Preserving the microbiome : quantifying collateral damage during antibiotic use

As living beings, we are as much defined by our own cellular composition as we are by by the diverse microbial ecosystem that exists within us all. Human-microbe interactions primarily benefit the human host, as our symbionts facilitate crucial host functions. Against this backdrop, the continued overuse of broad-spectrum antibiotics threatens the stability of the human microbiome and has caused a significant rise in the prevalence of antibiotic-resistant strains. Bacteriocins, highly specific killing proteins that —with few exceptions—target bacteria related to the producer provide a targeted alternative to broad-spectrum antibiotics in the fight against infection. Currently, no standard method has been developed to compare the effects on target and commensal bacteria of conventional antibiotics to those resulting from the use of alternative antibiotics. The long-term objective of this project is to develop a relatively quick, reliable, and repeatable quantitative test for collateral damage to the microbiome during narrow- and broad-spectrum antibiotic use. Here I outline my findings concerning the initial development of such an assay. I observed the growth of BZB Escherichia coli and Hafnia alvei in the presence of Ampicillin (AMP) and colicins E2 and E4 over time using OD670nm absorbance measurements and LIVE/DEAD viability assessments. Both types of measurement were effective at quantitatively capturing the dynamics of cell growth, but the LIVE/DEAD method requires additional optimization. A titration conducted on AMP and Col E4 indicates differential dose-dependent behaviors for these two compounds. Results also indicate that colicin activity is indeed limited to strains related to the producer (BZB), whereas AMP was effective against the target BZB and H. alvei, our model for a non-target commensal. This study has many implications for the design of targeted therapies that do not cause collateral damage, and further work will improve our understanding of human health as it relates to our microbial symbionts