Strain identifier

BacDive ID: 140359

Type strain: Yes

Species: Stenotrophomonas bentonitica

Strain Designation: BII-R7

Strain history: <- M. L. Merroun, University of Granada, Spain <- O. Fernández Sanfrancisco and M. López Fernández, University of Granada

NCBI tax ID(s): 1450134 (species)

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General

@ref: 42966

BacDive-ID: 140359

DSM-Number: 103927

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

description: Stenotrophomonas bentonitica BII-R7 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from soil, bentonitic formation.

NCBI tax id

  • NCBI tax id: 1450134
  • Matching level: species

strain history

  • @ref: 42966
  • history: <- M. L. Merroun, University of Granada, Spain <- O. Fernández Sanfrancisco and M. López Fernández, University of Granada

doi: 10.13145/bacdive140359.20250331.9.3

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 bentonitica
  • full scientific name: Stenotrophomonas bentonitica Sánchez-Castro et al. 2017

@ref: 42966

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Lysobacteraceae

genus: Stenotrophomonas

species: Stenotrophomonas bentonitica

full scientific name: Stenotrophomonas bentonitica Sánchez-Castro et al. 2017

strain designation: BII-R7

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43476negative0.92-1.55 µm0.45-0.65 µmrod-shapedno
125438negative97.744

colony morphology

  • @ref: 43476
  • colony color: light yellow
  • colony shape: circular
  • incubation period: 3 days
  • medium used: Luria Bertani agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43476LB (Luria-Bertani) MEDIUMyes
42966NUTRIENT 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

culture temp

@refgrowthtypetemperature
43476nogrowth4
43476nogrowth40
43476positivegrowth15-37
43476positiveoptimum28
42966positivegrowth28

culture pH

@refabilitytypepHPH range
43476nogrowth12
43476positivegrowth5-10alkaliphile
43476positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 43476
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
43476no
125439no93.2

halophily

@refsaltgrowthtested relationconcentration
43476NaClnogrowth5 %
43476NaClpositivegrowth0-2.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
43476161933-hydroxybenzoate-assimilation
43476178794-hydroxybenzoate-assimilation
4347617128adipate-assimilation
4347678208azelaate-assimilation
4347616958beta-alanine-assimilation
4347616383cis-aconitate-assimilation
4347615963ribitol-assimilation
4347615824D-fructose-assimilation
4347612936D-galactose-assimilation
4347618391D-gluconate-assimilation
4347616899D-mannitol-assimilation
43476DL-2-gamma-aminobutyrate-assimilation
43476370543-hydroxybutyrate-assimilation
4347617268myo-inositol-assimilation
4347617240itaconate-assimilation
4347616977L-alanine-assimilation
4347630849L-arabinose-assimilation
4347629991L-aspartate-assimilation
4347615971L-histidine-assimilation
4347615603L-leucine-assimilation
4347615729L-ornithine-assimilation
4347617295L-phenylalanine-assimilation
4347617203L-proline-assimilation
4347662345L-rhamnose-assimilation
4347617115L-serine-assimilation
4347616828L-tryptophan-assimilation
4347668428maltitol-assimilation
4347636986mesaconate-assimilation
43476309162-oxoglutarate-assimilation
4347618401phenylacetate-assimilation
4347617148putrescine-assimilation
4347630911sorbitol-assimilation
434769300suberic acid-assimilation
4347617992sucrose-assimilation
4347615708trans-aconitate-assimilation
4347615963ribitol-builds acid from
4347617057cellobiose-builds acid from
4347618333D-arabitol-builds acid from
4347616899D-mannitol-builds acid from
4347665327D-xylose-builds acid from
4347616813galactitol-builds acid from
4347617268myo-inositol-builds acid from
4347630849L-arabinose-builds acid from
4347662345L-rhamnose-builds acid from
4347617716lactose-builds acid from
4347628053melibiose-builds acid from
4347637657methyl D-glucoside-builds acid from
4347616634raffinose-builds acid from
4347630911sorbitol-builds acid from
43476901464-nitrophenyl beta-D-glucuronide-hydrolysis
4347618305arbutin+assimilation
4347617057cellobiose+assimilation
4347665327D-xylose+assimilation
4347617859glutaric acid+assimilation
4347628053melibiose+assimilation
4347617634D-glucose+builds acid from
4347616024D-mannose+builds acid from
4347617306maltose+builds acid from
4347630089acetate+carbon source
4347617634D-glucose+carbon source
4347616024D-mannose+carbon source
4347616988D-ribose+carbon source
4347624996lactate+carbon source
4347625115malate+carbon source
4347629806fumarate+carbon source
4347617306maltose+carbon source
4347628037N-acetylgalactosamine+carbon source
43476506227N-acetylglucosamine+carbon source
4347617272propionate+carbon source
4347615361pyruvate+carbon source
4347617814salicin+carbon source
4347627082trehalose+carbon source
43476911224-nitrophenyl alpha-D-glucopyranoside+hydrolysis
43476902594-nitrophenyl beta-D-glucopyranoside+hydrolysis
43476901484-nitrophenyl beta-D-xylopyranoside+hydrolysis
434763122bis-4-nitrophenyl phosphate+hydrolysis
4347655394bis-4-nitrophenyl-phosphorylcholine+hydrolysis
434764853esculin+hydrolysis
43476L-alanine 4-nitroanilide+hydrolysis
43476L-glutamate-gamma-3-carboxy-4-nitroanilide+hydrolysis
43476L-proline-4-nitroanilide+hydrolysis
43476O-nitrophenyl-beta-D-galactopyranosid+hydrolysis
4347691050p-nitrophenyl phenyl phosphonate+hydrolysis
4347617632nitrate+reduction

metabolite production

  • @ref: 43476
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
43476catalase+1.11.1.6
43476protease+
43476cytochrome oxidase-1.9.3.1
43476urease-3.5.1.5
43476beta-galactosidase+/-3.2.1.23
43476leucine arylamidase+3.4.11.1
43476esterase+
43476esterase Lipase (C 8)+
43476acid phosphatase+3.1.3.2
43476alkaline phosphatase+3.1.3.1
43476naphthol-AS-BI-phosphohydrolase+

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    43476C15:0 anteiso19.4
    43476C12:0 3OH3.6
    43476C13:0 2OH1.7
    43476C14:02.3
    43476C15:00.9
    43476C16:09.4
    43476C16:1ω7c / C15:0 iso 2OH9.2
    43476C16:1ω9c2.3
    43476cyclo-C17:01.7
    43476C11:0 iso3.7
    43476C11:0 iso 3OH2
    43476C13:0 iso 3OH3.2
    43476C14:0 iso1.4
    43476C15:0 iso23.8
    43476C15:1 iso1.1
    43476C16:0 iso4
    43476C17:0 iso2.8
    43476C17:1 iso ω9c7.5
    43476Unknown ECL 11.799111799
  • type of FA analysis: whole cell analysis
  • incubation medium: TSA
  • agar/liquid: agar
  • incubation temperature: 28
  • incubation time: 2
  • incubation pH: 7
  • incubation_oxygen: aerobic
  • software version: Sherlock 2.1
  • library/peak naming table: TSBA4.1
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
42966soil, bentonitic formationAlmeriaSpainESPEurope
43476Bentonite formationsSouthern SpainSpainESPEurope

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Environmental#Terrestrial#Geologic

taxonmaps

  • @ref: 69479
  • File name: preview.99_2601.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17;96_26;97_27;98_2015;99_2601&stattab=map
  • Last taxonomy: Stenotrophomonas
  • 16S sequence: LT622838
  • Sequence Identity:
  • Total samples: 80919
  • soil counts: 24235
  • aquatic counts: 14518
  • animal counts: 31589
  • plant counts: 10577

Safety information

risk assessment

  • @ref: 42966
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 42966
  • description: Stenotrophomonas sp. BIIR7 partial 16S rRNA gene, isolate BIIR7
  • accession: LT622838
  • length: 1385
  • database: nuccore
  • NCBI tax ID: 1904462

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Stenotrophomonas bentonitica DSM 103927GCA_013185915scaffoldncbi1450134
66792Stenotrophomonas bentonitica strain DSM 1039271450134.7wgspatric1450134

GC content

@refGC-contentmethod
4347666.5
4296666.5sequence analysis

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno97.744yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no98.881no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes84.133yes
125438spore-formingspore-formingAbility to form endo- or exosporesno89.917yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno98.5yes
125438motile2+flagellatedAbility to perform flagellated movementyes71.554no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno93.2
125439BacteriaNetmotilityAbility to perform movementyes75.2
125439BacteriaNetgram_stainReaction to gram-stainingnegative86.5
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe75

External links

@ref: 42966

culture collection no.: DSM 103927, CECT 9180, LMG 29893

straininfo link

  • @ref: 96657
  • straininfo: 400073

literature

topicPubmed-IDtitleauthorsjournalDOIyeartopic2mesh
Genetics28774976Draft Genome Sequence of Stenotrophomonas bentonitica BII-R7(T), a Selenite-Reducing Bacterium Isolated from Spanish Bentonites.Sanchez-Castro I, Bakkali M, Merroun MLGenome Announc10.1128/genomeA.00719-172017Phylogeny
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.0.0020162017TranscriptomeBacterial 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/chemistry
Transcriptome33264934Multisystem combined uranium resistance mechanisms and bioremediation potential of Stenotrophomonas bentonitica BII-R7: Transcriptomics and microscopic study.Pinel-Cabello M, Jroundi F, Lopez-Fernandez M, Geffers R, Jarek M, Jauregui R, Link A, Vilchez-Vargas R, Merroun MLJ Hazard Mater10.1016/j.jhazmat.2020.1238582020Biodegradation, Environmental, Stenotrophomonas, Transcriptome, *Uranium/toxicity
34111750Delineation of cellular stages and identification of key proteins for reduction and biotransformation of Se(IV) by Stenotrophomonas bentonitica BII-R7.Pinel-Cabello M, Chapon V, Ruiz-Fresneda MA, Alpha-Bazin B, Berthomieu C, Armengaud J, Merroun MLJ Hazard Mater10.1016/j.jhazmat.2021.1261502021Biodegradation, Environmental, Biotransformation, *Selenium, Stenotrophomonas
Phylogeny34559247Stenotrophomonas nematodicola sp. nov., isolated from Caenorhabditis elegans.Wei X, Lei S, Deng Y, Zhang Y, Zhang L, Niu QArch Microbiol10.1007/s00203-021-02586-y2021TranscriptomeAnimals, Bacterial Typing Techniques, *Caenorhabditis elegans, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Stenotrophomonas/genetics
Biotechnology36476772Genetic mechanisms for Se(VI) reduction and synthesis of trigonal 1-D nanostructures in Stenotrophomonas bentonitica: Perspectives in eco-friendly nanomaterial production and bioremediation.Pinel-Cabello M, Jauregui R, Jroundi F, Geffers R, Jarek M, Link A, Vilchez-Vargas R, Merroun MLSci Total Environ10.1016/j.scitotenv.2022.1606352022

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
42966Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-103927Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103927)
43476Ivan Sanchez-Castro, Miguel Angel Ruiz-Fresneda, Mohammed Bakkali, Peter Kaempfer, Stefanie P. Glaeser, Hans Jürgen Busse, Margarita López-Fern andez, Pablo Martínez-Rodríguez, Mohamed Larbi MerrounStenotrophomonas bentonitica sp. nov., isolated from bentonite formations10.1099/ijsem.0.002016IJSEM 67: 2779-2786 201728820086
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
96657Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID400073.1
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG