Strain identifier
BacDive ID: 6407
Type strain:
Species: Ligilactobacillus agilis
Strain Designation: 262
Strain history: CIP <- 1985, DSMZ <- N. Weiss: strain 262
NCBI tax ID(s): 1423718 (strain), 1601 (species)
General
@ref: 8858
BacDive-ID: 6407
DSM-Number: 20509
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, lactate production
description: Ligilactobacillus agilis 262 is an anaerobe, mesophilic bacterium that produces lactate and was isolated from municipal sewage.
NCBI tax id
NCBI tax id | Matching level |
---|---|
1423718 | strain |
1601 | species |
strain history
@ref | history |
---|---|
8858 | <- N. Weiss, 262 |
67770 | DSM 20509 <-- N. Weiss 262. |
116161 | CIP <- 1985, DSMZ <- N. Weiss: strain 262 |
doi: 10.13145/bacdive6407.20230509.8.1
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 agilis
- full scientific name: Ligilactobacillus agilis (Weiss et al. 1982) Zheng et al. 2020
synonyms
- @ref: 20215
- synonym: Lactobacillus agilis
@ref: 8858
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Lactobacillales
family: Lactobacillaceae
genus: Ligilactobacillus
species: Ligilactobacillus agilis
full scientific name: Ligilactobacillus agilis (Weiss et al. 1982) Zheng et al. 2020
strain designation: 262
type strain: yes
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
8858 | MRS MEDIUM WITH CYSTEINE (DSMZ Medium 232) | yes | https://mediadive.dsmz.de/medium/232 | Name: MRS MEDIUM WITH CYSTEINE (DSMZ Medium 232) 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)2 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 |
34906 | MEDIUM 40- for Lactobacillus and Leuconostoc | yes | Distilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g) | |
116161 | CIP Medium 40 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
8858 | positive | growth | 37 | mesophilic |
34906 | positive | growth | 37 | mesophilic |
50605 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
8858 | anaerobe |
8858 | microaerophile |
compound production
- @ref: 8858
- compound: (L+) lactic acid
murein
- @ref: 8858
- murein short key: A31
- type: A1gamma m-Dpm-direct
metabolite utilization
@ref | metabolite | utilization activity | kind of utilization tested | Chebi-ID |
---|---|---|---|---|
68371 | Potassium 5-ketogluconate | - | builds acid from | |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | gluconate | - | builds acid from | 24265 |
68371 | L-arabitol | - | builds acid from | 18403 |
68371 | D-arabitol | - | builds acid from | 18333 |
68371 | L-fucose | - | builds acid from | 18287 |
68371 | D-fucose | - | builds acid from | 28847 |
68371 | D-tagatose | - | builds acid from | 16443 |
68371 | D-lyxose | - | builds acid from | 62318 |
68371 | turanose | - | builds acid from | 32528 |
68371 | xylitol | - | builds acid from | 17151 |
68371 | glycogen | - | builds acid from | 28087 |
68371 | starch | - | builds acid from | 28017 |
68371 | melezitose | - | builds acid from | 6731 |
68371 | inulin | - | builds acid from | 15443 |
68371 | methyl alpha-D-glucopyranoside | - | builds acid from | 320061 |
68371 | methyl alpha-D-mannoside | - | builds acid from | 43943 |
68371 | D-sorbitol | - | builds acid from | 17924 |
68371 | myo-inositol | - | builds acid from | 17268 |
68371 | galactitol | - | builds acid from | 16813 |
68371 | L-rhamnose | - | builds acid from | 62345 |
68371 | L-sorbose | - | builds acid from | 17266 |
68371 | methyl beta-D-xylopyranoside | - | builds acid from | 74863 |
68371 | ribitol | - | builds acid from | 15963 |
68371 | L-xylose | - | builds acid from | 65328 |
68371 | D-xylose | - | builds acid from | 65327 |
68371 | L-arabinose | - | builds acid from | 30849 |
68371 | D-arabinose | - | builds acid from | 17108 |
68371 | erythritol | - | builds acid from | 17113 |
68371 | glycerol | - | builds acid from | 17754 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
8858 | - | - | - | - | - | +/- | - | - | - | - | + | + | + | + | - | - | - | - | + | - | - | - | + | + | + | + | + | + | + | + | + | + | + | - | - | + | - | - | - | + | - | - | - | - | - | - | - | - | - | - |
116161 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
8858 | municipal sewage | ||||
50605 | Municipal sewage | ||||
67770 | Municipal sewage | ||||
116161 | Environment, Municipal sewage | München | Germany | DEU | Europe |
isolation source categories
- Cat1: #Engineered
- Cat2: #Waste
- Cat3: #Wastewater
taxonmaps
- @ref: 69479
- File name: preview.99_6918.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_3250;97_3988;98_5089;99_6918&stattab=map
- Last taxonomy: Ligilactobacillus agilis subclade
- 16S sequence: LC065041
- Sequence Identity:
- Total samples: 41290
- soil counts: 1642
- aquatic counts: 1961
- animal counts: 36795
- plant counts: 892
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
8858 | 1 | Risk group (German classification) |
116161 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Lactobacillus agilis strain DSM 20509 16S ribosomal RNA gene, partial sequence | M58803 | 1511 | ena | 1601 |
20218 | Lactobacillus agilis gene for 16S rRNA, partial sequence, strain: JCM 1187 | AB596945 | 1485 | ena | 1601 |
67770 | Lactobacillus agilis gene for 16S ribosomal RNA, partial sequence, strain: JCM 1187 | LC065041 | 1462 | ena | 1601 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Lactobacillus agilis DSM 20509 | 1423718.3 | wgs | patric | 1423718 |
66792 | Ligilactobacillus agilis DSM 20509 | 2667527581 | draft | img | 1423718 |
67770 | Ligilactobacillus agilis DSM 20509 | GCA_001436215 | scaffold | ncbi | 1423718 |
GC content
@ref | GC-content | method |
---|---|---|
8858 | 43.6 | |
67770 | 41 | |
67770 | 41.7 | genome sequence analysis |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | yes | 53.049 | no |
gram-positive | yes | 94.259 | no |
anaerobic | no | 85.715 | no |
halophile | yes | 85.529 | no |
spore-forming | no | 89.936 | no |
glucose-util | yes | 92.208 | no |
thermophile | no | 97.98 | yes |
aerobic | no | 97.629 | yes |
flagellated | no | 88.762 | no |
glucose-ferment | yes | 91.68 | no |
External links
@ref: 8858
culture collection no.: DSM 20509, NCIB 11716, CCUG 31450, JCM 1187, BCRC 12931, CECT 4131, CIP 101264, KCTC 3606, LMG 9186, NCFB 2744, NCIMB 11716, NRIC 1642, NRRL B-14856, NCDO 2744
straininfo link
- @ref: 75880
- straininfo: 3201
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
8858 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20509) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-20509 | |||
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 | |
34906 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/12820 | ||||
50605 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 31450) | https://www.ccug.se/strain?id=31450 | |||
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) | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
75880 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID3201.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
116161 | Curators of the CIP | Collection of Institut Pasteur (CIP 101264) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20101264 |