Strain identifier

BacDive ID: 1737

Type strain: Yes

Species: Bifidobacterium porcinum

Strain Designation: P3-14

Strain history: LMG 21689 <-- CGMCC 1.3009 <-- L. Zhu and W. Li P3-14.

NCBI tax ID(s): 1435463 (strain), 212365 (species)

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General

@ref: 7169

BacDive-ID: 1737

DSM-Number: 17755

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

description: Bifidobacterium porcinum P3-14 is an anaerobe, mesophilic bacterium that was isolated from feces of piglet.

NCBI tax id

NCBI tax idMatching level
1435463strain
212365species

strain history

@refhistory
7169<- X. Dong; P3-14
67770LMG 21689 <-- CGMCC 1.3009 <-- L. Zhu and W. Li P3-14.

doi: 10.13145/bacdive1737.20230509.8.1

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 porcinum
  • full scientific name: Bifidobacterium porcinum (Zhu et al. 2003) Nouioui et al. 2018

  • synonyms

    • @ref: 20215
    • synonym: Bifidobacterium thermacidophilum subsp. porcinum

@ref: 7169

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Bifidobacteriales

family: Bifidobacteriaceae

genus: Bifidobacterium

species: Bifidobacterium porcinum

full scientific name: Bifidobacterium porcinum (Zhu et al. 2003) Nouioui et al. 2018

strain designation: P3-14

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no93.462
69480100positive

Culture and growth conditions

culture medium

  • @ref: 7169
  • 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
7169positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
7169anaerobe
69480anaerobe99.413

spore formation

@refspore formationconfidence
69481no100
69480no99.999

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
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
68371esculin+builds acid from4853
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
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

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
7169--------+/--+++--------+-+/-+/-++/--+-+++--+++-+/-+---------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7169feces of pigletBeijingChinaCHNAsia
67770Piglet 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: LC519870
  • Sequence Identity:
  • Total samples: 25358
  • soil counts: 263
  • aquatic counts: 756
  • animal counts: 24173
  • plant counts: 166

Safety information

risk assessment

  • @ref: 7169
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bifidobacterium thermacidophilum subsp porcinum 16S-23S ribosomal RNA intergenic spacer, culture collection DSM 17755AM991325482ena212365
20218Bifidobacterium thermacidophilum subsp. porcinum strain DSM 17755 16S ribosomal RNA gene, partial sequenceGQ487641138ena212365
7169Bifidobacterium suis strain JCM7139 heat shock protein 60 (hsp60) gene, partial cdsAY166575590ena1695
67770Bifidobacterium thermacidophilum subsp. porcinum gene for 16S ribosomal RNA, partial sequenceAB4373611512ena212365
67770Bifidobacterium thermacidophilum subsp. porcinum strain P3-14 16S ribosomal RNA gene, complete sequenceAY1484701523ena212365
67770Bifidobacterium thermacidophilum subsp. porcinum JCM 16945 gene for 16S rRNA, partial sequenceLC5198701467ena212365

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bifidobacterium porcinum DSM 17755GCA_000771045contigncbi1435463
66792Bifidobacterium thermacidophilum subsp. porcinum DSM 177551435463.3wgspatric1435463
66792Bifidobacterium thermacidophilum subsp. porcinum strain LMG 21689212365.3wgspatric212365
66792Bifidobacterium porcinum LMG 216892600254978draftimg212365
66792Bifidobacterium porcinum DSM 177552663763372draftimg1435463
67770Bifidobacterium porcinum LMG 21689GCA_000741445contigncbi212365

GC content

@refGC-contentmethod
716961.2
6777061.5thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno93.87no
gram-positiveyes92.54no
anaerobicyes98.337yes
halophileno69.338no
spore-formingno96.75no
thermophileno92.553yes
glucose-utilyes85.823no
aerobicno98.234yes
flagellatedno96.553no
glucose-fermentyes81.993no

External links

@ref: 7169

culture collection no.: DSM 17755, AS 1.3009, LMG 21689, JCM 16945, CGMCC 1.3009

straininfo link

  • @ref: 71384
  • straininfo: 93622

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7169Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17755)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17755
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/
68371Automatically annotated from API 50CH acid
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
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
71384Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID93622.1StrainInfo: A central database for resolving microbial strain identifiers