Strain identifier

BacDive ID: 1736

Type strain: Yes

Species: Bifidobacterium animalis

Strain Designation: R101-8

Strain history: CIP <- 1998, DSM <- T. Mitsuoka: strain R101-8, Bifidobacterium longum subsp. animalis biotype a

NCBI tax ID(s): 703613 (strain), 28025 (species)

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General

@ref: 8529

BacDive-ID: 1736

DSM-Number: 20104

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

description: Bifidobacterium animalis R101-8 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from rat faeces.

NCBI tax id

NCBI tax idMatching level
28025species
703613strain

strain history

@refhistory
8529<- T. Mitsuoka, R101-8 (Bifidobacterium longum subsp. animalis biotype a)
67770ATCC 25527 <-- T. Mitsuoka R 101-8 ("Bifidobacterium longum subsp. animalis" biotype a).
116391CIP <- 1998, DSM <- T. Mitsuoka: strain R101-8, Bifidobacterium longum subsp. animalis biotype a

doi: 10.13145/bacdive1736.20230509.8.1

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 animalis
  • full scientific name: Bifidobacterium animalis (Mitsuoka 1969) Scardovi and Trovatelli 1974 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Bifidobacterium longum subsp. animalis

@ref: 8529

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Bifidobacteriales

family: Bifidobacteriaceae

genus: Bifidobacterium

species: Bifidobacterium animalis subsp. animalis

full scientific name: Bifidobacterium animalis subsp. animalis (Mitsuoka 1969) Masco et al. 2004

strain designation: R101-8

type strain: yes

Morphology

cell morphology

@refgram stainconfidencemotility
69480positive99.999
116391positiveno

colony morphology

  • @ref: 116391

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8529BIFIDOBACTERIUM 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
39288MEDIUM 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)
116391CIP Medium 20yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20

culture temp

@refgrowthtypetemperaturerange
8529positivegrowth37mesophilic
39288positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
8529anaerobe
69480anaerobe98.855

spore formation

@refspore formationconfidence
69481no100
69480no99.997

murein

  • @ref: 8529
  • murein short key: A11.21
  • type: A3alpha L-Lys(L-Orn)-L-Ala(L-Ser)-L-Ala2

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
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371lactose+builds acid from17716
68371maltose+builds acid from17306
68371cellobiose-builds acid from17057
68371esculin+builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside+builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
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-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
116391D-arabinose+degradation17108
116391D-fructose+degradation15824
116391D-glucose+degradation17634
116391D-xylose+degradation65327
116391cellobiose-degradation17057
116391lactose+degradation17716
116391maltose+degradation17306
116391salicin-degradation17814
116391sucrose+degradation17992
116391esculin-hydrolysis4853
116391nitrate-reduction17632
116391nitrite-reduction16301
116391nitrate+respiration17632

metabolite production

  • @ref: 116391
  • 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
116391oxidase-
116391beta-galactosidase+3.2.1.23
116391gelatinase-
116391amylase-
116391DNase-
116391caseinase-3.4.21.50
116391catalase-1.11.1.6
116391tween esterase-
116391lecithinase-
116391lipase-
116391protease-
116391urease-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
116391--++-+-+--++++-++---

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
8529----+++---+++--------+---++/--++--------------------
8529----+++---++---------+---+--++++---+----+/----------

Isolation, sampling and environmental information

isolation

@refsample type
8529rat faeces
67770Rat feces
116391Animal, Rat, feces

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Muridae (Mouse/Rat)
#Host Body Product#Gastrointestinal tract#Feces (Stool)

taxonmaps

  • @ref: 69479
  • File name: preview.99_3607.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_24;96_259;97_283;98_316;99_3607&stattab=map
  • Last taxonomy: Bifidobacterium animalis subclade
  • 16S sequence: LC065042
  • Sequence Identity:
  • Total samples: 79510
  • soil counts: 1194
  • aquatic counts: 2336
  • animal counts: 75452
  • plant counts: 528

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
85291Risk group (German classification)
1163911Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bifidobacterium animalis ATCC 25527 16S rRNA-23S rRNA intergenic spacerU09858509ena703613
20218B.animalis DNA sequence for 16S rRNAX709711459ena703613
20218Bifidobacterium animalis subsp. animalis strain CCUG 24606 16S ribosomal RNA gene, partial sequenceGQ487634147ena302912
20218Bifidobacterium animalis gene for 16S rRNA, partial sequence, strain: JCM 1190AB116277481ena28025
20218Bifidobacterium animalis subsp. animalis gene for 16S rRNA, partial sequence, strain: JCM 1190AB507070652ena302912
20218Bifidobacterium animalis gene for 16S rRNA, partial sequence, strain: JCM 1190D861851529ena28025
20218Bifidobacterium animalis subsp. animalis strain KCTC 3219 16S ribosomal RNA gene, partial sequenceGU3618121493ena302912
67770Bifidobacterium animalis subsp. animalis gene for 16S ribosomal RNA, partial sequence, strain: JCM 1190LC0650421450ena302912

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bifidobacterium animalis subsp. animalis ATCC 25527GCA_000260715completencbi703613
66792Bifidobacterium animalis subsp. animalis ATCC 25527703613.4completepatric703613
66792Bifidobacterium animalis subsp. animalis strain LMG 10508302912.4wgspatric302912
66792Bifidobacterium animalis animalis ATCC 255272513237236completeimg703613
66792Bifidobacterium animalis animalis LMG 105082597490250draftimg302912
67770Bifidobacterium animalis subsp. animalis LMG 10508GCA_000741485contigncbi302912

GC content

@refGC-contentmethod
852960.1
6777061.4high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno93.782no
flagellatedno97.405no
gram-positiveyes91.255no
anaerobicyes98.546yes
aerobicno97.698no
halophileno63.821no
spore-formingno96.46no
glucose-utilyes83.046no
thermophileno96.434yes
glucose-fermentyes81.328no

External links

@ref: 8529

culture collection no.: DSM 20104, ATCC 25527, CIP 105419, JCM 1190, BCRC 14668, CCUG 24606, CGMCC 1.2268, KCTC 3125, LMG 10508, NCFB 2242, VTT E-96663, ISL 120

straininfo link

  • @ref: 71383
  • straininfo: 1236

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny7767228Characterization of fructose 6 phosphate phosphoketolases purified from Bifidobacterium species.Grill JP, Crociani J, Ballongue JCurr Microbiol10.1007/BF002946341995Adenosine Diphosphate/pharmacology, Adenosine Triphosphate/pharmacology, Aldehyde-Lyases/drug effects/*isolation & purification/metabolism, Bifidobacterium/drug effects/*enzymology/metabolism, Enzyme Inhibitors/*pharmacology, Methylene Blue/pharmacology, Molecular Weight, Organophosphates/metabolism, Species SpecificityMetabolism
Phylogeny11128064Bifidobacterium lactis Meile et al. 1997 is a subjective synonym of Bifidobacterium animalis (Mitsuoka 1969) Scardovi and Trovatelli 1974.Cai Y, Matsumoto M, Benno YMicrobiol Immunol10.1111/j.1348-0421.2000.tb02568.x2000Bifidobacterium/*classification/*genetics, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Terminology as TopicGenetics
Phylogeny12450873Rapid identification, differentiation, and proposed new taxonomic classification of Bifidobacterium lactis.Ventura M, Zink RAppl Environ Microbiol10.1128/AEM.68.12.6429-6434.20022002Animals, Base Sequence, Bifidobacterium/*classification/genetics/isolation & purification, Electrophoresis, Gel, Pulsed-Field, Humans, Molecular Sequence Data, Polymerase Chain ReactionEnzymology
Phylogeny15280282Polyphasic taxonomic analysis of Bifidobacterium animalis and Bifidobacterium lactis reveals relatedness at the subspecies level: reclassification of Bifidobacterium animalis as Bifidobacterium animalis subsp. animalis subsp. nov. and Bifidobacterium lactis as Bifidobacterium animalis subsp. lactis subsp. nov.Masco L, Ventura M, Zink R, Huys G, Swings JInt J Syst Evol Microbiol10.1099/ijs.0.03011-02004Animals, Bacterial Proteins/analysis/genetics, Bifidobacterium/*classification/genetics/growth & development/metabolism, Chaperonin 60/genetics, Colony Count, Microbial, DNA Fingerprinting, DNA, Bacterial/analysis/chemistry/isolation & purification, Genotype, Humans, Milk/metabolism, Molecular Sequence Data, Nucleic Acid Amplification Techniques, Phenotype, Phylogeny, Proteome, Sequence Analysis, DNA, Sequence HomologyGenetics
Pathogenicity15808363A dynamic model that simulates the human upper gastrointestinal tract for the study of probiotics.Mainville I, Arcand Y, Farnworth ERInt J Food Microbiol10.1016/j.ijfoodmicro.2004.08.0202005Bifidobacterium/growth & development/*physiology, Colony Count, Microbial, Digestion, Gastrointestinal Tract/*microbiology, Gastrointestinal Transit, Humans, Hydrogen-Ion Concentration, Lactobacillus/growth & development/*physiology, Models, Biological, *Probiotics, Regression Analysis, Time Factors
Genetics22118077Short communication: the complete genome sequence of Bifidobacterium animalis subspecies animalis ATCC 25527(T) and comparative analysis of growth in milk with B. animalis subspecies lactis DSM 10140(T).Loquasto JR, Barrangou R, Dudley EG, Roberts RFJ Dairy Sci10.3168/jds.2011-44992011Animals, Base Sequence, Bifidobacterium/*genetics/growth & development, DNA, Intergenic/genetics, Genome, Bacterial/*genetics, Inverted Repeat Sequences/genetics, Milk/*microbiology, Molecular Sequence Data, Sequence Alignment, Sequence Analysis, DNA/methods, Sequence Homology, Nucleic AcidTranscriptome
Metabolism22335359The potential of bifidobacteria as a source of natural folate.D'Aimmo MR, Mattarelli P, Biavati B, Carlsson NG, Andlid TJ Appl Microbiol10.1111/j.1365-2672.2012.05261.x2012Animals, Bifidobacterium/genetics/*growth & development/metabolism, Chromatography, High Pressure Liquid, Culture Media, Dairy Products/microbiology, Fermentation, Folic Acid/analysis/genetics/*metabolism, Humans, Intestinal Mucosa/metabolism, Intestines/chemistry/*microbiology, Metagenome, ProbioticsCultivation
Genetics30306201Staying alive: growth and survival of Bifidobacterium animalis subsp. animalis under in vitro and in vivo conditions.Egan M, Bottacini F, O'Connell Motherway M, Casey PG, Morrissey R, Melgar S, Faurie JM, Chervaux C, Smokvina T, van Sinderen DAppl Microbiol Biotechnol10.1007/s00253-018-9413-72018Animals, Bifidobacterium animalis/drug effects/*genetics/*growth & development, Carbohydrate Metabolism, Drug Resistance, Microbial, Female, Food Microbiology/*methods, Gastrointestinal Microbiome, Gene Expression Profiling, Gene Expression Regulation, Bacterial, Genome, Bacterial, Mice, Inbred BALB C, Milk/*microbiology, ProbioticsPathogenicity
Phylogeny32804603Bifidobacterium canis sp. nov., a novel member of the Bifidobacterium pseudolongum phylogenetic group isolated from faeces of a dog (Canis lupus f. familiaris).Neuzil-Bunesova V, Lugli GA, Modrackova N, Makovska M, Mrazek J, Mekadim C, Musilova S, Svobodova I, Spanek R, Ventura M, Killer JInt J Syst Evol Microbiol10.1099/ijsem.0.0043782020Aldehyde-Lyases, Animals, Bacterial Typing Techniques, Base Composition, Bifidobacterium/*classification, DNA, Bacterial/genetics, Dogs/*microbiology, Feces/microbiology, Genes, Bacterial, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome
Pathogenicity33135616Modulation of Proinflammatory Bacteria- and Lipid-Coupled Intracellular Signaling Pathways in a Transwell Triple Co-Culture Model by Commensal Bifidobacterium Animalis R101-8.Ghadimi D, Nielsen A, Hassan MFY, Folster-Holst R, Ebsen M, Frahm SO, Rocken C, de Vrese M, Heller KJAntiinflamm Antiallergy Agents Med Chem10.2174/18715230199992010291156182021Bifidobacterium animalis/*metabolism, Biomarkers, Cell Line, Coculture Techniques, Cytokines/biosynthesis, Humans, Inflammation/*physiopathology, Inflammation Mediators/*metabolism, Lipid Metabolism/genetics/*physiology, Lipopolysaccharides/pharmacology, Signal Transduction/*physiologyMetabolism
Metabolism34132282Different effects of soybean protein and its derived peptides on the growth and metabolism of Bifidobacterium animalis subsp. animalis JCM 1190.Li W, Li H, Zhang Y, He L, Zhang C, Liu XFood Funct10.1039/d1fo00480h2021Bifidobacterium animalis/*drug effects/*growth & development/*metabolism, Escherichia coli, Metabolic Networks and Pathways/drug effects, Nitrogen, Peptides/chemistry/*pharmacology, Probiotics, Soybean Proteins/*chemistry, Soybeans/chemistryPathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8529Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20104)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20104
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
39288Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17437
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
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
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
71383Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID1236.1StrainInfo: A central database for resolving microbial strain identifiers
116391Curators of the CIPCollection of Institut Pasteur (CIP 105419)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105419