Strain identifier

BacDive ID: 17817

Type strain: Yes

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)

For citation purpose refer to the digital object identifier (doi) of the current version.
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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

@refgram staincell lengthcell widthcell shapemotilityconfidence
30552negative7 µm0.25 µmrod-shapedyes
69480negative99.998

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

@refgrowthtypetemperaturerange
7830positivegrowth55thermophilic
30552positivegrowth35-55
30552positiveoptimum50thermophilic

culture pH

@refabilitytypepH
30552positivegrowth5.5-8
30552positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
7830anaerobe
30552anaerobe
69480anaerobe95.472

spore formation

@refspore formationconfidence
69481no100
69480no99.911

halophily

@refsaltgrowthtested relationconcentration
30552NaClpositivegrowth01-08 %
30552NaClpositiveoptimum3 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3055222599arabinose+carbon source
3055217057cellobiose+carbon source
3055228757fructose+carbon source
3055228260galactose+carbon source
3055217234glucose+carbon source
3055217716lactose+carbon source
3055217306maltose+carbon source
3055237684mannose+carbon source
3055226546rhamnose+carbon source
3055217992sucrose+carbon source
3055227082trehalose+carbon source
3055218222xylose+carbon source

enzymes

@refvalueactivityec
30552catalase+1.11.1.6
30552gelatinase+

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

Cat1Cat2Cat3
#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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Thermophagus xiamenensis HS1GCA_000220155contigncbi385682
66792Thermophagus xiamenensis DSM 19012GCA_900112795scaffoldncbi385682
66792Thermophagus xiamenensis strain DSM 19012385682.7wgspatric385682
66792Thermophagus xiamenensis HS12515154052draftimg385682
66792Thermophagus xiamenensis DSM 190122693429893draftimg385682

GC content

@refGC-contentmethod
783038.7high performance liquid chromatography (HPLC)
3055238.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno97.109no
gram-positiveno97.226yes
anaerobicyes93.585yes
aerobicno93.777yes
halophileno53.505no
spore-formingno94.286no
glucose-fermentyes51.123no
thermophileno87.809no
glucose-utilyes88.341yes
motileno70.246yes

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

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
7830Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19012)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19012
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
30552Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2688328776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
69479João 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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
86808Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID396897.1StrainInfo: A central database for resolving microbial strain identifiers