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BacDive ID 17555
Type strain
Strain Designation L2
Culture col. no. CCUG 46888 CIP 107228 LMG 22074 DSM 12575 ATCC BAA-12 L2 JCM 13311 2 more
NCBI tax ID(s) 83617
Links
For citation purpose refer to the digital object identifier (doi) of the current version.

Archive

version 9.3 (current version):
version 9.3 (current version)

General

@ref: 4680

BacDive-ID: 17555

DSM-Number: 12575

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

description: Stenotrophomonas nitritireducens L2 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from laboratory scale biofilter.

NCBI tax id

  • NCBI tax id: 83617
  • Matching level: species

strain history

@refhistory
4680<- A. Lipski; L2
337072001, A. Lipski, Univ. Osnabrück, Germany: strain L2
67770CIP 107228 <-- A. Lipski L2.
121310CIP <- 2001, A. Lipski, Osnabrück Univ., Osnabrück, Germany: strain L2

doi: 10.13145/bacdive17555.20250331.9.3

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 nitritireducens
  • full scientific name: Stenotrophomonas nitritireducens Finkmann et al. 2000

@ref: 4680

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Xanthomonadales

family: Lysobacteraceae

genus: Stenotrophomonas

species: Stenotrophomonas nitritireducens

full scientific name: Stenotrophomonas nitritireducens Finkmann et al. 2000

strain designation: L2

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
125438negative98.23
125439negative94.2
121310negativerod-shapedyes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4680NUTRIENT 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
33707MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121310CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperature
4680positivegrowth30
33707positivegrowth30
57385positivegrowth30
67770positivegrowth30
121310positivegrowth25-37
121310nogrowth5
121310nogrowth10
121310nogrowth41

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
57385aerobe
121310obligate aerobe
125439obligate aerobe98.6

spore formation

@refspore formationconfidence
125438no91.204
125439no96.7

halophily

@refsaltgrowthtested relationconcentration
121310NaClpositivegrowth0-4 %
121310NaClnogrowth6 %
121310NaClnogrowth8 %
121310NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12131016947citrate-carbon source
1213104853esculin+hydrolysis
12131017632nitrate-reduction
12131016301nitrite+reduction
12131017632nitrate-respiration
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

antibiotic resistance

  • @ref: 121310
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12131035581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382cystine arylamidase-3.4.11.3
68382trypsin+3.4.21.4
68382valine arylamidase-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382esterase lipase (C 8)+
121310oxidase+
121310beta-galactosidase+3.2.1.23
121310alcohol dehydrogenase-1.1.1.1
121310gelatinase+/-
121310amylase-
121310DNase-
121310caseinase-3.4.21.50
121310catalase+1.11.1.6
121310tween esterase+
121310lecithinase-
121310lipase-
121310lysine decarboxylase-4.1.1.18
121310ornithine decarboxylase-4.1.1.17
121310protease-
121310tryptophan deaminase-
121310urease+3.5.1.5
68382esterase (C 4)-
68382alkaline phosphatase+3.1.3.1
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    57385C14:01.814
    57385C15:01.515
    57385C16:01.916
    57385C11:0 ANTEISO0.410.693
    57385C11:0 iso10.210.605
    57385C11:0 ISO 3OH412.09
    57385C12:0 3OH1.213.455
    57385C12:0 ISO 3OH2.913.098
    57385C13:0 2OH0.514.191
    57385C13:0 iso1.912.612
    57385C13:0 ISO 3OH3.314.11
    57385C14:0 ISO9.413.618
    57385C15:0 ANTEISO4.714.711
    57385C15:0 ISO35.914.621
    57385C15:1 ISO F5.914.414
    57385C16:0 iso3.315.626
    57385C16:1 ω7c1.115.819
    57385C16:1 ω9c0.815.774
    57385C17:0 CYCLO1.116.888
    57385C17:0 iso0.616.629
    57385C17:1 ω9c ISO7.516.416
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121310-+-+-+--+-++-----+--

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
4680-----+------+-----+-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121310++----------------+--+-------------------------------+-----+--+--+---------+----------+-+-+++++-++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
4680laboratory scale biofilterOsnabrückGermanyDEUEurope
57385Biofilter,laboratory scaleOsnabrückGermanyDEUEurope1992
67770Experimental biofilter supplied with the waste gas of an animal-rendering plant
121310Laboratory scale biofilterOsnabrückGermanyDEUEurope1992

isolation source categories

Cat1Cat2Cat3
#Engineered#Bioremediation#Biofilter
#Engineered#Laboratory

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: AJ012229
  • 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
46801Risk group (German classification)
1213101Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Stenotrophomonas nitritireducens 16S rRNA gene, strain L2
  • accession: AJ012229
  • length: 1513
  • database: nuccore
  • NCBI tax ID: 83617

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Stenotrophomonas nitritireducens strain DSM 1257583617.3wgspatric83617
66792Stenotrophomonas nitritireducens DSM 125752713896755draftimg83617
67770Stenotrophomonas nitritireducens DSM 12575GCA_001431425contigncbi83617

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno98.23no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.851yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes82.736yes
125438spore-formingspore-formingAbility to form endo- or exosporesno91.204no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno95.657yes
125438motile2+flagellatedAbility to perform flagellated movementyes61.493no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno96.7
125439BacteriaNetmotilityAbility to perform movementyes81.6
125439BacteriaNetgram_stainReaction to gram-stainingnegative94.2
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe98.6

External links

@ref: 4680

culture collection no.: CCUG 46888, CIP 107228, LMG 22074, DSM 12575, ATCC BAA-12, JCM 13311

straininfo link

  • @ref: 86550
  • straininfo: 44253

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10826814Characterization of N2O-producing Xanthomonas-like isolates from biofilters as Stenotrophomonas nitritireducens sp. nov., Luteimonas mephitis gen. nov., sp. nov. and Pseudoxanthomonas broegbernensis gen. nov., sp. nov.Finkmann W, Altendorf K, Stackebrandt E, Lipski AInt J Syst Evol Microbiol10.1099/00207713-50-1-2732000DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Filtration/*instrumentation, Gammaproteobacteria/*classification/physiology, Gases, Industrial Waste, Molecular Sequence Data, Nitrites/metabolism, Nitrous Oxide/*metabolism, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Stenotrophomonas/*classification/physiology, Xanthomonas/chemistry/*classification/genetics/physiologyGenetics
Phylogeny11931169Stenotrophomonas acidaminiphila sp. nov., a strictly aerobic bacterium isolated from an upflow anaerobic sludge blanket (UASB) reactor.Assih EA, Ouattara AS, Thierry S, Cayol JL, Labat M, Macarie HInt J Syst Evol Microbiol10.1099/00207713-52-2-5592002Anaerobiosis, Anti-Bacterial Agents/pharmacology, DNA, Bacterial/chemistry, Environmental Microbiology, Industrial Waste, Microbial Sensitivity Tests, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/chemistry, Sequence Homology, Nucleic Acid, Sewage/*microbiology, Stenotrophomonas/*classification/drug effects/physiologyGenetics
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

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4680Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12575)https://www.dsmz.de/collection/catalogue/details/culture/DSM-12575
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
33707Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4641
57385Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 46888)https://www.ccug.se/strain?id=46888
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/
68369Automatically annotated from API 20NE
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
86550Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID44253.1StrainInfo: A central database for resolving microbial strain identifiers
121310Curators of the CIPCollection of Institut Pasteur (CIP 107228)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107228
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1

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