Strain identifier
BacDive ID: 24181
Type strain: 
Species: Agrococcus terreus
Strain Designation: DNG5
Strain history: CGMCC 1.6960 <-- J.-Y. Zhang et al. DNG5.
NCBI tax ID(s): 574649 (species)
version 8.1 (current version)
General
@ref: 20269
BacDive-ID: 24181
DSM-Number: 28114
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, rod-shaped
description: Agrococcus terreus DNG5 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from forest soil.
NCBI tax id
- NCBI tax id: 574649
- Matching level: species
strain history
| @ref | history |
|---|---|
| 20269 | <- NBRC <- CGMCC 1.6960 <- J.-Y. Zhang, CAS; DNG5 |
| 67770 | CGMCC 1.6960 <-- J.-Y. Zhang et al. DNG5. |
doi: 10.13145/bacdive24181.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Micrococcales
- family: Microbacteriaceae
- genus: Agrococcus
- species: Agrococcus terreus
- full scientific name: Agrococcus terreus Zhang et al. 2010
@ref: 20269
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Microbacteriaceae
genus: Agrococcus
species: Agrococcus terreus
full scientific name: Agrococcus terreus Zhang et al. 2010
strain designation: DNG5
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 29443 | positive | 0.8-1 µm | 0.4-0.5 µm | rod-shaped | no | |
| 69480 | positive | 100 |
pigmentation
- @ref: 29443
- production: yes
Culture and growth conditions
culture medium
- @ref: 20269
- 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 |
|---|---|---|---|---|
| 20269 | positive | growth | 28 | mesophilic |
| 29443 | positive | growth | 20-40 | |
| 29443 | positive | optimum | 30 | mesophilic |
| 67770 | positive | growth | 28 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 29443 | positive | growth | 5.5-9 | alkaliphile |
| 29443 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 29443
- oxygen tolerance: aerobe
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.998
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 29443 | NaCl | positive | growth | 0-4 % |
| 29443 | NaCl | positive | optimum | 1 % |
observation
| @ref | observation |
|---|---|
| 29443 | aggregates in chains |
| 67770 | quinones: MK-11, MK-10, MK-9 |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 29443 | 22599 | arabinose | + | carbon source |
| 29443 | 24265 | gluconate | + | carbon source |
| 29443 | 25115 | malate | + | carbon source |
| 29443 | 29864 | mannitol | + | carbon source |
| 29443 | 37684 | mannose | + | carbon source |
| 29443 | 4853 | esculin | + | hydrolysis |
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 |
|---|---|---|---|---|---|
| 20269 | forest soil | Changbai Mountain | 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 |
Safety information
risk assessment
- @ref: 20269
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20269
- description: Agrococcus terreus strain DNG5 16S ribosomal RNA gene, partial sequence
- accession: FJ423764
- length: 1516
- database: ena
- NCBI tax ID: 574649
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Agrococcus terreus CGMCC 1.6960 | GCA_014645235 | contig | ncbi | 574649 |
| 66792 | Agrococcus terreus strain CGMCC 1.6960 | 574649.3 | wgs | patric | 574649 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 20269 | 67.2 | thermal denaturation, midpoint method (Tm) |
| 29443 | 75.9 | |
| 67770 | 75.9 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 82 | no |
| gram-positive | yes | 93.36 | no |
| anaerobic | no | 99.537 | yes |
| halophile | no | 91.652 | yes |
| spore-forming | no | 94.503 | no |
| glucose-util | yes | 85.696 | no |
| flagellated | no | 97.741 | yes |
| aerobic | yes | 96.727 | yes |
| thermophile | no | 99.39 | yes |
| motile | no | 89.529 | yes |
| glucose-ferment | no | 91.214 | no |
External links
@ref: 20269
culture collection no.: DSM 28114, CGMCC 1.6960, JCM 17488, NBRC 104260
straininfo link
- @ref: 88134
- straininfo: 402013
literature
- topic: Phylogeny
- Pubmed-ID: 19783614
- title: Agrococcus terreus sp. nov. and Micrococcus terreus sp. nov., isolated from forest soil.
- authors: Zhang JY, Liu XY, Liu SJ
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.013235-0
- year: 2009
- mesh: 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
- topic2: Metabolism
Reference
| @id | authors | title | doi/url | catalogue | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 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 | |||
| 20269 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-28114 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28114) | |||
| 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 | |||
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 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 | |||
| 88134 | 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-ID402013.1 |