Identifying the antibiotics and antibiotic resistance genes that shape a microbiome

Scientific background

Microbiomes offer great benefits to their hosts, including nutrient acquisition, growth promotion, immunity, and defence against disease but they are complex and difficult to study. As a result, insects have emerged as simple, experimentally tractable models with which to study microbiomes.

Our model is the leafcutter ant Acromyrmex echinatior, which has a simple cuticular microbiome dominated by antibiotic-producing bacteria that protect the ants against disease. The question in this project is how do the ants recruit antibiotic-producing (useful) bacteria while keeping out all other (cheater) bacteria?

Hypothesis: We know the ants pass a single strain of antibiotic-producing Pseudonocardia bacteria from generation to generation. Preliminary data suggest these are bacteriocin-type antibiotics. We have shown in vitro that this vertically transmitted strain could result in selective acquisition of antibiotic-producing Streptomyces bacteria, resulting in a defensive microbiome producing multiple types of antibiotics that is robust to the evolution of resistance by pathogens.

Antibiotic-producing bacteria are necessarily themselves antibiotic resistant and are pre-adapted to the Pseudonocardia-toxin-infused ant cuticle, allowing them to consume nutrients provided by the ants to their cuticular microbiome. Research methodology

The student will test the prediction that only antibiotic-producing bacteria that are resistant to Pseudonocardia antibiotics can colonise the ant cuticle, and this is why the ants are able to selectively recruit a microbiome dominated by Pseudonocardia and Streptomyces bacteria. This will involve: 1. Identifying the antibiotics made by the Pseudonocardia bacteria.

2. Testing them for activity against a range of different bacteria. 3. Determining their mode(s) of action. 4. Identifying the antibiotic resistance genes (ARGs) that make Streptomyces bacteria resistant.