Strain identifier
BacDive ID: 140035
Type strain: 
Species: Neomicrococcus aestuarii
Strain Designation: DY66
Strain history: <- CN Seong, Sunchon Natl. Univ.
NCBI tax ID(s): 556325 (species)
version 9.3 (current version)
General
@ref: 42642
BacDive-ID: 140035
DSM-Number: 105783
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive
description: Neomicrococcus aestuarii DY66 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from tidal flat sediment.
NCBI tax id
- NCBI tax id: 556325
- Matching level: species
strain history
| @ref | history |
|---|---|
| 42642 | <- JCM, RIKEN BioResource Center, Tsukuba; JCM 16364 <- C. N. Seong, Sunchon Natl. Univ., South Korea; DY66 |
| 67770 | C. N. Seong DY66. |
| 67771 | <- CN Seong, Sunchon Natl. Univ. |
doi: 10.13145/bacdive140035.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Micrococcales
- family: Micrococcaceae
- genus: Neomicrococcus
- species: Neomicrococcus aestuarii
- full scientific name: Neomicrococcus aestuarii (Baik et al. 2011) Prakash et al. 2015
synonyms
- @ref: 20215
- synonym: Zhihengliuella aestuarii
@ref: 42642
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Micrococcaceae
genus: Neomicrococcus
species: Neomicrococcus aestuarii
full scientific name: Neomicrococcus aestuarii (Baik et al. 2011) Prakash et al. 2015
strain designation: DY66
type strain: yes
Morphology
cell morphology
| @ref | gram stain | motility | confidence |
|---|---|---|---|
| 67771 | positive | ||
| 125438 | no | 92 | |
| 125438 | positive | 94.32 |
Culture and growth conditions
culture medium
- @ref: 42642
- name: RICH MEDIUM (DSMZ Medium 736)
- growth: yes
- link: https://mediadive.dsmz.de/medium/736
- composition: Name: RICH MEDIUM (DSMZ Medium 736) Composition: Agar 20.0 g/l Bacto peptone 10.0 g/l Yeast extract 5.0 g/l Malt extract 5.0 g/l Casamino acids 5.0 g/l Glycerol 2.0 g/l Meat extract 2.0 g/l MgSO4 x 7 H2O 1.0 g/l Tween 80 0.05 g/l Distilled water
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 42642 | positive | growth | 28 |
| 67770 | positive | growth | 28 |
| 67771 | positive | growth | 30 |
Physiology and metabolism
oxygen tolerance
- @ref: 67771
- oxygen tolerance: aerobe
observation
- @ref: 67770
- observation: quinones: MK-10, MK-9
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 42642 | tidal flat sediment | Deukryang Bay | Republic of Korea | KOR | Asia |
| 67770 | Tidal flat sediment from Deukryang Bay | Republic of Korea | KOR | Asia | |
| 67771 | From tidal-flat sediment | Deukryang Bay | Republic of Korea | KOR | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Tidal flat |
| #Environmental | #Terrestrial | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_5539.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_2677;97_3285;98_4134;99_5539&stattab=map
- Last taxonomy: Neomicrococcus aestuarii
- 16S sequence: EU939716
- Sequence Identity:
- Total samples: 36
- soil counts: 8
- aquatic counts: 6
- animal counts: 21
- plant counts: 1
Safety information
risk assessment
- @ref: 42642
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 42642 | Zhihengliuella aestuarii strain DY66 16S ribosomal RNA gene, partial sequence | EU939716 | 1410 | nuccore | 556325 |
| 124043 | Neomicrococcus aestuarii gene for 16S ribosomal RNA, partial sequence. | AB778262 | 1479 | nuccore | 556325 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Neomicrococcus aestuarii DSM 105783 | GCA_014201135 | contig | ncbi | 556325 |
| 66792 | Neomicrococcus aestuarii strain DSM 105783 | 556325.12 | wgs | patric | 556325 |
| 66792 | Neomicrococcus aestuarii DSM 105783 | 2857395869 | draft | img | 556325 |
GC content
- @ref: 67770
- GC-content: 59.1
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 94.32 | yes |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 98.322 | yes |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 80.219 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 85.473 | yes |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 98 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | no | 92 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 89 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | no | 86.2 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | positive | 78.1 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 85.3 |
External links
@ref: 42642
culture collection no.: DSM 105783, JCM 16364, KCTC 19557, NBRC 109060
straininfo link
- @ref: 96457
- straininfo: 396879
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 20729314 | Zhihengliuella aestuarii sp. nov., isolated from tidal flat sediment. | Baik KS, Lim CH, Park SC, Choe HN, Kim HJ, Kim D, Lee KH, Seong CN | Int J Syst Evol Microbiol | 10.1099/ijs.0.026245-0 | 2010 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Micrococcaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Peptidoglycan/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/microbiology, Sequence Analysis, DNA, Vitamin K 2/chemistry | Genetics |
| Phylogeny | 26233517 | Proposal for creation of a new genus Neomicrococcus gen. nov. to accommodate Zhihengliuella aestuarii Baik et al. 2011 and Micrococcus lactis Chittpurna et al. 2011 as Neomicrococcus aestuarii comb. nov. and Neomicrococcus lactis comb. nov. | Prakash O, Sharma A, Nimonkar Y, Shouche YS | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000490 | 2015 | Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, Micrococcaceae/*classification, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Transcriptome |
Reference
| @id | authors | title | doi/url | catalogue | journal | 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 | |||
| 42642 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-105783 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 105783) | |||
| 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 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
| 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/ | |||
| 96457 | 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-ID396879.1 | |||
| 124043 | Isabel Schober, Julia Koblitz | Data extracted from sequence databases, automatically matched based on designation and taxonomy | ||||
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | 10.1101/2024.08.12.607695 | |||
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 | https://github.com/GenomeNet/deepG |