Strain identifier
BacDive ID: 1266
Type strain:
Species: Metabacillus idriensis
Strain history: CIP <- 2007, JCM <- 2005, K.S. Ko, ARFID, Seoul, Korea: strain SMC 4352-2
NCBI tax ID(s): 324768 (species)
General
@ref: 7888
BacDive-ID: 1266
DSM-Number: 19097
keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, spore-forming, mesophilic, motile, human pathogen
description: Metabacillus idriensis DSM 19097 is an obligate aerobe, spore-forming, mesophilic human pathogen that was isolated from new born child with sepsis.
NCBI tax id
- NCBI tax id: 324768
- Matching level: species
strain history
@ref | history |
---|---|
7888 | <- JCM <- K.S. Ko, SMC 4352-2 |
67770 | K. S. Ko SMC 4352-2. |
120043 | CIP <- 2007, JCM <- 2005, K.S. Ko, ARFID, Seoul, Korea: strain SMC 4352-2 |
doi: 10.13145/bacdive1266.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Caryophanales
- family: Bacillaceae
- genus: Metabacillus
- species: Metabacillus idriensis
- full scientific name: Metabacillus idriensis (Ko et al. 2006) Gupta et al. 2020
synonyms
- @ref: 20215
- synonym: Bacillus idriensis
@ref: 7888
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Bacillaceae
genus: Metabacillus
species: Metabacillus idriensis
full scientific name: Metabacillus idriensis (Ko et al. 2006) Gupta et al. 2020
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | yes | 96.543 | ||
69480 | 100 | positive | ||
120043 | no | positive | rod-shaped |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
7888 | CASO AGAR (MERCK 105458) (DSMZ Medium 220) | yes | https://mediadive.dsmz.de/medium/220 | Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water |
33304 | MEDIUM 45 - for Columbia agar with sheep blood | yes | Distilled water make up to (1000.000 ml);Columbia agar (39.000 g);Sheepblood (100.000 ml) | |
120043 | CIP Medium 45 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=45 | |
120043 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
7888 | positive | growth | 30 | mesophilic |
33304 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 120043
- oxygen tolerance: obligate aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | yes | 100 |
69480 | yes | 100 |
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 | gentiobiose | + | builds acid from | 28066 |
68371 | xylitol | - | builds acid from | 17151 |
68371 | raffinose | + | builds acid from | 16634 |
68371 | melezitose | - | builds acid from | 6731 |
68371 | inulin | - | builds acid from | 15443 |
68371 | trehalose | + | builds acid from | 27082 |
68371 | sucrose | + | builds acid from | 17992 |
68371 | melibiose | + | builds acid from | 28053 |
68371 | lactose | - | builds acid from | 17716 |
68371 | maltose | + | builds acid from | 17306 |
68371 | cellobiose | - | builds acid from | 17057 |
68371 | esculin | + | builds acid from | 4853 |
68371 | N-acetylglucosamine | + | builds acid from | 59640 |
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 | D-mannose | + | builds acid from | 16024 |
68371 | D-fructose | + | builds acid from | 15824 |
68371 | D-glucose | + | builds acid from | 17634 |
68371 | D-galactose | - | builds acid from | 12936 |
68371 | methyl beta-D-xylopyranoside | - | builds acid from | 74863 |
68371 | ribitol | - | builds acid from | 15963 |
68371 | L-xylose | - | builds acid from | 65328 |
68371 | L-arabinose | - | builds acid from | 30849 |
68371 | D-arabinose | - | builds acid from | 17108 |
68371 | erythritol | - | builds acid from | 17113 |
120043 | nitrate | - | reduction | 17632 |
120043 | nitrite | - | reduction | 16301 |
metabolite production
- @ref: 120043
- Chebi-ID: 35581
- metabolite: indole
- production: no
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 |
120043 | oxidase | + | |
120043 | catalase | + | 1.11.1.6 |
120043 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
120043 | - | - | + | + | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - |
API 50CHac
@ref | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
120043 | +/- | - | - | - | +/- | +/- | - | - | - | - | + | + | + | - | - | - | - | +/- | - | - | +/- | + | +/- | +/- | + | +/- | - | + | - | + | + | + | - | - | + | +/- | +/- | - | + | + | - | - | - | - | - | - | + | - | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent |
---|---|---|---|---|
7888 | new born child with sepsis | Republic of Korea | KOR | Asia |
67770 | Blood of a newborn child with sepsis | |||
120043 | Human, Blood |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Infection | #Disease | |
#Infection | #Patient | |
#Host | #Human | #Child |
taxonmaps
- @ref: 69479
- File name: preview.99_8187.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_3218;97_3948;98_5033;99_8187&stattab=map
- Last taxonomy: Bacillus idriensis
- 16S sequence: AY904033
- Sequence Identity:
- Total samples: 1681
- soil counts: 672
- aquatic counts: 269
- animal counts: 703
- plant counts: 37
Safety information
risk assessment
@ref | pathogenicity human | biosafety level | biosafety level comment |
---|---|---|---|
7888 | yes, in single cases | 1 | Risk group (German classification) |
120043 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 7888
- description: Bacillus idriensis strain SMC 4352-2 16S ribosomal RNA gene, partial sequence
- accession: AY904033
- length: 1437
- database: ena
- NCBI tax ID: 324768
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Bacillus idriensis strain DSM 19097 | 324768.4 | wgs | patric | 324768 |
67770 | Metabacillus idriensis DSM 19097 | GCA_009674765 | contig | ncbi | 324768 |
GC content
@ref | GC-content | method |
---|---|---|
7888 | 41.2 | |
67770 | 41.2 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
gram-positive | yes | 88.035 | no |
anaerobic | no | 97.58 | no |
halophile | no | 69.222 | no |
spore-forming | yes | 97.235 | no |
glucose-util | yes | 89.293 | no |
motile | yes | 84.65 | no |
flagellated | yes | 79.563 | no |
aerobic | yes | 86.502 | no |
thermophile | no | 98.064 | no |
glucose-ferment | no | 93.349 | no |
External links
@ref: 7888
culture collection no.: DSM 19097, CCUG 58726, JCM 13437, KCCM 90024, SMC 4352-2, ABB 0430, CIP 109494
straininfo link
- @ref: 70922
- straininfo: 297132
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 17082387 | Bacillus infantis sp. nov. and Bacillus idriensis sp. nov., isolated from a patient with neonatal sepsis. | Ko KS, Oh WS, Lee MY, Lee JH, Lee H, Peck KR, Lee NY, Song JH | Int J Syst Evol Microbiol | 10.1099/ijs.0.64213-0 | 2006 | Bacillus/*classification/genetics/*isolation & purification, Bacterial Typing Techniques, Carbohydrate Metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Female, Genes, rRNA, Humans, Infant, Newborn, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sepsis/*microbiology, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid | Pathogenicity |
Phylogeny | 26559004 | Bacillus ectoiniformans sp. nov., a halotolerant bacterium isolated from deep-sea sediments. | Zhu D, Zhang P, Niu L, Xie C, Li P, Sun J, Hang F | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000763 | 2015 | ||
Phylogeny | 35998028 | Metabacillus kandeliae sp. nov., isolated from the rhizosphere soil of a decayed mangrove plant Kandelia candel. | Cai H, Huang Y, Liu Y, Yang L, Zhou Y, Yang S, Chen X, Jiang C, Jiang M, Jiang Y, Singh P | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005538 | 2022 | *Bacillaceae, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizophoraceae/microbiology, Rhizosphere, Sequence Analysis, DNA, Soil, Soil Microbiology | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title |
---|---|---|---|---|
7888 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19097) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19097 | |
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 | |
33304 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/7244 | ||
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 | |
70922 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID297132.1 | StrainInfo: A central database for resolving microbial strain identifiers | |
120043 | Curators of the CIP | Collection of Institut Pasteur (CIP 109494) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109494 |