Strain identifier

BacDive ID: 1266

Type strain: Yes

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)

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General

@ref: 7888

BacDive-ID: 1266

DSM-Number: 19097

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, spore-forming, mesophilic, Gram-positive, rod-shaped

description: Metabacillus idriensis DSM 19097 is an obligate aerobe, spore-forming, mesophilic bacterium that was isolated from new born child with sepsis.

NCBI tax id

  • NCBI tax id: 324768
  • Matching level: species

strain history

@refhistory
7888<- JCM <- K.S. Ko, SMC 4352-2
67770K. S. Ko SMC 4352-2.
120043CIP <- 2007, JCM <- 2005, K.S. Ko, ARFID, Seoul, Korea: strain SMC 4352-2

doi: 10.13145/bacdive1266.20250331.9.3

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: 120043
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7888CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: 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
33304MEDIUM 45 - for Columbia agar with sheep bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Sheepblood (100.000 ml)
120043CIP Medium 45yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=45
120043CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperature
7888positivegrowth30
33304positivegrowth37
67770positivegrowth37

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
120043obligate aerobe
125439obligate aerobe90.7

spore formation

  • @ref: 125438
  • spore formation: yes
  • confidence: 95.273

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12004317632nitrate-reduction
12004316301nitrite-reduction
68371Potassium 5-ketogluconate+builds acid from
6837159640N-acetylglucosamine+builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate+builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose+builds acid from
6837128066gentiobiose+builds acid from
6837117151xylitol-builds acid from
6837116634raffinose+builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose+builds acid from
6837117992sucrose+builds acid from
6837128053melibiose+builds acid from
6837117716lactose-builds acid from
6837117306maltose+builds acid from
6837117057cellobiose-builds acid from
683714853esculin+builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from

metabolite production

  • @ref: 120043
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-glucosidase-3.2.1.20
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase-
68382acid phosphatase-3.1.3.2
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382cystine arylamidase-3.4.11.3
68382leucine arylamidase-3.4.11.1
68382valine arylamidase-
68382lipase (C 14)-
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382alkaline phosphatase-3.1.3.1
120043oxidase+
120043catalase+1.11.1.6
120043urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120043--++---------+------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120043+/----+/-+/-----+++----+/---+/-++/-+/-++/--+-+++--++/-+/--++------+-+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
7888new born child with sepsisRepublic of KoreaKORAsia
67770Blood of a newborn child with sepsis
120043Human, Blood

isolation source categories

Cat1Cat2Cat3
#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

@refpathogenicity humanbiosafety levelbiosafety level comment
7888yes, in single cases1Risk group (German classification)
1200431Risk 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: nuccore
  • NCBI tax ID: 324768

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bacillus idriensis strain DSM 19097324768.4wgspatric324768
67770Metabacillus idriensis DSM 19097GCA_009674765contigncbi324768

GC content

@refGC-contentmethod
788841.2
6777041.2thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes71.467no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no89.848yes
125438spore-formingspore-formingAbility to form endo- or exosporesyes95.273no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes73.452no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno95.295yes
125438motile2+flagellatedAbility to perform flagellated movementyes87.166no
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes76.8
125439BacteriaNetmotilityAbility to perform movementyes66.4
125439BacteriaNetgram_stainReaction to gram-stainingvariable78.1
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe90.7

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

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17082387Bacillus 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 JHInt J Syst Evol Microbiol10.1099/ijs.0.64213-02006Bacillus/*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 AcidPathogenicity
Phylogeny26559004Bacillus ectoiniformans sp. nov., a halotolerant bacterium isolated from deep-sea sediments.Zhu D, Zhang P, Niu L, Xie C, Li P, Sun J, Hang FInt J Syst Evol Microbiol10.1099/ijsem.0.0007632015
Phylogeny35998028Metabacillus 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 PInt J Syst Evol Microbiol10.1099/ijsem.0.0055382022*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 MicrobiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitle
7888Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19097)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19097
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
33304Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7244
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
69479João 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
70922Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297132.1StrainInfo: A central database for resolving microbial strain identifiers
120043Curators of the CIPCollection of Institut Pasteur (CIP 109494)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109494
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1