Commensal E. Coli  vs. Pathogenic E. Coli

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Using antiSMASH to Compare Antimicrobial Genes of Commensal E. coli (Normal Flora) to Pathogenic E. coli

Antibiotic resistance has plagued mankind for decades. Thus, the world is in much need of new antibiotics. Fortunately, bacteria themselves produce secondary metabolites (often antibiotics) to combat other bacteria. The question is which bacteria (commensal or pathogenic) is more likely to produce effective/new antibiotics. As part of a two-phase study, this phase of the study used a genetic approach to determine if there is a difference between commensal (good) and pathogenic (harmful) E. coli in terms of the secondary metabolites they produce. Using antiSMASH, a genome mining tool, it was established that commensal E. coli K-12 and pathogenic E. coli O157:H7 strains are different in the number and types of biosynthetic genes identified.  Furthermore, pathogenic E. coli O157:H7 strains yield more numbers and types of biosynthetic genes than commensal E. coli K-12. One of the secondary metabolites bacteriocin shows antimicrobial properties and may serve to combat bacterial infections. Finally, another secondary metabolite NRPS that emerged in the study was reported to be similar to turnerbactin which shows agronomic benefits. This study also validates the assertion that genetic approaches through the use of databases such as NCBI and software such as antiSMASH  are valid and useful in isolating bacterial strains that can then be cultured with the specific goal of isolating the secondary metabolites (antibiotics) they can produce. Thus, in the second phase study pathogenic (as opposed to commensal) E. coli will be co-cultured with soil bacteria to screen soil bacteria for antibiotic production.