Strain identifier

BacDive ID: 1735

Type strain: Yes

Species: Bifidobacterium thermacidophilum

Strain Designation: 36

Strain history: X. Dong 36.

NCBI tax ID(s): 246618 (species)

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General

@ref: 6050

BacDive-ID: 1735

DSM-Number: 15837

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic

description: Bifidobacterium thermacidophilum 36 is an anaerobe, mesophilic bacterium that was isolated from waste water of a bean-curd farm.

NCBI tax id

  • NCBI tax id: 246618
  • Matching level: species

strain history

@refhistory
6050<- JCM <- X. Dong; 36
67770X. Dong 36.

doi: 10.13145/bacdive1735.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Bifidobacteriales
  • family: Bifidobacteriaceae
  • genus: Bifidobacterium
  • species: Bifidobacterium thermacidophilum
  • full scientific name: Bifidobacterium thermacidophilum Dong et al. 2000

@ref: 6050

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Bifidobacteriales

family: Bifidobacteriaceae

genus: Bifidobacterium

species: Bifidobacterium thermacidophilum

full scientific name: Bifidobacterium thermacidophilum Dong et al. 2000 emend. Zhu et al. 2003 emend. Nouioui et al. 2018

strain designation: 36

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no94.358
69480100positive

Culture and growth conditions

culture medium

  • @ref: 6050
  • name: BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/58
  • composition: Name: BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58) Composition: Glucose 10.0 g/l Casein peptone 10.0 g/l Bacto Soytone 5.0 g/l Meat extract 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l MnSO4 x H2O 0.05 g/l KH2PO4 0.04 g/l K2HPO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Tween 80 Resazurin Distilled water

culture temp

@refgrowthtypetemperaturerange
6050positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
6050anaerobe
69480anaerobe99.592

spore formation

@refspore formationconfidence
69481no96
69480no99.995

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6050waste water of a bean-curd farmBeijingChinaCHNAsia
67770Wastewater of a bean-curd farmBeijingChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture
#Engineered#Waste#Wastewater

Safety information

risk assessment

  • @ref: 6050
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bifidobacterium thermacidophilum gene for 16S rRNA, partial sequence, strain: JCM 11165AB507157660ena246618
20218Bifidobacterium thermacidophilum subsp. thermacidophilum strain JCM 11165 16S ribosomal RNA gene, partial sequenceGQ227716308ena79262
20218Bifidobacterium thermacidophilum subsp. thermacidophilum strain DSM 15837 16S ribosomal RNA gene, partial sequenceGQ487647139ena79262
6050Bifidobacterium thermophilum 16S rRNA gene, complete sequenceAB0162461533ena33905
67770Bifidobacterium thermacidophilum subsp. thermacidophilum gene for 16S ribosomal RNA, partial sequenceAB4373621512ena79262
67770Bifidobacterium thermacidophilum subsp. thermacidophilum gene for 16S ribosomal RNA, partial sequence, strain: JCM 11165LC3117411467ena79262

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bifidobacterium thermacidophilum subsp. thermacidophilum DSM 158371121111.3wgspatric1121111
66792Bifidobacterium thermacidophilum subsp. thermacidophilum DSM 158371121111.4wgspatric1121111
66792Bifidobacterium thermacidophilum subsp. thermacidophilum strain LMG 2139579262.3wgspatric79262
66792Bifidobacterium thermacidophilum thermacidophilum DSM 158372524614678draftimg1121111
66792Bifidobacterium thermacidophilum thermacidophilum DSM 158372675903354draftimg1121111
66792Bifidobacterium thermacidophilum thermacidophilum LMG 213952600254984draftimg79262
67770Bifidobacterium thermacidophilum subsp. thermacidophilum DSM 15837GCA_000426425contigncbi1121111
67770Bifidobacterium thermacidophilum subsp. thermacidophilum DSM 15837GCA_000771005contigncbi1121111
67770Bifidobacterium thermacidophilum subsp. thermacidophilum LMG 21395GCA_000741455contigncbi79262

GC content

@refGC-contentmethod
605056.7
6777057.7thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno96no
motileno92.838no
flagellatedno96.661no
gram-positiveyes92.757no
anaerobicyes98.242no
aerobicno98.002yes
halophileno67.785no
spore-formingno95.862no
thermophileno92.949no
glucose-utilyes87.246no
glucose-fermentyes80.333no

External links

@ref: 6050

culture collection no.: DSM 15837, CGMCC AS 1.2282, JCM 11165, CGMCC 1.2282, KCTC 5850, LMG 21395, NBRC 106100, VTT E-052869

straininfo link

  • @ref: 71382
  • straininfo: 14991

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6050Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15837)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15837
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
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/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
71382Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID14991.1StrainInfo: A central database for resolving microbial strain identifiers