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Strain identifier

BacDive ID: 137143

Type strain: No

Species: Bifidobacterium bifidum

Strain history: T. Mitsuoka IV-4 <-- G. Reuter S28a (Variant b).

NCBI tax ID(s): 1207542 (strain), 1681 (species)

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For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 37007

BacDive-ID: 137143

keywords: genome sequence, Bacteria, mesophilic

description: Bifidobacterium bifidum CIP 64.65 is a mesophilic bacterium that was isolated from Intestine of infant.

NCBI tax id

NCBI tax idMatching level
1207542strain
1681species

strain history: T. Mitsuoka IV-4 <-- G. Reuter S28a (Variant b).

doi: 10.13145/bacdive137143.20221219.7.1

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 bifidum
  • full scientific name: Bifidobacterium bifidum (Tissier 1900) Orla-Jensen 1924 (Approved Lists 1980)

  • synonyms

    @refsynonym
    20215Bacterium bifidum
    20215Bacillus bifidus

@ref: 37007

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Bifidobacteriales

family: Bifidobacteriaceae

genus: Bifidobacterium

species: Bifidobacterium bifidum

type strain: no

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 82.451

Culture and growth conditions

culture medium

  • @ref: 37007
  • name: MEDIUM 20 - for Anaerobic bacteria
  • growth: yes
  • composition: Agar (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)

culture temp

@refgrowthtypetemperaturerange
37007positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 69480
  • oxygen tolerance: anaerobe
  • confidence: 94.332

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 98.638

halophily

  • @ref: 69480
  • halophily level: non-halophilic
  • confidence: 97.986

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838116199urea-hydrolysis
6838116443D-tagatose-builds acid from
68381320055methyl beta-D-glucopyranoside-builds acid from
683816731melezitose-builds acid from
6838128053melibiose-builds acid from
6838117306maltose-builds acid from
6838127941pullulan-builds acid from
6838128087glycogen-builds acid from
68381606565hippurate-hydrolysis
6838140585alpha-cyclodextrin-builds acid from
6838118333D-arabitol-builds acid from
6838130849L-arabinose-builds acid from
6838117992sucrose-builds acid from
6838116634raffinose-builds acid from
6838127082trehalose-builds acid from
6838117716lactose+builds acid from
6838130911sorbitol-builds acid from
6838116899D-mannitol-builds acid from
6838116988D-ribose-builds acid from
6838129016arginine-hydrolysis
6838027897tryptophan-energy source
6838017632nitrate-reduction
6838029985L-glutamate-degradation
6838016634raffinose-fermentation
6838016024D-mannose-fermentation
6838029016arginine-hydrolysis
6838016199urea-hydrolysis
6837928087glycogen-fermentation
6837917992sucrose-fermentation
6837917716lactose+fermentation
6837917306maltose+fermentation
6837916899D-mannitol-fermentation
6837965327D-xylose-fermentation
6837916988D-ribose-fermentation
6837917634D-glucose+fermentation
683795291gelatin-hydrolysis
6837916199urea-hydrolysis
683794853esculin-hydrolysis
6837917632nitrate-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6838115688acetoinno
6838035581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6838115688acetoin-
6838035581indole-

enzymes

@refvalueactivityec
68381urease-3.5.1.5
68381beta-mannosidase-3.2.1.25
68381glycyl tryptophan arylamidase-
68381N-acetyl-beta-glucosaminidase+3.2.1.52
68381pyrrolidonyl arylamidase+3.4.19.3
68381beta-galactosidase+3.2.1.23
68381Alanyl-Phenylalanyl-Proline arylamidase+
68381alkaline phosphatase-3.1.3.1
68381alpha-galactosidase+3.2.1.22
68381beta-glucuronidase-3.2.1.31
68381beta-glucosidase-3.2.1.21
68381arginine dihydrolase-3.5.3.6
68380serine arylamidase+
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase+
68380glycin arylamidase+
68380alanine arylamidase+3.4.11.2
68380tyrosine arylamidase+
68380pyrrolidonyl arylamidase+3.4.19.3
68380leucine arylamidase+3.4.11.1
68380phenylalanine arylamidase+
68380leucyl glycin arylamidase-3.4.11.1
68380proline-arylamidase+3.4.11.5
68380L-arginine arylamidase+
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase+3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
68380beta-glucosidase-3.2.1.21
68380alpha-glucosidase+3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase+3.2.1.23
68380alpha-galactosidase+3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5
68379catalase-1.11.1.6
68379gelatinase-
68379urease-3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase+3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase+3.5.1.B15

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELControlGLURIBXYLMANMALLACSACGLYGCAT
65639-+-+-+++----+---++---

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
65639--++-+---+-------++-+++++++-+

API rID32STR

@refADH Argbeta GLUbeta GARbeta GURalpha GALPALRIBMANSORLACTRERAFSACLARADARLCDEXVPAPPAbeta GALPyrAbeta NAGGTAHIPGLYGPULMALMELMLZMbeta DGTAGbeta MANURE
65639--+-+----+-------++++-----------

Isolation, sampling and environmental information

isolation

  • @ref: 67770
  • sample type: Intestine of infant

Sequence information

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bifidobacterium bifidum LMG 13195 JCM 7004GCA_003573955completencbi1207542
66792Bifidobacterium bifidum LMG 13195 strain JCM 70041207542.9completepatric1207542
66792Bifidobacterium bifidum JCM 70042859461767completeimg1681
66792Methanothermococcus sp. SCGC AD-155-N22 SCGC AD-155-N22GCA_019561535contigpatric2838159

External links

@ref: 37007

culture collection no.: CIP 64.65, ATCC 15696, NCDO 2203, CCUG 45219, JCM 7004, BCRC 14614, CCUG 17358, KCTC 3418, LMG 10644

straininfo link

@refpassport
20218http://www.straininfo.net/strains/233552
20218http://www.straininfo.net/strains/5392
20218http://www.straininfo.net/strains/149252
20218http://www.straininfo.net/strains/149253

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism7836576Growth and viability of Bifidobacterium bifidum in cheddar cheese.Dinakar P, Mistry VVJ Dairy Sci10.3168/jds.S0022-0302(94)77225-81994Bifidobacterium/growth & development/*physiology, Cheese/*microbiology, Chromatography, High Pressure Liquid, Dietary Proteins/metabolism, Microscopy, Electron, Scanning, Taste, Time Factors
Pathogenicity8872711Growth characteristics of bifidobacteria in infant formulas.Dubey UK, Mistry VVJ Dairy Sci10.3168/jds.S0022-0302(96)76468-81996Acetic Acid/metabolism, Animals, Bifidobacterium/cytology/*growth & development, Buffers, Caseins, Fats/analysis, Humans, Hydrogen-Ion Concentration, Infant Food/analysis/*microbiology, Infant, Newborn, Kinetics, Lactic Acid/biosynthesis, Milk, Protein Hydrolysates, Proteins/analysis, SoybeansEnzymology
Pathogenicity8872712Effect of bifidogenic factors on growth characteristics of bifidobacteria in infant formulas.Dubey UK, Mistry VVJ Dairy Sci10.3168/jds.S0022-0302(96)76469-X1996Acetic Acid/metabolism, Bifidobacterium/*drug effects/*growth & development, Caseins, Colony Count, Microbial, Fructose/*pharmacology, Humans, Hydrogen-Ion Concentration, Infant, Infant Food/analysis/*microbiology, Lactic Acid/biosynthesis, Lactulose/*pharmacology, Oligosaccharides/*pharmacology, Protein Hydrolysates, SoybeansMetabolism
Metabolism12926870Andean yacon root (Smallanthus sonchifolius Poepp. Endl) fructooligosaccharides as a potential novel source of prebiotics.Pedreschi R, Campos D, Noratto G, Chirinos R, Cisneros-Zevallos LJ Agric Food Chem10.1021/jf03447442003Asteraceae/*chemistry, Bifidobacterium/metabolism, Chromatography, Gel, Fermentation, Lactobacillus/metabolism, Lactobacillus acidophilus/metabolism, Oligosaccharides/*metabolism, Plant Roots/*chemistry, Probiotics/*metabolism
Metabolism15039348Probiotic bifidobacteria protect mice from lethal infection with Shiga toxin-producing Escherichia coli O157:H7.Asahara T, Shimizu K, Nomoto K, Hamabata T, Ozawa A, Takeda YInfect Immun10.1128/IAI.72.4.2240-2247.20042004Acetic Acid/pharmacology, Animals, Bifidobacterium/*growth & development, Disease Models, Animal, Escherichia coli Infections/microbiology/*prevention & control, Escherichia coli O157/*pathogenicity, Escherichia coli Proteins/metabolism, Gene Expression Regulation, Bacterial, Humans, Hydrogen-Ion Concentration, Intestines/microbiology, Male, Mice, Mice, Inbred BALB C, *Probiotics, Shiga Toxin 1/genetics/*metabolism, Shiga Toxin 2/genetics/*metabolismPathogenicity
Phylogeny26859305Routine Use of Probiotics in Preterm Infants: Longitudinal Impact on the Microbiome and Metabolome.Abdulkadir B, Nelson A, Skeath T, Marrs EC, Perry JD, Cummings SP, Embleton ND, Berrington JE, Stewart CJNeonatology10.1159/0004429362016Bifidobacterium/isolation & purification, Case-Control Studies, *Dietary Supplements, Feces/microbiology, Female, *Gastrointestinal Microbiome, Humans, Infant, Infant, Newborn, *Infant, Premature, Lactobacillus/isolation & purification, Male, *Metabolome, Probiotics/*administration & dosage, RNA, Ribosomal, 16S/analysisEnzymology
Metabolism28814130Identification and characterization of a sulfoglycosidase from Bifidobacterium bifidum implicated in mucin glycan utilization.Katoh T, Maeshibu T, Kikkawa KI, Gotoh A, Tomabechi Y, Nakamura M, Liao WH, Yamaguchi M, Ashida H, Yamamoto K, Katayama TBiosci Biotechnol Biochem10.1080/09168451.2017.13618102017Acetylglucosaminidase/chemistry/genetics/*metabolism, Amino Acid Sequence, Bifidobacterium bifidum/*enzymology/genetics/metabolism, Gene Expression Regulation, Bacterial, Mucins/*metabolism, Polysaccharides/*metabolismEnzymology
Metabolism28974612Bifidobacterium bifidum Extracellular Sialidase Enhances Adhesion to the Mucosal Surface and Supports Carbohydrate Assimilation.Nishiyama K, Yamamoto Y, Sugiyama M, Takaki T, Urashima T, Fukiya S, Yokota A, Okada N, Mukai TmBio10.1128/mBio.00928-172017Animals, *Bacterial Adhesion, Bifidobacterium bifidum/drug effects/*enzymology/genetics/*physiology, *Carbohydrate Metabolism, Colon/microbiology, Epithelial Cells/microbiology, Humans, Mice, Mucins/metabolism, Neuraminidase/*metabolism, Oligosaccharides/chemistry/pharmacology, Polysaccharides/metabolism, Protein Binding, Recombinant Proteins/genetics/metabolism, SwinePathogenicity
Metabolism30228375Sharing of human milk oligosaccharides degradants within bifidobacterial communities in faecal cultures supplemented with Bifidobacterium bifidum.Gotoh A, Katoh T, Sakanaka M, Ling Y, Yamada C, Asakuma S, Urashima T, Tomabechi Y, Katayama-Ikegami A, Kurihara S, Yamamoto K, Harata G, He F, Hirose J, Kitaoka M, Okuda S, Katayama TSci Rep10.1038/s41598-018-32080-32018Adult, Bacterial Proteins/genetics/*metabolism, Bifidobacteriales Infections/*metabolism/microbiology, Bifidobacterium/classification/genetics/*metabolism, Cells, Cultured, Child, Preschool, Dietary Supplements, Feces/*microbiology, Female, Gastrointestinal Microbiome, Genome, Bacterial, Humans, Infant, Male, Milk, Human/*metabolism, Oligosaccharides/*metabolismGenetics
Metabolism30683741Bifidobacterium bifidum ATCC 15696 and Bifidobacterium breve 24b Metabolic Interaction Based on 2'-O-Fucosyl-Lactose Studied in Steady-State Cultures in a Freter-Style Chemostat.Centanni M, Ferguson SA, Sims IM, Biswas A, Tannock GWAppl Environ Microbiol10.1128/AEM.02783-182019Batch Cell Culture Techniques, Bifidobacterium bifidum/genetics/*growth & development/*metabolism, Bifidobacterium breve/genetics/*growth & development/*metabolism, Coculture Techniques, Culture Media/chemistry, Ecosystem, Fucose/metabolism, Gastrointestinal Microbiome, Humans, Intestines/microbiology, Lactose/metabolism, Milk, Human/chemistry, Oligosaccharides/metabolism, Transcriptome, Trisaccharides/*metabolismPathogenicity
Pathogenicity34794372Effectiveness of two probiotics in preventing necrotising enterocolitis in a cohort of very-low-birth-weight premature new-borns.Uberos J, Campos-Martinez A, Fernandez-Marin E, Millan IC, Lopez AR, Blanca-Jover EBenef Microbes10.3920/BM2021.00882021*Enterocolitis, Necrotizing/epidemiology/prevention & control, Humans, Infant, Newborn, Infant, Premature, Infant, Very Low Birth Weight, Lactobacillus acidophilus, *Probiotics/therapeutic use

Reference

@idauthorstitledoi/urljournalpubmedcatalogue
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.StrainInfo introduces electronic passports for microorganisms.10.1016/j.syapm.2013.11.002Syst Appl Microbiol. 37: 42-50 201424321274
37007Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/10170 Collection of Institut Pasteur (CIP 64.65)
65639Curators of the CCUGhttps://www.ccug.se/strain?id=45219Culture Collection University of Gothenburg (CCUG) (CCUG 45219)
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/
68379Automatically annotated from API Coryne
68380Automatically annotated from API rID32A
68381Automatically annotated from API rID32STR
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