Strain identifier

BacDive ID: 1712

Type strain: Yes

Species: Bifidobacterium minimum

Strain Designation: F392

Strain history: ATCC 27538 <-- V. Scardovi F392.

NCBI tax ID(s): 1121109 (strain), 1693 (species)

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General

@ref: 8528

BacDive-ID: 1712

DSM-Number: 20102

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

description: Bifidobacterium minimum F392 is an anaerobe, mesophilic bacterium that was isolated from sewage.

NCBI tax id

NCBI tax idMatching level
1121109strain
1693species

strain history

@refhistory
8528<- V. Scardovi, F392
67770ATCC 27538 <-- V. Scardovi F392.

doi: 10.13145/bacdive1712.20230509.8.1

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

@ref: 8528

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Bifidobacteriales

family: Bifidobacteriaceae

genus: Bifidobacterium

species: Bifidobacterium minimum

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

strain designation: F392

type strain: yes

Culture and growth conditions

culture medium

  • @ref: 8528
  • 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
8528positivegrowth37mesophilic
52432positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
8528anaerobe
52432anaerobe

murein

  • @ref: 8528
  • murein short key: A11.14
  • type: A3alpha L-Lys-L-Ser

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-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

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    52432C10:00.510
    52432C12:01.712
    52432C14:07.614
    52432C16:03516
    52432C18:06.318
    52432C13:0 3OH/C15:1 i I/H1.414.469
    52432C13:1 at 12-130.412.931
    52432C16:0 3OH0.917.52
    52432C16:1 ω7c0.915.819
    52432C16:1 ω9c4.715.774
    52432C17:0 iso 3OH1.418.161
    52432C17:1 ω5c ISO0.616.461
    52432C17:1 ω9c0.916.773
    52432C18:1 ω9c17.317.769
    52432C18:2 ω6,9c/C18:0 ANTE4.717.724
    52432C19:0 CYCLO ω9c5.618.87
    52432C19:1 ISO I0.518.473
    52432Unidentified5.718.219
    52432Unidentified4.119.318
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
8528-----------++/----------------+-------++--+---------

Isolation, sampling and environmental information

isolation

@refsample type
8528sewage
52432Sewage
67770Sewage

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_2910.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_24;96_1536;97_1833;98_2250;99_2910&stattab=map
  • Last taxonomy: Bifidobacterium minimum subclade
  • 16S sequence: LC071835
  • Sequence Identity:
  • Total samples: 9916
  • soil counts: 215
  • aquatic counts: 472
  • animal counts: 9131
  • plant counts: 98

Safety information

risk assessment

  • @ref: 8528
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bifidobacterium minimum strain ATCC 27538 16S ribosomal RNA gene, partial sequenceM587411470ena1693
20218Bifidobacterium minimum strain DSM 20102 16S ribosomal RNA gene, partial sequenceGQ487640134ena1693
20218Bifidobacterium minimum gene for 16S rRNA, partial sequence, strain: JCM 5821AB116326475ena1693
20218Bifidobacterium minimum gene for 16S rRNA, partial sequence, strain: JCM 5821AB507130613ena1693
20218Bifidobacterium minimum strain KCTC 3273 16S ribosomal RNA gene, partial sequenceGU3618261476ena1693
20218Bifidobacterium minimum strain LMG11592 16S ribosomal RNA gene and 16S-23S ribosomal RNA intergenic spacer, partial sequenceFJ231743846ena1693
67770Bifidobacterium minimum gene for 16S ribosomal RNA, partial sequence, strain: YIT 4097AB4373501505ena1693
67770Bifidobacterium minimum gene for 16S ribosomal RNA, partial sequence, strain: JCM 5821LC0718351422ena1693

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bifidobacterium minimum DSM 201021121109.3wgspatric1121109
66792Bifidobacterium minimum DSM 201021121109.4wgspatric1121109
66792Bifidobacterium minimum strain LMG 115921693.3wgspatric1693
66792Bifidobacterium minimum LMG 115922597490263draftimg1693
66792Bifidobacterium minimum DSM 201022690316073draftimg1121109
66792Bifidobacterium minimum DSM 201022524023146draftimg1121109
67770Bifidobacterium minimum DSM 20102GCA_000421685contigncbi1121109
67770Bifidobacterium minimum DSM 20102GCA_000771245contigncbi1121109
67770Bifidobacterium minimum LMG 11592GCA_000741645contigncbi1693

GC content

@refGC-contentmethod
852861.6
6777061.6thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno94.665no
flagellatedno97.432no
gram-positiveyes92.413no
anaerobicyes95.029yes
aerobicno96.43yes
halophileno76.202no
spore-formingno95.928no
thermophileno98.127yes
glucose-utilyes88.133no
glucose-fermentyes80.07no

External links

@ref: 8528

culture collection no.: CCUG 34982, DSM 20102, ATCC 27538, JCM 5821, BCRC 14666, CGMCC 1.2233, KCTC 3273, LMG 11592

straininfo link

  • @ref: 71359
  • straininfo: 9645

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8528Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20102)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20102
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
52432Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 34982)https://www.ccug.se/strain?id=34982
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
71359Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID9645.1StrainInfo: A central database for resolving microbial strain identifiers