Microbial Bioinformatics Group, SKMML, SJTU 
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Horizontal gene transfer events have led to the integration of alien large DNA fragments into the genomic backbones of bacterial species.These genomic islands potentially allow host strains to enhance adaptations in new niches through the acquisition of new virulence factors, antimicrobial resistance, metabolic pathways and/or cell signaling systems, thus play key roles on bacterial evolution. Since June 2006, the Microbial Bioinformatics Group at MML, SJTU has been focused on in-depth mining for bacterial mobile genomes (mobilome), including:
(1) characterization of the mobile genetic elements in Klebsiella pneumoniae and the other opportunistic Gram-negative pathogens of the so-called ESKAPE group that have developed antibiotic resistances;
(2) development of bioinformatics tools and databases for identification of mobile genetic elements, analysis of genomic island mobility and stability;
(3) identification of biosynthetic gene clusters for antibiotics in Streptomyces genome sequences.
  (1) Characterization of novel mobile genetic elements in Klebsiella pneumoniae and the other opportunistic Gram-negative pathogens of the so-called ESKAPE group that have developed antibiotic resistances;
The bacterial species Klebsiella pneumoniae is an increasingly important pathogen of man. It is responsible for nosocomial and community-acquired infections of the urinary tract, upper respiratory tract, blood stream and other anatomical sites, and notably its namesake condition, pneumonia. K. pneumoniae and selected other members of this genus also afflict the animal agriculture and equine industries, and defined K. pneumoniae strains possessing particular properties have been exploited for biotechnological purposes and nitrogen-fixation in plant agriculture. Dramatic increases in the levels of multiple-antibiotic resistance associated with this species, particularly to agents of last-resort such as carbapenems, pose a major emerging global problem. Further accentuating the problem is the fact that Klebsiella serve as reservoirs for the spread of antibiotic resistance genes to many bacterial species, thus amplifying the hazard of antibiotic-recalcitrant infections both within and outside hospitals. We aim to clarify how horizontally-acquired genetic elements comprising the broader K. pneumoniae mobilome promote dissemination of bacterial adaption traits, with an emphasis on antibiotic resistances.
Fig. 1. Complete genome sequence of Klebsiella pneumoniae subsp. pneumoniae HS11286, a Carbapenem-resistant strain belonging to the dominant clone ST11 of Klebsiella pneumoniae in China [ Liu, et al. Journal of Bacteriology, 2012].
Fig. 2. Comparative schematic maps of tmRNA gene-associated islands in seven K. pneumoniae strains and one Salmonella enterica strain [Zhang, et al. Journal of Microbiological Methods, 2011; Chen, et al. Current Microbiol, 2010].
Fig. 3. Translational genomics to develop a Salmonella enterica Serovar Paratyphi A multiplex PCR assay [Ou, et al.Journal of Molecular Diagnostics, 2007 (cover story)].
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(2) Development of bioinformatics tools and databases for identification of mobile genetic elements,  analysis of genomic island mobility and stability. Click here to visit the bioinformatics resources.
Fig. 4. Bioinformatics tools and biological databased available at the Microbial Genomics and Bioinformatics Group, MML, SJTU.
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(3) Identification of mobile genetic elements and antibiotic biosynthetic gene clusters in Streptomyces genome sequences.
Fig. 5. Streptomyces cattleya is unusual for its capacity to biosynthesis of antibiotics and other secondary metabolites. The 1.8-Mb mega-plasmid pSCATT is densely packed with 12 putative secondary metabolite gene clusters, in addition to the chromosome that also harbors 17 such gene clusters [Zhao, et al. Bioorganic Chemistry, 2012]. Remarkably, the epsilon-poly-L-Lysine, used as a pollution-free food preservative, is encoded by the two synthetase genes, pls1 located in chromosome and pls2 in the mega-plasmid.
Fig. 6. The web-based tool ThioFinder for rapid identification of thiopeptide biosynthetic gene cluster from DNA sequence using a profile Hidden Markov Model approach [Li, et al. PloS ONE, 2012].
Fig. 7. The genomic island SLG of Streptomyces lividans is involved into the phosphorothioation of the DNA backbone. And the SLP island of Streptomyces coelicolor encoded the Type IV restriction endonuclease ScoMcrA that cleave phosphothioated DNA and methylated DNA [He, et al. Molecular Microbiology, 2007; Ou, et al., PLoS ONE, 2009; Liu, et al. PLoS Genetics, 2010].
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