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
1437596strain
33905species

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/bacdive1721.20250331.9.3

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

@refgram staincell shapemotilityconfidence
123507negativerod-shapedno
125438no93

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

@refgrowthtypetemperature
8479positivegrowth37
39289positivegrowth37
52433positivegrowth37
67770positivegrowth37

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
8479anaerobe
52433anaerobe

spore formation

@refspore formationconfidence
125438no91.443
125439no96.9

murein

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12350715824D-fructose+degradation
12350717634D-glucose+degradation
12350765327D-xylose-degradation
12350717057cellobiose-degradation
12350717716lactose-degradation
12350717306maltose+degradation
12350717814salicin-degradation
12350717992sucrose+degradation
1235074853esculin-hydrolysis
12350717632nitrate-reduction
12350716301nitrite-reduction
12350717632nitrate+respiration
68371Potassium 5-ketogluconate-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch+builds acid from
6837116634raffinose+builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose+builds acid from
6837128053melibiose+builds acid from
6837117716lactose-builds acid from
6837117306maltose+builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin+builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from

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
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-galactosidase+3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382valine arylamidase-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
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 spacerU09528478nuccore33905
20218Bifidobacterium thermophilum ATCC 25525 16S ribosomal RNAU101511453nuccore33905
20218Bifidobacterium thermophilum strain DSM 20210 16S ribosomal RNA gene, partial sequenceGQ487648138nuccore33905
20218Bifidobacterium thermophilum gene for 16S rRNA, partial sequence, strain: JCM 1207AB507158666nuccore33905
20218Bifidobacterium thermophilum strain JCM 1207 16S ribosomal RNA gene, partial sequenceGQ227712322nuccore33905
20218Bifidobacterium thermophilum strain KCTC 3225 16S ribosomal RNA gene, partial sequenceGU3618341483nuccore33905
20218Bifidobacterium thermophilum strain LMG 11573 16S ribosomal RNA gene, partial sequenceJX9869651451nuccore33905
67770Bifidobacterium thermophilum gene for 16S ribosomal RNA, partial sequenceAB4373641513nuccore33905
67770Bifidobacterium thermophilum gene for 16S ribosomal RNA, partial sequence, strain: JCM 1207LC0717981377nuccore33905

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

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes86.766no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)yes84.815yes
125438spore-formingspore-formingAbility to form endo- or exosporesno91.443no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no95.797yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno92.954no
125438motile2+flagellatedAbility to perform flagellated movementno93no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno96.9
125439BacteriaNetmotilityAbility to perform movementno58
125439BacteriaNetgram_stainReaction to gram-stainingpositive77
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthanaerobe73.2

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
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