Strain identifier

BacDive ID: 13966

Type strain: Yes

Species: Thalassospira xiamenensis

Strain Designation: M-5

Strain history: CIP <- 2007, DSMZ <- Z. Shao, Marine Biogen. Res., China: strain M-5

NCBI tax ID(s): 1123366 (strain), 220697 (species)

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General

@ref: 6981

BacDive-ID: 13966

DSM-Number: 17429

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, motile, rod-shaped

description: Thalassospira xiamenensis M-5 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from surface water sample collected in a waste-oil pool at the storage dock.

NCBI tax id

NCBI tax idMatching level
1123366strain
220697species

strain history

@refhistory
6981<- Z. Shao; M-5 <- C. Liu
123977CIP <- 2007, DSMZ <- Z. Shao, Marine Biogen. Res., China: strain M-5

doi: 10.13145/bacdive13966.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodospirillales
  • family: Thalassospiraceae
  • genus: Thalassospira
  • species: Thalassospira xiamenensis
  • full scientific name: Thalassospira xiamenensis Liu et al. 2007

@ref: 6981

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodospirillales

family: Thalassospiraceae

genus: Thalassospira

species: Thalassospira xiamenensis

full scientific name: Thalassospira xiamenensis Liu et al. 2007

strain designation: M-5

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31858negative5.5 µm1.55 µmrod-shapedyes
69480yes94.584
69480negative99.995
123977negativerod-shapedyes

pigmentation

  • @ref: 31858
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6981BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: 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
37759Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
123977CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
6981positivegrowth25mesophilic
31858positivegrowth04-40
31858positiveoptimum22psychrophilic
37759positivegrowth25mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31858anaerobe
123977obligate aerobe

spore formation

@refspore formationconfidence
31858no
69481no100
69480no99.999

halophily

@refsaltgrowthtested relationconcentration
31858NaClpositivegrowth0.5-10 %
31858NaClpositiveoptimum3 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3185821217L-alaninamide+carbon source
3185816449alanine+carbon source
3185822599arabinose+carbon source
3185818403L-arabitol+carbon source
3185822653asparagine+carbon source
3185817057cellobiose+carbon source
3185815740formate+carbon source
3185828757fructose+carbon source
3185828260galactose+carbon source
3185824265gluconate+carbon source
3185817234glucose+carbon source
3185829987glutamate+carbon source
3185817754glycerol+carbon source
3185827570histidine+carbon source
31858182404-hydroxy-L-proline+carbon source
3185824996lactate+carbon source
3185815792malonate+carbon source
3185817306maltose+carbon source
3185829864mannitol+carbon source
3185837684mannose+carbon source
3185851850methyl pyruvate+carbon source
3185817268myo-inositol+carbon source
31858506227N-acetylglucosamine+carbon source
3185818257ornithine+carbon source
3185826271proline+carbon source
3185817272propionate+carbon source
3185826490quinate+carbon source
3185817822serine+carbon source
3185830031succinate+carbon source
3185817992sucrose+carbon source
3185817748thymidine+carbon source
3185827082trehalose+carbon source
3185827248urocanic acid+carbon source
3185817632nitrate+reduction
12397717632nitrate+reduction
12397716301nitrite+reduction

metabolite production

  • @ref: 123977
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31858catalase+1.11.1.6
31858cytochrome oxidase+1.9.3.1
123977oxidase+
123977catalase+1.11.1.6
123977urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123977-++--+----++---+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6981surface water sample collected in a waste-oil pool at the storage dockXiamen, FujianChinaCHNAsia
123977Environment, Surface water sample, waste-oil pool storage dockChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Built environment#Water reservoir (Aquarium/pool)
#Engineered#Industrial#Oil reservoir
#Engineered#Waste
#Environmental#Aquatic#Surface water

taxonmaps

  • @ref: 69479
  • File name: preview.99_318.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_88;96_222;97_242;98_271;99_318&stattab=map
  • Last taxonomy: Thalassospira
  • 16S sequence: AY189753
  • Sequence Identity:
  • Total samples: 3490
  • soil counts: 250
  • aquatic counts: 2971
  • animal counts: 192
  • plant counts: 77

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
69811Risk group (German classification)
1239771Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6981
  • description: Thalassospira xiamenensis strain M-5 16S ribosomal RNA gene, partial sequence
  • accession: AY189753
  • length: 1439
  • database: ena
  • NCBI tax ID: 1123366

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Thalassospira xiamenensis M-5 = DSM 17429GCA_000300235contigncbi1123366
66792Thalassospira xiamenensis M-5 = DSM 17429GCA_900156715contigncbi1123366
66792Thalassospira xiamenensis M-5 = DSM 174291123366.3wgspatric1123366
66792Thalassospira xiamenensis M-5 = DSM 174291123366.7plasmidpatric1123366
66792Thalassospira xiamenensis M-5 = DSM 17429 strain DSM 174291123366.5wgspatric1123366
66792Thalassospira xiamenensis DSM 174292681813519draftimg1123366
66792Thalassospira xiamenensis M-5, DSM 174292534681947draftimg1123366

GC content

  • @ref: 6981
  • GC-content: 52.6

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes93.943yes
motileyes93.943yes
flagellatedyes89.364no
flagellatedyes89.364no
gram-positiveno98.746yes
gram-positiveno98.746yes
anaerobicno97.503no
anaerobicno97.503no
aerobicyes84.581no
aerobicyes84.581no
halophileno51.083no
halophileno51.083no
spore-formingno93.837yes
spore-formingno93.837yes
glucose-utilyes92.284yes
glucose-utilyes92.284yes
thermophileno98.542yes
thermophileno98.542yes
glucose-fermentno87.847no
glucose-fermentno87.847no

External links

@ref: 6981

culture collection no.: DSM 17429, CGMCC 1.3998, CIP 109533

straininfo link

  • @ref: 83138
  • straininfo: 297361

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17267971Thalassospira xiamenensis sp. nov. and Thalassospira profundimaris sp. nov.Liu C, Wu Y, Li L, Ma Y, Shao ZInt J Syst Evol Microbiol10.1099/ijs.0.64544-02007Bacterial Typing Techniques, Carbohydrate Metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis/chemistry, Flagella, Genes, rRNA, Geologic Sediments/*microbiology, Molecular Sequence Data, Movement, Nitrates/metabolism, Oxidation-Reduction, Pacific Ocean, Phylogeny, Polysorbates, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Rhodospirillaceae/*classification/genetics/*isolation & purification/physiology, Seawater/*microbiology, Sequence Analysis, DNA, TemperatureMetabolism
Phylogeny19666802Thalassospira xianhensis sp. nov., a polycyclic aromatic hydrocarbon-degrading marine bacterium.Zhao B, Wang H, Li R, Mao XInt J Syst Evol Microbiol10.1099/ijs.0.013201-02009Alphaproteobacteria/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Genotype, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Petroleum, Phenotype, Phylogeny, Polycyclic Aromatic Hydrocarbons/metabolism, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sodium Chloride, *Soil Pollutants, Species SpecificityGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6981Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17429)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17429
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
31858Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2812128776041
37759Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7287
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)
68382Automatically annotated from API zym
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
83138Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297361.1StrainInfo: A central database for resolving microbial strain identifiers
123977Curators of the CIPCollection of Institut Pasteur (CIP 109533)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109533