The Williams lab at Providence College has two research tracks: predatory bacteria and the microbiome. Read on to learn about our projects within these two tracks.
Predatory bacteria evolved to hunt, attack, and digest other bacteria. They are found in a wide range of environments, including soil, freshwater lakes and streams, oceans and estuaries, and even animal guts. We aren’t yet sure about the ecological roles of predatory bacteria in these environments, but initial studies indicate that they may shape microbial communities. In addition, studies using animal models have shown that predatory bacteria can reduce pathogen loads without toxicity to the animal host, suggesting that we may be able to use these tiny predators in clinical therapies to combat drug-resistant bacterial infections.
Below is a video of predatory bacteria (specifically, Bdellovibrio bacteriovorus) dividing within an E. coli prey cell after invasion. (Video credit: Liz Sockett, University of Nottingham, and the Biotechnology and Biological Sciences Research Council)
Our lab is using a combination of computational and wet lab techniques to reconstruct how the predatory lifestyle evolved in bacteria and to define molecular mechanisms governing variation in predation. We have isolated and sequenced predatory bacteria from different environments throughout Rhode Island and the surrounding area. We are using comparative genomics to examine the evolution of different gene families in these predatory bacteria, and we are assaying predatory phenotypes such as prey range and predation efficiency to determine variation in the outcomes of interactions between predatory bacteria and prey.
In September 2019, a manuscript was accepted at Microbiology featuring research by Nicole Cullen ’17, Justina Mellone ’17, Karla Martinez ’19, and Molly Oser ’19 on Bdellovibrio isolated from a bioswale on the Providence College campus. Phenotype assays showed that this isolate of Bdellovibrio kills fewer tested prey strains than B. bacteriovorus type strain HD100, and it is less efficient at killing E. coli ML35. Comparative genomics identified differences in gene content between Bdellovibrio from the bioswale and the type strain HD100 that may be linked to variation in predatory phenotypes. In particular, Bdellovibrio isolated from the bioswale is missing some genes that are classified as important for predation in the type strain. We are following up on these observations. The preprint of this article is available on bioRxiv. https://www.biorxiv.org/content/10.1101/551937v4
In January 2018, we published a paper in mSphere featuring research by Brett Enos ’16 and Molly Anthony ’18 on saltwater-adapted predatory bacteria that Brett isolated from Mount Hope Bay, RI. Using comparative genomics, we identified two regions in the genome where genes were likely acquired from other bacteria by horizontal gene transfer. We also showed that this isolate of predatory bacteria was able to attack and kill a range of different Gram-negative bacteria, including soil bacteria and E. coli. https://msphere.asm.org/content/3/1/e00508-17
In recent years, our view of the microbial world has shifted from an antagonistic relationship aimed at eradicating “germs” to an ecological perspective that considers the web of interactions among microbes and other organisms, including us. We know that microbes are essential for the health and development of humans, other animals and plants. The microbial communities occupying a particular habitat, whether it is our bodies, plant root systems, or man-made structures, are referred to as the “microbiome” of that site. Advances in sequencing technology and bioinformatics methods have enabled us to explore these microbiomes in more detail than ever before. In the Williams lab, we use microbiome data analysis to profile bacterial communities of different sites. We are currently collaborating with colleagues at the University of California-Davis to investigate the gut microbiome of titi monkeys, a non-human primate.
In 2018, we completed a project assessing changes in the bacterial communities of a microflush toilet system developed by Steve Mecca and his lab in Engineering-Physics-Systems at Providence College. Claire Kleinschmidt ’18 worked on this project from sample processing to data analysis. In a paper published in PeerJ, we used 16S rRNA amplicon data to confirm the capacity of the toilet system to contain and eliminate fecal-associated bacteria, thereby improving sanitation and public health. https://peerj.com/articles/6077/