Strain identifier
BacDive ID: 6646
Type strain:
Species: Ligilactobacillus apodemi
Strain Designation: ASB1, ASB-1
Strain history: CIP <- 2005, DSMZ <- R. Osawa, Kobe Univ., Kobe, Japan: strain ASB-1
NCBI tax ID(s): 307126 (species)
General
@ref: 6537
BacDive-ID: 6646
DSM-Number: 16634
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive, rod-shaped
description: Ligilactobacillus apodemi ASB1 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from feces, wild Japanese wood mouse.
NCBI tax id
- NCBI tax id: 307126
- Matching level: species
strain history
@ref | history |
---|---|
6537 | <- R. Osawa; ASB1 |
67770 | CIP 108913 <-- DSM 16634 <-- R. Osawa ASB1. |
116423 | CIP <- 2005, DSMZ <- R. Osawa, Kobe Univ., Kobe, Japan: strain ASB-1 |
doi: 10.13145/bacdive6646.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Lactobacillales
- family: Lactobacillaceae
- genus: Ligilactobacillus
- species: Ligilactobacillus apodemi
- full scientific name: Ligilactobacillus apodemi (Osawa et al. 2006) Zheng et al. 2020
synonyms
- @ref: 20215
- synonym: Lactobacillus apodemi
@ref: 6537
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Lactobacillales
family: Lactobacillaceae
genus: Ligilactobacillus
species: Ligilactobacillus apodemi
full scientific name: Ligilactobacillus apodemi (Osawa et al. 2006) Zheng et al. 2020
strain designation: ASB1, ASB-1
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
31735 | positive | 05-06 µm | 0.5-1 µm | rod-shaped | no | |
69480 | positive | 100 | ||||
116423 | positive | rod-shaped | no |
pigmentation
- @ref: 31735
- production: yes
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
6537 | MRS MEDIUM (DSMZ Medium 11) | yes | https://mediadive.dsmz.de/medium/11 | 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 |
38184 | MEDIUM 40- for Lactobacillus and Leuconostoc | yes | Distilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g) | |
116423 | CIP Medium 40 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
6537 | positive | growth | 37 | mesophilic |
31735 | positive | growth | 25-45 | |
31735 | positive | optimum | 25-37 | mesophilic |
38184 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
116423 | positive | growth | 30-37 | mesophilic |
116423 | no | growth | 10 | psychrophilic |
116423 | no | growth | 15 | psychrophilic |
116423 | no | growth | 22 | psychrophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
31735 | positive | growth | 7 |
31735 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
6537 | anaerobe |
6537 | microaerophile |
31735 | anaerobe |
116423 | facultative anaerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
31735 | no | |
69481 | no | 100 |
69480 | no | 99.987 |
observation
- @ref: 31735
- observation: aggregates in chains
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31735 | 28757 | fructose | + | carbon source |
31735 | 28260 | galactose | + | carbon source |
31735 | 17234 | glucose | + | carbon source |
31735 | 24996 | lactate | + | carbon source |
31735 | 17716 | lactose | + | carbon source |
31735 | 17306 | maltose | + | carbon source |
31735 | 37684 | mannose | + | carbon source |
31735 | 28053 | melibiose | + | carbon source |
31735 | 506227 | N-acetylglucosamine | + | carbon source |
31735 | 16634 | raffinose | + | carbon source |
31735 | 17992 | sucrose | + | carbon source |
31735 | 27082 | trehalose | + | 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 | 6731 | melezitose | - | builds acid from |
68371 | 15443 | inulin | - | 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 | 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 | 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 |
116423 | 17632 | nitrate | - | reduction |
116423 | 16301 | nitrite | - | reduction |
116423 | 17632 | nitrate | + | respiration |
metabolite tests
- @ref: 116423
- Chebi-ID: 15688
- metabolite: acetoin
- voges-proskauer-test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | + | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | + | 3.2.1.23 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | - | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | + | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | - | |
68382 | esterase (C 4) | - | |
68382 | alkaline phosphatase | - | 3.1.3.1 |
116423 | oxidase | - | |
116423 | alcohol dehydrogenase | - | 1.1.1.1 |
116423 | catalase | - | 1.11.1.6 |
116423 | lysine decarboxylase | - | 4.1.1.18 |
116423 | ornithine decarboxylase | - | 4.1.1.17 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
116423 | - | - | - | - | - | + | + | - | - | - | + | + | - | + | - | + | - | - | + | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
6537 | - | - | - | - | - | + | - | - | - | - | - | + | + | + | - | - | - | - | - | - | - | - | + | - | + | + | + | + | + | + | + | + | + | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
6537 | - | - | - | - | - | - | - | - | - | - | + | + | + | + | - | - | - | - | - | - | - | - | + | - | + | + | + | + | + | + | + | + | + | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
116423 | - | - | - | - | - | - | - | - | - | +/- | +/- | +/- | +/- | - | - | - | - | - | - | - | - | +/- | - | +/- | +/- | +/- | +/- | +/- | +/- | +/- | +/- | +/- | - | - | +/- | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | isolation date |
---|---|---|---|---|---|---|
6537 | feces, wild Japanese wood mouse | Kyotanabe | Japan | JPN | Asia | |
67770 | Wild mouse feces | Kyotanabe | Japan | JPN | Asia | |
116423 | Animal, Wild Japanese wood mouse | Kyotanabe | Japan | JPN | Asia | 2002 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Mammals | #Muridae (Mouse/Rat) |
#Host Body Product | #Gastrointestinal tract | #Feces (Stool) |
taxonmaps
- @ref: 69479
- File name: preview.99_7017.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_871;97_1018;98_1201;99_7017&stattab=map
- Last taxonomy: Ligilactobacillus apodemi
- 16S sequence: LC519852
- Sequence Identity:
- Total samples: 68252
- soil counts: 1119
- aquatic counts: 731
- animal counts: 66125
- plant counts: 277
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
6537 | 1 | Risk group (German classification) |
116423 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Lactobacillus apodemi gene for 16S ribosomal RNA, partial sequence, strain: DSM 16634 | AB370874 | 1487 | ena | 307126 |
6537 | Lactobacillus apodemi 16S rRNA gene, type strain ASB1T | AJ871178 | 1532 | ena | 307126 |
67770 | Lactobacillus apodemi JCM 16172 gene for 16S rRNA, partial sequence | LC519852 | 1504 | ena | 307126 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Lactobacillus apodemi DSM 16634 = JCM 16172 | 1423724.4 | wgs | patric | 1423724 |
66792 | Lactobacillus apodemi JCM 16172 | 1236952.3 | wgs | patric | 1423724 |
66792 | Ligilactobacillus apodemi JCM 16172 | 2585427873 | draft | img | 1423724 |
66792 | Ligilactobacillus apodemi DSM 16634 | 2675903500 | draft | img | 1423724 |
67770 | Ligilactobacillus apodemi DSM 16634 = JCM 16172 | GCA_001434405 | scaffold | ncbi | 1423724 |
67770 | Ligilactobacillus apodemi DSM 16634 = JCM 16172 | GCA_000615885 | contig | ncbi | 1423724 |
GC content
@ref | GC-content | method |
---|---|---|
6537 | 38.5 | |
67770 | 38.5 | high performance liquid chromatography (HPLC) |
67770 | 38.6 | genome sequence analysis |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 95.591 | yes |
gram-positive | yes | 95.176 | yes |
anaerobic | no | 90.125 | no |
halophile | yes | 86.851 | no |
spore-forming | no | 93.684 | yes |
glucose-util | yes | 92.54 | no |
thermophile | no | 97.939 | no |
aerobic | no | 98.086 | yes |
flagellated | no | 98.197 | yes |
glucose-ferment | yes | 91.967 | no |
External links
@ref: 6537
culture collection no.: DSM 16634, CIP 108913, JCM 16172, NCIMB 14359
straininfo link
- @ref: 76120
- straininfo: 292425
literature
- topic: Phylogeny
- Pubmed-ID: 16825652
- title: Lactobacillus apodemi sp. nov., a tannase-producing species isolated from wild mouse faeces.
- authors: Osawa R, Fujisawa T, Pukall R
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.64147-0
- year: 2006
- mesh: Animals, Bacterial Infections/*microbiology/*veterinary, Base Composition, Carbohydrate Metabolism, Carboxylic Ester Hydrolases/*biosynthesis, Cell Wall/chemistry, DNA Fingerprinting, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Feces/*microbiology, Genes, rRNA, Lactobacillus/*classification/cytology/*isolation & purification/physiology, Molecular Sequence Data, Murinae/*microbiology, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Ribotyping, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Spores, Bacterial
- topic2: Genetics
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed | ID_cross_reference |
---|---|---|---|---|---|---|---|
6537 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16634) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-16634 | ||||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | ||||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | ||
31735 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28776041 | 28011 | ||
38184 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/6596 | |||||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | ||||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||||
68371 | Automatically annotated from API 50CH acid | ||||||
68382 | Automatically annotated from API zym | ||||||
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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | ||||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | ||||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | ||||
76120 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID292425.1 | StrainInfo: A central database for resolving microbial strain identifiers | ||||
116423 | Curators of the CIP | Collection of Institut Pasteur (CIP 108913) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108913 |