Strain identifier
BacDive ID: 13861
Type strain:
Species: Celeribacter halophilus
Strain Designation: ZXM137
Strain history: <- LMG <- X.-H. Zhang, Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao
NCBI tax ID(s): 576117 (species)
General
@ref: 18180
BacDive-ID: 13861
DSM-Number: 26270
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped
description: Celeribacter halophilus ZXM137 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from seawater collected from a coastal region.
NCBI tax id
- NCBI tax id: 576117
- Matching level: species
strain history
- @ref: 18180
- history: <- LMG <- X.-H. Zhang, Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao
doi: 10.13145/bacdive13861.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodobacterales
- family: Roseobacteraceae
- genus: Celeribacter
- species: Celeribacter halophilus
- full scientific name: Celeribacter halophilus (Wang et al. 2012) Lai et al. 2014
synonyms
- @ref: 20215
- synonym: Huaishuia halophila
@ref: 18180
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Celeribacter
species: Celeribacter halophilus
full scientific name: Celeribacter halophilus (Wang et al. 2012) Lai et al. 2014
strain designation: ZXM137
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
29904 | negative | 0.8 µm | 0.3 µm | rod-shaped | no | |
69480 | negative | 99.997 |
pigmentation
- @ref: 29904
- production: yes
Culture and growth conditions
culture medium
- @ref: 18180
- name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
- growth: yes
- link: https://mediadive.dsmz.de/medium/514
- composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
18180 | positive | growth | 28 | mesophilic |
29904 | positive | growth | 04-45 | |
29904 | positive | optimum | 28 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
29904 | positive | growth | 06-09 | alkaliphile |
29904 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 29904
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.969 |
halophily
- @ref: 29904
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0.5-11 %
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
29904 | 28757 | fructose | + | carbon source |
29904 | 28260 | galactose | + | carbon source |
29904 | 17234 | glucose | + | carbon source |
29904 | 29864 | mannitol | + | carbon source |
29904 | 37684 | mannose | + | carbon source |
29904 | 4853 | esculin | + | hydrolysis |
68368 | 17632 | nitrate | - | reduction |
68368 | 30849 | L-arabinose | - | fermentation |
68368 | 27613 | amygdalin | - | fermentation |
68368 | 30911 | sorbitol | - | fermentation |
68368 | 17634 | D-glucose | - | fermentation |
68368 | 5291 | gelatin | - | hydrolysis |
68368 | 27897 | tryptophan | - | energy source |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68368 | 17997 | dinitrogen | no |
68368 | 16301 | nitrite | no |
68368 | 35581 | indole | no |
68368 | 16136 | hydrogen sulfide | no |
metabolite tests
- @ref: 68368
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
29904 | catalase | + | 1.11.1.6 |
29904 | cytochrome oxidase | + | 1.9.3.1 |
29904 | urease | + | 3.5.1.5 |
68368 | gelatinase | - | |
68368 | tryptophan deaminase | - | 4.1.99.1 |
68368 | beta-galactosidase | + | 3.2.1.23 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | - | |
68382 | esterase lipase (C 8) | - | |
68382 | lipase (C 14) | - | |
68382 | valine arylamidase | - | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | - | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | - | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
18180 | - | + | - | - | - | +/- | - | - | - | - | - | - | - | - | - | - | +/- | - | - | - |
API 20E
@ref | ONPG | ADH Arg | LDC Lys | ODC | CIT | H2S | URE | TDA Trp | IND | VP | GEL | GLU | MAN | INO | Sor | RHA | SAC | MEL | AMY | ARA | NO2 | N2 | OX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
18180 | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | |
18180 | + | + | + | + | + | - | + | - | - | + | - | - | - | + | - | + | + | + | - | - | + | ||
18180 | + | + | - | - | - | - | + | - | - | - | - | - | +/- | + | - | - | - | +/- | - | - | - |
Isolation, sampling and environmental information
isolation
- @ref: 18180
- sample type: seawater collected from a coastal region
- geographic location: Qingdao
- country: China
- origin.country: CHN
- continent: Asia
- latitude: 36.027
- longitude: 120.184
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Marine |
#Environmental | #Terrestrial | #Coast |
taxonmaps
- @ref: 69479
- File name: preview.99_2675.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_1423;97_1699;98_2073;99_2675&stattab=map
- Last taxonomy: Celeribacter halophilus
- 16S sequence: FJ436725
- Sequence Identity:
- Total samples: 1758
- soil counts: 95
- aquatic counts: 1574
- animal counts: 82
- plant counts: 7
Safety information
risk assessment
- @ref: 18180
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 18180
- description: Celeribacter halophilus strain ZXM137 16S ribosomal RNA gene, partial sequence
- accession: FJ436725
- length: 1370
- database: ena
- NCBI tax ID: 576117
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Celeribacter halophilus DSM 26270 | GCA_003254175 | scaffold | ncbi | 576117 |
66792 | Celeribacter halophilus CGMCC 1.8891 | GCA_900114135 | scaffold | ncbi | 576117 |
66792 | Celeribacter halophilus ZXM137 | GCA_001550085 | scaffold | ncbi | 576117 |
66792 | Celeribacter halophilus strain CGMCC 1.8891 | 576117.6 | wgs | patric | 576117 |
66792 | Celeribacter halophilus strain DSM 26270 | 576117.7 | wgs | patric | 576117 |
66792 | Celeribacter halophilus CGMCC 1.8891 | 2617270905 | draft | img | 576117 |
66792 | Celeribacter halophilus ZXM137 | 2728369168 | draft | img | 576117 |
66792 | Celeribacter halophilus DSM 26270 | 2593339274 | draft | img | 576117 |
GC content
@ref | GC-content | method |
---|---|---|
18180 | 60.1 | high performance liquid chromatography (HPLC) |
29904 | 60.1 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
flagellated | no | 85.399 | no |
gram-positive | no | 98.971 | no |
anaerobic | no | 96.576 | yes |
halophile | yes | 67.675 | no |
spore-forming | no | 97.768 | no |
aerobic | yes | 68.008 | no |
glucose-util | yes | 88.574 | no |
thermophile | no | 97.188 | no |
motile | no | 65.693 | no |
glucose-ferment | no | 88.064 | yes |
External links
@ref: 18180
culture collection no.: DSM 26270, CGMCC 1.8891, LMG 24854
straininfo link
- @ref: 83037
- straininfo: 360660
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 21398505 | Huaishuia halophila gen. nov., sp. nov., isolated from coastal seawater. | Wang H, Zhang X, Yan S, Qi Z, Yu Y, Zhang XH | Int J Syst Evol Microbiol | 10.1099/ijs.0.025536-0 | 2011 | Aerobiosis, Base Composition, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Hydroxybutyrates/metabolism, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Polyesters/metabolism, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Roseobacter/*classification/genetics/*isolation & purification/physiology, Seawater/*microbiology, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature | Metabolism |
Phylogeny | 25256706 | Celeribacter indicus sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium from deep-sea sediment and reclassification of Huaishuia halophila as Celeribacter halophilus comb. nov. | Lai Q, Cao J, Yuan J, Li F, Shao Z | Int J Syst Evol Microbiol | 10.1099/ijs.0.069039-0 | 2014 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Indian Ocean, Molecular Sequence Data, Phosphatidylglycerols/chemistry, *Phylogeny, Polycyclic Aromatic Hydrocarbons/*metabolism, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry | Genetics |
Phylogeny | 26297231 | Celeribacter naphthalenivorans sp. nov., a naphthalene-degrading bacterium from tidal flat sediment. | Taek Oh Y, Avedoza C, Lee SS, Jeong SE, Jia B, Jeon CO | Int J Syst Evol Microbiol | 10.1099/ijs.0.000381 | 2015 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/microbiology, Molecular Sequence Data, Naphthalenes, Phospholipids/chemistry, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhodobacteraceae/classification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone | Genetics |
Phylogeny | 26303941 | Celeribacter manganoxidans sp. nov., a manganese-oxidizing bacterium isolated from deep-sea sediment of a polymetallic nodule province. | Wang L, Liu Y, Wang Y, Dai X, Zhang XH | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000558 | 2015 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Manganese/*metabolism, Molecular Sequence Data, Pacific Ocean, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry | Genetics |
Phylogeny | 29388535 | Marivivens niveibacter sp. nov., isolated from the seawater of tropical mangrove. | Hu D, Wang L, Lai Q, Sun F, Shao Z | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002544 | 2018 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*chemistry, Sequence Analysis, DNA, Ubiquinone/chemistry, *Wetlands | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
18180 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26270) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-26270 | ||||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | ||||
29904 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 26276 | 28776041 | ||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | ||||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
68368 | Automatically annotated from API 20E | ||||||
68382 | Automatically annotated from API zym | ||||||
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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | ||||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | ||||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | ||||
83037 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID360660.1 | StrainInfo: A central database for resolving microbial strain identifiers |