Strain identifier

BacDive ID: 1717

Type strain: Yes

Species: Bifidobacterium pseudolongum

Strain Designation: PNC-2-9G (Biotype a), PNC-2-9G

Strain history: CIP <- 1998, ATCC <- T. Mitsuoka: strain PNC-2-9G

NCBI tax ID(s): 1694 (species), 31954 (subspecies)

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General

@ref: 8525

BacDive-ID: 1717

DSM-Number: 20099

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

description: Bifidobacterium pseudolongum PNC-2-9G is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from pig faeces.

NCBI tax id

NCBI tax idMatching level
31954subspecies
1694species

strain history

@refhistory
8525<- T. Mitsuoka, PNC-2-9G (Biotype a)
67770ATCC 25526 <-- T. Mitsuoka PNC-2-9G (biotype a).
121991CIP <- 1998, ATCC <- T. Mitsuoka: strain PNC-2-9G

doi: 10.13145/bacdive1717.20250331.9.3

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 pseudolongum
  • full scientific name: Bifidobacterium pseudolongum Mitsuoka 1969 (Approved Lists 1980)

@ref: 8525

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Bifidobacteriales

family: Bifidobacteriaceae

genus: Bifidobacterium

species: Bifidobacterium pseudolongum

full scientific name: Bifidobacterium pseudolongum Mitsuoka 1969 emend. Nouioui et al. 2018

strain designation: PNC-2-9G (Biotype a), PNC-2-9G

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
121991positiverod-shapedno
125439positive90.5
125439no91.7
125438no94

colony morphology

  • @ref: 121991

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8525BIFIDOBACTERIUM 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
35803MEDIUM 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)
121991CIP Medium 20yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20

culture temp

@refgrowthtypetemperature
8525positivegrowth37
35803positivegrowth37
52431positivegrowth37
67770positivegrowth37

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
8525anaerobe
52431anaerobe
125439anaerobe92.6

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 94.6

murein

  • @ref: 8525
  • murein short key: A21.02
  • type: A3ß L-Orn(L-Lys)-L-Ala2-3

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1219914853esculin+hydrolysis
12199117632nitrate-reduction
12199116301nitrite-reduction
12199117632nitrate+respiration
68371Potassium 5-ketogluconate-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose+builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen+builds acid from
6837128017starch+builds acid from
6837116634raffinose+builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose+builds acid from
6837128053melibiose+builds acid from
6837117716lactose+builds acid from
6837117306maltose+builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose+builds acid from
6837116988D-ribose+builds acid from
6837130849L-arabinose+builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from

metabolite production

  • @ref: 121991
  • 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
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-galactosidase+3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382cystine arylamidase+3.4.11.3
68382trypsin-3.4.21.4
68382valine arylamidase-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
121991oxidase-
121991beta-galactosidase-3.2.1.23
121991gelatinase-
121991amylase+
121991DNase-
121991caseinase-3.4.21.50
121991catalase-1.11.1.6
121991tween esterase-
121991lecithinase-
121991lipase-
121991urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    52431C12:03.912
    52431C14:018.314
    52431C16:031.616
    52431C18:03.118
    52431C13:0 3OH/C15:1 i I/H2.814.469
    52431C16:1 ω9c4.315.774
    52431C17:0 iso 3OH1.318.161
    52431C17:1 ω5c ISO1.216.461
    52431C18:1 ω6c1.617.858
    52431C18:1 ω9c15.317.769
    52431C18:2 ω6,9c/C18:0 ANTE6.317.724
    52431C19:0 CYCLO ω9c1.518.87
    52431Unidentified8.819.321
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121991--++-+-+--++++-++---

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
8525----+++---+++--------+---+--++++---+++--+---------
121991---+++---++----------------++++---+++--+---------

Isolation, sampling and environmental information

isolation

@refsample type
8525pig faeces
52431Pig feces
67770Swine feces

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Suidae (Pig,Swine)
#Host Body Product#Gastrointestinal tract#Feces (Stool)

taxonmaps

  • @ref: 69479
  • File name: preview.99_3954.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_24;96_1232;97_1460;98_1781;99_3954&stattab=map
  • Last taxonomy: Bifidobacterium pseudolongum subclade
  • 16S sequence: LC071797
  • Sequence Identity:
  • Total samples: 32537
  • soil counts: 398
  • aquatic counts: 229
  • animal counts: 31773
  • plant counts: 137

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
85251Risk group (German classification)
1219911Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bifidobacterium pseudolongum 16S ribosomal RNAM587421475nuccore1694
20218Bifidobacterium pseudolongum ATCC 25526 16S rRNA-23S rRNA intergenic spacerU09879541nuccore1694
20218Bifidobacterium pseudolongum subsp. pseudolongum strain DSM 20099 16S ribosomal RNA gene, partial sequenceGQ487642151nuccore31954
20218Bifidobacterium pseudolongum subsp. pseudolongum gene for 16S rRNA, partial sequence, strain: JCM 1205AB116335472nuccore31954
20218Bifidobacterium pseudolongum subsp. pseudolongum gene for 16S rRNA, partial sequence, strain: JCM 1205AB507141671nuccore31954
20218Bifidobacterium pseudolongum subsp. pseudolongum JCM 1205 gene for 16S rRNA, partial sequenceD861951527nuccore31954
20218Bifidobacterium pseudolongum subsp. pseudolongum strain KCTC 3224 16S ribosomal RNA gene, partial sequenceGU3618291490nuccore31954
20218Bifidobacterium pseudolongum subsp. pseudolongum strain LMG11571 16S ribosomal RNA gene and 16S-23S ribosomal RNA intergenic spacer, partial sequenceFJ231745812nuccore31954
67770Bifidobacterium pseudolongum subsp. pseudolongum gene for 16S ribosomal RNA, partial sequence, strain: JCM 1205LC0717971404nuccore31954

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bifidobacterium pseudolongum subsp. pseudolongum DSM 200991437595.3wgspatric1437595
66792Bifidobacterium pseudolongum subsp. pseudolongum strain LMG 1157131954.3wgspatric31954
66792Bifidobacterium pseudolongum pseudolongum LMG 115712597490262draftimg31954
66792Bifidobacterium pseudolongum pseudolongum DSM 200992663763404draftimg1437595
67770Bifidobacterium pseudolongum subsp. pseudolongum DSM 20099GCA_000771225contigncbi1437595
67770Bifidobacterium pseudolongum subsp. pseudolongum LMG 11571GCA_000741325contigncbi31954
66792Bifidobacterium pseudolongum subsp. pseudolongum ATCC 25526GCA_022691205chromosomencbi31954

GC content

@refGC-contentmethod
852559.5
6777059.5thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes87.121no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)yes83.396no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no94.589no
125438spore-formingspore-formingAbility to form endo- or exosporesno89.777no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno94yes
125438motile2+flagellatedAbility to perform flagellated movementno94no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno94.6
125439BacteriaNetmotilityAbility to perform movementno91.7
125439BacteriaNetgram_stainReaction to gram-stainingpositive90.5
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthanaerobe92.6

External links

@ref: 8525

culture collection no.: DSM 20099, ATCC 25526, CCUG 34981, CCM 7207, JCM 1205, BCRC 14673, CGMCC 1.2185, CIP 105352, KCTC 3224, LMG 11571, NCFB 2244

straininfo link

  • @ref: 71364
  • straininfo: 9647

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Biotechnology11472921Adhesion of bifidobacteria to granular starch and its implications in probiotic technologies.Crittenden R, Laitila A, Forssell P, Matto J, Saarela M, Mattila-Sandholm T, Myllarinen PAppl Environ Microbiol10.1128/AEM.67.8.3469-3475.20012001*Bacterial Adhesion, Bifidobacterium/*physiology, Biotechnology/methods, *Probiotics, Starch/*metabolism, Surface PropertiesMetabolism
33754306Investigation of Antibacterial Activity and Probiotic Properties of Strains Belonging to Lactobacillus and Bifidobacterium Genera for Their Potential Application in Functional Food and Feed Products.Cizeikiene D, Jagelaviciute JProbiotics Antimicrob Proteins10.1007/s12602-021-09777-52021Animal Feed, *Bifidobacterium, *Functional Food, *Lactobacillus, *Probiotics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8525Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20099)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20099
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
35803Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17362
52431Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 34981)https://www.ccug.se/strain?id=34981
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
71364Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID9647.1StrainInfo: A central database for resolving microbial strain identifiers
121991Curators of the CIPCollection of Institut Pasteur (CIP 105352)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105352
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1