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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  DSM14405 T  (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 DSM14405 T . Instead,  S. rhizophila  DSM14405 T  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. DSM14405 T  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.    Electronic supplementary material  The online version of this article (doi:10.1186/1471-2164-15-482) contains supplementary material, which is available to authorized users.

Stenotrophomonas comparative genomics reveals genes and functions that differentiate beneficial and pathogenic bacteria