Strain identifier

BacDive ID: 1713

Type strain: Yes

Species: Bifidobacterium pseudocatenulatum

Strain Designation: B1279

Strain history: CIP <- 1994, ATCC <- V. Scardovi: strain B1279

NCBI tax ID(s): 547043 (strain), 28026 (species)

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General

@ref: 8813

BacDive-ID: 1713

DSM-Number: 20438

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

description: Bifidobacterium pseudocatenulatum B1279 is an anaerobe, mesophilic bacterium that was isolated from infant faeces.

NCBI tax id

NCBI tax idMatching level
547043strain
28026species

strain history

@refhistory
8813<- ATCC <- V. Scardovi, B1279
67770ATCC 27919 <-- V. Scardovi B1279.
121984CIP <- 1994, ATCC <- V. Scardovi: strain B1279

doi: 10.13145/bacdive1713.20230509.8.1

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 pseudocatenulatum
  • full scientific name: Bifidobacterium pseudocatenulatum Scardovi et al. 1979 (Approved Lists 1980)

@ref: 8813

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Bifidobacteriales

family: Bifidobacteriaceae

genus: Bifidobacterium

species: Bifidobacterium pseudocatenulatum

full scientific name: Bifidobacterium pseudocatenulatum Scardovi et al. 1979 emend. Nouioui et al. 2018

strain designation: B1279

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no92.68
69480100positive
121984nopositiverod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8813BIFIDOBACTERIUM 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
40674MEDIUM 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)
121984CIP Medium 20yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20

culture temp

@refgrowthtypetemperaturerange
8813positivegrowth37mesophilic
40674positivegrowth37mesophilic
52437positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
8813anaerobe
52437anaerobe
69480anaerobe99.706
121984anaerobe

spore formation

@refspore formationconfidence
69481no90
69480no99.993

murein

  • @ref: 8813
  • murein short key: A11.11
  • type: A3alpha L-Lys(L-Orn)-L-Ala2-L-Ser

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
68371sucrose-builds acid from17992
68371lactose+builds acid from17716
68371cellobiose-builds acid from17057
68371esculin+builds acid from4853
68371amygdalin+builds acid from27613
68371N-acetylglucosamine-builds acid from59640
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-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
121984nitrate-reduction17632
121984nitrite-reduction16301

metabolite production

  • @ref: 121984
  • 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
121984oxidase-
121984catalase-1.11.1.6
121984urease-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
121984--+-------++--------

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
8813----+++---++++-----+-+-+-+--+++-----++-++---------
8813----+++---++++/------+-+/--++++--+-----+++-+----------

Isolation, sampling and environmental information

isolation

@refsample typeisolation date
8813infant faeces
52437Infant feces
67770Feces of an infant
121984Human, Infant, feces1974

isolation source categories

Cat1Cat2Cat3
#Infection#Patient
#Host Body Product#Gastrointestinal tract#Feces (Stool)
#Host#Human#Child

taxonmaps

  • @ref: 69479
  • File name: preview.99_1402.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_24;96_811;97_945;98_1109;99_1402&stattab=map
  • Last taxonomy: Actinobacteria
  • 16S sequence: LC071796
  • Sequence Identity:
  • Total samples: 282879
  • soil counts: 5076
  • aquatic counts: 13261
  • animal counts: 262631
  • plant counts: 1911

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
88131Risk group (German classification)
1219841Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bifidobacterium pseudocatenulatum (ATCC 27919) 16S ribosomal RNA gene, partialM84785641ena28026
20218Bifidobacterium pseudocatenulatum DSM 20438 strain JCM 1200 16S ribosomal RNA gene, partial sequenceGQ227711287ena547043
20218Bifidobacterium pseudocatenulatum gene for 16S rRNA, partial sequence, strain: JCM 1200AB507133684ena547043
20218Bifidobacterium pseudocatenulatum gene for 16S rRNA, partial sequence, strain: JCM 1200D861871519ena547043
20218Bifidobacterium pseudocatenulatum strain KCTC 3223 16S ribosomal RNA gene, partial sequenceGU3618271480ena28026
20218Bifidobacterium pseudocatenulatum strain LMG10505 16S ribosomal RNA gene and 16S-23S ribosomal RNA intergenic spacer, partial sequenceFJ231744792ena28026
67770Bifidobacterium pseudocatenulatum gene for 16S ribosomal RNA, partial sequence, strain: JCM 1200LC0717961392ena547043

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bifidobacterium pseudocatenulatum DSM 20438 = JCM 1200 = LMG 10505GCA_001025215completencbi547043
66792Bifidobacterium pseudocatenulatum DSM 20438 = JCM 1200547043.6wgspatric547043
66792Bifidobacterium pseudocatenulatum DSM 20438 = JCM 1200 = LMG 10505547043.16wgspatric547043
66792Bifidobacterium pseudocatenulatum DSM 20438 = JCM 1200 = LMG 10505547043.19completepatric547043
66792Bifidobacterium pseudocatenulatum DSM 20438 = JCM 1200 = LMG 10505547043.20wgspatric547043
66792Bifidobacterium pseudocatenulatum DSM 20438, JCM 1200, LMG 105052597490216draftimg547043
66792Bifidobacterium pseudocatenulatum DSM 20438, JCM 1200, LMG 105052562617145draftimg547043
66792Bifidobacterium pseudocatenulatum DSM 204382695420736draftimg547043
67770Bifidobacterium pseudocatenulatum DSM 20438 = JCM 1200 = LMG 10505GCA_000173435contigncbi547043
67770Bifidobacterium pseudocatenulatum DSM 20438 = JCM 1200 = LMG 10505GCA_000771445contigncbi547043
67770Bifidobacterium pseudocatenulatum DSM 20438 = JCM 1200 = LMG 10505GCA_000741685contigncbi547043

GC content

@refGC-contentmethod
881357.5
6777057.5thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno90no
motileno93.129no
flagellatedno96.197no
gram-positiveyes90.492no
anaerobicyes97.206yes
aerobicno96.319no
halophileno71.491no
spore-formingno94.023no
thermophileno94.315yes
glucose-utilyes87.722no
glucose-fermentyes81.326no

External links

@ref: 8813

culture collection no.: DSM 20438, ATCC 27919, CCUG 34989, JCM 1200, BCRC 15476, CCM 7094, CECT 5776, CGMCC 1.2277, CIP 104168, HAMBI 562, KCTC 3223, LMG 10505, NCAIM B.02022, VTT E-991439

straininfo link

  • @ref: 71360
  • straininfo: 1256

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism19674804Phytate degradation by human gut isolated Bifidobacterium pseudocatenulatum ATCC27919 and its probiotic potential.Haros M, Carlsson NG, Almgren A, Larsson-Alminger M, Sandberg AS, Andlid TInt J Food Microbiol10.1016/j.ijfoodmicro.2009.07.01520096-Phytase/*metabolism, Bacterial Adhesion/*physiology, Bifidobacterium/enzymology/metabolism/*physiology, Caco-2 Cells/microbiology, Humans, Inositol Phosphates/analysis/metabolism, Phytic Acid/*metabolism, Probiotics/*metabolismPathogenicity
Phylogeny21148680Bifidobacterium kashiwanohense sp. nov., isolated from healthy infant faeces.Morita H, Nakano A, Onoda H, Toh H, Oshima K, Takami H, Murakami M, Fukuda S, Takizawa T, Kuwahara T, Ohno H, Tanabe S, Hattori MInt J Syst Evol Microbiol10.1099/ijs.0.024521-02010Bacterial Proteins/genetics/metabolism, Base Composition, Bifidobacterium/*classification/genetics/*isolation & purification, Cellulases/genetics/metabolism, DNA, Bacterial/genetics, Fatty Acids/metabolism, Feces/*microbiology, Humans, Infant, Male, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, beta-Galactosidase/genetics/metabolismMetabolism
Metabolism22582052Novel phytases from Bifidobacterium pseudocatenulatum ATCC 27919 and Bifidobacterium longum subsp. infantis ATCC 15697.Tamayo-Ramos JA, Sanz-Penella JM, Yebra MJ, Monedero V, Haros MAppl Environ Microbiol10.1128/AEM.00782-1220126-Phytase/*genetics/metabolism, Bacterial Proteins/genetics/metabolism, Bifidobacterium/*classification/*enzymology/genetics, Humans, Hydrogen-Ion Concentration, Hydrolysis, Phytic Acid/*metabolism, Polymerase Chain Reaction, *Probiotics, Substrate Specificity, TemperaturePathogenicity
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
Phylogeny24158945Bifidobacterium moukalabense sp. nov., isolated from the faeces of wild west lowland gorilla (Gorilla gorilla gorilla).Tsuchida S, Takahashi S, Nguema PPM, Fujita S, Kitahara M, Yamagiwa J, Ngomanda A, Ohkuma M, Ushida KInt J Syst Evol Microbiol10.1099/ijs.0.055186-02013Animals, Base Composition, Bifidobacterium/*classification/genetics/isolation & purification, Chaperonin 60/genetics, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/*microbiology, Gabon, Genes, Bacterial, Gorilla gorilla/*microbiology, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Metabolism25704711Myo-inositol hexakisphosphate degradation by Bifidobacterium pseudocatenulatum ATCC 27919 improves mineral availability of high fibre rye-wheat sour bread.Garcia-Mantrana I, Monedero V, Haros MFood Chem10.1016/j.foodchem.2015.01.0992015Bifidobacterium/*metabolism, Biological Availability, Bread/analysis/*microbiology, Dietary Fiber/*metabolism, Fermentation, Flour/analysis/microbiology, Humans, Hydrolysis, Inositol Phosphates/chemistry/*metabolism, Minerals/*metabolism, Phytic Acid/metabolism, Secale/metabolism/*microbiology, Triticum/metabolism/microbiologyPathogenicity
Genetics26133926Complete genome sequence of Bifidobacterium pseudocatenulatum JCM 1200(T) isolated from infant feces.Morita H, Toh H, Oshima K, Nakano A, Arakawa K, Takayama Y, Kurokawa R, Takanashi K, Honda K, Hattori MJ Biotechnol10.1016/j.jbiotec.2015.06.4162015Base Composition, Bifidobacterium/*genetics, Feces/*microbiology, Genome Size, *Genome, Bacterial, Humans, Infant, Molecular Sequence Annotation, Molecular Sequence Data, Sequence Analysis, DNA/*methodsPathogenicity
28377750Measurements of Intra- and Extra-Cellular 5-Methyltetrahydrofolate Indicate that Bifidobacterium Adolescentis DSM 20083(T) and Bifidobacterium Pseudocatenulatum DSM 20438(T) Do Not Actively Excrete 5-Methyltetrahydrofolate In vitro.Kopp M, Durr K, Steigleder M, Clavel T, Rychlik MFront Microbiol10.3389/fmicb.2017.004452017

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8813Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20438)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20438
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
40674Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16047
52437Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 34989)https://www.ccug.se/strain?id=34989
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
71360Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID1256.1StrainInfo: A central database for resolving microbial strain identifiers
121984Curators of the CIPCollection of Institut Pasteur (CIP 104168)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104168