Strain identifier

BacDive ID: 1719

Type strain: Yes

Species: Bifidobacterium subtile

Strain Designation: F395

Strain history: <- V. Scardovi, F395

NCBI tax ID(s): 1121110 (strain), 77635 (species)

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General

@ref: 8522

BacDive-ID: 1719

DSM-Number: 20096

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

description: Bifidobacterium subtile F395 is an anaerobe, mesophilic bacterium that was isolated from sewage.

NCBI tax id

NCBI tax idMatching level
77635species
1121110strain

strain history

  • @ref: 8522
  • history: <- V. Scardovi, F395

doi: 10.13145/bacdive1719.20230509.8.1

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 subtile
  • full scientific name: Bifidobacterium subtile Biavati et al. 1982

@ref: 8522

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Bifidobacteriales

family: Bifidobacteriaceae

genus: Bifidobacterium

species: Bifidobacterium subtile

full scientific name: Bifidobacterium subtile Biavati et al. 1982 emend. Nouioui et al. 2018

strain designation: F395

type strain: yes

Culture and growth conditions

culture medium

  • @ref: 8522
  • 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
8522positivegrowth37mesophilic
52430positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
8522anaerobe
52430anaerobe

murein

  • @ref: 8522
  • murein short key: A11.31
  • type: A4alpha L-Lys-D-Asp

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-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
68380urea-hydrolysis16199
68380arginine-hydrolysis29016
68380D-mannose-fermentation16024
68380raffinose+fermentation16634
68380L-glutamate-degradation29985
68380nitrate-reduction17632
68380tryptophan-energy source27897

metabolite production

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68380serine arylamidase+
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase+
68380glycin arylamidase+
68380alanine arylamidase-3.4.11.2
68380tyrosine arylamidase+
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase+3.4.11.1
68380phenylalanine arylamidase+
68380leucyl glycin arylamidase-3.4.11.1
68380proline-arylamidase+3.4.11.5
68380L-arginine arylamidase+
68380alkaline phosphatase+3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase-3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
68380beta-glucosidase+3.2.1.21
68380alpha-glucosidase+3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase-3.2.1.23
68380alpha-galactosidase+3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    52430C12:02.312
    52430C14:015.514
    52430C16:034.816
    52430C18:03.218
    52430C13:0 3OH/C15:1 i I/H114.469
    52430C16:1 ω7c115.819
    52430C16:1 ω9c2.615.774
    52430C17:0 iso 3OH1.418.161
    52430C17:1 ω5c ISO0.616.461
    52430C17:1 ω9c0.916.773
    52430C18:1 ω9c12.817.769
    52430C18:1 ω9c DMA5.218.226
    52430C18:2 ω6,9c/C18:0 ANTE6.517.724
    52430C19:0 CYCLO ω9c918.87
    52430unknown 19.3203.319.32
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
8522-----+----+++-+/-----+/------++-+-++--++++--+---------

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
52430--+--++----+----+++-++-+-++-+

Isolation, sampling and environmental information

isolation

@refsample type
8522sewage
52430Sewage

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Waste
  • Cat3: #Wastewater

taxonmaps

  • @ref: 69479
  • File name: preview.99_1441.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_24;96_829;97_968;98_1139;99_1441&stattab=map
  • Last taxonomy: Bifidobacterium subtile subclade
  • 16S sequence: D89378
  • Sequence Identity:
  • Total samples: 4201
  • soil counts: 62
  • aquatic counts: 434
  • animal counts: 3697
  • plant counts: 8

Safety information

risk assessment

  • @ref: 8522
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bifidobacterium subtile gene for 16S rRNA, partial sequence, strain: DSM 20096D893781513ena77635
20218Bifidobacterium subtile strain DSM 20096 16S ribosomal RNA gene, partial sequenceGQ487645135ena77635
20218Bifidobacterium subtile gene for 16S rRNA, partial sequence, strain: JCM 5822AB116351476ena77635
20218Bifidobacterium subtile strain KCTC 3272 16S ribosomal RNA gene, partial sequenceGU3618331475ena77635

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bifidobacterium subtile DSM 20096GCA_000426405contigncbi1121110
66792Bifidobacterium subtile DSM 20096GCA_000771185contigncbi1121110
66792Bifidobacterium subtile DSM 200961121110.3wgspatric1121110
66792Bifidobacterium subtile DSM 200961121110.4wgspatric1121110
66792Bifidobacterium subtile DSM 200962524614804draftimg1121110
66792Bifidobacterium subtile DSM 200962663763018draftimg1121110

GC content

  • @ref: 8522
  • GC-content: 61.6

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno92.71no
flagellatedno96.575no
gram-positiveyes89.842no
anaerobicyes80.477no
aerobicno95.608no
halophileno66.654no
spore-formingno96.194no
thermophileno98.291yes
glucose-utilyes83.581no
glucose-fermentyes76.947no

External links

@ref: 8522

culture collection no.: DSM 20096, ATCC 27537, CCUG 34980

straininfo link

  • @ref: 71366
  • straininfo: 9650

literature

  • topic: Phylogeny
  • Pubmed-ID: 31860428
  • title: Bifidobacterium tibiigranuli sp. nov. isolated from homemade water kefir.
  • authors: Eckel VPL, Ziegler LM, Vogel RF, Ehrmann M
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.003936
  • year: 2020
  • mesh: Bacterial Typing Techniques, Base Composition, Bifidobacterium/*classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/microbiology, *Food Microbiology, Genes, Bacterial, Germany, Kefir/*microbiology, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Biotechnology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8522Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20096)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20096
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
52430Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 34980)https://www.ccug.se/strain?id=34980
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
68371Automatically annotated from API 50CH acid
68380Automatically annotated from API rID32A
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
71366Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID9650.1StrainInfo: A central database for resolving microbial strain identifiers