Strain identifier

BacDive ID: 1721

Type strain: Yes

Species: Bifidobacterium thermophilum

Strain Designation: P2-91

Strain history: CIP <- 1998, DSM <- T. Mitsuoka: strain P2-91

NCBI tax ID(s): 1437596 (strain), 33905 (species)

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General

@ref: 8479

BacDive-ID: 1721

DSM-Number: 20210

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

description: Bifidobacterium thermophilum P2-91 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from pig faeces.

NCBI tax id

NCBI tax idMatching level
33905species
1437596strain

strain history

@refhistory
8479<- T. Mitsuoka, P2-91
67770ATCC 25525 <-- T. Mitsuoka J18-P2-91.
123507CIP <- 1998, DSM <- T. Mitsuoka: strain P2-91

doi: 10.13145/bacdive1721.20230509.8.1

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 thermophilum
  • full scientific name: Bifidobacterium thermophilum corrig. Mitsuoka 1969 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Bifidobacterium thermophilium

@ref: 8479

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Bifidobacteriales

family: Bifidobacteriaceae

genus: Bifidobacterium

species: Bifidobacterium thermophilum

full scientific name: Bifidobacterium thermophilum Mitsuoka 1969 emend. Nouioui et al. 2018

strain designation: P2-91

type strain: yes

Morphology

cell morphology

  • @ref: 123507
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 123507

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8479BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58)yeshttps://mediadive.dsmz.de/medium/58Name: 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
39289MEDIUM 45 - for Columbia agar with sheep bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Sheepblood (100.000 ml)
123507CIP Medium 45yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=45

culture temp

@refgrowthtypetemperaturerange
8479positivegrowth37mesophilic
39289positivegrowth37mesophilic
52433positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
8479anaerobe
52433anaerobe

murein

  • @ref: 8479
  • murein short key: A21.06
  • type: A4ß L-Orn(L-Lys)-D-Glu

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch+builds acid from28017
68371raffinose+builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose+builds acid from17992
68371melibiose+builds acid from28053
68371lactose-builds acid from17716
68371maltose+builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin+builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose+builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
123507D-fructose+degradation15824
123507D-glucose+degradation17634
123507D-xylose-degradation65327
123507cellobiose-degradation17057
123507lactose-degradation17716
123507maltose+degradation17306
123507salicin-degradation17814
123507sucrose+degradation17992
123507esculin-hydrolysis4853
123507nitrate-reduction17632
123507nitrite-reduction16301
123507nitrate+respiration17632

metabolite production

  • @ref: 123507
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase+3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
123507oxidase-
123507beta-galactosidase+3.2.1.23
123507gelatinase-
123507amylase+
123507DNase-
123507caseinase-3.4.21.50
123507catalase-1.11.1.6
123507tween esterase-
123507lecithinase-
123507lipase-
123507urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    52433C10:01.310
    52433C12:03.712
    52433C14:021.514
    52433C16:023.216
    52433C18:02.418
    52433C13:0 3OH/C15:1 i I/H2.114.469
    52433C13:1 at 12-130.612.931
    52433C16:0 3OH0.517.52
    52433C16:1 ω9c7.615.774
    52433C17:1 ω5c ISO116.461
    52433C17:1 ω9c0.916.773
    52433C18:1 ω6c117.858
    52433C18:1 ω9c17.117.769
    52433C18:2 ω6,9c/C18:0 ANTE5.417.724
    52433C19:0 CYCLO ω9c3.718.87
    52433Unidentified0.513.772
    52433Unidentified0.516.238
    52433Unidentified1.118.179
    52433Unidentified2.518.225
    52433Unidentified2.819.323
    52433unknown 12.4860.512.486
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123507--++-+-----+++-+----

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
8479----------+++------------+--+-++---++-------------

Isolation, sampling and environmental information

isolation

@refsample type
8479pig faeces
52433Pig feces
67770Swine feces
123507Animal, Pig, feces

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Suidae (Pig,Swine)
#Host Body Product#Gastrointestinal tract#Feces (Stool)

taxonmaps

  • @ref: 69479
  • File name: preview.99_2657.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_24;96_607;97_710;98_829;99_2657&stattab=map
  • Last taxonomy: Bifidobacterium
  • 16S sequence: LC071798
  • Sequence Identity:
  • Total samples: 25358
  • soil counts: 263
  • aquatic counts: 756
  • animal counts: 24173
  • plant counts: 166

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
84791Risk group (German classification)
1235071Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bifidobacterium thermophilum ATCC25525 16S-23S intergenic spacerU09528478ena33905
20218Bifidobacterium thermophilum ATCC 25525 16S ribosomal RNAU101511453ena33905
20218Bifidobacterium thermophilum strain DSM 20210 16S ribosomal RNA gene, partial sequenceGQ487648138ena33905
20218Bifidobacterium thermophilum gene for 16S rRNA, partial sequence, strain: JCM 1207AB507158666ena33905
20218Bifidobacterium thermophilum strain JCM 1207 16S ribosomal RNA gene, partial sequenceGQ227712322ena33905
20218Bifidobacterium thermophilum strain KCTC 3225 16S ribosomal RNA gene, partial sequenceGU3618341483ena33905
20218Bifidobacterium thermophilum strain LMG 11573 16S ribosomal RNA gene, partial sequenceJX9869651451ena33905
67770Bifidobacterium thermophilum gene for 16S ribosomal RNA, partial sequenceAB4373641513ena33905
67770Bifidobacterium thermophilum gene for 16S ribosomal RNA, partial sequence, strain: JCM 1207LC0717981377ena33905

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bifidobacterium thermophilum DSM 202101437596.3wgspatric1437596
66792Bifidobacterium thermophilum strain JCM 120733905.21wgspatric33905
66792Bifidobacterium thermophilum JCM 12072600254976draftimg33905
66792Bifidobacterium thermophilum DSM 202102671180426draftimg1437596
67770Bifidobacterium thermophilum DSM 20210GCA_000771265contigncbi1437596
67770Bifidobacterium thermophilum JCM 1207GCA_000741495contigncbi33905

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno93.806no
gram-positiveyes92.897no
anaerobicyes98.394no
halophileno70.227no
spore-formingno96.073no
thermophileno93.164yes
glucose-utilyes85.859no
aerobicno98.569yes
flagellatedno96.574no
glucose-fermentyes80.991no

External links

@ref: 8479

culture collection no.: DSM 20210, ATCC 25525, CIP 105420, CCUG 34983, JCM 1207, BCRC 14669, CGMCC 1.2235, HAMBI 111, KCTC 3225, LMG 11573, LMG 21813, NCFB 2253, NCIMB 702253, ISL 118

straininfo link

  • @ref: 71368
  • straininfo: 217569

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny13130059Species identification of genus Bifidobacterium based on partial HSP60 gene sequences and proposal of Bifidobacterium thermacidophilum subsp. porcinum subsp. nov.Zhu L, Li W, Dong XInt J Syst Evol Microbiol10.1099/ijs.0.02617-02003Bifidobacterium/*classification/*genetics/metabolism, Chaperonin 60/*genetics, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, *Genes, Bacterial, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Species SpecificityGenetics
26441950Glycan cross-feeding activities between bifidobacteria under in vitro conditions.Turroni F, Ozcan E, Milani C, Mancabelli L, Viappiani A, van Sinderen D, Sela DA, Ventura MFront Microbiol10.3389/fmicb.2015.010302015
Phylogeny28714841Bifidobacterium apri sp. nov., a thermophilic actinobacterium isolated from the digestive tract of wild pigs (Sus scrofa).Pechar R, Killer J, Salmonova H, Geigerova M, Svejstil R, Svec P, Sedlacek I, Rada V, Benada OInt J Syst Evol Microbiol10.1099/ijsem.0.0019562017Aldehyde-Lyases/chemistry, Animals, Bacterial Typing Techniques, Base Composition, Bifidobacterium/*classification/genetics/isolation & purification, Czech Republic, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Intestines/*microbiology, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sus scrofa/*microbiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8479Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20210)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20210
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
39289Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17438
52433Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 34983)https://www.ccug.se/strain?id=34983
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/
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
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
71368Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID217569.1StrainInfo: A central database for resolving microbial strain identifiers
123507Curators of the CIPCollection of Institut Pasteur (CIP 105420)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105420