Strain identifier
BacDive ID: 17481
Type strain:
Species: Lysobacter gummosus
Strain history: <- ATCC <- P. Christensen, UASM 402 <- F.D. Cook
NCBI tax ID(s): 262324 (species)
General
@ref: 2935
BacDive-ID: 17481
DSM-Number: 6980
keywords: 16S sequence, Bacteria, aerobe, mesophilic, polysaccharide production
description: Lysobacter gummosus DSM 6980 is an aerobe, mesophilic bacterium that produces polysaccharides and was isolated from soil.
NCBI tax id
- NCBI tax id: 262324
- Matching level: species
strain history
- @ref: 2935
- history: <- ATCC <- P. Christensen, UASM 402 <- F.D. Cook
doi: 10.13145/bacdive17481.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Lysobacterales
- family: Lysobacteraceae
- genus: Lysobacter
- species: Lysobacter gummosus
- full scientific name: Lysobacter gummosus Christensen and Cook 1978 (Approved Lists 1980)
@ref: 2935
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Xanthomonadales
family: Lysobacteraceae
genus: Lysobacter
species: Lysobacter gummosus
full scientific name: Lysobacter gummosus Christensen and Cook 1978
type strain: yes
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
2935 | CY-AGAR (DSMZ Medium 67) | yes | https://mediadive.dsmz.de/medium/67 | Name: CY-AGAR (DSMZ Medium 67) Composition: Agar 15.0 g/l Casitone 3.0 g/l CaCl2 x 2 H2O 1.36 g/l Yeast extract 1.0 g/l Distilled water |
2935 | REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) | yes | https://mediadive.dsmz.de/medium/1a | Name: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water |
2935 | R2A MEDIUM (DSMZ Medium 830) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium830.pdf |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
2935 | positive | growth | 28 | mesophilic |
2935 | positive | growth | 30 | mesophilic |
60654 | positive | growth | 30 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 60654
- oxygen tolerance: aerobe
compound production
- @ref: 2935
- compound: polysaccharides
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
43356 | 2509 | agar | - | degradation |
43356 | 58187 | alginate | - | degradation |
43356 | 28938 | ammonium | + | nitrogen source |
43356 | 22653 | asparagine | + | nitrogen source |
43356 | 85146 | carboxymethylcellulose | + | degradation |
43356 | 62968 | cellulose | - | degradation |
43356 | 17029 | chitin | + | degradation |
43356 | 16947 | citrate | + | assimilation |
43356 | 5291 | gelatin | + | degradation |
43356 | 17234 | glucose | - | fermentation |
43356 | 68837 | pectate | + | degradation |
43356 | 28017 | starch | - | degradation |
43356 | 53424 | tween 20 | + | degradation |
43356 | 53426 | tween 80 | + | degradation |
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 |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
43356 | 15688 | acetoin | no |
43356 | 35581 | indole | no |
68369 | 35581 | indole | no |
metabolite tests
@ref | Chebi-ID | metabolite | methylred-test | voges-proskauer-test | indole test |
---|---|---|---|---|---|
43356 | 17234 | glucose | - | ||
43356 | 15688 | acetoin | - | ||
68369 | 35581 | indole | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
43356 | catalase | + | 1.11.1.6 |
43356 | cytochrome oxidase | + | 1.9.3.1 |
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 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
2935 | - | - | - | - | - | + | + | + | - | - | + | - | + | - | - | - | - | + | - | - | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
2935 | soil | Ottawa, Ontario | Canada | CAN | North America |
60654 | Soil | Ontario,Ottawa | Canada | CAN | North America |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
taxonmaps
- @ref: 69479
- File name: preview.99_2461.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17;96_647;97_1577;98_1919;99_2461&stattab=map
- Last taxonomy: Lysobacter
- 16S sequence: AB161361
- Sequence Identity:
- Total samples: 16578
- soil counts: 9924
- aquatic counts: 1340
- animal counts: 1424
- plant counts: 3890
Safety information
risk assessment
- @ref: 2935
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Lysobacter gummosus gene for 16S rRNA, partial sequence | AB166894 | 1482 | ena | 262324 |
2935 | Lysobacter gummosus gene for 16S rRNA, partial sequence | AB161361 | 1482 | ena | 262324 |
GC content
- @ref: 2935
- GC-content: 65.7
External links
@ref: 2935
culture collection no.: DSM 6980, ATCC 29489, NCIB 11896, CCUG 55586, LMG 8763, UASM 402
straininfo link
- @ref: 86478
- straininfo: 3552
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 16403891 | Lysobacter koreensis sp. nov., isolated from a ginseng field. | Lee JW, Im WT, Kim MK, Yang DC | Int J Syst Evol Microbiol | 10.1099/ijs.0.63955-0 | 2006 | Benzoquinones, Fatty Acids, Korea, Molecular Sequence Data, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, *Soil Microbiology, Species Specificity, Xanthomonadaceae/chemistry/*classification/isolation & purification/physiology | Genetics |
Phylogeny | 17329782 | Lysobacter niabensis sp. nov. and Lysobacter niastensis sp. nov., isolated from greenhouse soils in Korea. | Weon HY, Kim BY, Kim MK, Yoo SH, Kwon SW, Go SJ, Stackebrandt E | Int J Syst Evol Microbiol | 10.1099/ijs.0.64473-0 | 2007 | DNA, Bacterial, DNA, Ribosomal, Fatty Acids/analysis, Korea, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S, Soil Microbiology, Xanthomonadaceae/chemistry/*classification/genetics/isolation & purification | Genetics |
Phylogeny | 19406775 | Lysobacter panaciterrae sp. nov., isolated from soil of a ginseng field. | Ten LN, Jung HM, Im WT, Yoo SA, Oh HM, Lee ST | Int J Syst Evol Microbiol | 10.1099/ijs.0.002394-0 | 2009 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Korea, Lysobacter/*classification/genetics/isolation & purification/physiology, Molecular Sequence Data, *Panax, Phenotype, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity | Genetics |
Phylogeny | 19684312 | Lysobacter soli sp. nov., isolated from soil of a ginseng field. | Srinivasan S, Kim MK, Sathiyaraj G, Kim HB, Kim YJ, Yang DC | Int J Syst Evol Microbiol | 10.1099/ijs.0.016428-0 | 2009 | Base Composition, Base Sequence, Fatty Acids/analysis, Lysobacter/*classification/genetics/isolation & purification, Molecular Sequence Data, Panax/*microbiology, *Soil Microbiology | Genetics |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
2935 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6980) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-6980 | |||
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 | |
43356 | R.F. Sullivan, M.A. Holtman, G.J. Zylstra, J.F. White Jr, D.Y. Kobayashi | 10.1046/j.1365-2672.2003.01932 | Taxonomic positioning of two biological control agents for plant diseases as Lysobacter enzymogenes based on phylogenetic analysis of 16S rDNA, fatty acid composition and phenotypic characteristics | J. app. Microbiol. 94: 1079-1086 2003 | ||
60654 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 55586) | https://www.ccug.se/strain?id=55586 | |||
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 | |
68369 | Automatically annotated from API 20NE | |||||
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 | |||
86478 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID3552.1 | StrainInfo: A central database for resolving microbial strain identifiers |