Strain identifier
BacDive ID: 134285
Type strain:
Species: Paracoccus halophilus
Strain Designation: HN-182
Strain history: S. Liu HN-182.
NCBI tax ID(s): 376733 (species)
version 8.1 (current version)
General
@ref: 32272
BacDive-ID: 134285
keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, rod-shaped
description: Paracoccus halophilus HN-182 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from marine sediment.
NCBI tax id
- NCBI tax id: 376733
- Matching level: species
strain history
- @ref: 67770
- history: S. Liu HN-182.
doi: 10.13145/bacdive134285.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodobacterales
- family: Paracoccaceae
- genus: Paracoccus
- species: Paracoccus halophilus
- full scientific name: Paracoccus halophilus Liu et al. 2008
@ref: 32272
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Paracoccus
species: Paracoccus halophilus
strain designation: HN-182
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
32272 | negative | 0.9 µm | 0.45 µm | rod-shaped | no | |
69480 | negative | 99.994 |
Culture and growth conditions
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
32272 | positive | growth | 07-42 | |
32272 | positive | optimum | 25 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
32272 | positive | growth | 05-09 | alkaliphile |
32272 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 32272
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
32272 | no | |
69481 | no | 100 |
69480 | no | 99.999 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
32272 | NaCl | positive | growth | 0.5-8.5 % |
32272 | NaCl | positive | optimum | 4.5 % |
observation
- @ref: 67770
- observation: quinones: Q-10
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
32272 | 22599 | arabinose | + | carbon source |
32272 | 17057 | cellobiose | + | carbon source |
32272 | 28757 | fructose | + | carbon source |
32272 | 28260 | galactose | + | carbon source |
32272 | 17234 | glucose | + | carbon source |
32272 | 17754 | glycerol | + | carbon source |
32272 | 17306 | maltose | + | carbon source |
32272 | 29864 | mannitol | + | carbon source |
32272 | 37684 | mannose | + | carbon source |
32272 | 26546 | rhamnose | + | carbon source |
32272 | 33942 | ribose | + | carbon source |
32272 | 30911 | sorbitol | + | carbon source |
32272 | 18222 | xylose | + | carbon source |
enzymes
@ref | value | activity | ec |
---|---|---|---|
32272 | catalase | + | 1.11.1.6 |
32272 | cytochrome oxidase | + | 1.9.3.1 |
32272 | urease | + | 3.5.1.5 |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent |
---|---|---|---|---|
32272 | marine sediment | |||
67770 | Marine sediment from the South China Sea | China | CHN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Marine |
#Environmental | #Aquatic | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_3779.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_1674;97_2334;98_2880;99_3779&stattab=map
- Last taxonomy: Paracoccus halophilus subclade
- 16S sequence: DQ423482
- Sequence Identity:
- Total samples: 951
- soil counts: 94
- aquatic counts: 306
- animal counts: 541
- plant counts: 10
Sequence information
16S sequences
- @ref: 32272
- description: Paracoccus halophilus strain HN-182 16S ribosomal RNA gene, partial sequence
- accession: DQ423482
- length: 1428
- database: nuccore
- NCBI tax ID: 376733
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Paracoccus halophilus JCM 14014 | 376733.3 | wgs | patric | 376733 |
66792 | Paracoccus halophilus strain CGMCC 1.6117 | 376733.15 | wgs | patric | 376733 |
66792 | Paracoccus halophilus JCM 14014 | 2713897088 | draft | img | 376733 |
66792 | Paracoccus halophilus CGMCC 1.6117 | 2617270913 | draft | img | 376733 |
67770 | Paracoccus halophilus CGMCC 1.6117 | GCA_900111785 | scaffold | ncbi | 376733 |
67770 | Paracoccus halophilus JCM 14014 | GCA_000763905 | contig | ncbi | 376733 |
GC content
@ref | GC-content | method |
---|---|---|
32272 | 67.2 | |
67770 | 67.2 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
gram-positive | no | 98.677 | yes |
anaerobic | no | 98.199 | yes |
halophile | no | 50 | no |
spore-forming | no | 97.169 | yes |
glucose-util | yes | 91.546 | yes |
aerobic | yes | 86.072 | yes |
motile | no | 77.555 | yes |
flagellated | no | 89.203 | yes |
thermophile | no | 96.347 | yes |
glucose-ferment | no | 85.058 | no |
External links
@ref: 32272
culture collection no.: CGMCC 1.6117, JCM 14014
straininfo link
- @ref: 91871
- straininfo: 323987
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 18175718 | Paracoccus halophilus sp. nov., isolated from marine sediment of the South China Sea, China, and emended description of genus Paracoccus Davis 1969. | Liu ZP, Wang BJ, Liu XY, Dai X, Liu YH, Liu SJ | Int J Syst Evol Microbiol | 10.1099/ijs.0.65237-0 | 2008 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/analysis, Fatty Acids/analysis, Genes, rRNA, Geologic Sediments/*microbiology, Molecular Sequence Data, Paracoccus/*classification/genetics/isolation & purification/physiology, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, *Sodium Chloride, Species Specificity | Genetics |
Phylogeny | 20400662 | Paracoccus sphaerophysae sp. nov., a siderophore-producing, endophytic bacterium isolated from root nodules of Sphaerophysa salsula. | Deng ZS, Zhao LF, Xu L, Kong ZY, Zhao P, Qin W, Chang JL, Wei GH | Int J Syst Evol Microbiol | 10.1099/ijs.0.021071-0 | 2010 | Antibiosis, Antifungal Agents/metabolism, Bacterial Typing Techniques, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fabaceae/*microbiology, Fatty Acids/analysis, Molecular Sequence Data, Paracoccus/*classification/genetics/*isolation & purification/physiology, Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Siderophores/*metabolism | Metabolism |
Phylogeny | 31647401 | Paracoccus luteus sp. nov., isolated from the intestine of grass carp. | Ming H, Cheng LJ, Ding CL, Niu MM, Zhao ZL, Ji WL, Zhang LY, Zhang YM, Meng XL, Nie GX | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003790 | 2020 | Animals, Bacterial Typing Techniques, Base Composition, Carps/*microbiology, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Intestines/*microbiology, Nucleic Acid Hybridization, Paracoccus/*classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Transcriptome |
Reference
@id | authors | title | doi/url | 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 | |||
32272 | 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 | 28512 | 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 | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |||
91871 | 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-ID323987.1 |