Strain identifier

BacDive ID: 17570

Type strain: Yes

Species: Stenotrophomonas pavanii

Strain history: CIP <- 2019, LMG <- 2009, S. Van Trappen, LMG <- 2008, P.L. Ramos, Sao Paulo Univ., Sao Paulo, Brazil <- H.R. Barbosa, Biomedical Sciences Inst., Sao Paulo Univ., Sao Paulo, Brazil: strain ICB 89

NCBI tax ID(s): 487698 (species)

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General

@ref: 17917

BacDive-ID: 17570

DSM-Number: 25135

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

description: Stenotrophomonas pavanii CCUG 59972 is a mesophilic, Gram-negative, rod-shaped bacterium that was isolated from stems of sugar cane .

NCBI tax id

  • NCBI tax id: 487698
  • Matching level: species

strain history

@refhistory
17917<- LMG <- S. Van Trappen, Univ. Ghent, Belgium <- H. R. Barbosa, Univ. Sao Paulo, Brazil
121642CIP <- 2019, LMG <- 2009, S. Van Trappen, LMG <- 2008, P.L. Ramos, Sao Paulo Univ., Sao Paulo, Brazil <- H.R. Barbosa, Biomedical Sciences Inst., Sao Paulo Univ., Sao Paulo, Brazil: strain ICB 89

doi: 10.13145/bacdive17570.20230509.8.1

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 pavanii
  • full scientific name: Stenotrophomonas pavanii Ramos et al. 2011

@ref: 17917

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Xanthomonadales

family: Lysobacteraceae

genus: Stenotrophomonas

species: Stenotrophomonas pavanii

full scientific name: Stenotrophomonas pavanii Ramos et al. 2011

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
29715negativerod-shapedno
121642negativerod-shapedyes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17917NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
121642CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
17917positivegrowth28mesophilic
29715positivegrowth20-37
29715positiveoptimum28.5mesophilic

culture pH

@refabilitytypepHPH range
29715positivegrowth05-12alkaliphile
29715positiveoptimum8.5

Physiology and metabolism

spore formation

  • @ref: 29715
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
29715NaClpositivegrowth0.7-3.0 %
29715NaClpositiveoptimum1.85 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2971516947citrate+carbon source
29715506227N-acetylglucosamine+carbon source
2971553426tween 80+carbon source
297154853esculin+hydrolysis
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
29715catalase+1.11.1.6
29715gelatinase+
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
17917-----++++-+-++---++-+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
17917stems of sugar cane (Brazilian variety widely used in organic farming)Sao Francisco SertaozinhoBrazilBRAMiddle and South America
62173Sugarcane plant stem,organic cultivatedBrazilBRAMiddle and South America
121642Sugarcane, Saccharum officinarum, stemUsina Sao Francisco SertaozinhoBrazilBRAMiddle and South America2000-01-03

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Stem (Branch)

taxonmaps

  • @ref: 69479
  • File name: preview.99_31.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17;96_26;97_27;98_30;99_31&stattab=map
  • Last taxonomy: Stenotrophomonas
  • 16S sequence: HQ641452
  • Sequence Identity:
  • Total samples: 48176
  • soil counts: 6245
  • aquatic counts: 10099
  • animal counts: 29572
  • plant counts: 2260

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
179171Risk group (German classification)
1216421Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
29715Stenotrophomonas pavanii strain ICB 89 16S ribosomal RNA gene, partial sequenceFJ7486831483nuccore487698
17917Stenotrophomonas pavanii strain LMG 25348 16S ribosomal RNA gene, partial sequenceHQ6414521497ena487698

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Stenotrophomonas pavanii LMG 25348GCA_900101175scaffoldncbi487698
66792Stenotrophomonas pavanii DSM 25135GCA_001431565contigncbi487698
66792Stenotrophomonas pavanii strain DSM 25135487698.4wgspatric487698
66792Stenotrophomonas pavanii strain LMG 25348487698.5wgspatric487698
66792Stenotrophomonas pavanii LMG 253482623620583draftimg487698
66792Stenotrophomonas pavanii DSM 251352740892494draftimg487698

GC content

  • @ref: 17917
  • GC-content: 67.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes85.926yes
flagellatedno80.473yes
gram-positiveno97.906no
anaerobicno98.163no
aerobicyes88.203no
halophileno93.963no
spore-formingno95.752yes
glucose-fermentno90.766no
thermophileno99.528yes
glucose-utilyes86.747no

External links

@ref: 17917

culture collection no.: CCUG 59972, DSM 25135, CBMAI 564, ICB 89, LMG 25348, CIP 111741

straininfo link

  • @ref: 86566
  • straininfo: 363691

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20495025Screening for endophytic nitrogen-fixing bacteria in Brazilian sugar cane varieties used in organic farming and description of Stenotrophomonas pavanii sp. nov.Ramos PL, Van Trappen S, Thompson FL, Rocha RCS, Barbosa HR, De Vos P, Moreira-Filho CAInt J Syst Evol Microbiol10.1099/ijs.0.019372-02010Brazil, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Molecular Sequence Data, *Nitrogen Fixation, Nucleic Acid Hybridization, Organic Agriculture, Phylogeny, RNA, Ribosomal, 16S/genetics, Saccharum/*microbiology, Sequence Analysis, DNA, Stenotrophomonas/*classification/genetics/*isolation & purification/physiologyGenetics
Phylogeny22934997Isolation and molecular identification of landfill bacteria capable of growing on di-(2-ethylhexyl) phthalate and deteriorating PVC materials.Latorre I, Hwang S, Montalvo-Rodriguez RJ Environ Sci Health A Tox Hazard Subst Environ Eng10.1080/10934529.2012.7075492012Bacteria/*classification/genetics/*isolation & purification/metabolism, Biodegradation, Environmental, DNA, Bacterial/genetics, Diethylhexyl Phthalate/*metabolism, Endocrine Disruptors/*metabolism, Phylogeny, Polymerase Chain Reaction, Polyvinyl Chloride/*metabolism, RNA, Ribosomal, 16S/genetics, Refuse Disposal, Sequence Analysis, RNA, Water Pollutants, Chemical/*metabolismMetabolism
Phylogeny28820086Stenotrophomonas bentonitica sp. nov., isolated from bentonite formations.Sanchez-Castro I, Ruiz-Fresneda MA, Bakkali M, Kampfer P, Glaeser SP, Busse HJ, Lopez-Fernandez M, Martinez-Rodriguez P, Merroun MLInt J Syst Evol Microbiol10.1099/ijsem.0.0020162017Bacterial Typing Techniques, Base Composition, *Bentonite, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spain, Stenotrophomonas/*classification/genetics/isolation & purification, Ubiquinone/chemistryTranscriptome
Phylogeny32748076Stenotrophomonas cyclobalanopsidis sp. nov., isolated from the leaf spot disease of Cyclobalanopsis patelliformis.Bian DR, Xue H, Piao CG, Li YAntonie Van Leeuwenhoek10.1007/s10482-020-01453-y2020Genome, Bacterial, Genomics/methods, High-Throughput Nucleotide Sequencing, Phenotype, Phylogeny, Plant Diseases/*microbiology, Quercus/*microbiology, RNA, Ribosomal, 16S/genetics, Stenotrophomonas/chemistry/*classification/genetics/*isolation & purificationGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17917Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25135)https://www.dsmz.de/collection/catalogue/details/culture/DSM-25135
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
29715Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2609828776041
62173Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 59972)https://www.ccug.se/strain?id=59972
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
86566Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID363691.1StrainInfo: A central database for resolving microbial strain identifiers
121642Curators of the CIPCollection of Institut Pasteur (CIP 111741)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20111741