Strain identifier

BacDive ID: 1752

Type strain: Yes

Species: Bifidobacterium saguini

Strain Designation: AFB23-1

Strain history: A. Endo AFB23-1.

NCBI tax ID(s): 1437607 (strain), 762210 (species)

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

@ref: 17458

BacDive-ID: 1752

DSM-Number: 23967

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

description: Bifidobacterium saguini AFB23-1 is an anaerobe, mesophilic bacterium that was isolated from feces of tamarin .

NCBI tax id

NCBI tax idMatching level
1437607strain
762210species

strain history

@refhistory
17458<- A. Endo, Dept. Microbiology, Stellenbosch Univ., South Africa; AFB23-1
67770A. Endo AFB23-1.

doi: 10.13145/bacdive1752.20250331.9.3

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

@ref: 17458

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Bifidobacteriales

family: Bifidobacteriaceae

genus: Bifidobacterium

species: Bifidobacterium saguini

full scientific name: Bifidobacterium saguini Endo et al. 2012

strain designation: AFB23-1

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
125438no93
12543890.208positive

Culture and growth conditions

culture medium

  • @ref: 17458
  • 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

@refgrowthtypetemperature
17458positivegrowth37
67770positivegrowth37

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
17458anaerobe
125439anaerobe97

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 99.2

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371methyl alpha-D-glucopyranoside+builds acid from320061
68371glycerol-builds acid from17754
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-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

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
17458----+++---+++--------+-+++++++++---+---++------+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
17458feces 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_7782.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_24;96_39;97_4436;98_5688;99_7782&stattab=map
  • Last taxonomy: Bifidobacterium
  • 16S sequence: LC519987
  • Sequence Identity:
  • Total samples: 82751
  • soil counts: 346
  • aquatic counts: 990
  • animal counts: 81242
  • plant counts: 173

Safety information

risk assessment

  • @ref: 17458
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
17458Bifidobacterium saguini gene for 16S rRNA, partial sequenceAB5595041433nuccore1437607
67770Bifidobacterium saguini JCM 17297 gene for 16S rRNA, partial sequenceLC5199871090nuccore762210

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bifidobacterium saguini DSM 239671437607.3wgspatric1437607
66792Bifidobacterium saguini DSM 239671437607.4wgspatric1437607
66792Bifidobacterium saguini strain DSMZ 23967762210.5completepatric762210
66792Bifidobacterium saguini DSM 239672597490226draftimg1437607
66792Bifidobacterium saguini DSM 239672663763274draftimg1437607
67770Bifidobacterium saguini DSM 23967GCA_000771625contigncbi1437607
67770Bifidobacterium saguini DSM 23967GCA_000741715contigncbi1437607

GC content

@refGC-contentmethod
1745857.3high performance liquid chromatography (HPLC)
6777057.3

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes90.208no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)yes85.349yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no92.823yes
125438spore-formingspore-formingAbility to form endo- or exosporesno88.985no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno90.487no
125438motile2+flagellatedAbility to perform flagellated movementno93no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno99.2
125439BacteriaNetmotilityAbility to perform movementno69.4
125439BacteriaNetgram_stainReaction to gram-stainingnegative73.9
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthanaerobe97

External links

@ref: 17458

culture collection no.: DSM 23967, JCM 17297, KCTC 15335

straininfo link

  • @ref: 71399
  • straininfo: 405768

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
Phylogeny25736415Bifidobacterium lemurum sp. nov., from faeces of the ring-tailed lemur (Lemur catta).Modesto M, Michelini S, Stefanini I, Sandri C, Spiezio C, Pisi A, Filippini G, Biavati B, Mattarelli PInt J Syst Evol Microbiol10.1099/ijs.0.0001622015Animals, Bacterial Typing Techniques, Base Composition, Bifidobacterium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Feces/microbiology, Genes, Bacterial, Lemur/*microbiology, Molecular Sequence Data, Multilocus Sequence Typing, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny29116036Bifidobacterium callitrichidarum sp. nov. from the faeces of the emperor tamarin (Saguinus imperator).Modesto M, Michelini S, Sansosti MC, De Filippo C, Cavalieri D, Qvirist L, Andlid T, Spiezio C, Sandri C, Pascarelli S, Sgorbati B, Mattarelli PInt J Syst Evol Microbiol10.1099/ijsem.0.0024722017Aldehyde-Lyases/chemistry, Animals, Bacterial Typing Techniques, Base Composition, Bifidobacterium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/microbiology, Multilocus Sequence Typing, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Saguinus/*microbiology, Sequence Analysis, DNATranscriptome
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

Reference

@idauthorscataloguedoi/urltitle
17458Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23967)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23967
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)
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
71399Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID405768.1StrainInfo: A central database for resolving microbial strain identifiers
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