Strain identifier
BacDive ID: 17568
Type strain: 
Species: Stenotrophomonas chelatiphaga
Strain Designation: LPM-5
Strain history: <- Y. A. Trotsenko, Inst. Biochem. Physiol. Microorg., Pushchino, Russia; LPM-5 <- E.N. Kaparullina <- T. I. Chistyakova
NCBI tax ID(s): 517011 (species)
version 9.3 (current version)
General
@ref: 15753
BacDive-ID: 17568
DSM-Number: 21508
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative
description: Stenotrophomonas chelatiphaga LPM-5 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sewage sludge.
NCBI tax id
- NCBI tax id: 517011
- Matching level: species
strain history
- @ref: 15753
- history: <- Y. A. Trotsenko, Inst. Biochem. Physiol. Microorg., Pushchino, Russia; LPM-5 <- E.N. Kaparullina <- T. I. Chistyakova
doi: 10.13145/bacdive17568.20250331.9.3
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 chelatiphaga
- full scientific name: Stenotrophomonas chelatiphaga Kaparullina et al. 2010
@ref: 15753
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Xanthomonadales
family: Lysobacteraceae
genus: Stenotrophomonas
species: Stenotrophomonas chelatiphaga
full scientific name: Stenotrophomonas chelatiphaga Kaparullina et al. 2010
strain designation: LPM-5
type strain: yes
Morphology
cell morphology
| @ref | gram stain | confidence |
|---|---|---|
| 125438 | negative | 98.994 |
| 125439 | negative | 96.4 |
colony morphology
- @ref: 61226
- incubation period: 2 days
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 15753 | EDTA-MEDIUM (DSMZ Medium 463a) | yes | https://mediadive.dsmz.de/medium/463a | Name: EDTA-MEDIUM (DSMZ Medium 463a) Composition: MgSO4 x 7 H2O 1.0 g/l EDTA 0.5 g/l Na2HPO4 x 2 H2O 0.41 g/l CaCl2 x 2 H2O 0.4 g/l KH2PO4 0.26 g/l FeCl2 x 4 H2O 0.0015 g/l CoCl2 x 6 H2O 0.00012 g/l MnCl2 x 4 H2O 0.0001 g/l ZnCl2 6.8e-05 g/l H3BO3 6.2e-05 g/l Thiamine-HCl x 2 H2O 5e-05 g/l p-Aminobenzoic acid 5e-05 g/l alpha-lipoic acid 5e-05 g/l Vitamin B12 5e-05 g/l Pantothenic acid 5e-05 g/l Riboflavin 5e-05 g/l Nicotine amide 2.5e-05 g/l Nicotinic acid 2.5e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l Na2MoO4 x 2 H2O 2.4e-05 g/l Folic acid 2e-05 g/l Biotin 2e-05 g/l CuCl2 x 2 H2O 1.7e-05 g/l Pyridoxamine hydrochloride 1e-05 g/l HCl Distilled water |
| 15753 | 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 |
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 15753 | positive | growth | 28 |
| 61226 | positive | growth | 30 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 61226 | aerobe | |
| 125439 | obligate aerobe | 99.8 |
spore formation
- @ref: 125439
- spore formation: no
- confidence: 95
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | sampling date |
|---|---|---|---|---|---|---|
| 15753 | sewage sludge | Tartarstan, Kazan City | Russia | RUS | Europe | |
| 61226 | Sewage sludge | Tatarstan,Kazan City | Russia | RUS | Europe | 2005 |
isolation source categories
- Cat1: #Engineered
- Cat2: #Waste
- Cat3: #Sewage sludge
taxonmaps
- @ref: 69479
- File name: preview.99_3305.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17;96_26;97_27;98_30;99_3305&stattab=map
- Last taxonomy: Stenotrophomonas
- 16S sequence: EU573216
- Sequence Identity:
- Total samples: 2553
- soil counts: 455
- aquatic counts: 340
- animal counts: 566
- plant counts: 1192
Safety information
risk assessment
- @ref: 15753
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 15753
- description: Stenotrophomonas chelatiphaga strain LPM-5 16S ribosomal RNA gene, partial sequence
- accession: EU573216
- length: 1454
- database: nuccore
- NCBI tax ID: 517011
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Stenotrophomonas chelatiphaga DSM 21508 | GCA_001431535 | contig | ncbi | 517011 |
| 66792 | Stenotrophomonas chelatiphaga strain DSM 21508 | 517011.3 | wgs | patric | 517011 |
| 66792 | Stenotrophomonas chelatiphaga DSM 21508 | 2713896757 | draft | img | 517011 |
GC content
- @ref: 15753
- GC-content: 68.3
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 98.994 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 97.818 | yes |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 88.949 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 86.321 | yes |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 97.672 | no |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 63.422 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 95 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 76.5 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 96.4 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 99.8 |
External links
@ref: 15753
culture collection no.: DSM 21508, CCUG 57178, VKM B-2486
straininfo link
- @ref: 86563
- straininfo: 400160
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 19216044 | Stenotrophomonas chelatiphaga sp. nov., a new aerobic EDTA-degrading bacterium. | Kaparullina E, Doronina N, Chistyakova T, Trotsenko Y | Syst Appl Microbiol | 10.1016/j.syapm.2008.12.003 | 2009 | Aerobiosis, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Edetic Acid/*metabolism, Fatty Acids/analysis, Genes, rRNA, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/microbiology, Species Specificity, Stenotrophomonas/*classification/genetics/isolation & purification/physiology | Transcriptome |
| Phylogeny | 26653171 | Stenotrophomonas tumulicola sp. nov., a major contaminant of the stone chamber interior in the Takamatsuzuka Tumulus. | Handa Y, Tazato N, Nagatsuka Y, Koide T, Kigawa R, Sano C, Sugiyama J | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000843 | 2015 | ||
| Phylogeny | 28820086 | Stenotrophomonas 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 ML | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002016 | 2017 | Bacterial 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 | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 15753 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21508) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21508 | |||
| 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 | |||
| 61226 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 57178) | https://www.ccug.se/strain?id=57178 | |||
| 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) | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 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 | |||
| 86563 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID400160.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | 10.1101/2024.08.12.607695 | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | |||
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | https://github.com/GenomeNet/deepG | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 |