Strain identifier

BacDive ID: 160002

Type strain: Yes

Species: Bifidobacterium saimiriisciurei

Strain history: <- P. Mattarelli, Dept. Agricult. Scs., Univ. Bologna, Italy; SMA 1 <- M. Modesto

NCBI tax ID(s): 2661627 (species)

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General

@ref: 66906

BacDive-ID: 160002

DSM-Number: 106020

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, rod-shaped, colony-forming

description: Bifidobacterium saimiriisciurei DSM 106020 is an aerobe, mesophilic, Gram-positive bacterium that forms circular colonies and was isolated from Feces of Saimiri sciureus.

NCBI tax id

  • NCBI tax id: 2661627
  • Matching level: species

strain history

  • @ref: 66906
  • history: <- P. Mattarelli, Dept. Agricult. Scs., Univ. Bologna, Italy; SMA 1 <- M. Modesto

doi: 10.13145/bacdive160002.20230509.8.1

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 saimiriisciurei
  • full scientific name: Bifidobacterium saimiriisciurei Modesto et al. 2020

@ref: 66906

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Bifidobacteriales

family: Bifidobacteriaceae

genus: Bifidobacterium

species: Bifidobacterium saimiriisciurei

full scientific name: Bifidobacterium saimiriisciurei Modesto et al. 2020

type strain: yes

Morphology

cell morphology

  • @ref: 69629
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 69629
  • type of hemolysis: gamma
  • colony size: 1-2 mm
  • colony color: white
  • colony shape: circular
  • incubation period: 3 days
  • medium used: TPY agar

multicellular morphology

  • @ref: 69629
  • forms multicellular complex: yes
  • further description: frequently forming filaments, with irregular contractions along the cells and bifurcations

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
66906BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58)yeshttps://mediadive.dsmz.de/medium/58Name: 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
69629TPY brothyes
69629TPY agaryes

culture temp

@refgrowthtypetemperaturerange
66906positivegrowth37mesophilic
69629positivegrowth25-46
69629positiveoptimum37mesophilic

culture pH

@refabilitytypepH
69629positivegrowth5.5-7
69629positiveoptimum6.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
69629aerobe
69629microaerophile

spore formation

  • @ref: 69629
  • type of spore: spore
  • spore formation: no

observation

  • @ref: 69629
  • observation: In TPY broth rods form a branched structure with a Y shape at both sides

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
69629168082-dehydro-D-gluconate-fermentation
69629581435-dehydro-D-gluconate-fermentation
6962918305arbutin-fermentation
6962917057cellobiose-fermentation
6962962318D-lyxose-fermentation
6962916024D-mannose-fermentation
6962928066gentiobiose-fermentation
6962924265gluconate-fermentation
6962965328L-xylose-fermentation
696296731melezitose-fermentation
69629320061methyl alpha-D-glucopyranoside-fermentation
6962943943methyl alpha-D-mannoside-fermentation
69629506227N-acetyl-D-glucosamine-fermentation
6962928017starch-fermentation
6962917151xylitol-fermentation
6962917632nitrate-reduction
6962918333D-arabitol+fermentation
6962912936D-galactose+fermentation
6962917634D-glucose+fermentation
6962916988D-ribose+fermentation
6962917924D-sorbitol+fermentation
6962965327D-xylose+fermentation
6962917992sucrose+fermentation
696294853esculin+hydrolysis
6962927613amygdalin+/-fermentation
6962915824D-fructose+/-fermentation
6962916899D-mannitol+/-fermentation
6962916551D-trehalose+/-fermentation
6962916813galactitol+/-fermentation
6962928087glycogen+/-fermentation
6962917716lactose+/-fermentation
6962917306maltose+/-fermentation
6962928053melibiose+/-fermentation
6962974863methyl beta-D-xylopyranoside+/-fermentation
6962916634raffinose+/-fermentation
6962917814salicin+/-fermentation
6962932528turanose+/-fermentation

enzymes

@refvalueactivityec
69629L-arginine arylamidase-
69629alpha-galactosidase+3.2.1.22
69629beta-galactosidase-3.2.1.23
69629alpha-glucosidase-3.2.1.20
69629beta-glucosidase-3.2.1.21
69629alpha-arabinosidase-
69629beta-glucuronidase-3.2.1.31
69629alkaline phosphatase+3.1.3.1
69629arginine arylamidase+
69629proline-arylamidase-3.4.11.5
69629leucyl glycin arylamidase-3.4.11.1
69629phenylalanine arylamidase-
69629leucine arylamidase-3.4.11.1
69629pyroglutamic acid arylamidase+
69629glycin arylamidase+
69629tyrosine arylamidase-
69629histidine arylamidase+
69629glutamyl-glutamate arylamidase+
69629serine arylamidase-
69629fructose-6-phosphate phosphoketolase+4.1.2.22
69629urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    69629C13:11.2
    69629C14:04
    69629C16:054.3
    69629C17:0 2OH1.1
    69629C17:1 w8c2.1
    69629C18:013.1
    69629C18:1 w7c/C18:1 w6c2.1
    69629C18:1 w9c15
    69629iso-C15:1 H/C13:0 3OH/C15:1 I H4.2
  • type of FA analysis: whole cell analysis
  • incubation medium: MRS supplemented with 0.05% cysteine
  • agar/liquid: agar
  • incubation temperature: 37
  • incubation time: 1
  • incubation_oxygen: anaerobic
  • library/peak naming table: TSBA50
  • system: MIS MIDI
  • instrument: Agilent 6890N

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling datelatitudelongitudeenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperatureisolation date
66906Feces of Saimiri sciureusBussolengo, VeronaItalyITAEurope
69629Faecal samples of an adult male of Saimiri sciureusParco Natura Viva - Garda Zoological Park (Bussolengo,Verona)ItalyITAEurope2016-12-0245.477710.794MRS agarsupplemented with mupirocin (100 mg/L)2-3 days372016-12-09

Sequence information

16S sequences

  • @ref: 66906
  • description: Bifidobacterium sp. SMA1 16S ribosomal RNA gene, partial sequence
  • accession: MN722462
  • length: 1534
  • database: ena
  • NCBI tax ID: 2661627

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
69629Bifidobacterium saimiriisciurei SMA1GCA_010667655scaffoldncbi2661627
69629Whole genome shotgunWHZU00000000ncbi2661627

GC content

  • @ref: 69629
  • GC-content: 63.6
  • method: genome sequence analysis

External links

@ref: 66906

culture collection no.: DSM 106020, SMA 1, BCRC 81223, NBRC 114049

literature

  • topic: Phylogeny
  • Pubmed-ID: 32847786
  • title: Phylogenetic characterization of two novel species of the genus Bifidobacterium: Bifidobacterium saimiriisciurei sp. nov. and Bifidobacterium platyrrhinorum sp. nov.
  • authors: Modesto M, Satti M, Watanabe K, Scarafile D, Huang CH, Liou JS, Tamura T, Saito S, Watanabe M, Mori K, Huang L, Sandri C, Spiezio C, Arita M, Mattarelli P
  • journal: Syst Appl Microbiol
  • DOI: 10.1016/j.syapm.2020.126111
  • year: 2020
  • mesh: Aldehyde-Lyases/metabolism, Animals, Bacterial Typing Techniques, Base Composition, Bifidobacterium/*classification/genetics/*isolation & purification/physiology, Computer Simulation, Culture Media, DNA, Bacterial/chemistry/genetics, Feces/microbiology, Genes, Bacterial, Genes, rRNA, Genetic Variation, Genome, Bacterial, Male, Phylogeny, RNA, Ribosomal, 16S/genetics, Saimiri/*microbiology, Sequence Analysis, DNA, Temperature
  • topic2: Cultivation

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
66906Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-106020Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 106020)
69629Monica Modesto, Maria Satti, Koichi Watanabe, Donatella Scarafile, Chien-Hsun Huang, Jong-Shian Liou, Tomohiko Tamura, Satomi Saito, Mizuki Watanabe, Koji Mori, Lina Huang, Camillo Sandri, Caterina Spiezio, Masanori Arita, Paola MattarelliPhylogenetic characterization of two novel species of the genus Bifidobacterium: Bifidobacterium saimiriisciurei sp. nov. and Bifidobacterium platyrrhinorum sp. Nov10.1016/j.syapm.2020.126111