Strain identifier

BacDive ID: 17566

Type strain: Yes

Species: Stenotrophomonas humi

Strain Designation: R-32729

Strain history: <- K. Heylen, Ghent Univ.; R-32729

NCBI tax ID(s): 405444 (species)

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General

@ref: 7790

BacDive-ID: 17566

DSM-Number: 18929

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

description: Stenotrophomonas humi R-32729 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 405444
  • Matching level: species

strain history

  • @ref: 7790
  • history: <- K. Heylen, Ghent Univ.; R-32729

doi: 10.13145/bacdive17566.20230509.8.1

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 humi
  • full scientific name: Stenotrophomonas humi Heylen et al. 2007

@ref: 7790

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Xanthomonadales

family: Lysobacteraceae

genus: Stenotrophomonas

species: Stenotrophomonas humi

full scientific name: Stenotrophomonas humi Heylen et al. 2007

strain designation: R-32729

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
32152negativerod-shapedyes
69480yes93.583
69480negative99.998

pigmentation

  • @ref: 32152
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 7790
  • name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/535
  • composition: Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
7790positivegrowth28mesophilic
32152positivegrowth15-37
32152positiveoptimum26mesophilic
60368positivegrowth30mesophilic

culture pH

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

Physiology and metabolism

oxygen tolerance

  • @ref: 60368
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
32152no
69481no100
69480no99.999

halophily

@refsaltgrowthtested relationconcentration
32152NaClpositivegrowth2.25 %
32152NaClpositiveoptimum0.5-4 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3215216947citrate+carbon source
3215228757fructose+carbon source
3215225115malate+carbon source
3215217306maltose+carbon source
3215237684mannose+carbon source
32152506227N-acetylglucosamine+carbon source
3215217632nitrate+reduction
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

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

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

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
7790+-----+-+-+-++-+-++--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7790soilGentBelgiumBELEurope
60368Soil,enrichment with ethanol and nitrate

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_383.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17;96_26;97_288;98_321;99_383&stattab=map
  • Last taxonomy: Stenotrophomonas
  • 16S sequence: AM403587
  • Sequence Identity:
  • Total samples: 294
  • soil counts: 83
  • aquatic counts: 65
  • animal counts: 115
  • plant counts: 31

Safety information

risk assessment

  • @ref: 7790
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 32152
  • description: Stenotrophomonas humi partial 16S rRNA gene, type strain R-32729T
  • accession: AM403587
  • length: 1494
  • database: nuccore
  • NCBI tax ID: 405444

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Stenotrophomonas humi DSM 18929GCA_001431415contigncbi405444
66792Stenotrophomonas humi strain DSM 18929405444.3wgspatric405444
66792Stenotrophomonas humi DSM 189292713896756draftimg405444

GC content

  • @ref: 32152
  • GC-content: 64

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.38yes
anaerobicno98.581yes
halophileno92.594no
spore-formingno95.371yes
glucose-utilyes88.25yes
aerobicyes93.145no
flagellatedno73.484no
motileyes90.151yes
thermophileno98.719yes
glucose-fermentno89.02yes

External links

@ref: 7790

culture collection no.: DSM 18929, LMG 23959, CCUG 54881

straininfo link

  • @ref: 86561
  • straininfo: 290571

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
Phylogeny20221726Stenotrophomonas panacihumi sp. nov., isolated from soil of a ginseng field.Yi H, Srinivasan S, Kim MKJ Microbiol10.1007/s12275-010-0006-02010Carotenoids/analysis, Fatty Acids/analysis, Genes, Bacterial, *Panax, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Soil Microbiology, Stenotrophomonas/chemistry/classification/genetics/*isolation & purificationEnzymology
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_referencepubmed
7790Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18929)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18929
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
60368Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 54881)https://www.ccug.se/strain?id=54881
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)
68369Automatically annotated from API 20NE
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
86561Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID290571.1StrainInfo: A central database for resolving microbial strain identifiers