Strains of the Burkholderia cepacia complex (Bcc) are able to colonize many different environments; they can have a free living lifestyle, but they may also colonize multicellular eukaryotes intracellularly and, although they are considered highly beneficial in the environment, they can also cause lifethreatening infections in immuno-compromised and Cystic Fibrosis (CF) patients. This heterogeneous lifestyle and the consequent high metabolic versatility is accompanied by unusually large genomes (7,5-8,5 Mb, with a GC content of approximately 67% and divided in multiple replicons), suggesting that particular genome structures and genetic content may support and explain in evolutionary terms such high metabolic diversity. Then, the purpose of this work was to provide a model framework of relationships between genomes and phenotypic diversity in the 18 Bcc type strains, through a multi-level, systems biology approach. The genome sequences of these 18 strains were obtained and their assembly revealed that sizes vary between 6,23 and 9,72 Mb. In addition a Pulse Field Gel Electrophoresis analysis was performed, confirming the presence of multiple replicons in each strain. Further analysis on the sequences obtained allowed the identification of peculiar patterns as concerning, on one hand, genes involved in pathogenesis, virulence and antibiotics resistance and on the other hand genes involved in plants growth promotion, nitrogen fixation and degradation of toxic agents. Large scale phenotypic characterization was also performed on these strains, adopting the Phenotype MicroArray (PM) technique. The ability of these strains to grow using different sources of carbon, nitrogen, sulfur and phosphorus and also to grow in the presence of different pH, osmolytes and toxic compounds was tested. In addition the M.I.C. of different classes of antibiotics were determined. All those data were then used to perform an analysis of relationships between genome data and phenome results with the software suite DuctApe, to provide a first model of genome-metabolic description and differentiation of Bcc strains.
From Genome to phenome and back: understanding the high metabolic versatility of Burkholderia cepacia complex / E. Perrin; M. Fondi; I. Maida; V. Orlandini; E. Bosi; A. Mengoni; M. Galardini; P. Vandamme; F. Decorosi; C. Viti; L. Giovannetti; S. Buroni; G. Riccardi; R. Alduina; G. Gallo; A.M. Puglia; A. Fiore; G. Giuliano; R. Fani. - STAMPA. - (2014), pp. 24-24. (Intervento presentato al convegno Internationa Burkholderia cepacia working group,18th Annual meeting tenutosi a Nimes, France).
From Genome to phenome and back: understanding the high metabolic versatility of Burkholderia cepacia complex
PERRIN, ELENA;FONDI, MARCO;MAIDA, ISABEL;BOSI, EMANUELE;MENGONI, ALESSIO;DECOROSI, FRANCESCA;VITI, CARLO;GIOVANNETTI, LUCIANA;FANI, RENATO
2014
Abstract
Strains of the Burkholderia cepacia complex (Bcc) are able to colonize many different environments; they can have a free living lifestyle, but they may also colonize multicellular eukaryotes intracellularly and, although they are considered highly beneficial in the environment, they can also cause lifethreatening infections in immuno-compromised and Cystic Fibrosis (CF) patients. This heterogeneous lifestyle and the consequent high metabolic versatility is accompanied by unusually large genomes (7,5-8,5 Mb, with a GC content of approximately 67% and divided in multiple replicons), suggesting that particular genome structures and genetic content may support and explain in evolutionary terms such high metabolic diversity. Then, the purpose of this work was to provide a model framework of relationships between genomes and phenotypic diversity in the 18 Bcc type strains, through a multi-level, systems biology approach. The genome sequences of these 18 strains were obtained and their assembly revealed that sizes vary between 6,23 and 9,72 Mb. In addition a Pulse Field Gel Electrophoresis analysis was performed, confirming the presence of multiple replicons in each strain. Further analysis on the sequences obtained allowed the identification of peculiar patterns as concerning, on one hand, genes involved in pathogenesis, virulence and antibiotics resistance and on the other hand genes involved in plants growth promotion, nitrogen fixation and degradation of toxic agents. Large scale phenotypic characterization was also performed on these strains, adopting the Phenotype MicroArray (PM) technique. The ability of these strains to grow using different sources of carbon, nitrogen, sulfur and phosphorus and also to grow in the presence of different pH, osmolytes and toxic compounds was tested. In addition the M.I.C. of different classes of antibiotics were determined. All those data were then used to perform an analysis of relationships between genome data and phenome results with the software suite DuctApe, to provide a first model of genome-metabolic description and differentiation of Bcc strains.
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