Strain identifier

BacDive ID: 13802

Type strain: Yes

Species: Thalassobius mediterraneus

Strain Designation: XSM19

Strain history: CIP <- 2004, M.J. Pujalte, Burjassot, Spain: strain XSM19

NCBI tax ID(s): 340021 (species)

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General

@ref: 6428

BacDive-ID: 13802

DSM-Number: 16398

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

description: Thalassobius mediterraneus XSM19 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from water from the Mediterranean Sea.

NCBI tax id

  • NCBI tax id: 340021
  • Matching level: species

strain history

@refhistory
6428<- M. J. Pujalte, Dept. Microbiol. and Ecol., ICBiBE, Univ. Valencia, Spain; XSM19
327782004, M.J. Pujalte, Burjassot, Spain: strain XSM19
120879CIP <- 2004, M.J. Pujalte, Burjassot, Spain: strain XSM19

doi: 10.13145/bacdive13802.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Thalassobius
  • species: Thalassobius mediterraneus
  • full scientific name: Thalassobius mediterraneus Arahal et al. 2005

  • synonyms

    • @ref: 20215
    • synonym: Thalassovita mediterranea

@ref: 6428

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Thalassobius

species: Thalassobius mediterraneus

full scientific name: Thalassobius mediterraneus Arahal et al. 2005

strain designation: XSM19

type strain: yes

Morphology

cell morphology

  • @ref: 120879
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 58556
  • incubation period: 2 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6428BACTO 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
32778Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
120879CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
6428positivegrowth28mesophilic
32778positivegrowth25mesophilic
58556positivegrowth20-30
120879positivegrowth15-30
120879nogrowth5psychrophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
58556aerobe
120879facultative anaerobe

halophily

@refsaltgrowthtested relationconcentration
120879NaClpositivegrowth6-10 %
120879NaClnogrowth0 %
120879NaClnogrowth2 %
120879NaClnogrowth4 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12087916947citrate-carbon source
1208794853esculin-hydrolysis
120879606565hippurate+hydrolysis
12087917632nitrate-builds gas from
12087917632nitrate-reduction
12087916301nitrite-builds gas from
12087916301nitrite-reduction
12087915792malonate-assimilation
12087917632nitrate-respiration

metabolite production

  • @ref: 120879
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12087915688acetoin-
12087917234glucose-

enzymes

@refvalueactivityec
120879oxidase+
120879beta-galactosidase-3.2.1.23
120879alcohol dehydrogenase-1.1.1.1
120879gelatinase-
120879amylase-
120879caseinase-3.4.21.50
120879catalase+1.11.1.6
120879tween esterase-
120879gamma-glutamyltransferase+2.3.2.2
120879lecithinase-
120879lipase-
120879lysine decarboxylase-4.1.1.18
120879ornithine decarboxylase-4.1.1.17
120879phenylalanine ammonia-lyase-4.3.1.24
120879protease-
120879tryptophan deaminase-
120879urease-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
120879-+++-+----+---------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
6428water from the Mediterranean SeaValenciaSpainESPEurope
58556Oyster meatValenciaSpainESPEurope1989-10-01
120879Environment, Sea waterValenciaSpainESPEurope

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Marine

taxonmaps

  • @ref: 69479
  • File name: preview.99_1342.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_777;97_905;98_1061;99_1342&stattab=map
  • Last taxonomy: Thalassobius
  • 16S sequence: AJ878874
  • Sequence Identity:
  • Total samples: 4274
  • soil counts: 70
  • aquatic counts: 3934
  • animal counts: 257
  • plant counts: 13

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
64281Risk group (German classification)
1208791Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6428
  • description: Thalassobius mediterraneus 16S rRNA gene, type strain CECT 5383
  • accession: AJ878874
  • length: 1456
  • database: ena
  • NCBI tax ID: 340021

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Thalassovita mediterranea DSM 16398GCA_900156595contigncbi340021
66792Thalassovita mediterranea CECT 5383GCA_001458435contigncbi340021
66792Thalassobius mediterraneus strain DSM 16398340021.11wgspatric340021
66792Thalassobius mediterraneus DSM 163982681813506draftimg340021
66792Thalassobius mediterraneus CECT 53832713896964draftimg340021

GC content

  • @ref: 6428
  • GC-content: 57.0

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveno98.695no
anaerobicno98.502yes
halophileyes78.798no
spore-formingno96.355no
glucose-utilyes54.729no
motileno72.122no
flagellatedno86.149no
thermophileno95.231yes
aerobicyes88.708yes
glucose-fermentno88.738no

External links

@ref: 6428

culture collection no.: DSM 16398, CCUG 49438, CECT 5383, CIP 108400

straininfo link

  • @ref: 82980
  • straininfo: 281471

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16280499Thalassobius mediterraneus gen. nov., sp. nov., and reclassification of Ruegeria gelatinovorans as Thalassobius gelatinovorus comb. nov.Arahal DR, Macian MC, Garay E, Pujalte MJInt J Syst Evol Microbiol10.1099/ijs.0.63842-02005Mediterranean Sea, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/*analysis/genetics, Rhodobacteraceae/chemistry/*classification/genetics/growth & development, Seawater/*microbiology, Sequence Analysis, DNAGenetics
Genetics26981416Draft genome sequence of Thalassobius mediterraneus CECT 5383(T), a poly-beta-hydroxybutyrate producer.Rodrigo-Torres L, Pujalte MJ, Arahal DRGenom Data10.1016/j.gdata.2016.01.0132016
Genetics29375512Comparative Genomics of Thalassobius Including the Description of Thalassobius activus sp. nov., and Thalassobius autumnalis sp. nov.Pujalte MJ, Lucena T, Rodrigo-Torres L, Arahal DRFront Microbiol10.3389/fmicb.2017.026452018Phylogeny
Phylogeny33974534Isolation of Thalassobius mangrovi sp. nov., a novel bacterium in the family Rhodobacteraceae, from marine mangrove sediment.Chen S, Zheng S, Zhang D, Hetharua B, Gui J, An X, Xu HInt J Syst Evol Microbiol10.1099/ijsem.0.0048012021Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/isolation & purification, Sequence Analysis, DNA, WetlandsTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6428Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16398)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16398
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
32778Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6019
58556Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 49438)https://www.ccug.se/strain?id=49438
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 updatesNucleic Acids Res. 49: D498-D508 202033211880
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
82980Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID281471.1StrainInfo: A central database for resolving microbial strain identifiers
120879Curators of the CIPCollection of Institut Pasteur (CIP 108400)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108400