Strain identifier

BacDive ID: 1748

Type strain: No

Species: Bifidobacterium adolescentis

Strain Designation: Eg1

Strain history: M.-S. Kim Eg1.

NCBI tax ID(s): 1437612 (strain), 1680 (species)

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General

@ref: 17786

BacDive-ID: 1748

DSM-Number: 24849

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

description: Bifidobacterium adolescentis Eg1 is an anaerobe, mesophilic, Gram-positive human pathogen that was isolated from feces of a healthy, 27-year-old male.

NCBI tax id

NCBI tax idMatching level
1680species
1437612strain

strain history

@refhistory
17786<- JCM <- M.-S. Kim, Kyung Hee Univ., Seoul, Republic of Korea; Eg1
67770M.-S. Kim Eg1.

doi: 10.13145/bacdive1748.20230509.8.1

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

  • synonyms

    • @ref: 20215
    • synonym: Bifidobacterium stercoris

@ref: 17786

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Bifidobacteriales

family: Bifidobacteriaceae

genus: Bifidobacterium

species: Bifidobacterium adolescentis

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

strain designation: Eg1

type strain: no

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29746positive04-06 µm1 µmrod-shapedno
69480positive100

pigmentation

  • @ref: 29746
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 17786
  • name: BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/58
  • composition: Name: 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

culture temp

@refgrowthtypetemperaturerange
29746positivegrowth37mesophilic
17786positivegrowth37mesophilic
29746positiveoptimum37mesophilic
67770positivegrowth37mesophilic

culture pH

@refabilitytypepH
29746positivegrowth6.8
29746positiveoptimum6.8

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
17786anaerobe
29746anaerobe
69480anaerobe99.723

spore formation

@refspore formationconfidence
29746no
69481no100
69480no99.998

observation

  • @ref: 29746
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2974622599arabinose+carbon source
2974617057cellobiose+carbon source
2974617234glucose+carbon source
2974628087glycogen+carbon source
2974617716lactose+carbon source
2974617306maltose+carbon source
2974629864mannitol+carbon source
2974628053melibiose+carbon source
2974616634raffinose+carbon source
2974633942ribose+carbon source
2974617814salicin+carbon source
2974627082trehalose+carbon source
2974618222xylose+carbon source
297464853esculin+hydrolysis
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-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
683714853esculin+builds acid from
6837118305arbutin+builds acid from
6837127613amygdalin+builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside+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
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+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

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
17786----+++---+++-----+--+-+++++++++++++++-++------+/---

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
17786feces of a healthy, 27-year-old maleRepublic of KoreaKORAsia
67770Feces of a healthy, 27-year-old male

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_3042.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_24;96_920;97_1072;98_1898;99_3042&stattab=map
  • Last taxonomy: Bifidobacterium
  • 16S sequence: KF147852
  • Sequence Identity:
  • Total samples: 38958
  • soil counts: 167
  • aquatic counts: 1297
  • animal counts: 37409
  • plant counts: 85

Safety information

risk assessment

  • @ref: 17786
  • pathogenicity human: yes, in single cases
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bifidobacterium stercoris strain Eg1 16S ribosomal RNA gene, partial sequenceKF1478521523ena1437612
17786Bifidobacterium stercoris strain Eg1 16S ribosomal RNA gene, partial sequenceFJ6117931416ena1437612

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bifidobacterium stercoris JCM 159181437612.3wgspatric1437612
66792Bifidobacterium stercoris strain DSM 24849592977.3wgspatric1680
66792Bifidobacterium stercoris JCM 159182671180988draftimg1437612
66792Bifidobacterium stercoris DSM 248492597490242draftimg1437612
67770Bifidobacterium adolescentis JCM 15918GCA_000771705contigncbi1437612
67770Bifidobacterium adolescentis JCM 15918GCA_000741415contigncbi1437612

GC content

@refGC-contentmethod
1778660.6high performance liquid chromatography (HPLC)
1778657.8thermal denaturation, midpoint method (Tm)
2974657.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno92.931yes
gram-positiveyes92.746yes
anaerobicyes98.175no
halophileno74.798no
spore-formingno95.92no
glucose-utilyes86.075no
thermophileno96.744yes
aerobicno97.834yes
flagellatedno95.965no
glucose-fermentyes84.926no

External links

@ref: 17786

culture collection no.: DSM 24849, JCM 15918, KCTC 5756, BCRC 80257

straininfo link

  • @ref: 71395
  • straininfo: 374227

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20081020Bifidobacterium stercoris sp. nov., isolated from human faeces.Kim MS, Roh SW, Bae JWInt J Syst Evol Microbiol10.1099/ijs.0.019943-02010Adult, Aldehyde-Lyases/metabolism, Bacterial Typing Techniques, Base Composition, Bifidobacterium/*classification/genetics/isolation & purification, Chaperonin 60/genetics, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/*microbiology, Humans, Male, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAPathogenicity
Phylogeny24187022Reclassification of Bifidobacterium stercoris Kim et al. 2010 as a later heterotypic synonym of Bifidobacterium adolescentis.Killer J, Sedlacek I, Rada V, Havlik J, Kopecny JInt J Syst Evol Microbiol10.1099/ijs.0.054957-02013Aldehyde-Lyases/genetics, Bacterial Typing Techniques, Bifidobacterium/*classification/genetics, DNA Gyrase/genetics, DNA, Bacterial/genetics, DNA-Directed RNA Polymerases/genetics, Molecular Sequence Data, Multilocus Sequence Typing, Nucleic Acid Hybridization, Peptide Elongation Factor G/genetics, Phenotype, *Phylogeny, RNA, Ribosomal, 16S/genetics, Ribosomal Proteins/genetics, Sequence Analysis, DNAGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
17786Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24849)https://www.dsmz.de/collection/catalogue/details/culture/DSM-24849
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
29746Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604126128
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
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
71395Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID374227.1StrainInfo: A central database for resolving microbial strain identifiers