Strain identifier

BacDive ID: 24132

Type strain: Yes

Species: Paucilactobacillus hokkaidonensis

Strain Designation: LOOC260

Strain history: CIP <- 2014, DSMZ <- M. Tohno, NARO, Tochigi, Japan: strain LOOC260

NCBI tax ID(s): 1291742 (strain), 1193095 (species)

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General

@ref: 20992

BacDive-ID: 24132

DSM-Number: 26202

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

description: Paucilactobacillus hokkaidonensis LOOC260 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from timothy grass silage.

NCBI tax id

NCBI tax idMatching level
1291742strain
1193095species

strain history

@refhistory
20992<- M. Tohno, National Agriculture and Food Res. Org. (NARO), Nat. Inst. of Livestock and Grassland Science, Tochigi, Japan; LOOC260
67770M. Tohno LOOC260.
67771<- DSM <- M Tohno, National Agriculture and Food Res Org (NARO), Nat. Inst. of Livestock and Grassland Science, Tochigi, Japan, LOOC260
119929CIP <- 2014, DSMZ <- M. Tohno, NARO, Tochigi, Japan: strain LOOC260

doi: 10.13145/bacdive24132.20250331.9.3

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 hokkaidonensis
  • full scientific name: Paucilactobacillus hokkaidonensis (Tohno et al. 2013) Zheng et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Lactobacillus hokkaidonensis

@ref: 20992

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Paucilactobacillus

species: Paucilactobacillus hokkaidonensis

full scientific name: Paucilactobacillus hokkaidonensis (Tohno et al. 2013) Zheng et al. 2020

strain designation: LOOC260

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30898positive2.25 µm1 µmrod-shapedno
67771rod-shapedno
67771positive
125438no93.5
125438positive96.011
119929positiverod-shapedno

pigmentation

  • @ref: 30898
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
41596MEDIUM 40- for Lactobacillus and LeuconostocyesDistilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g)
20992MRS MEDIUM (DSMZ Medium 11)yesName: 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 waterhttps://mediadive.dsmz.de/medium/11
119929CIP Medium 40yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40

culture temp

@refgrowthtypetemperature
20992positivegrowth25
30898positivegrowth04-37
30898positiveoptimum25
41596positivegrowth25
67770positivegrowth30
67771positivegrowth25

culture pH

  • @ref: 30898
  • ability: positive
  • type: growth
  • pH: 4.0-7.0
  • PH range: acidophile

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
20992anaerobe
20992microaerophile
30898facultative anaerobe
67771microaerophile
125439microaerophile96.7

spore formation

  • @ref: 30898
  • spore formation: no

halophily

  • @ref: 30898
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-4 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3089822599arabinose+carbon source
3089817234glucose+carbon source
3089817306maltose+carbon source
30898506227N-acetylglucosamine+carbon source
3089833942ribose+carbon source
3089818222xylose+carbon source
68371Potassium 5-ketogluconate-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
683714853esculin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-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

enzymes

@refvalueactivityec
30898acid phosphatase+3.1.3.2
30898alpha-galactosidase+3.2.1.22

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
20992----+++--+-+----------------+---------------------
20992----+++--+-+----------+/------+---------------------

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
20992timothy grass (Phleum pratense L.) silagePhleum pratenseHokkaidoJapanJPNAsia
67770Timothy grass (Phleum pratense L.) silage producedPhleum pratenseHokkaidoJapanJPNAsia
67771From timothy grass, `Phleum pratense` L. silageHokkaidoJapanJPNAsia
119929Timothy grass, Phleum pratense L. silageHokkaidoJapanJPNAsia

isolation source categories

  • Cat1: #Host
  • Cat2: #Plants
  • Cat3: #Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_1860.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_563;97_653;98_755;99_1860&stattab=map
  • Last taxonomy: Paucilactobacillus hokkaidonensis
  • 16S sequence: LC521988
  • Sequence Identity:
  • Total samples: 2034
  • soil counts: 146
  • aquatic counts: 211
  • animal counts: 1507
  • plant counts: 170

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
209921Risk group (German classification)
1199291Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20992Lactobacillus hokkaidonensis gene for 16S ribosomal RNA, partial sequenceAB7215491502nuccore1291742
67770Lactobacillus hokkaidonensis JCM 18461 gene for 16S rRNA, partial sequenceLC5219881515nuccore1291742

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paucilactobacillus hokkaidonensis JCM 18461 LOOC260GCA_000829395completencbi1291742
66792Paucilactobacillus hokkaidonensis JCM 18461GCA_001311505contigncbi1291742
66792Lactobacillus hokkaidonensis JCM 184611291742.4wgspatric1291742
66792Lactobacillus hokkaidonensis JCM 18461 strain LOOC2601291742.5plasmidpatric1291742
66792Lactobacillus hokkaidonensis JCM 18461 strain LOOC2601291742.6plasmidpatric1291742
66792Lactobacillus hokkaidonensis strain DSM 262021193095.8wgspatric1193095
66792Paucilactobacillus hokkaidonensis DSM 262022660237970draftimg1193095
66792Paucilactobacillus hokkaidonensis LOOC2602651869714completeimg1291742
66792Paucilactobacillus hokkaidonensis JCM 184612728369688draftimg1291742
67771Paucilactobacillus hokkaidonensis DSM 26202GCA_001437505scaffoldncbi1193095

GC content

@refGC-contentmethod
2099239.4high performance liquid chromatography (HPLC)
3089839.4
6777038.1genome sequence analysis
6777039-39.8high performance liquid chromatography (HPLC)
6777139.0-39.08high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthmicroaerophile96.7
125439BacteriaNetgram_stainReaction to gram-stainingpositive83.7
125439BacteriaNetmotilityAbility to perform movementno57
125439BacteriaNetspore_formationAbility to form endo- or exosporesno57.4
125438gram-positivegram-positivePositive reaction to Gram-stainingyes96.011yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no80.19no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no95.428yes
125438spore-formingspore-formingAbility to form endo- or exosporesno87.496yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno99yes
125438motile2+flagellatedAbility to perform flagellated movementno93.5yes

External links

@ref: 20992

culture collection no.: DSM 26202, CIP 110792, JCM 18461, KCTC 21044

straininfo link

  • @ref: 88090
  • straininfo: 390269

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
Metabolism25879859Complete genome sequence and analysis of Lactobacillus hokkaidonensis LOOC260(T), a psychrotrophic lactic acid bacterium isolated from silage.Tanizawa Y, Tohno M, Kaminuma E, Nakamura Y, Arita MBMC Genomics10.1186/s12864-015-1435-22015Bacterial Proteins/genetics/metabolism, Chromosome Mapping, Chromosomes, Bacterial/chemistry/metabolism, Comparative Genomic Hybridization, *Genome, Bacterial, Lactobacillus/classification/*genetics/isolation & purification, NADP/metabolism, NADP Transhydrogenases/genetics/metabolism, Phylogeny, Plasmids/genetics/metabolism, Sequence Analysis, DNA, Silage/*microbiologyPhylogeny
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

@idauthorstitledoi/urlcatalogueID_cross_referencepubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
20992Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-26202Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26202)
30898Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172722828776041
41596Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/30604
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
88090Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID390269.1
119929Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110792Collection of Institut Pasteur (CIP 110792)
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG