Strain identifier
BacDive ID: 17817
Type strain:
Species: Thermophagus xiamenensis
Strain Designation: HS1
Strain history: <- X. Xu, Third Inst. Oceanography, State Oceanic Administration, Xiamen, China; HS1 <- X. Liu and X. Zhang {2006}
NCBI tax ID(s): 385682 (species)
General
@ref: 7830
BacDive-ID: 17817
DSM-Number: 19012
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, thermophilic, Gram-negative, motile, rod-shaped
description: Thermophagus xiamenensis HS1 is an anaerobe, thermophilic, Gram-negative bacterium that was isolated from sediment from an offshore hot spring.
NCBI tax id
- NCBI tax id: 385682
- Matching level: species
strain history
- @ref: 7830
- history: <- X. Xu, Third Inst. Oceanography, State Oceanic Administration, Xiamen, China; HS1 <- X. Liu and X. Zhang {2006}
doi: 10.13145/bacdive17817.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Bacteroidia
- order: Bacteroidales
- family: Marinilabiliaceae
- genus: Thermophagus
- species: Thermophagus xiamenensis
- full scientific name: Thermophagus xiamenensis Gao et al. 2013
@ref: 7830
domain: Bacteria
phylum: Bacteroidetes
class: Bacteroidia
order: Bacteroidales
family: Marinilabiliaceae
genus: Thermophagus
species: Thermophagus xiamenensis
full scientific name: Thermophagus xiamenensis Gao et al. 2013
strain designation: HS1
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
30552 | negative | 7 µm | 0.25 µm | rod-shaped | yes | |
69480 | negative | 99.998 |
pigmentation
- @ref: 30552
- production: no
Culture and growth conditions
culture medium
- @ref: 7830
- name: ANAEROBIC SEAWATER (SWM) MEDIUM (DSMZ Medium 504)
- growth: yes
- link: https://mediadive.dsmz.de/medium/504
- composition: Name: ANAEROBIC SEAWATER (SWM) MEDIUM (DSMZ Medium 504; with strain-specific modifications) Composition: NaCl 19.9402 g/l MgCl2 x 6 H2O 2.99102 g/l D-Glucose 1.99402 g/l Na2CO3 1.49551 g/l KCl 0.498505 g/l Yeast extract 0.498504 g/l Na2S x 9 H2O 0.299103 g/l NH4Cl 0.249252 g/l KH2PO4 0.199402 g/l CaCl2 x 2 H2O 0.149552 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l Sodium resazurin 0.000498505 g/l NaOH 0.000498504 g/l Pyridoxine hydrochloride 0.000299103 g/l Nicotinic acid 0.000199402 g/l Thiamine-HCl x 2 H2O 0.000199402 g/l CoCl2 x 6 H2O 0.000189432 g/l Calcium pantothenate 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l Vitamin B12 9.97009e-05 g/l p-Aminobenzoic acid 7.97607e-05 g/l ZnCl2 6.97906e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l D-(+)-biotin 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
7830 | positive | growth | 55 | thermophilic |
30552 | positive | growth | 35-55 | |
30552 | positive | optimum | 50 | thermophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
30552 | positive | growth | 5.5-8 |
30552 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
7830 | anaerobe | |
30552 | anaerobe | |
69480 | anaerobe | 95.472 |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.911 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
30552 | NaCl | positive | growth | 01-08 % |
30552 | NaCl | positive | optimum | 3 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
30552 | 22599 | arabinose | + | carbon source |
30552 | 17057 | cellobiose | + | carbon source |
30552 | 28757 | fructose | + | carbon source |
30552 | 28260 | galactose | + | carbon source |
30552 | 17234 | glucose | + | carbon source |
30552 | 17716 | lactose | + | carbon source |
30552 | 17306 | maltose | + | carbon source |
30552 | 37684 | mannose | + | carbon source |
30552 | 26546 | rhamnose | + | carbon source |
30552 | 17992 | sucrose | + | carbon source |
30552 | 27082 | trehalose | + | carbon source |
30552 | 18222 | xylose | + | carbon source |
enzymes
@ref | value | activity | ec |
---|---|---|---|
30552 | catalase | + | 1.11.1.6 |
30552 | gelatinase | + |
Isolation, sampling and environmental information
isolation
- @ref: 7830
- sample type: sediment from an offshore hot spring
- geographic location: Xiamen
- country: China
- origin.country: CHN
- continent: Asia
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Sediment |
#Environmental | #Aquatic | #Thermal spring |
#Condition | #Thermophilic (>45°C) |
taxonmaps
- @ref: 69479
- File name: preview.99_7971.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_275;96_3690;97_4530;98_5814;99_7971&stattab=map
- Last taxonomy: Thermophagus xiamenensis subclade
- 16S sequence: DQ517535
- Sequence Identity:
- Total samples: 1345
- soil counts: 162
- aquatic counts: 597
- animal counts: 550
- plant counts: 36
Safety information
risk assessment
- @ref: 7830
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 7830
- description: Thermophagus xiamenensis strain HS1 16S ribosomal RNA gene, partial sequence
- accession: DQ517535
- length: 1488
- database: ena
- NCBI tax ID: 385682
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Thermophagus xiamenensis HS1 | GCA_000220155 | contig | ncbi | 385682 |
66792 | Thermophagus xiamenensis DSM 19012 | GCA_900112795 | scaffold | ncbi | 385682 |
66792 | Thermophagus xiamenensis strain DSM 19012 | 385682.7 | wgs | patric | 385682 |
66792 | Thermophagus xiamenensis HS1 | 2515154052 | draft | img | 385682 |
66792 | Thermophagus xiamenensis DSM 19012 | 2693429893 | draft | img | 385682 |
GC content
@ref | GC-content | method |
---|---|---|
7830 | 38.7 | high performance liquid chromatography (HPLC) |
30552 | 38.7 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
flagellated | no | 97.109 | no |
gram-positive | no | 97.226 | yes |
anaerobic | yes | 93.585 | yes |
aerobic | no | 93.777 | yes |
halophile | no | 53.505 | no |
spore-forming | no | 94.286 | no |
glucose-ferment | yes | 51.123 | no |
thermophile | no | 87.809 | no |
glucose-util | yes | 88.341 | yes |
motile | no | 70.246 | yes |
External links
@ref: 7830
culture collection no.: DSM 19012, CGMCCC 1.5071
straininfo link
- @ref: 86808
- straininfo: 396897
literature
- topic: Phylogeny
- Pubmed-ID: 22345138
- title: Thermophagus xiamenensis gen. nov., sp. nov., a moderately thermophilic and strictly anaerobic bacterium isolated from hot spring sediment.
- authors: Gao ZM, Liu X, Zhang XY, Ruan LW
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.038547-0
- year: 2012
- mesh: Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Gram-Negative Anaerobic Straight, Curved, and Helical Rods/*classification/genetics/isolation & purification, Hot Springs/*microbiology, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Water Microbiology
- topic2: Genetics
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
7830 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19012) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19012 | ||||
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 | ||||
30552 | 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 | 26883 | 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 | ||
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 | ||||
86808 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID396897.1 | StrainInfo: A central database for resolving microbial strain identifiers |