; YUAN-3
67770D. Xing et al. YUAN-3.

doi: 10.13145/bacdive17689.20250331.9.3

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

@refgram staincell lengthcell widthcell shapemotilityconfidence
31627positive1.5-8 µm0.4-0.8 µmrod-shapedyes
125439negative94.5

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

@refgrowthtypetemperature
7556positivegrowth37
31627positivegrowth20-44
31627positiveoptimum35
67770positivegrowth37

culture pH

@refabilitytypepHPH range
31627positivegrowth3.5-9alkaliphile
31627positiveoptimum4.5-5

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
7556anaerobe
31627anaerobe
125438anaerobe94.406
125439obligate anaerobe94.8

spore formation

@refspore formationconfidence
31627no
125439no96

halophily

@refsaltgrowthtested relationconcentration
31627NaClpositivegrowth0-2 %
31627NaClpositiveoptimum0-2 %

observation

  • @ref: 31627
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3162717057cellobiose+carbon source
3162728757fructose+carbon source
3162728260galactose+carbon source
3162717234glucose+carbon source
3162717716lactose+carbon source
3162717306maltose+carbon source
3162737684mannose+carbon source
3162728053melibiose+carbon source
3162733942ribose+carbon source
3162717992sucrose+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

@refsample typegeographic locationcountryorigin.countrycontinent
7556anaerobic sludge of molasses wastewater in a CSTRHarbinChinaCHNAsia
67770Anaerobic sludge of molasses wastewater

isolation source categories

Cat1Cat2Cat3
#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: nuccore
  • NCBI tax ID: 663278

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Ethanoligenens harbinense YUAN-3GCA_003020045completencbi663278
66792Ethanoligenens harbinense YUAN-3GCA_000178115completencbi663278
66792Ethanoligenens harbinense YUAN-3663278.4completepatric663278
66792Ethanoligenens harbinense YUAN-3T, DSM 18485649633043completeimg663278

GC content

@refGC-contentmethod
755647.8-49.0
3162747.8
6777047.8thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes70.185yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)yes94.406yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no96.936no
125438spore-formingspore-formingAbility to form endo- or exosporesno51.639yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno75.793no
125438motile2+flagellatedAbility to perform flagellated movementyes66.762no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno96
125439BacteriaNetmotilityAbility to perform movementyes50.1
125439BacteriaNetgram_stainReaction to gram-stainingnegative94.5
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate anaerobe94.8

External links

@ref: 7556

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

straininfo link

  • @ref: 86680
  • straininfo: 290972

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16585689Ethanoligenens harbinense gen. nov., sp. nov., isolated from molasses wastewater.Xing D, Ren N, Li Q, Lin M, Wang A, Zhao LInt J Syst Evol Microbiol10.1099/ijs.0.63926-02006Anaerobiosis, Gram-Positive Bacteria/*classification/*isolation & purification/physiology, Molasses/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/analysis/genetics, *Water MicrobiologyGenetics
Metabolism19502053Composition of extracellular polymeric substances influences the autoaggregation capability of hydrogen-producing bacterium Ethanoligenens harbinense.Ren N, Xie T, Xing DBioresour Technol10.1016/j.biortech.2009.05.0212009Biopolymers/*chemistry, Cation Exchange Resins/chemistry, Extracellular Space/*chemistry, Gram-Positive Bacteria/*cytology/growth & development, Hydrogen/*metabolism, Time Factors
Phylogeny26474980Caproiciproducens 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 BIInt J Syst Evol Microbiol10.1099/ijsem.0.0006652015Bacterial 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/*microbiologyMetabolism
Metabolism31085357Insights 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 DEnviron Int10.1016/j.envint.2019.05.0132019Acetic Acid/*metabolism, Bacterial Proteins/*analysis, Clostridiales/*metabolism, Ethanol/*metabolism, Fermentation, Proteome/*analysis, Stress, PhysiologicalProteome
Metabolism31297154Quantitative 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 DBiotechnol Biofuels10.1186/s13068-019-1511-y2019

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7556Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18485)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18485
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
31627Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2791228776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
69479João 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
86680Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID290972.1StrainInfo: A central database for resolving microbial strain identifiers
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1