Strain identifier

BacDive ID: 160370

Type strain: No

Species: Bifidobacterium sp.

Strain Designation: Cla-CZ-59

Strain history: <- T. Clavel; RWTH Aachen, Germany; Cla-CZ-59

NCBI tax ID(s): 41200 (species)

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General

@ref: 67276

BacDive-ID: 160370

DSM-Number: 108971

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

description: Bifidobacterium sp. Cla-CZ-59 is a mesophilic bacterium that was isolated from chicken colon content, adult.

NCBI tax id

  • NCBI tax id: 41200
  • Matching level: species

strain history

  • @ref: 67276
  • history: <- T. Clavel; RWTH Aachen, Germany; Cla-CZ-59

doi: 10.13145/bacdive160370.20250331.9.3

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 sp.
  • full scientific name: Bifidobacterium Orla-Jensen 1924 (Approved Lists 1980)

@ref: 67276

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Bifidobacteriales

family: Bifidobacteriaceae

genus: Bifidobacterium

species: Bifidobacterium sp.

full scientific name: Bifidobacterium sp.

strain designation: Cla-CZ-59

type strain: no

Morphology

cell morphology

  • @ref: 125438
  • motility: no
  • confidence: 93.5

Culture and growth conditions

culture medium

  • @ref: 67276
  • 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

  • @ref: 67276
  • growth: positive
  • type: growth
  • temperature: 37

Physiology and metabolism

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 91.1

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838027897tryptophan-energy source
6838017632nitrate-reduction
6838029985L-glutamate-degradation
6838016634raffinose+fermentation
6838029016arginine-hydrolysis
6838016199urea-hydrolysis
6838016024D-mannose-fermentation

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

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
67276--++-+++/----+------+-+--------
67276--++-+++/----+------+-+--------

Isolation, sampling and environmental information

isolation

  • @ref: 67276
  • sample type: chicken colon content, adult
  • geographic location: Dietramszell (Bavaria)
  • country: Germany
  • origin.country: DEU
  • continent: Europe
  • latitude: 47.8589
  • longitude: 11.5894

Sequence information

16S sequences

  • @ref: 67276
  • description: Bifidobacterium pullorum subsp. saeculare strain ClaCZ59 16S ribosomal RNA gene, partial sequence
  • accession: MN055938.1
  • length: 1468
  • database: nuccore
  • NCBI tax ID: 78257

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bifidobacterium pullorum subsp. saeculare DSM 108971GCA_014983005contigncbi78257
66792Bifidobacterium saeculare strain DSM 10897178257.7wgspatric78257

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes82.906no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)yes86.141no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no96.613no
125438spore-formingspore-formingAbility to form endo- or exosporesno89.198no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno92.989no
125438motile2+flagellatedAbility to perform flagellated movementno93.5no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno91.1
125439BacteriaNetmotilityAbility to perform movementno62.1
125439BacteriaNetgram_stainReaction to gram-stainingpositive89.9
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate anaerobe89.1

External links

@ref: 67276

culture collection no.: DSM 108971

straininfo link

  • @ref: 112619
  • straininfo: 397662

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
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
67276Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-108971Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 108971)
68380Automatically annotated from API rID32A
112619Reimer, 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-ID397662.1
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG