Strain identifier
BacDive ID: 6410
Type strain:
Species: Companilactobacillus alimentarius
Strain Designation: R 13, R13
Strain history: CIP <- 1987, DSM <- G. Reuter: strain R13
NCBI tax ID(s): 1423720 (strain), 1602 (species)
General
@ref: 8660
BacDive-ID: 6410
DSM-Number: 20249
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, lactate production
description: Companilactobacillus alimentarius R 13 is an anaerobe, mesophilic bacterium that produces lactate and was isolated from marinated fish product.
NCBI tax id
NCBI tax id | Matching level |
---|---|
1423720 | strain |
1602 | species |
strain history
@ref | history |
---|---|
8660 | <- G. Reuter, R 13 |
67770 | T. Mitsuoka S8-17 <-- DSM 20249 (Lactobacillus sp.) <-- G. Reuter R13. |
116236 | CIP <- 1987, DSM <- G. Reuter: strain R13 |
doi: 10.13145/bacdive6410.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Lactobacillales
- family: Lactobacillaceae
- genus: Companilactobacillus
- species: Companilactobacillus alimentarius
- full scientific name: Companilactobacillus alimentarius (Reuter 1983 ex Reuter 1970) Zheng et al. 2020
synonyms
- @ref: 20215
- synonym: Lactobacillus alimentarius
@ref: 8660
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Lactobacillales
family: Lactobacillaceae
genus: Companilactobacillus
species: Companilactobacillus alimentarius
full scientific name: Companilactobacillus alimentarius (Reuter 1983) Zheng et al. 2020
strain designation: R 13, R13
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | no | 96.425 | ||
69480 | 100 | positive | ||
116236 | no | positive | rod-shaped |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
8660 | 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 |
40496 | MEDIUM 40- for Lactobacillus and Leuconostoc | yes | Distilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g) | |
116236 | CIP Medium 40 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
8660 | positive | growth | 30 | mesophilic |
40496 | positive | growth | 30 | mesophilic |
50209 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
116236 | positive | growth | 30-37 | mesophilic |
116236 | no | growth | 10 | psychrophilic |
116236 | no | growth | 15 | psychrophilic |
116236 | no | growth | 22 | psychrophilic |
116236 | no | growth | 45 | thermophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 50209
- oxygen tolerance: anaerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.997 |
compound production
- @ref: 8660
- compound: L(+) lactic acid
murein
- @ref: 8660
- murein short key: A11.31
- type: A4alpha L-Lys-D-Asp
metabolite utilization
@ref | metabolite | utilization activity | kind of utilization tested | Chebi-ID |
---|---|---|---|---|
68371 | Potassium 5-ketogluconate | - | builds acid from | |
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 | raffinose | - | builds acid from | 16634 |
68371 | melezitose | - | builds acid from | 6731 |
68371 | inulin | - | builds acid from | 15443 |
68371 | melibiose | - | builds acid from | 28053 |
68371 | lactose | - | builds acid from | 17716 |
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 | D-mannitol | - | builds acid from | 16899 |
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 | D-arabinose | - | builds acid from | 17108 |
68371 | erythritol | - | builds acid from | 17113 |
68371 | glycerol | - | builds acid from | 17754 |
116236 | nitrate | - | reduction | 17632 |
116236 | nitrite | - | reduction | 16301 |
116236 | nitrate | + | respiration | 17632 |
metabolite tests
- @ref: 116236
- 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 |
116236 | oxidase | - | |
116236 | alcohol dehydrogenase | - | 1.1.1.1 |
116236 | catalase | - | 1.11.1.6 |
116236 | lysine decarboxylase | - | 4.1.1.18 |
116236 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
116236 | - | - | - | - | - | - | - | - | - | - | + | + | - | - | - | - | + | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
8660 | - | - | - | - | + | - | - | - | - | - | - | + | + | + | - | - | - | - | - | - | - | - | + | + | + | + | + | + | - | - | - | + | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
8660 | - | - | - | - | + | + | - | - | - | - | + | + | + | + | - | - | - | - | - | - | - | - | + | + | + | + | + | + | + | - | - | + | + | - | - | - | - | - | - | + | - | - | - | - | - | - | - | + | + | - |
116236 | - | - | - | +/- | +/- | - | - | - | - | - | +/- | +/- | +/- | - | - | - | - | - | - | - | - | +/- | +/- | - | +/- | +/- | +/- | - | - | - | +/- | +/- | - | - | - | - | - | - | +/- | - | - | - | - | - | - | - | +/- | - | - |
API biotype100
@ref | GLU | FRU | GAL | TRE | MNE | SBE | MEL | SAC | RAF | MTE | MAL | LAC | LTE | MbGa | MaGa | CEL | GEN | MbGu | ESC | RIB | ARA | XYL | PLE | RHA | FUC | MLZ | DARL | LARL | XLT | DUL | TAG | GLY | INO | MAN | MTL | TUR | SOR | ADO | HBG | LYX | ERY | MDG | 3MDG | SAT | MUC | LTAT | DTAT | MTAT | DMLT | LMLT | CATE | TATE | TTE | CIT | GRT | GAT | 2KG | 5KG | TRY | NAG | GNT | PAC | PAT | pOBE | QAT | GTE | mOBE | BAT | PPAT | CMT | TGE | BET | PCE | ABT | HIN | LAT | CAP | CYT | HIS | SUC | FUM | GRE | GYT | AVT | ETN | TTN | GLN | ITA | 3OBU | APT | GTT | PRO | DALA | LALA | SER | MNT | PROP | TYR | 2KT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
116236 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type |
---|---|
8660 | marinated fish product |
50209 | Marinated fish product |
67770 | Marinated fish product |
116236 | Food, Marinated fish product |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Food production | #Food |
#Host | #Fishes |
taxonmaps
- @ref: 69479
- File name: preview.99_7133.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_954;97_1113;98_2270;99_7133&stattab=map
- Last taxonomy: Companilactobacillus alimentarius
- 16S sequence: LC063166
- Sequence Identity:
- Total samples: 631
- soil counts: 61
- aquatic counts: 47
- animal counts: 461
- plant counts: 62
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
8660 | 1 | Risk group (German classification) |
116236 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Lactobacillus alimentarius 16S-23S ribosomal RNA small intergenic spacer region, complete sequence | AF500492 | 230 | ena | 1602 |
20218 | Lactobacillus alimentarius 16S-23S ribosomal RNA large intergenic spacer region; and tRNA-Ile and tRNA-Ala genes, complete sequence | AF500493 | 425 | ena | 1602 |
20218 | Lactobacillus alimentarius strain DSM 20249 16S ribosomal RNA gene, partial sequence | M58804 | 1514 | ena | 1602 |
20218 | Lactobacillus alimentarius gene for 16S rRNA, partial sequence, strain: JCM 1095 | AB289025 | 694 | ena | 1602 |
20218 | Lactobacillus alimentarius gene for 16S ribosomal RNA, partial sequence | D31677 | 187 | ena | 1602 |
20218 | Lactobacillus alimentarius partial 23S rRNA gene and 16S-23S IGS, strain LMG 9187 | AJ616015 | 701 | ena | 1602 |
67770 | Lactobacillus alimentarius gene for 16S ribosomal RNA, partial sequence, strain: JCM 1095 | LC063166 | 1528 | ena | 1602 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Companilactobacillus alimentarius DSM 20249 | GCA_002849895 | complete | ncbi | 1423720 |
66792 | Lactobacillus alimentarius DSM 20249 | 1423720.3 | wgs | patric | 1423720 |
66792 | Lactobacillus alimentarius DSM 20249 | 1423720.4 | patric | 1423720 | |
66792 | Lactobacillus alimentarius strain NBRC 106464 | 1602.4 | wgs | patric | 1602 |
66792 | Lactobacillus alimentarius DSM 20249 | 2700989133 | draft | img | 1423720 |
66792 | Lactobacillus alimentarius DSM 20249 | 2802429297 | complete | img | 1423720 |
67770 | Companilactobacillus alimentarius DSM 20249 | GCA_001434745 | scaffold | ncbi | 1423720 |
67770 | Companilactobacillus alimentarius NBRC 106464 | GCA_007991795 | contig | ncbi | 1602 |
GC content
@ref | GC-content | method |
---|---|---|
8660 | 37.0 | |
67770 | 35.4 | genome sequence analysis |
67770 | 37 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
flagellated | no | 98.271 | no |
gram-positive | yes | 97.307 | no |
anaerobic | no | 83.944 | yes |
aerobic | no | 93.552 | yes |
halophile | yes | 88.308 | no |
spore-forming | no | 95.307 | no |
thermophile | no | 99.342 | yes |
glucose-util | yes | 92.419 | no |
motile | no | 94.677 | no |
glucose-ferment | yes | 90.737 | no |
External links
@ref: 8660
culture collection no.: DSM 20249, ATCC 29643, CCUG 30672, JCM 1095, BCRC 12932, CECT 570, CIP 102986, KACC 12425, KCTC 3593, LMG 9187, NBRC 106464, NCFB 2329, NCIMB 11994, NRIC 1640, NCDO 2329
straininfo link
- @ref: 75883
- straininfo: 8644
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 11034488 | Lactobacillus kimchii sp. nov., a new species from kimchi. | Yoon JH, Kang SS, Mheen TI, Ahn JS, Lee HJ, Kim TK, Park CS, Kho YH, Kang KH, Park YH | Int J Syst Evol Microbiol | 10.1099/00207713-50-5-1789 | 2000 | Bacterial Typing Techniques, Bacteriocins/biosynthesis, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/analysis/genetics, Fatty Acids/analysis, Fermentation, *Food Microbiology, Korea, Lactobacillus/chemistry/*classification/*genetics/physiology, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vegetables/*microbiology | Biotechnology |
Phylogeny | 12710620 | Lactobacillus versmoldensis sp. nov., isolated from raw fermented sausage. | Krockel L, Schillinger U, Franz CMAP, Bantleon A, Ludwig W | Int J Syst Evol Microbiol | 10.1099/ijs.0.02387-0 | 2003 | Fermentation, *Food Microbiology, Lactobacillus/chemistry/*classification/genetics/physiology, Meat/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/*analysis/genetics, Sequence Analysis, DNA | Biotechnology |
Phylogeny | 23194598 | Lactobacillus alimentarius sp. nov., nom rev. and Lactobacillus farciminis sp. nov., nom. rev. | Reuter G | Syst Appl Microbiol | 10.1016/S0723-2020(83)80055-1 | 1983 | ||
Phylogeny | 31668878 | Polyphasic characterization of two novel Lactobacillus spp. isolated from blown salami packages: Description of Lactobacillus halodurans sp. nov. and Lactobacillus salsicarnum sp. nov. | Schuster JA, Klingl A, Vogel RF, Ehrmann MA | Syst Appl Microbiol | 10.1016/j.syapm.2019.126023 | 2019 | Animals, Base Composition, Fatty Acids/analysis, Fermented Foods/*microbiology, *Food Microbiology, Genes, Bacterial/genetics, Genome, Bacterial/genetics, Lactobacillus/chemistry/*classification/genetics/ultrastructure, Meat Products/*microbiology, Nucleic Acid Hybridization, Peptidoglycan/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Swine | Biotechnology |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
8660 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20249) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-20249 | |||
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 | |
40496 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/14732 | ||||
50209 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 30672) | https://www.ccug.se/strain?id=30672 | |||
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 | |||
75883 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID8644.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
116236 | Curators of the CIP | Collection of Institut Pasteur (CIP 102986) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20102986 |