Strain identifier
BacDive ID: 6674
Type strain:
Species: Companilactobacillus nodensis
Strain Designation: IZ4B, iz4b-1
Strain history: CIP <- 2009, DSMZ <- T. Kashiwagi, Tokyo Univ. of Science, Chiba, Japan: strain IZ4B
NCBI tax ID(s): 460870 (species)
General
@ref: 8253
BacDive-ID: 6674
DSM-Number: 19682
keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, Gram-positive, rod-shaped
description: Companilactobacillus nodensis IZ4B is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from Japanese pickles.
NCBI tax id
- NCBI tax id: 460870
- Matching level: species
strain history
@ref | history |
---|---|
8253 | <- T. Kashiwagi, Tokyo University of Science;IZ4B |
67770 | T. Kashiwagi iz4b-1. |
121322 | CIP <- 2009, DSMZ <- T. Kashiwagi, Tokyo Univ. of Science, Chiba, Japan: strain IZ4B |
doi: 10.13145/bacdive6674.20230509.8.1
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 nodensis
- full scientific name: Companilactobacillus nodensis (Kashiwagi et al. 2009) Zheng et al. 2020
synonyms
- @ref: 20215
- synonym: Lactobacillus nodensis
@ref: 8253
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Lactobacillales
family: Lactobacillaceae
genus: Companilactobacillus
species: Companilactobacillus nodensis
full scientific name: Companilactobacillus nodensis (Kashiwagi et al. 2009) Zheng et al. 2020
strain designation: IZ4B, iz4b-1
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
32611 | positive | 5 µm | 1.8 µm | rod-shaped | no | |
69480 | no | 96.423 | ||||
69480 | positive | 100 | ||||
121322 | positive | rod-shaped | no |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
8253 | 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 |
40607 | MEDIUM 40- for Lactobacillus and Leuconostoc | yes | Distilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g) | |
121322 | CIP Medium 40 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
8253 | positive | growth | 30 | mesophilic |
32611 | positive | growth | 15-37 | |
32611 | positive | optimum | 26 | mesophilic |
40607 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
121322 | positive | growth | 15-37 | |
121322 | no | growth | 45 | thermophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
8253 | microaerophile |
32611 | anaerobe |
121322 | facultative anaerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
32611 | no | |
69481 | no | 100 |
69480 | no | 99.999 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
32611 | NaCl | positive | growth | 0-15 % |
32611 | NaCl | positive | optimum | 7.5 % |
murein
- @ref: 8253
- murein short key: A11.31
- type: A4alpha L-Lys-D-Asp
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
32611 | 22599 | arabinose | + | carbon source |
32611 | 28757 | fructose | + | carbon source |
32611 | 28260 | galactose | + | carbon source |
32611 | 17234 | glucose | + | carbon source |
32611 | 37684 | mannose | + | carbon source |
32611 | 506227 | N-acetylglucosamine | + | carbon source |
32611 | 33942 | ribose | + | carbon source |
32611 | 4853 | esculin | + | hydrolysis |
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 | 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 | 17108 | D-arabinose | + | builds acid from |
68371 | 17113 | erythritol | - | builds acid from |
68371 | 17754 | glycerol | - | builds acid from |
121322 | 17632 | nitrate | - | reduction |
121322 | 16301 | nitrite | - | reduction |
121322 | 17632 | nitrate | + | respiration |
metabolite production
- @ref: 121322
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 121322
- 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 |
121322 | oxidase | - | |
121322 | alcohol dehydrogenase | + | 1.1.1.1 |
121322 | catalase | - | 1.11.1.6 |
121322 | lysine decarboxylase | - | 4.1.1.18 |
121322 | ornithine decarboxylase | - | 4.1.1.17 |
121322 | urease | - | 3.5.1.5 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121322 | - | + | - | - | - | + | - | - | - | - | + | + | - | - | - | + | + | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
8253 | - | - | - | + | - | - | - | - | - | - | + | + | + | + | - | - | - | - | - | - | - | - | + | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
8253 | Japanese pickles | Tochigi prefecture, Utsunomiya city | Japan | JPN | Asia |
67770 | Rice bran | ||||
121322 | Food, Rice bran, Japanse pickles | Utsunomiya | Japan | JPN | Asia |
isolation source categories
- Cat1: #Engineered
- Cat2: #Food production
- Cat3: #Food
taxonmaps
- @ref: 69479
- File name: preview.99_3365.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_1756;97_2100;98_2579;99_3365&stattab=map
- Last taxonomy: Companilactobacillus
- 16S sequence: LC258158
- Sequence Identity:
- Total samples: 357
- soil counts: 37
- aquatic counts: 22
- animal counts: 270
- plant counts: 28
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
8253 | 1 | Risk group (German classification) |
121322 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
8253 | Lactobacillus nodensis gene for 16S ribosomal RNA, partial sequence | AB332024 | 1556 | ena | 460870 |
67770 | Lactobacillus nodensis gene for 16S ribosomal RNA, partial sequence, strain: JCM 14932 | LC258158 | 1513 | ena | 460870 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Lactobacillus nodensis DSM 19682 = JCM 14932 = NBRC 107160 | 1423775.4 | wgs | patric | 1423775 |
66792 | Lactobacillus nodensis DSM 19682 = JCM 14932 = NBRC 107160 | 1423775.5 | wgs | patric | 1423775 |
66792 | Lactobacillus nodensis JCM 14932 | 1236953.3 | wgs | patric | 1423775 |
66792 | Lactobacillus nodensis JCM 14932 | 2585427881 | draft | img | 1423775 |
66792 | Lactobacillus nodensis NBRC 107160 | 2681812987 | draft | img | 1423775 |
66792 | Lactobacillus nodensis DSM 19682 | 2690315703 | draft | img | 1423775 |
67770 | Companilactobacillus nodensis DSM 19682 = JCM 14932 = NBRC 107160 | GCA_001435555 | scaffold | ncbi | 1423775 |
67770 | Companilactobacillus nodensis DSM 19682 = JCM 14932 = NBRC 107160 | GCA_000615905 | contig | ncbi | 1423775 |
67770 | Companilactobacillus nodensis DSM 19682 = JCM 14932 = NBRC 107160 | GCA_001592065 | contig | ncbi | 1423775 |
GC content
@ref | GC-content | method |
---|---|---|
8253 | 40.6 | |
67770 | 37.6 | genome sequence analysis |
67770 | 40.6 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 95.082 | yes |
gram-positive | yes | 94.104 | no |
anaerobic | no | 90.404 | no |
halophile | yes | 86.03 | no |
spore-forming | no | 94.843 | yes |
glucose-util | yes | 89.701 | yes |
thermophile | no | 99.216 | yes |
aerobic | no | 97.073 | no |
flagellated | no | 98.05 | yes |
glucose-ferment | yes | 90.495 | no |
External links
@ref: 8253
culture collection no.: DSM 19682, CIP 109958, JCM 14932, NBRC 107160
straininfo link
- @ref: 76148
- straininfo: 360509
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 19126729 | Lactobacillus nodensis sp. nov., isolated from rice bran. | Kashiwagi T, Suzuki T, Kamakura T | Int J Syst Evol Microbiol | 10.1099/ijs.0.65772-0 | 2009 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/genetics, Fermentation, Genes, rRNA, Japan, Lactobacillus/*classification/genetics/*isolation & purification/physiology, Nucleic Acid Hybridization, Oryza/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity | Transcriptome |
Phylogeny | 26486967 | Lactobacillus insicii sp. nov., isolated from fermented raw meat. | Ehrmann MA, Krockel L, Lick S, Radmann P, Bantleon A, Vogel RF | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000705 | 2015 | Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Dipeptides/chemistry, Fatty Acids/chemistry, Fermentation, *Food Microbiology, Lactobacillus/*cytology/genetics/isolation & purification, Meat Products/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Swine | Biotechnology |
Phylogeny | 30010525 | Lactobacillus terrae sp. nov., a novel species isolated from soil samples in the Republic of Korea. | Kim HJ, Lee HJ, Lim B, Kim E, Kim HY, Suh M, Hur M | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002918 | 2018 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lactobacillus/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
8253 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19682) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19682 | |||
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 | |||
32611 | 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 | 28824 | 28776041 | |
40607 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/7760 | ||||
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 | |||
76148 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID360509.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
121322 | Curators of the CIP | Collection of Institut Pasteur (CIP 109958) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109958 |