Strain identifier

BacDive ID: 17567

Type strain: Yes

Species: Stenotrophomonas terrae

Strain Designation: R-32768

Strain history: CIP <- 2008, DSMZ <- K. Heylen, Ghent Univ., Ghent, Belgium

NCBI tax ID(s): 405446 (species)

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General

@ref: 7799

BacDive-ID: 17567

DSM-Number: 18941

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

description: Stenotrophomonas terrae R-32768 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 405446
  • Matching level: species

strain history

@refhistory
7799<- K. Heylen, Ghent Univers.; R-32768
123465CIP <- 2008, DSMZ <- K. Heylen, Ghent Univ., Ghent, Belgium

doi: 10.13145/bacdive17567.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Lysobacterales
  • family: Lysobacteraceae
  • genus: Stenotrophomonas
  • species: Stenotrophomonas terrae
  • full scientific name: Stenotrophomonas terrae Heylen et al. 2007

@ref: 7799

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Xanthomonadales

family: Lysobacteraceae

genus: Stenotrophomonas

species: Stenotrophomonas terrae

full scientific name: Stenotrophomonas terrae Heylen et al. 2007

strain designation: R-32768

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
32152negativerod-shapedyes
123465negativerod-shapedno

pigmentation

  • @ref: 32152
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7799TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
36119MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123465CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
7799positivegrowth28mesophilic
32152positivegrowth15-37
32152positiveoptimum26mesophilic
36119positivegrowth30mesophilic
60367positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
32152positivegrowth5-10.5alkaliphile
32152positiveoptimum7.75

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
60367aerobe
123465obligate aerobe

spore formation

  • @ref: 32152
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
32152NaClpositivegrowth0.5-5 %
32152NaClpositiveoptimum2.75 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3215216947citrate+carbon source
3215228757fructose+carbon source
3215217234glucose+carbon source
3215217306maltose+carbon source
3215237684mannose+carbon source
32152506227N-acetylglucosamine+carbon source
321524853esculin+hydrolysis
3215217632nitrate+reduction
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837117634D-glucose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose+assimilation
6836959640N-acetylglucosamine+assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose+assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose+assimilation
683695291gelatin+hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction
12346517632nitrate+reduction
12346516301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12346535581indoleno

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
32152alkaline phosphatase+3.1.3.1
32152catalase+1.11.1.6
32152cytochrome oxidase+1.9.3.1
68369cytochrome oxidase-1.9.3.1
68369gelatinase+
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
123465oxidase+
123465catalase+1.11.1.6
123465urease-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
123465-+++-++-+-++---+-+--

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
7799+----++++-+-++----+--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123465---+/------+/--+/-+/---------+/---+/---+/--------+/-----+/--+/-------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7799soilGentBelgiumBELEurope
60367Soil,enrichment with ethanol and nitrate
123465Environment, SoilBelgiumBELEurope

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_3356.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17;96_26;97_288;98_321;99_3356&stattab=map
  • Last taxonomy: Stenotrophomonas
  • 16S sequence: AM403589
  • Sequence Identity:
  • Total samples: 3361
  • soil counts: 667
  • aquatic counts: 1046
  • animal counts: 1355
  • plant counts: 293

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
77991Risk group (German classification)
1234651Risk group (French classification)

Sequence information

16S sequences

  • @ref: 32152
  • description: Stenotrophomonas terrae partial 16S rRNA gene, type strain R-32768T
  • accession: AM403589
  • length: 1512
  • database: nuccore
  • NCBI tax ID: 405446

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Stenotrophomonas terrae DSM 18941GCA_001431465contigncbi405446
66792Stenotrophomonas terrae strain DSM 18941405446.3wgspatric405446
66792Stenotrophomonas terrae DSM 189412675903279draftimg405446

GC content

  • @ref: 32152
  • GC-content: 65

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveno98.314yes
anaerobicno98.228yes
halophileno93.949no
spore-formingno95.128yes
glucose-utilyes88.536yes
aerobicyes91.471yes
flagellatedno72.656no
motileyes89.976yes
thermophileno99.15yes
glucose-fermentno89.808yes

External links

@ref: 7799

culture collection no.: CCUG 54880, DSM 18941, CIP 109813, LMG 23958

straininfo link

  • @ref: 86562
  • straininfo: 290725

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17766871Stenotrophomonas terrae sp. nov. and Stenotrophomonas humi sp. nov., two nitrate-reducing bacteria isolated from soil.Heylen K, Vanparys B, Peirsegaele F, Lebbe L, De Vos PInt J Syst Evol Microbiol10.1099/ijs.0.65044-02007Bacterial Proteins/analysis, Bacterial Typing Techniques, Carbohydrate Metabolism, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Electrophoresis, Polyacrylamide Gel, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Nitrates/*metabolism, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology, Spores, Bacterial/cytology, Stenotrophomonas/chemistry/*classification/genetics/*isolation & purificationEnzymology
Phylogeny19684314Stenotrophomonas ginsengisoli sp. nov., isolated from a ginseng field.Kim HB, Srinivasan S, Sathiyaraj G, Quan LH, Kim SH, Bui TPN, Liang ZQ, Kim YJ, Yang DCInt J Syst Evol Microbiol10.1099/ijs.0.014662-02009Fatty Acids/analysis, Nucleic Acid Hybridization, Panax/*microbiology, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Stenotrophomonas/*classification/genetics/isolation & purificationPhenotype
Phylogeny20400671Stenotrophomonas daejeonensis sp. nov., isolated from sewage.Lee M, Woo SG, Chae M, Shin MC, Jung HM, Ten LNInt J Syst Evol Microbiol10.1099/ijs.0.017780-02010Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Stenotrophomonas/*classification/genetics/*isolation & purification/physiologyGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
7799Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18941)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18941
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
32152Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2839528776041
36119Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7598
60367Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 54880)https://www.ccug.se/strain?id=54880
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
68369Automatically annotated from API 20NE
68371Automatically annotated from API 50CH acid
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
86562Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID290725.1StrainInfo: A central database for resolving microbial strain identifiers
123465Curators of the CIPCollection of Institut Pasteur (CIP 109813)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109813