Strain identifier
BacDive ID: 7450
Type strain:
Species: Microbacterium humi
Strain Designation: CC-012309, CC-12309
Strain history: CCM 7687 <-- P. Kämpfer CC-12309.
NCBI tax ID(s): 640635 (species)
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
@ref | history |
---|---|
15962 | <- P. Kämpfer, Univ. Giessen, Germany <- College of Agriculture and Natural Resources, University Taichung; CC-12309 |
67770 | CCM 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
@ref | gram stain | cell length | cell width | cell shape | confidence |
---|---|---|---|---|---|
29488 | positive | 2.5 µm | 1.1 µm | rod-shaped | |
69480 | positive | 100 |
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
@ref | growth | type | temperature | range |
---|---|---|---|---|
15962 | positive | growth | 28 | mesophilic |
29488 | positive | growth | 25-30 | mesophilic |
61573 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
29488 | aerobe |
61573 | aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 99 |
69480 | no | 99.984 |
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
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
29488 | 22599 | arabinose | + | carbon source |
29488 | 35391 | aspartate | + | carbon source |
29488 | 28260 | galactose | + | carbon source |
29488 | 25115 | malate | + | carbon source |
29488 | 28053 | melibiose | + | carbon source |
29488 | 506227 | N-acetylglucosamine | + | carbon source |
29488 | 15361 | pyruvate | + | carbon source |
29488 | 26546 | rhamnose | + | carbon source |
29488 | 33942 | ribose | + | carbon source |
29488 | 30911 | sorbitol | + | carbon source |
29488 | 18222 | xylose | + | carbon source |
29488 | 4853 | esculin | + | hydrolysis |
enzymes
@ref | value | activity | ec |
---|---|---|---|
29488 | catalase | + | 1.11.1.6 |
29488 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | country | origin.country | continent |
---|---|---|---|---|---|
15962 | basidiomycete fungus Agaricus blazei Murill | Agaricus blazei | Taiwan | TWN | Asia |
61573 | Stalk of the mushroom Agaricus brasiliensi | Taiwan | TWN | Asia | |
67770 | Stalk of the edible mushroom Agaricus blazei grown in the laboratory | Agaricus blazei |
isolation source categories
Cat1 | Cat2 |
---|---|
#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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Microbacterium humi strain DSM 21799 | 640635.3 | wgs | patric | 640635 |
66792 | Microbacterium humi DSM 21799 | 2630968996 | draft | img | 640635 |
67770 | Microbacterium humi DSM 21799 | GCA_900105715 | contig | ncbi | 640635 |
GC content
- @ref: 67770
- GC-content: 67.3
- method: genome sequence analysis
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 99 | no |
gram-positive | yes | 90.934 | yes |
anaerobic | no | 99.282 | yes |
halophile | no | 80.798 | no |
spore-forming | no | 91.123 | no |
glucose-util | yes | 82.704 | no |
thermophile | no | 97.657 | no |
flagellated | no | 94.475 | no |
aerobic | yes | 89.737 | yes |
motile | yes | 61.333 | no |
glucose-ferment | no | 88.833 | no |
External links
@ref: 15962
culture collection no.: CCUG 58052, DSM 21799, CCM 7687, JCM 18706
straininfo link
- @ref: 76898
- straininfo: 402227
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 19661494 | Microbacterium 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 P | Int J Syst Evol Microbiol | 10.1099/ijs.0.014092-0 | 2009 | Actinomycetales/*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 Specificity | Genetics |
Phylogeny | 34232856 | Microbacterium 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 J | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004858 | 2021 | Animals, 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/chemistry | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
15962 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21799) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21799 | ||||
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 | ||||
29488 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 25888 | 28776041 | ||
61573 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 58052) | https://www.ccug.se/strain?id=58052 | ||||
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) | ||||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||||
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 | ||||
76898 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID402227.1 | StrainInfo: A central database for resolving microbial strain identifiers |