Strain identifier
BacDive ID: 162136
Type strain: 
Species: Kocuria sediminis
Strain history: S. Mayilraj FCS-11.
NCBI tax ID(s): 1038857 (species)
version 8.1 (current version)
General
@ref: 67770
BacDive-ID: 162136
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-positive
description: Kocuria sediminis JCM 17929 is a mesophilic, Gram-positive bacterium that was isolated from Marine sediment from Kochi fort area.
NCBI tax id
- NCBI tax id: 1038857
- Matching level: species
strain history
- @ref: 67770
- history: S. Mayilraj FCS-11.
doi: 10.13145/bacdive162136.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Micrococcales
- family: Micrococcaceae
- genus: Kocuria
- species: Kocuria sediminis
- full scientific name: Kocuria sediminis Bala et al. 2012
@ref: 67770
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Micrococcales
family: Micrococcaceae
genus: Kocuria
species: Kocuria sediminis
full scientific name: Kocuria sediminis Bala et al.
type strain: yes
Morphology
cell morphology
| @ref | gram stain | confidence | motility |
|---|---|---|---|
| 69480 | positive | 100 | |
| 69480 | 93.126 | no |
Culture and growth conditions
culture temp
- @ref: 67770
- growth: positive
- type: growth
- temperature: 28
- range: mesophilic
Physiology and metabolism
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.997
observation
- @ref: 67770
- observation: quinones: MK-7(H2), MK-8(H2), MK-9(H2)
Isolation, sampling and environmental information
isolation
- @ref: 67770
- sample type: Marine sediment from Kochi fort area
- geographic location: Kerala
- country: India
- origin.country: IND
- continent: Asia
taxonmaps
- @ref: 69479
- File name: preview.99_4042.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_424;97_1751;98_2142;99_4042&stattab=map
- Last taxonomy: Kocuria
- 16S sequence: JF896464
- Sequence Identity:
- Total samples: 378
- soil counts: 69
- aquatic counts: 42
- animal counts: 266
- plant counts: 1
Sequence information
16S sequences
- @ref: 67770
- description: Kocuria sediminis strain FCS-11 16S ribosomal RNA gene, partial sequence
- accession: JF896464
- length: 1429
- database: ena
- NCBI tax ID: 1038857
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Kocuria sediminis strain JCM 17929 | 1038857.3 | wgs | patric | 1038857 |
| 66792 | Kocuria sediminis JCM 17929 | 2898378665 | draft | img | 1038857 |
| 67770 | Kocuria sediminis JCM 17929 | GCA_009735315 | scaffold | ncbi | 1038857 |
GC content
- @ref: 67770
- GC-content: 60.7
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 86 | no |
| motile | no | 90.301 | no |
| flagellated | no | 96.962 | no |
| gram-positive | yes | 95.279 | no |
| anaerobic | no | 99.458 | no |
| aerobic | yes | 95.279 | no |
| halophile | yes | 57.402 | no |
| spore-forming | no | 91.758 | no |
| thermophile | no | 98.672 | yes |
| glucose-util | yes | 90.834 | no |
| glucose-ferment | no | 84.797 | no |
External links
@ref: 67770
culture collection no.: JCM 17929, MTCC 10969
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 22012251 | Kocuria sediminis sp. nov., isolated from a marine sediment sample. | Bala M, Kaur C, Kaur I, Khan F, Mayilraj S | Antonie Van Leeuwenhoek | 10.1007/s10482-011-9654-2 | 2011 | Carbohydrates/analysis, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/microbiology, India, Micrococcaceae/chemistry/classification/genetics/*isolation & purification, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Ribotyping, Species Specificity | Genetics |
| Phylogeny | 27902231 | Kocuria oceani sp. nov., isolated from a deep-sea hydrothermal plume. | Zhang L, Xi L, Ruan J, Huang Y | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001599 | 2017 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hydrothermal Vents/*microbiology, Micrococcaceae/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/chemistry | Transcriptome |
Reference
| @id | authors | title | doi/url |
|---|---|---|---|
| 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 |
| 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/ | |
| 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 |