Strain identifier

BacDive ID: 17949

Type strain: Yes

Species: Thiomonas intermedia

Strain history: CIP <- 1995, IFO <- 1987, IAM <- ATCC <- J. London

NCBI tax ID(s): 926 (species)

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General

@ref: 7339

BacDive-ID: 17949

DSM-Number: 18155

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

description: Thiomonas intermedia DSM 18155 is a mesophilic, Gram-negative bacterium that was isolated from mud at the bank of a freshwater stream.

NCBI tax id

  • NCBI tax id: 926
  • Matching level: species

strain history

@refhistory
7339<- K. Woodward, NCIMB <- J. London, University of California, Los Angeles, USA
67770IAM 12131 <-- ATCC 15466 <-- J. London.
120147CIP <- 1995, IFO <- 1987, IAM <- ATCC <- J. London

doi: 10.13145/bacdive17949.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Comamonadaceae
  • genus: Thiomonas
  • species: Thiomonas intermedia
  • full scientific name: Thiomonas intermedia (London 1963) Moreira and Amils 1997

  • synonyms

    • @ref: 20215
    • synonym: Thiobacillus intermedius

@ref: 7339

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Thiomonas

species: Thiomonas intermedia

full scientific name: Thiomonas intermedia (London 1963) Moreira and Amils 1997

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative100
120147negativerod-shapedyes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7339THIOMONAS MEDIUM (DSMZ Medium 35a)yeshttps://mediadive.dsmz.de/medium/35aName: THIOMONAS MEDIUM (DSMZ Medium 35a) Composition: Agar 19.4175 g/l (optional) Na2S2O3 x 5 H2O 4.85437 g/l KH2PO4 2.91262 g/l Yeast extract 0.970874 g/l CaCl2 x 2 H2O 0.135922 g/l MgCl2 x 6 H2O 0.0970874 g/l NH4Cl 0.0970873 g/l Distilled water
34702MEDIUM 126 - for ThiomonasyesDistilled water make up to (1000.000 ml);Magnesium sulphate heptahydrate (0.100 g);Agar (15.000 g);Yeast extract (5.000 g);Potassium di-hydrogen phosphate (1.500 g);Ammonium chloride (0.300 g);Sodium thiosulphate pentahydrate (5.000 g);Di Sodium hydrogen
120147CIP Medium 126yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=126

culture temp

@refgrowthtypetemperaturerange
7339positivegrowth30mesophilic
34702positivegrowth30mesophilic
67770positivegrowth30mesophilic
120147positivegrowth30mesophilic
120147nogrowth10psychrophilic
120147nogrowth37mesophilic
120147nogrowth45thermophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no97
69480no99.999

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
120147nitrate-reduction17632
120147nitrite-reduction16301
120147nitrate-respiration17632

metabolite production

  • @ref: 120147
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 120147
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
120147oxidase+
120147beta-galactosidase-3.2.1.23
120147alcohol dehydrogenase-1.1.1.1
120147gelatinase-
120147catalase-1.11.1.6
120147lysine decarboxylase-4.1.1.18
120147ornithine decarboxylase-4.1.1.17
120147urease-3.5.1.5

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120147----------+/---------------------------------------

Isolation, sampling and environmental information

isolation

@refsample type
7339mud at the bank of a freshwater stream
67770Mud
120147Environment, Soil

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Freshwater
#Environmental#Aquatic#River (Creek)

taxonmaps

  • @ref: 69479
  • File name: preview.99_3097.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_1616;97_1933;98_2377;99_3097&stattab=map
  • Last taxonomy: Thiomonas
  • 16S sequence: AY455809
  • Sequence Identity:
  • Total samples: 3123
  • soil counts: 388
  • aquatic counts: 2269
  • animal counts: 312
  • plant counts: 154

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
73391Risk group (German classification)
1201471Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7339
  • description: Thiomonas intermedia 16S ribosomal RNA gene, partial sequence
  • accession: AY455809
  • length: 1390
  • database: ena
  • NCBI tax ID: 926

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Thiomonas intermedia ATCC 15466GCA_002028405completencbi926
66792Thiomonas intermedia strain ATCC 15466926.5plasmidpatric926
66792Thiomonas intermedia strain ATCC 15466926.3completepatric926
66792Thiomonas intermedia ATCC 154662772190779completeimg926

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno97no
flagellatedyes67.465no
gram-positiveno97.963no
anaerobicno98.544no
aerobicyes81.307no
halophileno95.928no
spore-formingno96.267no
glucose-utilno59.971no
thermophileno96.965yes
motileyes91.794no
glucose-fermentno88.365no

External links

@ref: 7339

culture collection no.: DSM 18155, ATCC 15466, CIP 104401, IAM 12131, IFO 14564, NBRC 14564, NCIMB 9515, JCM 20425

straininfo link

  • @ref: 86937
  • straininfo: 10392

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19605731Thiomonas bhubaneswarensis sp. nov., an obligately mixotrophic, moderately thermophilic, thiosulfate-oxidizing bacterium.Panda SK, Jyoti V, Bhadra B, Nayak KC, Shivaji S, Rainey FA, Das SKInt J Syst Evol Microbiol10.1099/ijs.0.007120-02009Aerobiosis, Bacterial Typing Techniques, Base Composition, Betaproteobacteria/*classification/genetics/*isolation & purification/physiology, Catalase/metabolism, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids, Geologic Sediments/*microbiology, Hot Springs, Hydrogen-Ion Concentration, India, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Oxidation-Reduction, Oxidoreductases/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Temperature, Thiosulfates/*metabolismMetabolism
Phylogeny20173005Thiomonas islandica sp. nov., a moderately thermophilic, hydrogen- and sulfur-oxidizing betaproteobacterium isolated from a hot spring.Vesteinsdottir H, Reynisdottir DB, Orlygsson JInt J Syst Evol Microbiol10.1099/ijs.0.015511-02010Aerobiosis, Base Composition, Betaproteobacteria/*classification/genetics/*isolation & purification/physiology, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Hot Springs/*microbiology, Hydrogen/*metabolism, Hydrogen-Ion Concentration, Iceland, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Organic Chemicals/metabolism, Oxidation-Reduction, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sulfur/*metabolism, Temperature, Thiosulfates/metabolismMetabolism
Phylogeny20970324Bacteria involved in sulfur amendment oxidation and acidification processes of alkaline 'alperujo' compost.Garcia-de-la-Fuente R, Cuesta G, Sanchis-Jimenez E, Botella S, Abad M, Fornes FBioresour Technol10.1016/j.biortech.2010.09.1032010Acids/*metabolism, Alkalies/*metabolism, Bacteria/isolation & purification/*metabolism, Biodegradation, Environmental, DNA, Ribosomal/genetics, Electric Conductivity, Hydrogen-Ion Concentration, Industrial Waste/*analysis, Oxidation-Reduction, Phylogeny, *Soil, *Soil Microbiology, Sulfur/*isolation & purificationMetabolism
Metabolism27542742Response of cbb gene transcription levels of four typical sulfur-oxidizing bacteria to the CO2 concentration and its effect on their carbon fixation efficiency during sulfur oxidation.Wang YN, Wang L, Tsang YF, Fu X, Hu J, Li H, Le YEnzyme Microb Technol10.1016/j.enzmictec.2016.06.0152016Alphaproteobacteria/genetics/metabolism, Bacteria/*genetics/*metabolism, Bacterial Proteins/genetics/metabolism, Betaproteobacteria/genetics/metabolism, Carbon Cycle/genetics, Carbon Dioxide/metabolism, Genes, Bacterial, Halothiobacillus/genetics/metabolism, Oxidation-Reduction, Ribulose-Bisphosphate Carboxylase/genetics/metabolism, Sulfur/*metabolism, Thiobacillus/genetics/metabolism, Transcription, Genetic
Cultivation32579519Key internal factors leading to the variability in CO2 fixation efficiency of different sulfur-oxidizing bacteria during autotrophic cultivation.Wang YN, Kai Y, Wang L, Tsang YF, Fu X, Hu J, Xie YJ Environ Manage10.1016/j.jenvman.2020.1109572020Alphaproteobacteria, Bacteria, Burkholderiales, *Carbon Dioxide, Oxidation-Reduction, *Sulfur

Reference

@idauthorscataloguedoi/urltitle
7339Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18155)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18155
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
34702Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16305
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
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
86937Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10392.1StrainInfo: A central database for resolving microbial strain identifiers
120147Curators of the CIPCollection of Institut Pasteur (CIP 104401)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104401