Strain identifier

BacDive ID: 159320

Type strain: Yes

Species: Bifidobacterium jacchi

Strain history: P. Mattarelli; Dept. of Agric. Sci., Bologna Univ., Italy; MRM 9.3.

NCBI tax ID(s): 2490545 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 8.1 (current version)

General

@ref: 66143

BacDive-ID: 159320

DSM-Number: 103362

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

description: Bifidobacterium jacchi DSM 103362 is an aerobe, mesophilic, Gram-positive bacterium that forms circular colonies and was isolated from Faeces of Saguinus oedipus.

NCBI tax id

  • NCBI tax id: 2490545
  • Matching level: species

strain history

@refhistory
66143<- P. Mattarelli, Univ. Bologna, Italy; MRM 9.3 <- M. Modesto and S. Michelini
67770P. Mattarelli; Dept. of Agric. Sci., Bologna Univ., Italy; MRM 9.3.

doi: 10.13145/bacdive159320.20230509.8.1

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 jacchi
  • full scientific name: Bifidobacterium jacchi Modesto et al. 2019

@ref: 66143

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Bifidobacteriales

family: Bifidobacteriaceae

genus: Bifidobacterium

species: Bifidobacterium jacchi

full scientific name: Bifidobacterium jacchi Modesto et al. 2019

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
67988positive8.0-12.0 µm2 µmrod-shapedno
69480no95.125
69480positive100

colony morphology

  • @ref: 67988
  • colony size: 1.0-2.0 mm
  • colony color: white
  • colony shape: circular
  • incubation period: 3 days
  • medium used: TPY agar

Culture and growth conditions

culture medium

  • @ref: 66143
  • 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
66143positivegrowth37mesophilic
67770positivegrowth37mesophilic
67988positivegrowth22-48
67988positiveoptimum37mesophilic

culture pH

@refabilitytypepHPH range
67988positivegrowth4.0-7.5acidophile
67988positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
67988aerobe
67988microaerophile
69480anaerobe99.281

spore formation

@refspore formationconfidence
67988no
69480no99.999
69481no91

observation

@refobservation
67988cells form a branched structure with 'Y' at the both side
67988The peptidoglycan type is L-Orn - L-Ser - L-Ala
67988Colonies on the surface of are white, smooth and circular with entire edges, while the embedded colonies are lens-shaped or elliptical

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
679884853esculin-hydrolysis
6798817632nitrate-reduction
67988esculin ferric citrate-builds acid from
6798865327D-xylose-builds acid from
6798816988D-ribose+builds acid from
67988potassium 5-dehydro-D-gluconate-builds acid from
6798830849L-arabinose+builds acid from
6798816443D-tagatose-builds acid from
6798817634D-glucose+builds acid from
6798817306maltose+builds acid from
67988potassium 2-dehydro-D-gluconate-builds acid from
6798827082trehalose+builds acid from
6798832528turanose+/-builds acid from
6798812936D-galactose+builds acid from
6798815824D-fructose+builds acid from
6798817992sucrose+builds acid from
6798817057cellobiose-builds acid from
6798828053melibiose+/-builds acid from
6798818305arbutin+builds acid from
6798816024D-mannose+builds acid from
6798817814salicin-builds acid from
6798817716lactose+builds acid from
6798816899D-mannitol+builds acid from
6798828087glycogen-builds acid from
6798828017starch-builds acid from
6798817108D-arabinose-builds acid from
679886731melezitose-builds acid from
6798818287L-fucose-builds acid from
6798862345L-rhamnose-builds acid from
6798828066gentiobiose-builds acid from
6798817924D-sorbitol-builds acid from
6798818333D-arabitol-builds acid from
6798862318D-lyxose-builds acid from
6798828847D-fucose-builds acid from
6798817754glycerol-builds acid from
6798859640N-acetylglucosamine+/-builds acid from
67988320061methyl alpha-D-glucopyranoside-builds acid from
6798817268myo-inositol-builds acid from
6798832032potassium gluconate-builds acid from
6798874863methyl beta-D-xylopyranoside+builds acid from
6798816634raffinose+builds acid from
6798827613amygdalin-builds acid from
6798843943methyl alpha-D-mannoside-builds acid from
6798817113erythritol-builds acid from
6798865328L-xylose-builds acid from
6798815963ribitol-builds acid from
6798817266L-sorbose-builds acid from
6798816813galactitol-builds acid from
6798815443inulin-builds acid from
6798817151xylitol-builds acid from
6798818403L-arabitol-builds acid from

metabolite production

  • @ref: 67988
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
67988urease-3.5.1.5
67988alkaline phosphatase+/-3.1.3.1
67988glycin arylamidase+/-
67988alpha-galactosidase+3.2.1.22
67988beta-galactosidase+3.2.1.23
67988alpha-glucosidase+3.2.1.20
67988N-acetyl-beta-glucosaminidase+3.2.1.52
67988L-arginine arylamidase+
67988proline-arylamidase+3.4.11.5
67988phenylalanine arylamidase+
67988leucine arylamidase+3.4.11.1
67988tyrosine arylamidase+
67988histidine arylamidase+
67988serine arylamidase+
67988catalase-1.11.1.6
67988cytochrome oxidase-1.9.3.1
67988fructose-6-phosphate phosphoketolase+4.1.2.22

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinenthost species
66143Faeces of Saguinus oedipusVeronaItalyITAEurope
67770Feces of a baby common marmoset (Callithrix jacchus)ItalyITAEuropeCallithrix jacchus
67988faeces of a baby common marmoset

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_160161.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_24;96_60313;97_78079;98_105432;99_160161&stattab=map
  • Last taxonomy: Bifidobacterium
  • 16S sequence: KP718960
  • Sequence Identity:
  • Total samples: 11293
  • soil counts: 68
  • aquatic counts: 64
  • animal counts: 11142
  • plant counts: 19

Sequence information

16S sequences

  • @ref: 66143
  • description: Bifidobacterium sp. MRM 9.03 16S ribosomal RNA gene, partial sequence
  • accession: KP718960
  • length: 1466
  • database: ena
  • NCBI tax ID: 1630179

Genome sequences

  • @ref: 67988
  • description: Bifidobacterium jacchi MRM 9.3
  • accession: GCA_009078285
  • assembly level: scaffold
  • database: ncbi
  • NCBI tax ID: 2490545

GC content

  • @ref: 67988
  • GC-content: 61.5
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno91no
flagellatedno96.154no
gram-positiveyes93.459yes
anaerobicyes97.592no
aerobicno96.577no
halophileno82.098no
spore-formingno96.066no
thermophileno97.799yes
glucose-utilyes89.009no
motileno94.933no
glucose-fermentyes82.927no

External links

@ref: 66143

culture collection no.: DSM 103362, JCM 31788, MRM 9.3

straininfo link

  • @ref: 111819
  • straininfo: 404258

literature

  • topic: Phylogeny
  • Pubmed-ID: 31180316
  • title: Bifidobacterium jacchi sp. nov., isolated from the faeces of a baby common marmoset (Callithrix jacchus).
  • authors: Modesto M, Watanabe K, Arita M, Satti M, Oki K, Sciavilla P, Patavino C, Camma C, Michelini S, Sgorbati B, Mattarelli P
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.003518
  • year: 2019
  • mesh: Animals, Bacterial Typing Techniques, Base Composition, Bifidobacterium/*classification/isolation & purification, Callithrix/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/*microbiology, Genes, Bacterial, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournal
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
66143Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-103362Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103362)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67988Monica Modesto, Koichi Watanabe, Masanori Arita, Maria Satti, Kaihei Oki, Piero Sciavilla, Claudio Patavino, Cesare Cammà, Samanta Michelini, Barbara Sgorbati, Paola MattarelliBifidobacterium jacchi sp. nov., isolated from the faeces of a baby common marmoset (Callithrix jacchus)10.1099/ijsem.0.003518IJSEM 69: 2477-2485 2019
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
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
111819Reimer, 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-ID404258.1