Strain identifier

BacDive ID: 1696

Type strain: No

Species: Bifidobacterium breve

Strain Designation: S50 (Variant a), S50

Strain history: CIP <- 1964, Lab. Ident. Inst. Pasteur, Paris, France <- M. Sebald, Inst. Pasteur, Paris, France <- H. Werner <- G. Reuter: strain S50

NCBI tax ID(s): 1385941 (strain), 1685 (species)

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General

@ref: 8517

BacDive-ID: 1696

DSM-Number: 20091

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, Gram-positive, human pathogen

description: Bifidobacterium breve S50 is an anaerobe, Gram-positive human pathogen that was isolated from intestine of infant.

NCBI tax id

NCBI tax idMatching level
1385941strain
1685species

strain history

@refhistory
8517<- G. Reuter, S50 (Bifidobacterium parvulorum) (Variant a)
67770DSM 20091 <-- G. Reuter S50 ("Bifidobacterium parvulorum") (Variant a).
117002CIP <- 1964, Lab. Ident. Inst. Pasteur, Paris, France <- M. Sebald, Inst. Pasteur, Paris, France <- H. Werner <- G. Reuter: strain S50

doi: 10.13145/bacdive1696.20240916.9.1

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 breve
  • full scientific name: Bifidobacterium breve Reuter 1963 (Approved Lists 1980)

@ref: 8517

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Bifidobacteriales

family: Bifidobacteriaceae

genus: Bifidobacterium

species: Bifidobacterium breve

full scientific name: Bifidobacterium breve Reuter 1963 emend. Nouioui et al. 2018

strain designation: S50 (Variant a), S50

type strain: no

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
117002positiverod-shapedno
69480no91

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8517BIFIDOBACTERIUM 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
33435MEDIUM 20 - for Anaerobic bacteriayesAgar (15.000 g);Glucose (5.000 g);Yeast extract (20.000 g);Tryptone (30.000 g);Cysteine hydrochloride (0.500 g);distilled water (1000.000 ml);Hemin solution -M00149 (25.000 ml)
117002CIP Medium 20yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20

culture temp

@refgrowthtypetemperature
8517positivegrowth37
33435positivegrowth37
67770positivegrowth37

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
8517anaerobe
117002anaerobe

spore formation

  • @ref: 69481
  • spore formation: no
  • confidence: 100

murein

  • @ref: 8517
  • murein short key: A11.01
  • type: A3alpha L-Lys-Gly

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
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
68371melibiose+builds acid from28053
68371lactose+builds acid from17716
68371maltose+builds acid from17306
68371cellobiose+builds acid from17057
68371salicin+builds acid from17814
68371esculin+builds acid from4853
68371N-acetylglucosamine+builds acid from59640
68371methyl alpha-D-glucopyranoside+builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
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
117002nitrate-reduction17632
117002nitrite-reduction16301

metabolite production

  • @ref: 117002
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase-
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
117002oxidase-
117002catalase-1.11.1.6
117002urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
117002--+--+-------+--+---

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
8517---+-+----++++-------+++/-+/-++++++----+++------+-----
8517---+-+----++++-----+-+++++++++++---+++-++---+-----

Isolation, sampling and environmental information

isolation

@refsample type
8517intestine of infant
67770Intestine of infant
117002Human, Intestine of infant

isolation source categories

Cat1Cat2Cat3
#Host#Human#Child
#Host Body-Site#Gastrointestinal tract

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
8517yes, in single cases1Risk group (German classification)
1170021Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bifidobacterium breve ATCC15698 16S-23S intergenic spacerU09518488nuccore1685
20218B.breve (ATCC 15698) DNA sequence for 16S rRNAX709721464nuccore1685
124043Bifidobacterium breve gene for 16S rRNA, partial sequence, strain: JCM 1273.AB116289479nuccore1685
124043Bifidobacterium breve gene for 16S rRNA, partial sequence, strain: JCM 1273.AB507085607nuccore1685
124043Bifidobacterium breve strain JCM 1273 16S ribosomal RNA gene, partial sequence.AF4918321454nuccore1685

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bifidobacterium breve NCFB 2258GCA_000569035completencbi1385941
66792Bifidobacterium breve NCFB 22581385941.3completepatric1385941
66792Bifidobacterium breve strain NCFB 22581685.70plasmidpatric1685
66792Bifidobacterium breve NCFB 22582565956583completeimg1385941

GC content

@refGC-contentmethod
851759.4
6777059.4thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes87.079no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)yes82.585no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no92.158yes
69480spore-formingspore-formingAbility to form endo- or exosporesno86.766no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno92.965yes
69480flagellatedmotile2+Ability to perform flagellated movementno91no

External links

@ref: 8517

culture collection no.: DSM 20091, ATCC 15698, JCM 1273, CCUG 24611, CIP 64.66, KCTC 3461, LMG 10737, NCFB 2258, NCDO 2258, CCUG 45220

straininfo link

  • @ref: 71343
  • straininfo: 125611

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology7745146Viability and enzymatic activity of bifidobacteria in milk.Hughes DB, Hoover DGJ Dairy Sci10.3168/jds.S0022-0302(95)76634-61995Animals, Bifidobacterium/*enzymology/*growth & development, Cold Temperature, Freezing, Milk/*microbiology, alpha-Galactosidase/*metabolismMetabolism
Enzymology8100545Analysis of the genome of the five Bifidobacterium breve strains: plasmid content, pulsed-field gel electrophoresis genome size estimation and rrn loci number.Bourget N, Simonet JM, Decaris BFEMS Microbiol Lett10.1111/j.1574-6968.1993.tb06288.x1993Bifidobacterium/*genetics, Electrophoresis, Gel, Pulsed-Field, *Genome, Bacterial, Plasmids, Polymorphism, Genetic, Polymorphism, Restriction Fragment Length, RNA, Ribosomal/genetics, Restriction Mapping, Species Specificity, rRNA OperonGenetics
Genetics10339821Molecular characterisation of a 5.75-kb cryptic plasmid from Bifidobacterium breve NCFB 2258 and determination of mode of replication.O'Riordan K, Fitzgerald GFFEMS Microbiol Lett10.1111/j.1574-6968.1999.tb13581.x1999Amino Acid Sequence, Base Sequence, Bifidobacterium/*genetics, Cloning, Molecular, *DNA Replication, DNA, Bacterial/chemistry/genetics, Humans, Molecular Sequence Data, Open Reading Frames, Plasmids/*physiology, Sequence Alignment, Sequence Analysis, DNA, Single-Strand Specific DNA and RNA Endonucleases/metabolismEnzymology
Genetics17467795Characterization of plasmid pASV479 from Bifidobacterium pseudolongum subsp. globosum and its use for expression vector construction.Sangrador-Vegas A, Stanton C, van Sinderen D, Fitzgerald GF, Ross RPPlasmid10.1016/j.plasmid.2007.02.0042007Amino Acid Motifs, Amino Acid Sequence, Bacterial Proteins/genetics, Base Pairing, Base Sequence, Bifidobacterium/*genetics, Chromosomes, Bacterial, Conserved Sequence, DNA, Bacterial/chemistry/genetics, Genetic Vectors/*genetics, Glucuronidase/analysis, Molecular Sequence Data, Open Reading Frames, Physical Chromosome Mapping, Plasmids/*genetics, Promoter Regions, Genetic, RNA, Bacterial/genetics, RNA, Ribosomal/genetics, Sequence Analysis, DNA, Sequence Homology, Amino AcidTranscriptome
Metabolism19118369Mechanism of conjugated linoleic acid and vaccenic acid formation in human faecal suspensions and pure cultures of intestinal bacteria.McIntosh FM, Shingfield KJ, Devillard E, Russell WR, Wallace RJMicrobiology (Reading)10.1099/mic.0.022921-02009Adult, Butyrivibrio/*growth & development/isolation & purification/metabolism, Culture Media/metabolism, Feces/chemistry/*microbiology, Gram-Positive Bacteria/*growth & development/isolation & purification/metabolism, Humans, Intestines/*microbiology, Isomerism, Linoleic Acids, Conjugated/chemistry/*metabolism, Middle Aged, Oleic Acids/chemistry/*metabolismEnzymology
Pathogenicity22940065Prebiotic-non-digestible oligosaccharides preference of probiotic bifidobacteria and antimicrobial activity against Clostridium difficile.Kondepudi KK, Ambalam P, Nilsson I, Wadstrom T, Ljungh AAnaerobe10.1016/j.anaerobe.2012.08.0052012Acids/toxicity, Anti-Infective Agents/metabolism, *Antibiosis, Bifidobacterium/drug effects/metabolism/*physiology, Bile/metabolism, Clostridioides difficile/*drug effects/*growth & development, Humans, Microbial Viability/drug effects, Oligosaccharides/*metabolism, *Prebiotics, *ProbioticsMetabolism
Pathogenicity23737995Transposon mutagenesis in Bifidobacterium breve: construction and characterization of a Tn5 transposon mutant library for Bifidobacterium breve UCC2003.Ruiz L, Motherway MO, Lanigan N, van Sinderen DPLoS One10.1371/journal.pone.00646992013Bifidobacterium/drug effects/*genetics/growth & development, Carbohydrates/pharmacology, Carbon/pharmacology, DNA Transposable Elements/*genetics, *Gene Library, *Mutagenesis, Mutagenesis, Insertional/drug effects, *Mutation/drug effects, PhenotypePhenotype
Metabolism23851389Identification and characterization of an oleate hydratase-encoding gene from Bifidobacterium breve.O'Connell KJ, Motherway MO, Hennessey AA, Brodhun F, Ross RP, Feussner I, Stanton C, Fitzgerald GF, van Sinderen DBioengineered10.4161/bioe.241592013Bacterial Proteins/genetics/*metabolism, Bifidobacterium/enzymology/*genetics, Gene Expression, Hydro-Lyases/genetics/*metabolism, Linoleic Acids, Conjugated/metabolism, Mutagenesis, Insertional, Oleic Acids/*metabolismEnzymology
Metabolism31747272Structural Identity of Galactooligosaccharide Molecules Selectively Utilized by Single Cultures of Probiotic Bacterial Strains.Boger M, van Leeuwen SS, Lammerts van Bueren A, Dijkhuizen LJ Agric Food Chem10.1021/acs.jafc.9b059682019Bifidobacterium/growth & development/*metabolism, Lactobacillus/growth & development/*metabolism, Lactobacillus acidophilus/growth & development/metabolism, Oligosaccharides/*chemistry/*metabolism, Prebiotics/analysis, Probiotics/metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8517Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20091)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20091
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
33435Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/10171
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
71343Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID125611.1StrainInfo: A central database for resolving microbial strain identifiers
117002Curators of the CIPCollection of Institut Pasteur (CIP 64.66)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2064.66
124043Dr. Isabel Schober, Dr. Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy