Strain identifier

BacDive ID: 7463

Type strain: Yes

Species: Microbacterium immunditiarum

Strain Designation: SK 18

Strain history: T. Chakrabarti SK18.

NCBI tax ID(s): 337480 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 17724

BacDive-ID: 7463

DSM-Number: 24662

keywords: genome sequence, 16S sequence, Bacteria, Gram-positive, rod-shaped

description: Microbacterium immunditiarum SK 18 is a Gram-positive, rod-shaped bacterium that was isolated from surface soil from a municipal landfill.

NCBI tax id

  • NCBI tax id: 337480
  • Matching level: species

strain history

@refhistory
17724<- T. Chakrabarti, NCCS Complex, Univ. of Pune Campus, India; SK 18 <- S. Krishnamurthi, MTCC, Institute of Microbial Technology, Chandigarh
67770T. Chakrabarti SK18.

doi: 10.13145/bacdive7463.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Microbacterium
  • species: Microbacterium immunditiarum
  • full scientific name: Microbacterium immunditiarum Krishnamurthi et al. 2012

@ref: 17724

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium immunditiarum

full scientific name: Microbacterium immunditiarum Krishnamurthi et al. 2012

strain designation: SK 18

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
30321positiverod-shapedno
69480positive100

pigmentation

  • @ref: 30321
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
30321positivegrowth15-37
30321positiveoptimum30mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepH
30321positivegrowth06-08
30321positiveoptimum7.5

Physiology and metabolism

spore formation

@refspore formationconfidence
30321no
69481no100
69480no99.309

halophily

  • @ref: 30321
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <3 %

observation

  • @ref: 67770
  • observation: quinones: MK-13, MK-12

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
303214853esculin+hydrolysis
3032117632nitrate+reduction

enzymes

@refvalueactivityec
30321catalase+1.11.1.6
30321gelatinase+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
17724surface soil from a municipal landfillChandigarhIndiaINDAsia
67770Landfill surface soil in ChandigarhIndiaINDAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Waste#Landfill
#Environmental#Terrestrial#Soil

Safety information

risk assessment

  • @ref: 17724
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17724
  • description: Microbacterium immunditiarum strain SK 18 16S ribosomal RNA gene, partial sequence
  • accession: DQ119293
  • length: 1432
  • database: ena
  • NCBI tax ID: 337480

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microbacterium immunditiarum strain DSM 24662337480.3wgspatric337480
66792Microbacterium immunditiarum DSM 246622845010473draftimg337480
67770Microbacterium immunditiarum DSM 24662GCA_013409785contigncbi337480

GC content

@refGC-contentmethod
1772476.6thermal denaturation, midpoint method (Tm)
3032176.6

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveyes88.722no
anaerobicno99.6no
halophileno89.509no
spore-formingno91.571yes
glucose-utilyes86.569no
motileno91.047yes
flagellatedno98.798yes
thermophileno97.102no
aerobicyes93.724no
glucose-fermentno90.735no

External links

@ref: 17724

culture collection no.: DSM 24662, JCM 14034, MTCC 7185

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22058326Microbacterium immunditiarum sp. nov., an actinobacterium isolated from landfill surface soil, and emended description of the genus Microbacterium.Krishnamurthi S, Bhattacharya A, Schumann P, Dastager SG, Tang SK, Li WJ, Chakrabarti TInt J Syst Evol Microbiol10.1099/ijs.0.033373-02011Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Peptidoglycan/analysis, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Refuse Disposal, Sequence Analysis, DNA, Soil/analysis, *Soil MicrobiologyGenetics
Phylogeny25056298Microbacterium mangrovi sp. nov., an amylolytic actinobacterium isolated from mangrove forest soil.Lee LH, Azman AS, Zainal N, Eng SK, Mutalib NA, Yin WF, Chan KGInt J Syst Evol Microbiol10.1099/ijs.0.062414-02014Actinomycetales/*classification/genetics/isolation & purification, Avicennia/*microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Forests, Glycolipids/chemistry, Malaysia, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistryGenetics
Phylogeny27688210Microbacterium rhizosphaerae sp. nov., isolated from a Ginseng field, South Korea.Cho SJ, Lee SSAntonie Van Leeuwenhoek10.1007/s10482-016-0768-42016Actinomycetales/classification/genetics/*isolation & purification/metabolism, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry/metabolism, Panax/*growth & development, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Soil MicrobiologyMetabolism
Phylogeny32053092Microbacterium protaetiae sp. nov., isolated from gut of larva of Protaetia brevitarsis seulensis.Heo J, Cho H, Kim MA, Hamada M, Tamura T, Saitou S, Kim SK, Kwon SWInt J Syst Evol Microbiol10.1099/ijsem.0.0039672020Actinobacteria/*classification/isolation & purification, Animals, Bacterial Typing Techniques, Base Composition, Coleoptera/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gastrointestinal Tract/*microbiology, Glycolipids/chemistry, Larva/microbiology, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17724Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24662)https://www.dsmz.de/collection/catalogue/details/culture/DSM-24662
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
30321Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2666228776041
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/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1