Strain identifier

BacDive ID: 7450

Type strain: Yes

Species: Microbacterium humi

Strain Designation: CC-012309, CC-12309

Strain history: CCM 7687 <-- P. Kämpfer CC-12309.

NCBI tax ID(s): 640635 (species)

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General

@ref: 15962

BacDive-ID: 7450

DSM-Number: 21799

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

description: Microbacterium humi CC-012309 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from basidiomycete fungus Agaricus blazei Murill.

NCBI tax id

  • NCBI tax id: 640635
  • Matching level: species

strain history

@refhistory
15962<- P. Kämpfer, Univ. Giessen, Germany <- College of Agriculture and Natural Resources, University Taichung; CC-12309
67770CCM 7687 <-- P. Kämpfer CC-12309.

doi: 10.13145/bacdive7450.20230509.8.1

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 humi
  • full scientific name: Microbacterium humi Young et al. 2010

@ref: 15962

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium humi

full scientific name: Microbacterium humi Young et al. 2010 emend. Nouioui et al. 2018

strain designation: CC-012309, CC-12309

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapeconfidence
29488positive2.5 µm1.1 µmrod-shaped
69480positive100

colony morphology

  • @ref: 61573
  • incubation period: 1-2 days

pigmentation

  • @ref: 29488
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 15962
  • 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
15962positivegrowth28mesophilic
29488positivegrowth25-30mesophilic
61573positivegrowth30mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29488aerobe
61573aerobe

spore formation

@refspore formationconfidence
69481no99
69480no99.984

murein

  • @ref: 15962
  • murein short key: B12
  • type: B2alpha {Gly} [L-Orn] D-Glu-Gly-D-Orn

observation

  • @ref: 67770
  • observation: quinones: MK-11, MK-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2948822599arabinose+carbon source
2948835391aspartate+carbon source
2948828260galactose+carbon source
2948825115malate+carbon source
2948828053melibiose+carbon source
29488506227N-acetylglucosamine+carbon source
2948815361pyruvate+carbon source
2948826546rhamnose+carbon source
2948833942ribose+carbon source
2948830911sorbitol+carbon source
2948818222xylose+carbon source
294884853esculin+hydrolysis

enzymes

@refvalueactivityec
29488catalase+1.11.1.6
29488cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinent
15962basidiomycete fungus Agaricus blazei MurillAgaricus blazeiTaiwanTWNAsia
61573Stalk of the mushroom Agaricus brasiliensiTaiwanTWNAsia
67770Stalk of the edible mushroom Agaricus blazei grown in the laboratoryAgaricus blazei

isolation source categories

Cat1Cat2
#Host#Fungi
#Host Body-Site#Plant

taxonmaps

  • @ref: 69479
  • File name: preview.99_87031.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_27915;97_45951;98_60185;99_87031&stattab=map
  • Last taxonomy: Microbacterium humi subclade
  • 16S sequence: FJ865215
  • Sequence Identity:
  • Total samples: 111
  • soil counts: 63
  • aquatic counts: 18
  • animal counts: 24
  • plant counts: 6

Safety information

risk assessment

  • @ref: 15962
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15962
  • description: Microbacterium humi strain CC-012309 16S ribosomal RNA gene, partial sequence
  • accession: FJ865215
  • length: 1430
  • database: ena
  • NCBI tax ID: 640635

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microbacterium humi strain DSM 21799640635.3wgspatric640635
66792Microbacterium humi DSM 217992630968996draftimg640635
67770Microbacterium humi DSM 21799GCA_900105715contigncbi640635

GC content

  • @ref: 67770
  • GC-content: 67.3
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
gram-positiveyes90.934yes
anaerobicno99.282yes
halophileno80.798no
spore-formingno91.123no
glucose-utilyes82.704no
thermophileno97.657no
flagellatedno94.475no
aerobicyes89.737yes
motileyes61.333no
glucose-fermentno88.833no

External links

@ref: 15962

culture collection no.: CCUG 58052, DSM 21799, CCM 7687, JCM 18706

straininfo link

  • @ref: 76898
  • straininfo: 402227

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19661494Microbacterium agarici sp. nov., Microbacterium humi sp. nov. and Microbacterium pseudoresistens sp. nov., isolated from the base of the mushroom Agaricus blazei.Young CC, Busse HJ, Langer S, Chu JN, Schumann P, Arun AB, Shen FT, Rekha PD, Kampfer PInt J Syst Evol Microbiol10.1099/ijs.0.014092-02009Actinomycetales/*classification/genetics/*isolation & purification/physiology, *Agaricus, Bacterial Typing Techniques, DNA, Ribosomal/analysis/genetics, Fatty Acids/analysis, Genes, rRNA, Genotype, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Plant Stems/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny34232856Microbacterium chengjingii sp. nov. and Microbacterium fandaimingii sp. nov., isolated from bat faeces of Hipposideros and Rousettus species.Zhou J, Huang Y, Yang J, Lai XH, Jin D, Lu S, Pu J, Zhang S, Zhu W, Xu M, Huang Y, Liang J, Zheng H, Xu JInt J Syst Evol Microbiol10.1099/ijsem.0.0048582021Animals, Bacterial Typing Techniques, Base Composition, China, Chiroptera/classification/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/*microbiology, Microbacterium/*classification/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
15962Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21799)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21799
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
29488Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2588828776041
61573Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 58052)https://www.ccug.se/strain?id=58052
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
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
76898Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID402227.1StrainInfo: A central database for resolving microbial strain identifiers