Strain identifier

BacDive ID: 1754

Type strain: Yes

Species: Bifidobacterium callitrichos

Strain Designation: AFB22-5

Strain history: A. Endo AFB22-5.

NCBI tax ID(s): 1437609 (strain), 762209 (species)

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General

@ref: 17464

BacDive-ID: 1754

DSM-Number: 23973

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

description: Bifidobacterium callitrichos AFB22-5 is an anaerobe, mesophilic bacterium that was isolated from feces of common marmoset.

NCBI tax id

NCBI tax idMatching level
1437609strain
762209species

strain history

@refhistory
17464<- A. Endo, Dept. Microbiology, Stellenbosch Univ., South Africa; AFB22-5
67770A. Endo AFB22-5.

doi: 10.13145/bacdive1754.20230509.8.1

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

@ref: 17464

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Bifidobacteriales

family: Bifidobacteriaceae

genus: Bifidobacterium

species: Bifidobacterium callitrichos

full scientific name: Bifidobacterium callitrichos Endo et al. 2012

strain designation: AFB22-5

type strain: yes

Culture and growth conditions

culture medium

  • @ref: 17464
  • 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
17464positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 17464
  • oxygen tolerance: anaerobe

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
68371gentiobiose+builds acid from28066
68371xylitol+builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose+builds acid from16634
68371melezitose+builds acid from6731
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
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
17464---++-+---++++----++++++/-++++++++++/-++--+++/-+/---+--+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
17464feces of common marmosetCape TownSouth AfricaZAFAfrica
67770Feces of a common marmosetCape TownSouth AfricaZAFAfrica

isolation source categories

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

Safety information

risk assessment

  • @ref: 17464
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
17464Bifidobacterium callitrichos gene for 16S rRNA, partial sequenceAB5595031502ena1437609
67770Bifidobacterium callitrichos JCM 17296 gene for 16S rRNA, partial sequenceLC5199861461ena762209

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bifidobacterium callitrichos DSM 239731437609.3wgspatric1437609
66792Bifidobacterium callitrichos DSM 239731437609.4wgspatric1437609
66792Bifidobacterium callitrichos DSM 239732700989375draftimg1437609
66792Bifidobacterium callitrichos DSM 239732597490241draftimg1437609
67770Bifidobacterium callitrichos DSM 23973GCA_000771665contigncbi1437609
67770Bifidobacterium callitrichos DSM 23973GCA_000741175contigncbi1437609

GC content

@refGC-contentmethod
1746464.3high performance liquid chromatography (HPLC)
6777064.3

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno91.803no
gram-positiveyes93.261no
anaerobicyes96.682no
halophileno78.518no
spore-formingno93.892no
glucose-utilyes88.922no
thermophileno96.656yes
aerobicno94.093no
flagellatedno95.489no
glucose-fermentyes83.697no

External links

@ref: 17464

culture collection no.: DSM 23973, JCM 17296, KCTC 15334

straininfo link

  • @ref: 71401
  • straininfo: 379793

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
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
Phylogeny31585749Characterization of Bifidobacterium species in feaces of the Egyptian fruit bat: Description of B. vespertilionis sp. nov. and B. rousetti sp. nov.Modesto M, Satti M, Watanabe K, Puglisi E, Morelli L, Huang CH, Liou JS, Miyashita M, Tamura T, Saito S, Mori K, Huang L, Sciavilla P, Sandri C, Spiezio C, Vitali F, Cavalieri D, Perpetuini G, Tofalo R, Bonetti A, Arita M, Mattarelli PSyst Appl Microbiol10.1016/j.syapm.2019.1260172019Amino Acids/analysis, Animals, Base Composition, Bifidobacterium/chemistry/*classification/genetics/growth & development, Chiroptera/*microbiology, DNA, Bacterial/genetics, Egypt, Fatty Acids/analysis, Feces/*microbiology, Genes, Essential/genetics, Genetic Variation, Genome, Bacterial/genetics, Nucleic Acid Hybridization, Peptidoglycan/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
17464Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23973)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23973
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
71401Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID379793.1StrainInfo: A central database for resolving microbial strain identifiers