Strain identifier

BacDive ID: 6600

Type strain: Yes

Species: Paucilactobacillus vaccinostercus

Strain Designation: X-94

Strain history: CIP <- 1987, DSMZ <- ATCC <- S. Okada: strain X-94

NCBI tax ID(s): 1423813 (strain), 176291 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 8980

BacDive-ID: 6600

DSM-Number: 20634

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

description: Paucilactobacillus vaccinostercus X-94 is an anaerobe, mesophilic bacterium that was isolated from cow dung.

NCBI tax id

NCBI tax idMatching level
176291species
1423813strain

strain history

@refhistory
8980<- ATCC <- S. Okada, X-94
67770M. Kozaki and S. Okada X-94.
123771CIP <- 1987, DSMZ <- ATCC <- S. Okada: strain X-94

doi: 10.13145/bacdive6600.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Lactobacillaceae
  • genus: Paucilactobacillus
  • species: Paucilactobacillus vaccinostercus
  • full scientific name: Paucilactobacillus vaccinostercus (Kozaki and Okada 1983) Zheng et al. 2020

  • synonyms

    @refsynonym
    20215Lactobacillus durianis
    20215Lactobacillus vaccinostercus

@ref: 8980

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Paucilactobacillus

species: Paucilactobacillus vaccinostercus

full scientific name: Paucilactobacillus vaccinostercus (Kozaki and Okada 1983) Zheng et al. 2020

strain designation: X-94

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no95.851
69480100positive

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8980MRS 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
40458MEDIUM 51 - for Lactobacillus vaccinostercusyesDistilled water make up to (1000.000 ml);Man Rogosa Sharp broth (55.000 g);Xylose (10.000 g)
123771CIP Medium 41yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=41

culture temp

@refgrowthtypetemperaturerange
8980positivegrowth30mesophilic
40458positivegrowth37mesophilic
50244positivegrowth30mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 50244
  • oxygen tolerance: anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.99

murein

  • @ref: 8980
  • murein short key: A31
  • type: A1gamma m-Dpm-direct

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
8980cow dung
50244Cow dungKanagawa,Atsugi-shiJapanJPNAsia
67770Cow dung
123771Animal, Dried cow dungTokyoJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Bovinae (Cow, Cattle)
#Host Body Product#Gastrointestinal tract#Feces (Stool)

taxonmaps

  • @ref: 69479
  • File name: preview.99_1677.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_563;97_653;98_1325;99_1677&stattab=map
  • Last taxonomy: Paucilactobacillus vaccinostercus
  • 16S sequence: AM113786
  • Sequence Identity:
  • Total samples: 5611
  • soil counts: 307
  • aquatic counts: 795
  • animal counts: 4111
  • plant counts: 398

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
89801Risk group (German classification)
1237711Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Lactobacillus vaccinostercus gene for 16S rRNA, partial sequence, strain: NRIC 1075 (= ATCC 33310, = JCM 1716)AB3627031479ena176291
20218Lactobacillus vaccinostercus partial 16S rRNA gene, strain DSM 20634AJ417735508ena176291
20218Lactobacillus vaccinostercus partial 16S rRNA gene, strain type strain:DSM 20634AM1137861553ena176291
20218Lactobacillus vaccinostercus gene for 16S rRNA, partial sequence, strain: JCM 1716AB289310639ena176291
20218Lactobacillus vaccinostercus partial 16S rRNA gene, strain LMG 9215TAJ6215561529ena176291
20218Lactobacillus vaccinostercus strain LMG 9215 16S-23S ribosomal RNA intergenic spacer and 23S ribosomal RNA gene, partial sequenceEU161603796ena176291
20218Lactobacillus vaccinostercus gene for 16S rRNA, partial sequence, strain:NRIC 1075AB2120871563ena176291
67770Lactobacillus vaccinostercus gene for 16S ribosomal RNA, partial sequence, strain: JCM 1716LC0718231504ena176291

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lactobacillus vaccinostercus DSM 206341423813.3wgspatric1423813
66792Paucilactobacillus vaccinostercus DSM 206342660237943draftimg1423813
67770Paucilactobacillus vaccinostercus DSM 20634GCA_001436295scaffoldncbi1423813

GC content

@refGC-contentmethod
898036.0
6777043.9genome sequence analysis
6777036

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno93.907no
gram-positiveyes97.103no
anaerobicno93.222no
halophileyes89.987no
spore-formingno92.629no
thermophileno99.613yes
glucose-utilyes90.307no
aerobicno97.575yes
flagellatedno97.23no
glucose-fermentyes87.759no

External links

@ref: 8980

culture collection no.: DSM 20634, ATCC 33310, LMG 9215, NCIMB 11808, NRIC 1075, CCUG 30723, JCM 1716, BCRC 14005, CECT 5925, CIP 102807, KCTC 3608, NCFB 2784, TUA 055B

straininfo link

  • @ref: 76075
  • straininfo: 3385

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23223820Lactobacillus hokkaidonensis sp. nov., isolated from subarctic timothy grass (Phleum pratense L.) silage.Tohno M, Kitahara M, Uegaki R, Irisawa T, Ohkuma M, Tajima KInt J Syst Evol Microbiol10.1099/ijs.0.047027-02012Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Genes, Bacterial, Japan, Lactobacillus/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phleum/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Silage/*microbiologyGenetics
Phylogeny26475452Lactobacillus wasatchensis sp. nov., a non-starter lactic acid bacteria isolated from aged Cheddar cheese.Oberg CJ, Oberg TS, Culumber MD, Ortakci F, Broadbent JR, McMahon DJInt J Syst Evol Microbiol10.1099/ijsem.0.0006892015Bacterial Typing Techniques, Base Composition, Cheese/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fermentation, Lactic Acid/metabolism, Lactobacillus/*classification/genetics/isolation & purification, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8980Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20634)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20634
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
40458Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14535
50244Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 30723)https://www.ccug.se/strain?id=30723
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
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
76075Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID3385.1StrainInfo: A central database for resolving microbial strain identifiers
123771Curators of the CIPCollection of Institut Pasteur (CIP 102807)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20102807