Strain identifier
BacDive ID: 6668
Type strain:
Species: Agrilactobacillus composti
Strain history: CIP <- 2007, JCM <- 2006, NRIC
NCBI tax ID(s): 398555 (species)
General
@ref: 7578
BacDive-ID: 6668
DSM-Number: 18527
keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, Gram-positive, rod-shaped
description: Agrilactobacillus composti DSM 18527 is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from composting material of distilled shochu residue.
NCBI tax id
- NCBI tax id: 398555
- Matching level: species
strain history
@ref | history |
---|---|
7578 | <- Akihito Endo, NRIC 0689 |
67770 | A. Endo NRIC 0689. |
118715 | CIP <- 2007, JCM <- 2006, NRIC |
doi: 10.13145/bacdive6668.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Lactobacillales
- family: Lactobacillaceae
- genus: Agrilactobacillus
- species: Agrilactobacillus composti
- full scientific name: Agrilactobacillus composti (Endo and Okada 2007) Zheng et al. 2020
synonyms
- @ref: 20215
- synonym: Lactobacillus composti
@ref: 7578
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Lactobacillales
family: Lactobacillaceae
genus: Agrilactobacillus
species: Agrilactobacillus composti
full scientific name: Agrilactobacillus composti (Endo and Okada 2007) Zheng et al. 2020
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
31976 | positive | 02-06 µm | 0.8 µm | rod-shaped | no | |
69480 | no | 94.21 | ||||
69480 | positive | 100 | ||||
118715 | positive | rod-shaped | no |
pigmentation
- @ref: 31976
- production: yes
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
7578 | 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 |
37769 | MEDIUM 40- for Lactobacillus and Leuconostoc | yes | Distilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g) | |
118715 | CIP Medium 40 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
7578 | positive | growth | 30 | mesophilic |
31976 | positive | growth | 10-37 | |
31976 | positive | optimum | 23.5 | psychrophilic |
37769 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
118715 | positive | growth | 10-37 | |
118715 | no | growth | 45 | thermophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
31976 | positive | growth | 3.5-9 | alkaliphile |
31976 | positive | optimum | 6.25 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
7578 | microaerophile |
31976 | anaerobe |
118715 | facultative anaerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.995 |
observation
- @ref: 31976
- observation: aggregates in chains
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31976 | 22599 | arabinose | + | carbon source |
31976 | 28757 | fructose | + | carbon source |
31976 | 28260 | galactose | + | carbon source |
31976 | 17234 | glucose | + | carbon source |
31976 | 17306 | maltose | + | carbon source |
31976 | 29864 | mannitol | + | carbon source |
31976 | 37684 | mannose | + | carbon source |
31976 | 28053 | melibiose | + | carbon source |
31976 | 26546 | rhamnose | + | carbon source |
31976 | 17814 | salicin | + | carbon source |
31976 | 30911 | sorbitol | + | carbon source |
31976 | 17992 | sucrose | + | carbon source |
31976 | 27082 | trehalose | + | carbon source |
31976 | 18222 | xylose | + | carbon source |
68371 | Potassium 5-ketogluconate | - | 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 | 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 | 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 | 59640 | N-acetylglucosamine | + | 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 | 17113 | erythritol | - | builds acid from |
118715 | 17632 | nitrate | - | reduction |
118715 | 16301 | nitrite | - | reduction |
118715 | 17632 | nitrate | + | respiration |
metabolite tests
- @ref: 118715
- 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 |
118715 | oxidase | - | |
118715 | alcohol dehydrogenase | - | 1.1.1.1 |
118715 | catalase | - | 1.11.1.6 |
118715 | lysine decarboxylase | - | 4.1.1.18 |
118715 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
118715 | - | - | + | - | - | + | + | - | - | - | + | + | + | - | - | + | + | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
7578 | - | - | - | - | + | - | + | - | - | + | + | + | + | + | + | + | - | - | + | + | - | - | + | - | + | + | + | - | + | - | +/- | + | + | - | + | - | - | - | - | - | + | - | - | - | + | - | - | - | - | - |
7578 | - | +/- | - | - | + | - | + | - | - | + | + | + | + | + | + | + | - | - | + | + | - | - | + | - | + | + | + | - | + | - | - | + | + | - | + | - | - | - | - | - | + | - | - | - | + | - | - | + | + | - |
118715 | - | - | +/- | + | - | + | - | - | + | + | + | + | + | + | + | - | - | + | + | - | - | + | - | + | + | + | - | + | - | - | + | + | - | + | - | +/- | - | - | - | + | - | - | - | + | - | - | +/- | + | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
7578 | composting material of distilled shochu residue | Miyazaki prefecture | Japan | JPN | Asia |
67770 | Compost of distilled shochu residue | ||||
118715 | Environment, Compost of distilled shochu residue | Miyazaki, Kyushu | Japan | JPN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Biodegradation | #Composting |
#Engineered | #Food production | #Fermented |
#Engineered | #Food production | #Beverage |
taxonmaps
- @ref: 69479
- File name: preview.99_8049.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_3720;97_4572;98_5867;99_8049&stattab=map
- Last taxonomy: Agrilactobacillus composti subclade
- 16S sequence: LC480800
- Sequence Identity:
- Total samples: 2461
- soil counts: 76
- aquatic counts: 201
- animal counts: 1912
- plant counts: 272
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
7578 | 1 | Risk group (German classification) |
118715 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
7578 | Lactobacillus composti gene for 16S rRNA, partial sequence, strain:NRIC 0689 | AB268118 | 1522 | ena | 398555 |
67770 | Lactobacillus composti JCM 14202 gene for 16S ribosomal RNA, partial sequence | LC480800 | 1499 | ena | 398555 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Lactobacillus composti DSM 18527 = JCM 14202 | 1423734.3 | wgs | patric | 1423734 |
66792 | Lactobacillus composti JCM 14202 | 1236950.3 | wgs | patric | 1423734 |
66792 | Agrilactobacillus composti JCM 14202 | 2576861770 | draft | img | 1423734 |
66792 | Agrilactobacillus composti DSM 18527 | 2700989152 | draft | img | 1423734 |
67770 | Agrilactobacillus composti DSM 18527 = JCM 14202 | GCA_001436375 | scaffold | ncbi | 1423734 |
67770 | Agrilactobacillus composti DSM 18527 = JCM 14202 | GCA_000583695 | contig | ncbi | 1423734 |
GC content
@ref | GC-content | method |
---|---|---|
7578 | 47 | |
67770 | 47 | high performance liquid chromatography (HPLC) |
67770 | 44 | genome sequence analysis |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 91.571 | yes |
gram-positive | yes | 95.603 | yes |
anaerobic | no | 91.81 | no |
halophile | yes | 71.517 | no |
spore-forming | no | 86.329 | no |
thermophile | no | 98.068 | yes |
glucose-util | yes | 89.711 | yes |
aerobic | no | 94.439 | yes |
flagellated | no | 95.173 | yes |
glucose-ferment | yes | 83.448 | no |
External links
@ref: 7578
culture collection no.: DSM 18527, JCM 14202, NRIC 0689, CIP 109571
straininfo link
- @ref: 76142
- straininfo: 302642
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 17392222 | Lactobacillus composti sp. nov., a lactic acid bacterium isolated from a compost of distilled shochu residue. | Endo A, Okada S | Int J Syst Evol Microbiol | 10.1099/ijs.0.64743-0 | 2007 | Alcoholic Beverages/*microbiology, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Lactobacillus/*classification/genetics/isolation & purification/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics | Genetics |
Genetics | 24675866 | Draft Genome Sequences of Two Lactobacillus Strains, L. farraginis JCM 14108T and L. composti JCM 14202T, Isolated from Compost of Distilled Shochu Residue. | Yuki M, Oshima K, Suda W, Kitahara M, Kitamura K, Iida T, Hattori M, Ohkuma M | Genome Announc | 10.1128/genomeA.00257-14 | 2014 | Phylogeny | |
Enzymology | 28623564 | An NADPH-dependent Lactobacillus composti short-chain dehydrogenase/reductase: characterization and application to (R)-1-phenylethanol synthesis. | Wang YJ, Ying BB, Chen M, Shen W, Liu ZQ, Zheng YG | World J Microbiol Biotechnol | 10.1007/s11274-017-2311-9 | 2017 | Acetophenones/metabolism, Amino Acid Sequence, Bacterial Proteins/genetics/metabolism, Biocatalysis, Cloning, Molecular/*drug effects, Hydrogen-Ion Concentration, Lactobacillus/*enzymology/genetics, Molecular Weight, NADH, NADPH Oxidoreductases/*genetics/*metabolism, Open Reading Frames, Substrate Specificity, Temperature | Metabolism |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
7578 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18527) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-18527 | ||||
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 | ||||
31976 | 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 | 28231 | 28776041 | ||
37769 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/7329 | |||||
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 | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
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 | ||||
76142 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID302642.1 | StrainInfo: A central database for resolving microbial strain identifiers | ||||
118715 | Curators of the CIP | Collection of Institut Pasteur (CIP 109571) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109571 |