Strain identifier

BacDive ID: 7465

Type strain: Yes

Species: Microbacterium murale

Strain Designation: 01-Gi-001

Strain history: CCM 7640 <-- P. Kämpfer; Justus-Liebig-Univ. Giessen, Germany; 01-Gi-001.

NCBI tax ID(s): 1081040 (species)

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General

@ref: 16133

BacDive-ID: 7465

DSM-Number: 22178

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

description: Microbacterium murale 01-Gi-001 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from indoor wall colonized with moulds.

NCBI tax id

  • NCBI tax id: 1081040
  • Matching level: species

strain history

@refhistory
16133<- P. Kämpfer, Univ. Giessen, Germany; 01-Gi-001 <- J. Schäfer
67770CCM 7640 <-- P. Kämpfer; Justus-Liebig-Univ. Giessen, Germany; 01-Gi-001.

doi: 10.13145/bacdive7465.20230509.8.1

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 murale
  • full scientific name: Microbacterium murale Kämpfer et al. 2012

@ref: 16133

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium murale

full scientific name: Microbacterium murale Kämpfer et al. 2012

strain designation: 01-Gi-001

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapeconfidence
30509positive2.5 µm1.1 µmrod-shaped
69480positive100

pigmentation

  • @ref: 30509
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 16133
  • name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/92
  • composition: Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
16133positivegrowth28mesophilic
30509positivegrowth25-30mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 30509
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
30509no
69481no98
69480no99.959

murein

  • @ref: 16133
  • murein short key: B05
  • type: B2ß {Gly} [L-Hsr] D-Glu-D-Orn

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
30509370543-hydroxybutyrate+carbon source
3050916449alanine+carbon source
3050922599arabinose+carbon source
3050935391aspartate+carbon source
3050917057cellobiose+carbon source
3050928757fructose+carbon source
3050928260galactose+carbon source
3050924265gluconate+carbon source
3050917234glucose+carbon source
3050927570histidine+carbon source
3050924996lactate+carbon source
3050925017leucine+carbon source
3050925115malate+carbon source
3050917306maltose+carbon source
3050937684mannose+carbon source
30509506227N-acetylglucosamine+carbon source
3050918401phenylacetate+carbon source
3050928044phenylalanine+carbon source
3050917148putrescine+carbon source
3050915361pyruvate+carbon source
3050933942ribose+carbon source
3050917992sucrose+carbon source
3050927082trehalose+carbon source
3050918222xylose+carbon source
305094853esculin+hydrolysis

enzymes

@refvalueactivityec
30509catalase+1.11.1.6
30509cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
16133indoor wall colonized with mouldsGiessenGermanyDEUEurope
67770Indoor wall colonized with mouldsGiessenGermanyDEUEurope

isolation source categories

Cat1Cat2Cat3
#Engineered#Built environment#Indoor
#Host#Fungi

taxonmaps

  • @ref: 69479
  • File name: preview.99_7463.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_137;97_148;98_165;99_7463&stattab=map
  • Last taxonomy: Microbacterium
  • 16S sequence: HE585693
  • Sequence Identity:
  • Total samples: 224
  • soil counts: 50
  • aquatic counts: 29
  • animal counts: 126
  • plant counts: 19

Safety information

risk assessment

  • @ref: 16133
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16133
  • description: Microbacterium murale partial 16S rRNA gene, type strain 01-Gi-001T
  • accession: HE585693
  • length: 1356
  • database: ena
  • NCBI tax ID: 1081040

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microbacterium murale CCM 7640GCA_014635185scaffoldncbi1081040
66792Microbacterium murale strain CCM 76401081040.3wgspatric1081040

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno98no
flagellatedno91.879no
gram-positiveyes93.63yes
anaerobicno99.673yes
aerobicyes93.61yes
halophileno83.497no
spore-formingno85.493yes
thermophileno99.719yes
glucose-utilyes87.874yes
motileyes65.005no
glucose-fermentno88.667no

External links

@ref: 16133

culture collection no.: DSM 22178, CCM 7640, JCM 30494

straininfo link

  • @ref: 76910
  • straininfo: 405357

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22199224Microbacterium murale sp. nov., isolated from an indoor wall.Kampfer P, Schafer J, Lodders N, Martin KInt J Syst Evol Microbiol10.1099/ijs.0.037705-02011Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, DNA, Bacterial/genetics, Environmental Microbiology, Fatty Acids/analysis, Molecular Sequence Data, Peptidoglycan/analysis, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny25253073Microbacterium petrolearium sp. nov., isolated from an oil-contaminated water sample.Wang H, Xiang T, Wang Y, Song J, Zhai Y, Chen X, Li Y, Zhao B, Zhao B, Ruan ZInt J Syst Evol Microbiol10.1099/ijs.0.061119-02014Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Oil and Gas Fields/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistry, *Water Microbiology, Water Pollution, ChemicalGenetics
Phylogeny25678679Microbacterium shaanxiense sp. nov., isolated from the nodule surface of soybean.Peng S, Dongying L, Bingxin Y, Mingjun L, Gehong WInt J Syst Evol Microbiol10.1099/ijs.0.0001162015Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Root Nodules, Plant/*microbiology, Sequence Analysis, DNA, *Soil Microbiology, Soybeans/*microbiology, Vitamin K 2/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
16133Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22178)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22178
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
30509Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2684128776041
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/
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
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
76910Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID405357.1StrainInfo: A central database for resolving microbial strain identifiers