Strain identifier

BacDive ID: 1755

Type strain: Yes

Species: Bifidobacterium stellenboschense

Strain Designation: AFB23-3

Strain history: A. Endo AFB23-3.

NCBI tax ID(s): 762211 (species)

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General

@ref: 17459

BacDive-ID: 1755

DSM-Number: 23968

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

description: Bifidobacterium stellenboschense AFB23-3 is an anaerobe, mesophilic bacterium that was isolated from feces of tamarin .

NCBI tax id

  • NCBI tax id: 762211
  • Matching level: species

strain history

@refhistory
17459<- A. Endo, Dept. Microbiology, Stellenbosch Univ., South Africa; AFB23-3
67770A. Endo AFB23-3.

doi: 10.13145/bacdive1755.20230509.8.1

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 stellenboschense
  • full scientific name: Bifidobacterium stellenboschense Endo et al. 2012

@ref: 17459

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Bifidobacteriales

family: Bifidobacteriaceae

genus: Bifidobacterium

species: Bifidobacterium stellenboschense

full scientific name: Bifidobacterium stellenboschense Endo et al. 2012

strain designation: AFB23-3

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no94.606
6948099.999positive

Culture and growth conditions

culture medium

  • @ref: 17459
  • 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
17459positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
17459anaerobe
69480anaerobe99.999

spore formation

@refspore formationconfidence
69481no94
69480no99.997

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
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
68371D-sorbitol+builds acid from17924
68371D-mannitol+builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
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
17459----+++---+++-+/----+++/-++++++++++++-++---++------+/---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
17459feces of tamarin (red-handed marmoset)Cape TownSouth AfricaZAFAfrica
67770Feces of a red-handed tamarin collected at Cape TownSouth AfricaZAFAfrica

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Primates
#Host Body Product#Gastrointestinal tract#Feces (Stool)

taxonmaps

  • @ref: 69479
  • File name: preview.99_4153.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_24;96_2103;97_2534;98_3136;99_4153&stattab=map
  • Last taxonomy: Bifidobacterium stellenboschense subclade
  • 16S sequence: LC519988
  • Sequence Identity:
  • Total samples: 5879
  • soil counts: 7
  • aquatic counts: 54
  • animal counts: 5815
  • plant counts: 3

Safety information

risk assessment

  • @ref: 17459
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
17459Bifidobacterium stellenboschense gene for 16S rRNA, partial sequenceAB5595051437ena762211
67770Bifidobacterium stellenboschense JCM 17298 gene for 16S rRNA, partial sequenceLC5199881027ena762211

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bifidobacterium stellenboschense strain DSM 23968762211.3wgspatric762211
66792Bifidobacterium stellenboschense DSM 239682597489947draftimg762211
67770Bifidobacterium stellenboschense DSM 23968GCA_000741785contigncbi762211

GC content

@refGC-contentmethod
1745966.3high performance liquid chromatography (HPLC)
6777066.3

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno94no
motileno94.014no
flagellatedno96.232no
gram-positiveyes92.031no
anaerobicyes97.542no
aerobicno96.714no
halophileno80.14no
spore-formingno94.117no
glucose-utilyes87.449no
thermophileno95.129yes
glucose-fermentyes85.838no

External links

@ref: 17459

culture collection no.: DSM 23968, JCM 17298, KCTC 15336

straininfo link

  • @ref: 71402
  • straininfo: 406613

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22225994Bifidobacterium reuteri sp. nov., Bifidobacterium callitrichos sp. nov., Bifidobacterium saguini sp. nov., Bifidobacterium stellenboschense sp. nov. and Bifidobacterium biavatii sp. nov. isolated from faeces of common marmoset (Callithrix jacchus) and red-handed tamarin (Saguinus midas).Endo A, Futagawa-Endo Y, Schumann P, Pukall R, Dicks LMSyst Appl Microbiol10.1016/j.syapm.2011.11.0062012Aldehyde-Lyases/metabolism, Animals, Bacterial Typing Techniques, Base Composition, Base Sequence, Bifidobacterium/*classification/*genetics/isolation & purification, Callithrix/*microbiology, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Feces/microbiology, HSP40 Heat-Shock Proteins/genetics, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/analysis/genetics, Saguinus/*microbiology, Sequence Alignment, Sequence Analysis, DNAGenetics
Phylogeny24867172Bifidobacterium aesculapii sp. nov., from the faeces of the baby common marmoset (Callithrix jacchus).Modesto M, Michelini S, Stefanini I, Ferrara A, Tacconi S, Biavati B, Mattarelli PInt J Syst Evol Microbiol10.1099/ijs.0.056937-02014Aldehyde-Lyases/chemistry, Animals, Bacterial Typing Techniques, Base Composition, Bifidobacterium/*classification/genetics/isolation & purification, Callithrix/*microbiology, DNA, Bacterial/genetics, Feces/*microbiology, Genes, Bacterial, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny26515885Bifidobacterium myosotis sp. nov., Bifidobacterium tissieri sp. nov. and Bifidobacterium hapali sp. nov., isolated from faeces of baby common marmosets (Callithrix jacchus L.).Michelini S, Oki K, Yanokura E, Shimakawa Y, Modesto M, Mattarelli P, Biavati B, Watanabe KInt J Syst Evol Microbiol10.1099/ijsem.0.0007082015Aldehyde-Lyases/metabolism, Animals, Bacterial Proteins/genetics, Bacterial Typing Techniques, Base Composition, Bifidobacterium/classification/genetics/isolation & purification, Callithrix/*microbiology, Chaperonin 60/genetics, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/*microbiology, Heat-Shock Proteins/genetics, Molecular Sequence Data, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny26823373Bifidobacterium eulemuris sp. nov., isolated from faeces of black lemurs (Eulemur macaco).Michelini S, Modesto M, Pisi AM, Filippini G, Sandri C, Spiezio C, Biavati B, Sgorbati B, Mattarelli PInt J Syst Evol Microbiol10.1099/ijsem.0.0009242016
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
Phylogeny32847786Phylogenetic characterization of two novel species of the genus Bifidobacterium: Bifidobacterium saimiriisciurei sp. nov. and Bifidobacterium platyrrhinorum sp. nov.Modesto M, Satti M, Watanabe K, Scarafile D, Huang CH, Liou JS, Tamura T, Saito S, Watanabe M, Mori K, Huang L, Sandri C, Spiezio C, Arita M, Mattarelli PSyst Appl Microbiol10.1016/j.syapm.2020.1261112020Aldehyde-Lyases/metabolism, Animals, Bacterial Typing Techniques, Base Composition, Bifidobacterium/*classification/genetics/*isolation & purification/physiology, Computer Simulation, Culture Media, DNA, Bacterial/chemistry/genetics, Feces/microbiology, Genes, Bacterial, Genes, rRNA, Genetic Variation, Genome, Bacterial, Male, Phylogeny, RNA, Ribosomal, 16S/genetics, Saimiri/*microbiology, Sequence Analysis, DNA, TemperatureCultivation

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
17459Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23968)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23968
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
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
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
71402Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID406613.1StrainInfo: A central database for resolving microbial strain identifiers