title: Stenotrophomonas comparative genomics reveals genes and functions that differentiate beneficial and pathogenic bacteria.
abstract: BACKGROUND
  In recent years, the number of human infections caused by opportunistic pathogens has increased dramatically. Plant rhizospheres are one of the most typical natural reservoirs for these pathogens but they also represent a great source for beneficial microbes with potential for biotechnological applications. However, understanding the natural variation and possible differences between pathogens and beneficials is the main challenge in furthering these possibilities. The genus Stenotrophomonas contains representatives found to be associated with human and plant host.
  
  
  RESULTS
  We used comparative genomics as well as transcriptomic and physiological approaches to detect significant borders between the Stenotrophomonas strains: the multi-drug resistant pathogenic S. maltophilia and the plant-associated strains S. maltophilia R551-3 and S. rhizophila DSM14405T (both are biocontrol agents). We found an overall high degree of sequence similarity between the genomes of all three strains. Despite the notable similarity in potential factors responsible for host invasion and antibiotic resistance, other factors including several crucial virulence factors and heat shock proteins were absent in the plant-associated DSM14405T. Instead, S. rhizophila DSM14405T possessed unique genes for the synthesis and transport of the plant-protective spermidine, plant cell-wall degrading enzymes, and high salinity tolerance. Moreover, the presence or absence of bacterial growth at 37°C was identified as a very simple method in differentiating between pathogenic and non-pathogenic isolates. DSM14405T is not able to grow at this human-relevant temperature, most likely in great part due to the absence of heat shock genes and perhaps also because of the up-regulation at increased temperatures of several genes involved in a suicide mechanism.
  
  
  CONCLUSIONS
  While this study is important for understanding the mechanisms behind the emerging pattern of infectious diseases, it is, to our knowledge, the first of its kind to assess the risk of beneficial strains for biotechnological applications. We identified certain traits typical of pathogens such as growth at the human body temperature together with the production of heat shock proteins as opposed to a temperature-regulated suicide system that is harnessed by beneficials.
authors.affiliation: Graz University of Technology; Environmental Biotechnology, Petersgasse 12, 8010 Graz, Austria. alavi@tugraz.at.
authors.forename: Peyman
authors.initials: P
authors.lastname: Alavi
authors.forename: Margaret R
authors.initials: MR
authors.lastname: Starcher
authors.forename: Gerhard G
authors.initials: GG
authors.lastname: Thallinger
authors.forename: Christin
authors.initials: C
authors.lastname: Zachow
authors.forename: Henry
authors.initials: H
authors.lastname: Müller
authors.forename: Gabriele
authors.initials: G
authors.lastname: Berg
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics; D058947:Bacterial Secretion Systems / Q000235:genetics; D002688:Chitinases / Q000235:genetics; D010861:Fimbriae, Bacterial / Q000235:genetics; D059647:Gene-Environment Interaction; D005798:Genes, Bacterial; D018869:Heat-Shock Response; D054884:Host-Pathogen Interactions; D006801:Humans; D010944:Plants / Q000382:microbiology; D011135:Polysaccharides, Bacterial / Q000235:genetics; D053038:Quorum Sensing / Q000235:genetics; D058441:Rhizosphere; D013045:Species Specificity; D020588:Stenotrophomonas / Q000201:enzymology / Q000235:genetics* / Q000472:pathogenicity
chemical_list: D001426:Bacterial Proteins; D058947:Bacterial Secretion Systems; D011135:Polysaccharides, Bacterial; D002688:Chitinases