Effects of Carbon Metabolism on the growth of bacteria and antibiotic efficacy

With the rise of antibiotic resistance, there is ongoing need to find new antibiotics. As bacteria develop resistance to the current classes of antibiotics available, it is imperative to discover new ways to target bacteria. In this thesis, I focused on one of the basic components that all bacteria need to survive: a source of carbon. Here, I explore whether we can exploit this aspect for drug discovery. For bacteria to colonize a host and cause an infection, it must first be able to meet its nutritional needs for growth. Different host infection sites will have different carbon sources available. Some sites, like the gut, will have commensal bacteria which will compete with invading pathogens for carbon sources. While we still lack understanding of the specific growth environment bacteria experience during infection, it is important to understand how bacteria grow when given different nutrients. For the first part of my work, I systematically probed the gene essentiality patterns of E. coli grown in different carbon sources. I generated a large dataset of growth phenotypes that I compiled into a user-friendly web-application, Carbon Phenotype Explorer (CarPE). I identified many poorly annotated genes, and further characterized the gene ydhC as an adenosine transporter. After characterizing how the growth of E. coli and the genes essential for survival change depending on each carbon source, I looked at whether antibiotic efficacy changed depending on the carbon source used. I found that growth in oxaloacetate alters the proton motive force and potentiates macrolide antibiotics. I also found that linezolid, a compound that does not work on gram-negative bacteria due to efflux, is more effective when adenosine is the carbon source. Together, this work forms a foundation for future research into studying how carbon sources can be exploited in the field of antibiotic discovery. Thesis Candidate in Philosophy There is an urgent need for new antibiotics. Previous antibiotic discovery has primarily been conducted on bacteria growing in nutrient rich laboratory conditions. This led to antibiotics that targeted the same few bacterial processes. However, since bacteria need to survive in a host to cause an infection, there are targets that may be viable during an infection that we miss by using standard laboratory media. Bacteria need a source of carbon to survive, and each infection site contains different chemicals that bacteria can use as a source of carbon. My work studies how bacteria grow in the presence of different carbon sources. First, I systematically tested which bacterial genes are required for E. coli to grow in 30 different carbon sources. I then examined the effectiveness of antibiotics on bacteria grown using these different carbon sources. Together, this work helps us understand how changing carbon sources in the growth media we use to cultivate bacteria can change which genes are required and how it may change how bacteria survive antibiotic stress. When we discover the specific compositions of host infection environments, we can leverage this knowledge to find antibiotics that target these carbon acquisition pathways in bacteria.