Bee gut as a model microbiome
Social bees, such as honey bees and bumble bees, fulfill crucial roles in both natural ecosystems and human agriculture. We have discovered that they house a unique gut microbial community that has coexisted with bees for millions of years. These microbes confer many benefits including helping in the digestion of pollen and protecting against pathogens. Hence, the bee gut offers an excellent model system for the study of microbial community assembly, host-microbe and microbe-microbe interactions, and the evolution and ecology of microbiome mutualisms. We are currently working to unravel how this unique gut community persists, from its molecular underpinnings through to the ecological forces at play across populations. Understanding these factors will help us preserve these precious pollinators, and also reveal general principles that can be applied to the gut microbiomes of other animals.
Marine microbial symbioses
Life began in the oceans, and marine environments continue to harbor some of the most unexplored and diverse organisms. We are investigating the microbiota associated with coral reefs and other colonial animals, such as anemones, in both tropical and temperate waters. Using environmental sampling, single-cell approaches, and high-throughput sequencing, we are examining the composition and functional capabilities of these microbial communities. These include communities of micro-eukaryotes (protists), which are often understudied and under-appreciated components of ecosystems, but which inhabit critical niches as primary producers and parasites. Uncovering how these microbes interact with each other and with their hosts is key to filling in the picture of ocean biodiversity and nutrient cycling, which can ultimately help in guiding the conservation of our blue planet.
High-throughput DNA sequencing has revolutionized microbiology by opening up the vast, invisible world of uncultured microorganisms. However, even as we begin to better survey and grasp the identities of these new taxa, it is becoming obvious that we know very little about how they live and function; most microbial lineages remain scantly characterized, and their genomes are filled with enigmatic genes. The next frontier of microbiological research is to go beyond mere cataloging of "who is there", and towards "how do they function?". New advancements in '-omics' technologies and in ways of manipulating and engineering non-model taxa is now making this easier (or at least, more feasible!) than ever before. Along the way, we will uncover unique molecular mechanisms and functional novelties that will expand our perception of microbial capabilities.
Examples of past projects include functional characterization of genes involved in gut colonization (Powell et al. 2016), carbohydrate metabolism (Zheng et al. 2016), the TCA cycle (Kwong et al. 2017c), antimicrobial toxins (Steele et al. 2017), and protein trafficking (Bean et al. 2018).
Microbial diversity and its classification
Microbes are the oldest and most diverse organisms on the planet. Bacteria possess unparalleled biochemical innovations and molecular machines, while protist cells can have organelles, morphologies, behaviors completely foreign to a typical animal cell. We often encounter new microbial species in our work, and therefore devote a part of our time to describing and taxonomically classifying these unnamed organisms. To do this, we employ ecological survey data, comparative genomics, microscopy, and phylogenetics to give novel species/lineages their rightful place in the great Tree of Life.