Strain identifier

BacDive ID: 132546

Type strain: Yes

Species: Bifidobacterium ramosum

Strain history: P. Mattarelli; Dept. of Agric. Sci., Bologna Univ., Italy; TRE M.

NCBI tax ID(s): 1798158 (species)

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General

@ref: 24335

BacDive-ID: 132546

DSM-Number: 100688

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

description: Bifidobacterium ramosum DSM 100688 is an anaerobe, mesophilic bacterium that was isolated from faeces of an adult cotton-top tamarin L..

NCBI tax id

  • NCBI tax id: 1798158
  • Matching level: species

strain history

@refhistory
24335<- P. Mattarelli, Dept. Agricult. Scs., Univ. Bologna, Italy; TRE M <- M. Modesto and S. Michelini
67770P. Mattarelli; Dept. of Agric. Sci., Bologna Univ., Italy; TRE M.

doi: 10.13145/bacdive132546.20230509.8.1

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 ramosum
  • full scientific name: Bifidobacterium ramosum Michelini et al. 2017

@ref: 24335

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Bifidobacteriales

family: Bifidobacteriaceae

genus: Bifidobacterium

species: Bifidobacterium ramosum

full scientific name: Bifidobacterium ramosum Michelini et al. 2017

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no94.811
69480100positive

Culture and growth conditions

culture medium

  • @ref: 24335
  • 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
24335positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 69480
  • oxygen tolerance: anaerobe
  • confidence: 99.999

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.998

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-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
24335---------+++++-----------+---++-----++-+----------

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
24335faeces of an adult cotton-top tamarin (Saguinus oedipus) L.Saguinus oedipusVerona, Bussolengo, Parco Natura VivaItalyITAEurope
67770Faeces of an adult subject of the cotton-top tamarin

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_40525.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_24;96_18896;97_23406;98_29565;99_40525&stattab=map
  • Last taxonomy: Bifidobacterium ramosum subclade
  • 16S sequence: KU051447
  • Sequence Identity:
  • Total samples: 20386
  • soil counts: 246
  • aquatic counts: 165
  • animal counts: 19947
  • plant counts: 28

Safety information

risk assessment

  • @ref: 24335
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24335
  • description: Bifidobacterium ramosum strain TRE M 16S ribosomal RNA gene, partial sequence
  • accession: KU051447
  • length: 1382
  • database: ena
  • NCBI tax ID: 1798158

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bifidobacterium ramosum DSM 100688GCA_009299505contigncbi1798158
66792Bifidobacterium ramosum strain DSM 1006881798158.5wgspatric1798158

GC content

  • @ref: 24335
  • GC-content: 63
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes61no
motileno94.873no
gram-positiveyes94.615no
anaerobicyes95.204no
aerobicno95.958no
halophileno85.319no
spore-formingno96.17no
glucose-utilyes86.534no
flagellatedno96.805no
thermophileno97.595yes
glucose-fermentyes81.958no

External links

@ref: 24335

culture collection no.: DSM 100688, JCM 30944, TRE M

straininfo link

  • @ref: 90871
  • straininfo: 407015

literature

  • topic: Phylogeny
  • Pubmed-ID: 27236565
  • title: Bifidobacterium aerophilum sp. nov., Bifidobacterium avesanii sp. nov. and Bifidobacterium ramosum sp. nov.: Three novel taxa from the faeces of cotton-top tamarin (Saguinus oedipus L.).
  • authors: Michelini S, Modesto M, Filippini G, Spiezio C, Sandri C, Biavati B, Pisi A, Mattarelli P
  • journal: Syst Appl Microbiol
  • DOI: 10.1016/j.syapm.2016.04.005
  • year: 2016
  • mesh: Aldehyde-Lyases/genetics, Animals, Base Composition, Base Sequence, *Bifidobacterium/classification/genetics/isolation & purification, Chaperonin 60/genetics, DNA Primase/genetics, DNA, Bacterial/genetics, DNA-Directed RNA Polymerases/genetics, Feces/microbiology, HSP40 Heat-Shock Proteins/genetics, *Multilocus Sequence Typing, Peptidoglycan/classification/genetics, Phylogeny, RNA, Ribosomal, 16S/genetics, Saguinus/*microbiology, Sequence Analysis, DNA
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
24335Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100688Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100688)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
90871Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID407015.1