Strain identifier
BacDive ID: 17555
Type strain:
Species: Stenotrophomonas nitritireducens
Strain Designation: L2
Strain history: CIP <- 2001, A. Lipski, Osnabrück Univ., Osnabrück, Germany: strain L2
NCBI tax ID(s): 83617 (species)
General
@ref: 4680
BacDive-ID: 17555
DSM-Number: 12575
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative
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
@ref | history |
---|---|
4680 | <- A. Lipski; L2 |
33707 | 2001, A. Lipski, Univ. Osnabrück, Germany: strain L2 |
67770 | CIP 107228 <-- A. Lipski L2. |
121310 | CIP <- 2001, A. Lipski, Osnabrück Univ., Osnabrück, Germany: strain L2 |
doi: 10.13145/bacdive17555.20230509.8.1
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 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
@ref | gram stain | confidence | cell shape | motility |
---|---|---|---|---|
69480 | negative | 99.991 | ||
121310 | negative | rod-shaped | yes |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
4680 | NUTRIENT AGAR (DSMZ Medium 1) | yes | https://mediadive.dsmz.de/medium/1 | Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water |
33707 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
121310 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
4680 | positive | growth | 30 | mesophilic |
33707 | positive | growth | 30 | mesophilic |
57385 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
121310 | positive | growth | 25-37 | mesophilic |
121310 | no | growth | 5 | psychrophilic |
121310 | no | growth | 10 | psychrophilic |
121310 | no | growth | 41 | thermophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
57385 | aerobe |
121310 | obligate aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.995 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
121310 | NaCl | positive | growth | 0-4 % |
121310 | NaCl | no | growth | 6 % |
121310 | NaCl | no | growth | 8 % |
121310 | NaCl | no | growth | 10 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68369 | 25115 | malate | - | assimilation |
68369 | 17128 | adipate | - | assimilation |
68369 | 27689 | decanoate | - | assimilation |
68369 | 24265 | gluconate | - | assimilation |
68369 | 17306 | maltose | - | assimilation |
68369 | 59640 | N-acetylglucosamine | + | assimilation |
68369 | 16899 | D-mannitol | - | assimilation |
68369 | 16024 | D-mannose | - | assimilation |
68369 | 30849 | L-arabinose | - | assimilation |
68369 | 17634 | D-glucose | - | assimilation |
68369 | 5291 | gelatin | - | hydrolysis |
68369 | 4853 | esculin | + | hydrolysis |
68369 | 16199 | urea | - | hydrolysis |
68369 | 29016 | arginine | - | hydrolysis |
68369 | 17634 | D-glucose | - | fermentation |
68369 | 27897 | tryptophan | - | energy source |
68369 | 17632 | nitrate | - | reduction |
121310 | 16947 | citrate | - | carbon source |
121310 | 4853 | esculin | + | hydrolysis |
121310 | 17632 | nitrate | - | reduction |
121310 | 16301 | nitrite | + | reduction |
121310 | 17632 | nitrate | - | respiration |
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
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68369 | 35581 | indole | no |
121310 | 35581 | indole | no |
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
68369 | cytochrome oxidase | + | 1.9.3.1 |
68369 | gelatinase | - | |
68369 | beta-glucosidase | + | 3.2.1.21 |
68369 | urease | - | 3.5.1.5 |
68369 | arginine dihydrolase | - | 3.5.3.6 |
121310 | oxidase | + | |
121310 | beta-galactosidase | + | 3.2.1.23 |
121310 | alcohol dehydrogenase | - | 1.1.1.1 |
121310 | gelatinase | +/- | |
121310 | amylase | - | |
121310 | DNase | - | |
121310 | caseinase | - | 3.4.21.50 |
121310 | catalase | + | 1.11.1.6 |
121310 | tween esterase | + | |
121310 | lecithinase | - | |
121310 | lipase | - | |
121310 | lysine decarboxylase | - | 4.1.1.18 |
121310 | ornithine decarboxylase | - | 4.1.1.17 |
121310 | protease | - | |
121310 | tryptophan deaminase | - | |
121310 | urease | + | 3.5.1.5 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | - | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | - | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | + | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
fatty acid profile
fatty acids
@ref fatty acid percentage ECL 57385 C14:0 1.8 14 57385 C15:0 1.5 15 57385 C16:0 1.9 16 57385 C11:0 ANTEISO 0.4 10.693 57385 C11:0 iso 10.2 10.605 57385 C11:0 ISO 3OH 4 12.09 57385 C12:0 3OH 1.2 13.455 57385 C12:0 ISO 3OH 2.9 13.098 57385 C13:0 2OH 0.5 14.191 57385 C13:0 iso 1.9 12.612 57385 C13:0 ISO 3OH 3.3 14.11 57385 C14:0 ISO 9.4 13.618 57385 C15:0 ANTEISO 4.7 14.711 57385 C15:0 ISO 35.9 14.621 57385 C15:1 ISO F 5.9 14.414 57385 C16:0 iso 3.3 15.626 57385 C16:1 ω7c 1.1 15.819 57385 C16:1 ω9c 0.8 15.774 57385 C17:0 CYCLO 1.1 16.888 57385 C17:0 iso 0.6 16.629 57385 C17:1 ω9c ISO 7.5 16.416 - type of FA analysis: whole cell analysis
- method/protocol: CCUG
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121310 | - | + | - | + | - | + | - | - | + | - | + | + | - | - | - | - | - | + | - | - |
API 20NE
@ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC | OX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
4680 | - | - | - | - | - | + | - | - | - | - | - | - | + | - | - | - | - | - | + | - | + |
API biotype100
@ref | GLU | FRU | GAL | TRE | MNE | SBE | MEL | SAC | RAF | MTE | MAL | LAC | LTE | MbGa | MaGa | CEL | GEN | MbGu | ESC | RIB | ARA | XYL | PLE | RHA | FUC | MLZ | DARL | LARL | XLT | DUL | TAG | GLY | INO | MAN | MTL | TUR | SOR | ADO | HBG | LYX | ERY | MDG | 3MDG | SAT | MUC | LTAT | DTAT | MTAT | DMLT | LMLT | CATE | TATE | TTE | CIT | GRT | GAT | 2KG | 5KG | TRY | NAG | GNT | PAC | PAT | pOBE | QAT | GTE | mOBE | BAT | PPAT | CMT | TGE | BET | PCE | ABT | HIN | LAT | CAP | CYT | HIS | SUC | FUM | GRE | GYT | AVT | ETN | TTN | GLN | ITA | 3OBU | APT | GTT | PRO | DALA | LALA | SER | MNT | PROP | TYR | 2KT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121310 | + | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | + | - | - | + | - | - | + | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | + | - | + | - | + | + | + | + | + | - | + | + | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | sampling date | isolation date |
---|---|---|---|---|---|---|---|
4680 | laboratory scale biofilter | Osnabrück | Germany | DEU | Europe | ||
57385 | Biofilter,laboratory scale | Osnabrück | Germany | DEU | Europe | 1992 | |
67770 | Experimental biofilter supplied with the waste gas of an animal-rendering plant | ||||||
121310 | Laboratory scale biofilter | Osnabrück | Germany | DEU | Europe | 1992 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | biosafety level | biosafety level comment |
---|---|---|
4680 | 1 | Risk group (German classification) |
121310 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 20218
- description: Stenotrophomonas nitritireducens 16S rRNA gene, strain L2
- accession: AJ012229
- length: 1513
- database: ena
- NCBI tax ID: 83617
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Stenotrophomonas nitritireducens strain DSM 12575 | 83617.3 | wgs | patric | 83617 |
66792 | Stenotrophomonas nitritireducens DSM 12575 | 2713896755 | draft | img | 83617 |
67770 | Stenotrophomonas nitritireducens DSM 12575 | GCA_001431425 | contig | ncbi | 83617 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 89.695 | no |
flagellated | no | 77.195 | no |
gram-positive | no | 98.05 | no |
anaerobic | no | 98.351 | no |
halophile | no | 96.21 | no |
spore-forming | no | 94.01 | no |
thermophile | no | 99.252 | yes |
glucose-util | yes | 73.2 | yes |
aerobic | yes | 84.324 | no |
glucose-ferment | no | 89.929 | yes |
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
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 10826814 | Characterization 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 A | Int J Syst Evol Microbiol | 10.1099/00207713-50-1-273 | 2000 | DNA, 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/physiology | Genetics |
Phylogeny | 11931169 | Stenotrophomonas 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 H | Int J Syst Evol Microbiol | 10.1099/00207713-52-2-559 | 2002 | Anaerobiosis, 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/physiology | Genetics |
Phylogeny | 19684314 | Stenotrophomonas 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 DC | Int J Syst Evol Microbiol | 10.1099/ijs.0.014662-0 | 2009 | Fatty Acids/analysis, Nucleic Acid Hybridization, Panax/*microbiology, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Stenotrophomonas/*classification/genetics/isolation & purification | Phenotype |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
4680 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12575) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-12575 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
33707 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/4641 | ||||
57385 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 46888) | https://www.ccug.se/strain?id=46888 | |||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68369 | Automatically annotated from API 20NE | |||||
68382 | Automatically annotated from API zym | |||||
69479 | João 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 | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
86550 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID44253.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
121310 | Curators of the CIP | Collection of Institut Pasteur (CIP 107228) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107228 |