Strain identifier
BacDive ID: 24203
Type strain:
Species: Micrococcus terreus
Strain Designation: V3M1
Strain history: CGMCC 1.7054 <-- J.-Y. Zhang et al. V3M1.
NCBI tax ID(s): 574650 (species)
General
@ref: 20655
BacDive-ID: 24203
DSM-Number: 28110
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, coccus-shaped
description: Micrococcus terreus V3M1 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from forest soil.
NCBI tax id
- NCBI tax id: 574650
- Matching level: species
strain history
@ref | history |
---|---|
20655 | <- NBRC; NBRC 104258 <- J.-Y. Zhang, Chinese Acad. Sci. (CAS), Beijing; V3M1 |
67770 | CGMCC 1.7054 <-- J.-Y. Zhang et al. V3M1. |
doi: 10.13145/bacdive24203.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Micrococcales
- family: Micrococcaceae
- genus: Micrococcus
- species: Micrococcus terreus
- full scientific name: Micrococcus terreus Zhang et al. 2010
@ref: 20655
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Micrococcaceae
genus: Micrococcus
species: Micrococcus terreus
full scientific name: Micrococcus terreus Zhang et al. 2010 emend. Nouioui et al. 2018
strain designation: V3M1
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|
29443 | positive | 0.6-0.7 µm | coccus-shaped | no | |
69480 | positive | 100 |
pigmentation
- @ref: 29443
- production: yes
Culture and growth conditions
culture medium
- @ref: 20655
- 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 |
---|---|---|---|---|
20655 | positive | growth | 28 | mesophilic |
29443 | positive | growth | 20-35 | |
29443 | positive | optimum | 33 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
29443 | positive | growth | 05-09 | alkaliphile |
29443 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 29443
- oxygen tolerance: aerobe
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.999
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
29443 | NaCl | positive | growth | 0-2 % |
29443 | NaCl | positive | optimum | 1 % |
observation
@ref | observation |
---|---|
29443 | aggregates in chains |
67770 | quinones: MK-7, MK-7(H?n(2)), MK-8, MK-8(H2) |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
29443 | 17128 | adipate | + | carbon source |
29443 | 16947 | citrate | + | carbon source |
29443 | 24265 | gluconate | + | carbon source |
29443 | 25115 | malate | + | carbon source |
29443 | 17306 | maltose | + | carbon source |
29443 | 18401 | phenylacetate | + | carbon source |
29443 | 53426 | tween 80 | + | carbon source |
enzymes
- @ref: 29443
- value: catalase
- activity: +
- ec: 1.11.1.6
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
20655 | forest soil | Changbai mountains, Heilongjiang Province | China | CHN | Asia |
67770 | Forest soil of the Changbai mountains | China | CHN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Terrestrial | #Forest |
#Environmental | #Terrestrial | #Soil |
taxonmaps
- @ref: 69479
- File name: preview.99_11844.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_453;97_519;98_8896;99_11844&stattab=map
- Last taxonomy: Micrococcus
- 16S sequence: FJ423763
- Sequence Identity:
- Total samples: 6920
- soil counts: 1821
- aquatic counts: 771
- animal counts: 3656
- plant counts: 672
Safety information
risk assessment
- @ref: 20655
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20655
- description: Micrococcus terreus strain V3M1 16S ribosomal RNA gene, partial sequence
- accession: FJ423763
- length: 1514
- database: ena
- NCBI tax ID: 574650
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Micrococcus terreus strain CGMCC 1.7054 | 574650.4 | wgs | patric | 574650 |
66792 | Micrococcus terreus CGMCC 1.7054 | 2617270780 | draft | img | 574650 |
67770 | Micrococcus terreus CGMCC 1.7054 | GCA_900116905 | contig | ncbi | 574650 |
GC content
@ref | GC-content | method |
---|---|---|
20655 | 67.2 | |
67770 | 67.2 | thermal denaturation, midpoint method (Tm) |
67770 | 68.9 | genome sequence analysis |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 78 | no |
gram-positive | yes | 93.001 | yes |
anaerobic | no | 99.451 | no |
halophile | no | 81.93 | yes |
spore-forming | no | 92.927 | no |
glucose-util | yes | 79.791 | no |
thermophile | no | 99.413 | yes |
flagellated | no | 98.319 | yes |
aerobic | yes | 92.844 | yes |
motile | no | 94.722 | yes |
glucose-ferment | no | 89.967 | no |
External links
@ref: 20655
culture collection no.: DSM 28110, CGMCC 1.7054, NBRC 104258, JCM 17489
straininfo link
- @ref: 88150
- straininfo: 404630
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 19783614 | Agrococcus terreus sp. nov. and Micrococcus terreus sp. nov., isolated from forest soil. | Zhang JY, Liu XY, Liu SJ | Int J Syst Evol Microbiol | 10.1099/ijs.0.013235-0 | 2009 | DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Micrococcaceae/*classification/genetics/*isolation & purification/metabolism, Micrococcus/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology | Metabolism |
Phylogeny | 21239567 | Micrococcus lactis sp. nov., isolated from dairy industry waste. | Chittpurna, Singh PK, Verma D, Pinnaka AK, Mayilraj S, Korpole S | Int J Syst Evol Microbiol | 10.1099/ijs.0.028043-0 | 2011 | Animals, Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Dairy Products/microbiology, Fatty Acids/metabolism, Food Industry, Micrococcus/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sewage/*microbiology | Metabolism |
Reference
@id | authors | title | doi/url | catalogue | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | ||||
20655 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-28110 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28110) | ||||
29443 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 25849 | 28776041 | ||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | ||||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | ||||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | ||||
88150 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID404630.1 |