Strain identifier

BacDive ID: 6536

Type strain: Yes

Species: Lactobacillus hamsteri

Strain Designation: Ha5F1

Strain history: CIP <- 1989, JCM <- T. Fujisawa: strain Ha5F1

NCBI tax ID(s): 1423754 (strain), 96565 (species)

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General

@ref: 2149

BacDive-ID: 6536

DSM-Number: 5661

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

description: Lactobacillus hamsteri Ha5F1 is an anaerobe, mesophilic bacterium that was isolated from faeces of hamster.

NCBI tax id

NCBI tax idMatching level
96565species
1423754strain

strain history

@refhistory
2149<- JCM <- Fujisawa, Ha5F1
67770T. Fujisawa Ha5F1.
119832CIP <- 1989, JCM <- T. Fujisawa: strain Ha5F1

doi: 10.13145/bacdive6536.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Lactobacillaceae
  • genus: Lactobacillus
  • species: Lactobacillus hamsteri
  • full scientific name: Lactobacillus hamsteri Mitsuoka and Fujisawa 1988

@ref: 2149

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Lactobacillus

species: Lactobacillus hamsteri

full scientific name: Lactobacillus hamsteri Mitsuoka and Fujisawa 1988

strain designation: Ha5F1

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no92.609
69480100positive

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2149MRS MEDIUM (DSMZ Medium 11)yeshttps://mediadive.dsmz.de/medium/11Name: MRS MEDIUM (DSMZ Medium 11) Composition: Glucose 20.0 g/l Casein peptone 10.0 g/l Meat extract 10.0 g/l Na-acetate 5.0 g/l Yeast extract 5.0 g/l (NH4)3 citrate 2.0 g/l K2HPO4 2.0 g/l Tween 80 1.0 g/l MgSO4 x 7 H2O 0.2 g/l MnSO4 x H2O 0.05 g/l Distilled water
39674MEDIUM 43 - for Lactobacillus hamsteri and Lactobacillus ruminisyesDistilled water make up to (900.000 ml);Man Rogosa Sharp broth (55.000 g);Cysteine hydrochloride 5 % solution - M0172 (100.000 ml)
119832CIP Medium 41yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=41

culture temp

@refgrowthtypetemperaturerange
2149positivegrowth37mesophilic
39674positivegrowth37mesophilic
50247positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
2149anaerobe
50247anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.968

murein

  • @ref: 2149
  • murein short key: A11.31
  • type: A4alpha L-Lys-D-Asp

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    50247C14:03.114
    50247C16:031.816
    50247C18:012.118
    50247C16:1 ω7c2.615.819
    50247C18:1 ω9c22.717.769
    50247C18:2 ω6,9c/C18:0 ANTE24.217.724
    50247C19:0 CYCLO ω9c3.518.87
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

Isolation, sampling and environmental information

isolation

@refsample type
2149faeces of hamster
50247Hamster feces
67770Hamster feces
119832Animal, Hamster, feces

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Rodentia (Other)
#Host Body Product#Gastrointestinal tract#Feces (Stool)

taxonmaps

  • @ref: 69479
  • File name: preview.99_4128.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_46;96_1120;97_2520;98_3118;99_4128&stattab=map
  • Last taxonomy: Lactobacillus
  • 16S sequence: LC071843
  • Sequence Identity:
  • Total samples: 2166
  • soil counts: 17
  • aquatic counts: 12
  • animal counts: 2099
  • plant counts: 38

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
21491Risk group (German classification)
1198321Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Lactobacillus hamsteri 16S-23S ribosomal RNA intergenic spacer region, complete sequenceAF113601202ena96565
20218Lactobacillus hamsteri partial 16S rRNA gene, type strain JCM 6256TFR6830941494ena96565
20218Lactobacillus hamsteri 16S rRNA gene, strain DSM 5661TAJ3062981510ena96565
20218Lactobacillus hamsteri gene for 16S rRNA, partial sequence, strain: JCM 6256AB289146664ena96565
67770Lactobacillus hamsteri gene for 16S ribosomal RNA, partial sequence, strain: JCM 6256LC0718431496ena96565

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lactobacillus hamsteri DSM 5661 = JCM 62561423754.3wgspatric1423754
66792Lactobacillus hamsteri JCM 62561236945.3wgspatric1423754
66792Lactobacillus hamsteri DSM 56612700989155draftimg1423754
66792Lactobacillus hamsteri JCM 62562585427879draftimg1423754
67770Lactobacillus hamsteri DSM 5661 = JCM 6256GCA_001434515scaffoldncbi1423754
67770Lactobacillus hamsteri DSM 5661 = JCM 6256GCA_000615445contigncbi1423754

GC content

@refGC-contentmethod
6777035.1genome sequence analysis
6777033.1

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno95.612no
gram-positiveyes96.815no
anaerobicyes87.181yes
halophileyes88.046no
spore-formingno97.158no
glucose-utilyes93.024no
thermophileno99.593yes
aerobicno97.974yes
flagellatedno98.227no
glucose-fermentyes92.284no

External links

@ref: 2149

culture collection no.: DSM 5661, ATCC 43851, JCM 6256, CCUG 30726, LMG 10754, BCRC 14740, CIP 103365, KCTC 5066, NCFB 2795, NCIMB 702795

straininfo link

  • @ref: 76008
  • straininfo: 3303

literature

  • topic: Phylogeny
  • Pubmed-ID: 31560297
  • title: Lactobacillus xujianguonis sp. nov., isolated from faeces of Marmota himalayana.
  • authors: Meng J, Jin D, Yang J, Lai XH, Pu J, Zhu W, Huang Y, Liang H, Lu S
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.003598
  • year: 2020
  • mesh: Animals, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/microbiology, Genes, Bacterial, Lactobacillus/*classification/isolation & purification, Marmota/*microbiology, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Tibet
  • topic2: Transcriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2149Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5661)https://www.dsmz.de/collection/catalogue/details/culture/DSM-5661
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
39674Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15154
50247Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 30726)https://www.ccug.se/strain?id=30726
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/
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
76008Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID3303.1StrainInfo: A central database for resolving microbial strain identifiers
119832Curators of the CIPCollection of Institut Pasteur (CIP 103365)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103365