Strain identifier

BacDive ID: 1699

Type strain: Yes

Species: Bifidobacterium choerinum

Strain Designation: SU806

Strain history: CIP <- 2019, DSMZ <- 1990, DSMZ <- ATCC <- V. Scardovi <- D. Matteuzzi: strain SU806

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 8810

BacDive-ID: 1699

DSM-Number: 20434

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

description: Bifidobacterium choerinum SU806 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from piglet faeces.

NCBI tax id

NCBI tax idMatching level
35760species
1121107strain

strain history

@refhistory
8810<- ATCC <- V. Scardovi, SU806
67770ATCC 27686 <-- V. Scardovi <-- D. Matteuzzi SU 806.
118249CIP <- 2019, DSMZ <- 1990, DSMZ <- ATCC <- V. Scardovi <- D. Matteuzzi: strain SU806

doi: 10.13145/bacdive1699.20230509.8.1

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 choerinum
  • full scientific name: Bifidobacterium choerinum Scardovi et al. 1979 (Approved Lists 1980)

@ref: 8810

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Bifidobacteriales

family: Bifidobacteriaceae

genus: Bifidobacterium

species: Bifidobacterium choerinum

full scientific name: Bifidobacterium choerinum Scardovi et al. 1979

strain designation: SU806

type strain: yes

Morphology

cell morphology

  • @ref: 118249
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8810BIFIDOBACTERIUM 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
118249CIP Medium 20yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20

culture temp

@refgrowthtypetemperaturerange
8810positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 8810
  • oxygen tolerance: anaerobe

murein

  • @ref: 8810
  • murein short key: A11.21
  • type: A3alpha L-Lys(L-Orn)-L-Ala(L-Ser)-L-Ala2

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

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
8810-----++----+----------------++++---+++------------

Isolation, sampling and environmental information

isolation

@refsample typesampling date
8810piglet faeces
47994Swine feces1989-05-02
67770Pig feces
118249Animal, Piglet, feces

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_5739.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_24;96_259;97_3388;98_4273;99_5739&stattab=map
  • Last taxonomy: Bifidobacterium
  • 16S sequence: LC071800
  • Sequence Identity:
  • Total samples: 42281
  • soil counts: 410
  • aquatic counts: 231
  • animal counts: 41508
  • plant counts: 132

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
88101Risk group (German classification)
1182491Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bifidobacterium choerinum gene for 16S rRNA, partial sequence, strain: ATCC 27686D861861530ena35760
20218Bifidobacterium choerinum 16S-23S rRNA intergenic spacer regionL36968552ena35760
20218Bifidobacterium choerinum strain DSM 20434 16S ribosomal RNA gene, partial sequenceGQ487638148ena35760
20218Bifidobacterium choerinum gene for 16S rRNA, partial sequence, strain: JCM 1212AB116296489ena35760
20218Bifidobacterium choerinum gene for 16S rRNA, partial sequence, strain: JCM 1212AB507092658ena35760
20218Bifidobacterium choerinum strain KCTC 3275 16S ribosomal RNA gene, partial sequenceGU3618171494ena35760
67770Bifidobacterium choerinum gene for 16S ribosomal RNA, partial sequence, strain: JCM 1212LC0718001466ena35760

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bifidobacterium choerinum DSM 204341121107.3wgspatric1121107
66792Bifidobacterium choerinum DSM 204341121107.4wgspatric1121107
66792Bifidobacterium choerinum strain LMG 1051035760.3wgspatric35760
66792Bifidobacterium choerinum DSM 204342529292584draftimg1121107
66792Bifidobacterium choerinum LMG 105102597490261draftimg35760
66792Bifidobacterium choerinum DSM 204342660238656draftimg1121107
67770Bifidobacterium choerinum DSM 20434GCA_000484675contigncbi1121107
67770Bifidobacterium choerinum DSM 20434GCA_000771425contigncbi1121107
67770Bifidobacterium choerinum LMG 10510GCA_000741135contigncbi35760

GC content

  • @ref: 8810
  • GC-content: 66.3

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno94.54no
flagellatedno97.228no
gram-positiveyes88.994no
anaerobicyes98.495yes
aerobicno97.759yes
halophileno70.184no
spore-formingno96.69no
thermophileno95.533yes
glucose-utilyes83.511no
glucose-fermentyes79.585no

External links

@ref: 8810

culture collection no.: DSM 20434, ATCC 27686, CCUG 24609, JCM 1212, CGMCC 1.2276, CIP 103378, KCTC 3275, LMG 10510

straininfo link

  • @ref: 71346
  • straininfo: 13594

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny29395537Phylogenetic classification of six novel species belonging to the genus Bifidobacterium comprising Bifidobacterium anseris sp. nov., Bifidobacterium criceti sp. nov., Bifidobacterium imperatoris sp. nov., Bifidobacterium italicum sp. nov., Bifidobacterium margollesii sp. nov. and Bifidobacterium parmae sp. nov.Lugli GA, Mangifesta M, Duranti S, Anzalone R, Milani C, Mancabelli L, Alessandri G, Turroni F, Ossiprandi MC, van Sinderen D, Ventura MSyst Appl Microbiol10.1016/j.syapm.2018.01.0022018Animals, Bacterial Typing Techniques, Base Sequence, Bifidobacterium/*classification/genetics, Callithrix/microbiology, Cricetinae/microbiology, DNA, Bacterial/genetics, Fatty Acids/analysis, Feces/*microbiology, Geese/microbiology, High-Throughput Nucleotide Sequencing, Italy, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rabbits/microbiology, Saguinus/microbiology, Sequence Analysis, DNATranscriptome
Phylogeny30789326Characterization of the phylogenetic diversity of five novel species belonging to the genus Bifidobacterium: Bifidobacterium castoris sp. nov., Bifidobacterium callimiconis sp. nov., Bifidobacterium goeldii sp. nov., Bifidobacterium samirii sp. nov. and Bifidobacterium dolichotidis sp. nov.Duranti S, Lugli GA, Napoli S, Anzalone R, Milani C, Mancabelli L, Alessandri G, Turroni F, Ossiprandi MC, van Sinderen D, Ventura MInt J Syst Evol Microbiol10.1099/ijsem.0.0033062019Animals, Bacterial Typing Techniques, Base Composition, Bifidobacterium/*classification, Callithrix/*microbiology, DNA, Bacterial/genetics, Feces/microbiology, Genes, Bacterial, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rodentia/*microbiology, Saimiri/*microbiology, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8810Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20434)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20434
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
47994Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 24609)https://www.ccug.se/strain?id=24609
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
71346Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13594.1StrainInfo: A central database for resolving microbial strain identifiers
118249Curators of the CIPCollection of Institut Pasteur (CIP 103378)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103378