Strain identifier
BacDive ID: 24132
Type strain:
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)
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 id | Matching level |
---|---|
1193095 | species |
1291742 | strain |
strain history
@ref | history |
---|---|
20992 | <- M. Tohno, National Agriculture and Food Res. Org. (NARO), Nat. Inst. of Livestock and Grassland Science, Tochigi, Japan; LOOC260 |
67770 | M. Tohno LOOC260. |
67771 | <- DSM <- M Tohno, National Agriculture and Food Res Org (NARO), Nat. Inst. of Livestock and Grassland Science, Tochigi, Japan, LOOC260 |
119929 | CIP <- 2014, DSMZ <- M. Tohno, NARO, Tochigi, Japan: strain LOOC260 |
doi: 10.13145/bacdive24132.20230509.8.1
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 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
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
30898 | positive | 2.25 µm | 1 µm | rod-shaped | no | |
67771 | rod-shaped | no | ||||
67771 | positive | |||||
69480 | no | 97.437 | ||||
69480 | positive | 100 | ||||
119929 | positive | rod-shaped | no |
pigmentation
- @ref: 30898
- production: yes
Culture and growth conditions
culture medium
@ref | name | growth | composition | link |
---|---|---|---|---|
41596 | MEDIUM 40- for Lactobacillus and Leuconostoc | yes | Distilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g) | |
20992 | MRS MEDIUM (DSMZ Medium 11) | yes | Name: 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 | https://mediadive.dsmz.de/medium/11 |
119929 | CIP Medium 40 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
20992 | positive | growth | 25 | mesophilic |
30898 | positive | growth | 04-37 | |
30898 | positive | optimum | 25 | mesophilic |
41596 | positive | growth | 25 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
67771 | positive | growth | 25 | mesophilic |
culture pH
- @ref: 30898
- ability: positive
- type: growth
- pH: 4.0-7.0
- PH range: acidophile
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
20992 | anaerobe |
20992 | microaerophile |
30898 | facultative anaerobe |
67771 | microaerophile |
spore formation
@ref | spore formation | confidence |
---|---|---|
30898 | no | |
69481 | no | 100 |
69480 | no | 99.997 |
halophily
- @ref: 30898
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-4 %
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
30898 | 22599 | arabinose | + | carbon source |
30898 | 17234 | glucose | + | carbon source |
30898 | 17306 | maltose | + | carbon source |
30898 | 506227 | N-acetylglucosamine | + | carbon source |
30898 | 33942 | ribose | + | carbon source |
30898 | 18222 | xylose | + | carbon source |
68371 | Potassium 5-ketogluconate | - | builds acid from | |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | 24265 | gluconate | - | builds acid from |
68371 | 18403 | L-arabitol | - | builds acid from |
68371 | 18333 | D-arabitol | - | builds acid from |
68371 | 18287 | L-fucose | - | builds acid from |
68371 | 28847 | D-fucose | - | builds acid from |
68371 | 16443 | D-tagatose | - | builds acid from |
68371 | 62318 | D-lyxose | - | builds acid from |
68371 | 32528 | turanose | - | builds acid from |
68371 | 28066 | gentiobiose | - | builds acid from |
68371 | 17151 | xylitol | - | builds acid from |
68371 | 28087 | glycogen | - | builds acid from |
68371 | 28017 | starch | - | builds acid from |
68371 | 16634 | raffinose | - | builds acid from |
68371 | 6731 | melezitose | - | builds acid from |
68371 | 15443 | inulin | - | builds acid from |
68371 | 27082 | trehalose | - | builds acid from |
68371 | 17992 | sucrose | - | builds acid from |
68371 | 28053 | melibiose | - | builds acid from |
68371 | 17716 | lactose | - | builds acid from |
68371 | 17306 | maltose | + | builds acid from |
68371 | 17057 | cellobiose | - | builds acid from |
68371 | 17814 | salicin | - | builds acid from |
68371 | 4853 | esculin | - | builds acid from |
68371 | 18305 | arbutin | - | builds acid from |
68371 | 27613 | amygdalin | - | builds acid from |
68371 | 320061 | methyl alpha-D-glucopyranoside | - | builds acid from |
68371 | 43943 | methyl alpha-D-mannoside | - | builds acid from |
68371 | 17924 | D-sorbitol | - | builds acid from |
68371 | 16899 | D-mannitol | - | builds acid from |
68371 | 17268 | myo-inositol | - | builds acid from |
68371 | 16813 | galactitol | - | builds acid from |
68371 | 62345 | L-rhamnose | - | builds acid from |
68371 | 17266 | L-sorbose | - | builds acid from |
68371 | 16024 | D-mannose | - | builds acid from |
68371 | 15824 | D-fructose | - | builds acid from |
68371 | 17634 | D-glucose | + | builds acid from |
68371 | 12936 | D-galactose | - | builds acid from |
68371 | 74863 | methyl beta-D-xylopyranoside | + | builds acid from |
68371 | 15963 | ribitol | - | builds acid from |
68371 | 65328 | L-xylose | - | builds acid from |
68371 | 65327 | D-xylose | + | builds acid from |
68371 | 16988 | D-ribose | + | builds acid from |
68371 | 30849 | L-arabinose | + | builds acid from |
68371 | 17108 | D-arabinose | - | builds acid from |
68371 | 17113 | erythritol | - | builds acid from |
68371 | 17754 | glycerol | - | builds acid from |
enzymes
@ref | value | activity | ec |
---|---|---|---|
30898 | acid phosphatase | + | 3.1.3.2 |
30898 | alpha-galactosidase | + | 3.2.1.22 |
API 50CHac
@ref | Q | GLY | ERY | DARA | LARA | RIB | DXYL | LXYL | ADO | MDX | GAL | GLU | FRU | MNE | SBE | RHA | DUL | INO | MAN | SOR | MDM | MDG | NAG | AMY | ARB | ESC | SAL | CEL | MAL | LAC | MEL | SAC | TRE | INU | MLZ | RAF | AMD | GLYG | XLT | GEN | TUR | LYX | TAG | DFUC | LFUC | DARL | LARL | GNT | 2KG | 5KG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
20992 | - | - | - | - | + | + | + | - | - | + | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
20992 | - | - | - | - | + | + | + | - | - | + | - | + | - | - | - | - | - | - | - | - | - | - | +/- | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | geographic location | country | origin.country | continent |
---|---|---|---|---|---|---|
20992 | timothy grass (Phleum pratense L.) silage | Phleum pratense | Hokkaido | Japan | JPN | Asia |
67770 | Timothy grass (Phleum pratense L.) silage produced | Phleum pratense | Hokkaido | Japan | JPN | Asia |
67771 | From timothy grass, `Phleum pratense` L. silage | Hokkaido | Japan | JPN | Asia | |
119929 | Timothy grass, Phleum pratense L. silage | Hokkaido | Japan | JPN | Asia |
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
@ref | biosafety level | biosafety level comment |
---|---|---|
20992 | 1 | Risk group (German classification) |
119929 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20992 | Lactobacillus hokkaidonensis gene for 16S ribosomal RNA, partial sequence | AB721549 | 1502 | ena | 1291742 |
67770 | Lactobacillus hokkaidonensis JCM 18461 gene for 16S rRNA, partial sequence | LC521988 | 1515 | ena | 1291742 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Paucilactobacillus hokkaidonensis JCM 18461 LOOC260 | GCA_000829395 | complete | ncbi | 1291742 |
66792 | Paucilactobacillus hokkaidonensis JCM 18461 | GCA_001311505 | contig | ncbi | 1291742 |
66792 | Lactobacillus hokkaidonensis JCM 18461 | 1291742.4 | wgs | patric | 1291742 |
66792 | Lactobacillus hokkaidonensis JCM 18461 strain LOOC260 | 1291742.5 | plasmid | patric | 1291742 |
66792 | Lactobacillus hokkaidonensis JCM 18461 strain LOOC260 | 1291742.6 | plasmid | patric | 1291742 |
66792 | Lactobacillus hokkaidonensis strain DSM 26202 | 1193095.8 | wgs | patric | 1193095 |
66792 | Paucilactobacillus hokkaidonensis DSM 26202 | 2660237970 | draft | img | 1193095 |
66792 | Paucilactobacillus hokkaidonensis LOOC260 | 2651869714 | complete | img | 1291742 |
66792 | Paucilactobacillus hokkaidonensis JCM 18461 | 2728369688 | draft | img | 1291742 |
67771 | Paucilactobacillus hokkaidonensis DSM 26202 | GCA_001437505 | scaffold | ncbi | 1193095 |
GC content
@ref | GC-content | method |
---|---|---|
20992 | 39.4 | high performance liquid chromatography (HPLC) |
30898 | 39.4 | |
67770 | 38.1 | genome sequence analysis |
67770 | 39-39.8 | high performance liquid chromatography (HPLC) |
67771 | 39.0-39.08 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 96.368 | yes |
flagellated | no | 98.332 | yes |
gram-positive | yes | 96.233 | yes |
anaerobic | no | 95.43 | no |
aerobic | no | 96.165 | no |
halophile | yes | 94.333 | no |
spore-forming | no | 93.878 | yes |
glucose-util | yes | 88.147 | no |
thermophile | no | 99.69 | yes |
glucose-ferment | yes | 89.25 | no |
External links
@ref: 20992
culture collection no.: DSM 26202, CIP 110792, JCM 18461, KCTC 21044
straininfo link
- @ref: 88090
- straininfo: 390269
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 23223820 | Lactobacillus hokkaidonensis sp. nov., isolated from subarctic timothy grass (Phleum pratense L.) silage. | Tohno M, Kitahara M, Uegaki R, Irisawa T, Ohkuma M, Tajima K | Int J Syst Evol Microbiol | 10.1099/ijs.0.047027-0 | 2012 | Bacterial 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/*microbiology | Genetics |
Metabolism | 25879859 | Complete 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 M | BMC Genomics | 10.1186/s12864-015-1435-2 | 2015 | Bacterial 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/*microbiology | Phylogeny |
Phylogeny | 26475452 | Lactobacillus 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 DJ | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000689 | 2015 | Bacterial 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, DNA | Genetics |
Reference
@id | authors | title | doi/url | catalogue | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | |||
20992 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-26202 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26202) | |||
30898 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 27228 | 28776041 | |
41596 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/30604 | ||||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
68371 | Automatically annotated from API 50CH acid | |||||
69479 | João 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 beta | https://microbeatlas.org/ | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |||
88090 | Reimer, 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 identifiers | 10.60712/SI-ID390269.1 | |||
119929 | Curators of the CIP | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110792 | Collection of Institut Pasteur (CIP 110792) |