Strain identifier
BacDive ID: 24127
Type strain:
Species: Ligilactobacillus pobuzihii
Strain Designation: E100301
Strain history: CIP <- 2011, KCTC
NCBI tax ID(s): 449659 (species)
General
@ref: 20987
BacDive-ID: 24127
DSM-Number: 28122
keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, Gram-positive, rod-shaped
description: Ligilactobacillus pobuzihii E100301 is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from fermented cummingcordia .
NCBI tax id
- NCBI tax id: 449659
- Matching level: species
strain history
@ref | history |
---|---|
37969 | 2011, KCTC |
20987 | <- NBRC; NBRC 103219 <- Y.-S. Chen, Yamanashi Univerity; RIFY 6501 |
67770 | KCTC 13174 <-- Y.-S. Chen E100301. |
67771 | <- Y Chen, Yamanashi Univ., Japan |
121918 | CIP <- 2011, KCTC |
doi: 10.13145/bacdive24127.20230509.8.1
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 pobuzihii
- full scientific name: Ligilactobacillus pobuzihii (Chen et al. 2010) Zheng et al. 2020
synonyms
- @ref: 20215
- synonym: Lactobacillus pobuzihii
@ref: 20987
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Lactobacillales
family: Lactobacillaceae
genus: Ligilactobacillus
species: Ligilactobacillus pobuzihii
full scientific name: Ligilactobacillus pobuzihii (Chen et al. 2010) Zheng et al. 2020
strain designation: E100301
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility |
---|---|---|---|---|---|
29607 | positive | 2.2-3.9 µm | 0.5 µm | rod-shaped | |
67771 | rod-shaped | ||||
67771 | positive | ||||
121918 | positive | rod-shaped | no |
pigmentation
- @ref: 29607
- production: yes
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
20987 | MRS MEDIUM (DSMZ Medium 11) | yes | https://mediadive.dsmz.de/medium/11 | Name: MRS MEDIUM (DSMZ Medium 11; with strain-specific modifications) Composition: NaCl 50.0 g/l Glucose 20.0 g/l Meat extract 10.0 g/l Casein peptone 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 |
37969 | MEDIUM 40- for Lactobacillus and Leuconostoc | yes | Distilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g) | |
121918 | CIP Medium 40 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
20987 | positive | growth | 37 | mesophilic |
29607 | positive | growth | 30-37 | mesophilic |
29607 | positive | optimum | 37 | mesophilic |
37969 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
67771 | positive | growth | 37 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
29607 | positive | growth | 7 |
29607 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
20987 | microaerophile |
29607 | facultative anaerobe |
67771 | facultative anaerobe |
121918 | facultative anaerobe |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
29607 | NaCl | positive | growth | 10 % |
29607 | NaCl | positive | optimum | 10 % |
observation
- @ref: 29607
- observation: aggregates in chains
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
29607 | 58143 | 5-dehydro-D-gluconate | + | carbon source |
29607 | 22599 | arabinose | + | carbon source |
29607 | 28757 | fructose | + | carbon source |
29607 | 17234 | glucose | + | carbon source |
29607 | 17716 | lactose | + | carbon source |
29607 | 17306 | maltose | + | carbon source |
29607 | 26546 | rhamnose | + | carbon source |
29607 | 33942 | ribose | + | carbon source |
29607 | 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 | 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 |
121918 | 17632 | nitrate | - | reduction |
121918 | 16301 | nitrite | - | reduction |
metabolite production
- @ref: 121918
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
121918 | oxidase | - | |
121918 | catalase | - | 1.11.1.6 |
121918 | urease | - | 3.5.1.5 |
68382 | alkaline phosphatase | - | 3.1.3.1 |
68382 | esterase (C 4) | - | |
68382 | esterase lipase (C 8) | - | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | + | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | - | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121918 | - | - | - | - | - | + | + | - | - | - | - | + | - | - | - | + | - | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
20987 | - | - | - | - | + | + | - | - | - | - | + | + | + | + | - | - | - | - | - | - | - | - | + | - | - | + | - | + | - | + | - | - | + | - | - | - | - | - | - | + | - | - | + | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent | geographic location |
---|---|---|---|---|---|
20987 | fermented cummingcordia (pobuzihi) | Taiwan | TWN | Asia | |
67770 | Fermented cummingcordia (pobuzihi) | Taiwan | TWN | Asia | |
67771 | From pobuzih, fermented cummingcordia | Taiwan | TWN | Asia | Taichung city |
121918 | Food, Fermented cummingcordia, food | Taiwan | TWN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Food production | #Vegetable (incl. Grains) |
#Engineered | #Food production | #Food |
#Engineered | #Food production | #Fermented |
taxonmaps
- @ref: 69479
- File name: preview.99_7875.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_937;97_1090;98_1300;99_7875&stattab=map
- Last taxonomy: Ligilactobacillus pobuzihii
- 16S sequence: LC521982
- Sequence Identity:
- Total samples: 2466
- soil counts: 81
- aquatic counts: 41
- animal counts: 2303
- plant counts: 41
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
20987 | 1 | Risk group (German classification) |
121918 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20987 | Lactobacillus pobuzihii gene for 16S rRNA, partial sequence, strain: NBRC 103219 | AB326358 | 1489 | ena | 1242253 |
67770 | Lactobacillus pobuzihii JCM 18084 gene for 16S rRNA, partial sequence | LC521982 | 1500 | ena | 449659 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Ligilactobacillus pobuzihii NBRC 103219 | GCA_007991295 | contig | ncbi | 449659 |
66792 | Lactobacillus pobuzihii E100301 = KCTC 13174 | 1242253.4 | wgs | patric | 1242253 |
66792 | Lactobacillus pobuzihii strain NBRC 103219 | 449659.4 | wgs | patric | 449659 |
66792 | Lactobacillus pobuzihii strain NBRC 103219 | 449659.10 | wgs | patric | 449659 |
66792 | Ligilactobacillus pobuzihii E100301 | 2554235039 | draft | img | 1242253 |
66792 | Ligilactobacillus pobuzihii NBRC 103219 | 2667528017 | draft | img | 449659 |
66792 | Ligilactobacillus pobuzihii E100301 | 2700989127 | draft | img | 1242253 |
67770 | Ligilactobacillus pobuzihii NBRC 103219 | GCA_001438865 | scaffold | ncbi | 449659 |
67771 | Ligilactobacillus pobuzihii E100301 = KCTC 13174 | GCA_000349725 | scaffold | ncbi | 1242253 |
67771 | Ligilactobacillus pobuzihii E100301 = KCTC 13174 | GCA_001433815 | contig | ncbi | 1242253 |
GC content
@ref | GC-content | method |
---|---|---|
20987 | 37.2 | |
67770 | 37.7 | genome sequence analysis |
67771 | 37.2 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | no | 93.882 | no |
gram-positive | yes | 96.858 | no |
anaerobic | no | 90.807 | yes |
aerobic | no | 95.934 | no |
halophile | yes | 95.166 | no |
spore-forming | no | 95.639 | no |
glucose-util | yes | 91.656 | yes |
flagellated | no | 97.789 | no |
thermophile | no | 99.518 | yes |
glucose-ferment | yes | 90.299 | no |
External links
@ref: 20987
culture collection no.: DSM 28122, KCTC 13174, NBRC 103219, RIFY 6501, JCM 18084, CIP 110289
straininfo link
- @ref: 88086
- straininfo: 370396
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 19783610 | Lactobacillus pobuzihii sp. nov., isolated from pobuzihi (fermented cummingcordia). | Chen YS, Miyashita M, Suzuki KI, Sato H, Hsu JS, Yanagida F | Int J Syst Evol Microbiol | 10.1099/ijs.0.016873-0 | 2009 | Carbohydrate Metabolism, Cordia/metabolism/*microbiology, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fermentation, Lactobacillus/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics | Metabolism |
Genetics | 23661478 | Draft Genome Sequence of Lactobacillus pobuzihii E100301T. | Chiu CM, Chang CH, Pan SF, Wu HC, Li SW, Chang CH, Lee YS, Chiang CM, Chen YS | Genome Announc | 10.1128/genomeA.00185-13 | 2013 | ||
Phylogeny | 30628884 | Lactobacillus salitolerans sp. nov., a novel lactic acid bacterium isolated from spent mushroom substrates. | Tohno M, Tanizawa Y, Kojima Y, Sakamoto M, Nakamura Y, Ohkuma M, Kobayashi H | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003224 | 2019 | *Agaricales, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Japan, Lactobacillus/*classification/isolation & purification, Multilocus Sequence Typing, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Transcriptome |
Reference
@id | authors | title | doi/url | catalogue | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | |||
20987 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-28122 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28122) | |||
29607 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 25997 | 28776041 | |
37969 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/8132 | ||||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |||
88086 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID370396.1 | |||
121918 | Curators of the CIP | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110289 | Collection of Institut Pasteur (CIP 110289) |