Strain identifier

BacDive ID: 24302

Type strain: Yes

Species: Tepidibacter mesophilus

Strain Designation: B1

Strain history: X.-Y. Wu B1.

NCBI tax ID(s): 655607 (species)

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General

@ref: 20850

BacDive-ID: 24302

DSM-Number: 28717

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

description: Tepidibacter mesophilus B1 is an anaerobe, spore-forming, mesophilic bacterium that was isolated from soil polluted by crude oil.

NCBI tax id

  • NCBI tax id: 655607
  • Matching level: species

strain history

@refhistory
20850<- T. Itoh, JCM <- X.-Y. Wu, Zhejiang Univ., Hangzhou, China; B1
67770X.-Y. Wu B1.

doi: 10.13145/bacdive24302.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Peptostreptococcaceae
  • genus: Tepidibacter
  • species: Tepidibacter mesophilus
  • full scientific name: Tepidibacter mesophilus Tan et al. 2012

@ref: 20850

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Peptostreptococcaceae

genus: Tepidibacter

species: Tepidibacter mesophilus

full scientific name: Tepidibacter mesophilus Tan et al. 2012

strain designation: B1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29955positive2.3-4.7 µm1.1-1.6 µmrod-shapedyes
69480yes95.989
69480positive100

pigmentation

  • @ref: 29955
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 20850
  • name: RCM MEDIUM (N2/CO2) (DSMZ Medium 634c)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/634c
  • composition: Name: RCM MEDIUM (N2/CO2) (DSMZ Medium 634c) Composition: dehydrated RCM medium 38.0 g/l Sodium carbonate 1.0 g/l Sodium resazurin 0.0005 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
20850positivegrowth30mesophilic
29955positivegrowth10-40
29955positiveoptimum28-32mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
29955positivegrowth6.0-8.9alkaliphile
29955positiveoptimum7.3

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
20850anaerobe
29955facultative anaerobe
69480anaerobe100

spore formation

@refspore formationconfidence
29955yes
69481yes96
69480yes100

halophily

@refsaltgrowthtested relationconcentration
29955NaClpositivegrowth<9 %
29955NaClpositiveoptimum1 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2995516449alanine+carbon source
2995528757fructose+carbon source
2995528260galactose+carbon source
2995517234glucose+carbon source
2995515428glycine+carbon source
2995517306maltose+carbon source
2995526271proline+carbon source
2995526546rhamnose+carbon source
2995533942ribose+carbon source
2995527082trehalose+carbon source
2995518222xylose+carbon source

metabolite production

  • @ref: 29955
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: yes

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
20850soil polluted by crude oilKaramay Oil FieldChinaCHNAsia45.684.95
67770Soil polluted by crude oil in the Karamay Oil FieldChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination#Oil (Fuel)
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_23623.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_2;96_4986;97_6034;98_7553;99_23623&stattab=map
  • Last taxonomy: Tepidibacter mesophilus subclade
  • 16S sequence: GQ231514
  • Sequence Identity:
  • Total samples: 3758
  • soil counts: 449
  • aquatic counts: 2923
  • animal counts: 354
  • plant counts: 32

Safety information

risk assessment

  • @ref: 20850
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20850
  • description: Tepidibacter mesophilus strain B1 16S ribosomal RNA gene, partial sequence
  • accession: GQ231514
  • length: 1438
  • database: ena
  • NCBI tax ID: 655607

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Tepidibacter mesophilus strain JCM 16806655607.3wgspatric655607
66792Tepidibacter mesophilus JCM 168062832628248draftimg655607
67770Tepidibacter mesophilus JCM 16806GCA_002724055contigncbi655607

GC content

@refGC-contentmethod
2995529.8
2085029.8high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes96no
gram-positiveyes84.085yes
anaerobicyes99.338no
halophileno85.662no
spore-formingyes95.631yes
glucose-utilyes86.872yes
thermophileno97.316yes
flagellatedno55.898no
motileyes90.994yes
aerobicno98.372yes
glucose-fermentyes52.702no

External links

@ref: 20850

culture collection no.: DSM 28717, CGMCC 1.5148, JCM 16806

straininfo link

  • @ref: 88235
  • straininfo: 399234

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21335504Tepidibacter mesophilus sp. nov., a mesophilic fermentative anaerobe isolated from soil polluted by crude oil, and emended description of the genus Tepidibacter.Tan HQ, Wu XY, Zhang XQ, Wu M, Zhu XFInt J Syst Evol Microbiol10.1099/ijs.0.027409-02011Anaerobiosis, Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Fermentation, Flagella/physiology, Gram-Positive Bacteria/*classification/genetics/*isolation & purification/physiology, Hydrogen-Ion Concentration, Locomotion, Molecular Sequence Data, Petroleum, Phylogeny, RNA, Ribosomal, 16S/genetics, Salts/metabolism, Sequence Analysis, DNA, *Soil Microbiology, Soil Pollutants, TemperatureGenetics
Genetics29167249Draft Genome Sequence of Tepidibacter mesophilus Strain JCM 16806(T) Isolated from Soil Polluted by Crude Oil in China.Lee CG, Yuki M, Iida T, Nakaho K, Ohkuma MGenome Announc10.1128/genomeA.01308-172017Phylogeny

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmed
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
20850Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-28717Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28717)
29955Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172632428776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
88235Reimer, 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 identifiers10.60712/SI-ID399234.1