Microbiomes colonize diverse hosts and environments, shape host health and environmental biochemistry, and are promising engineering targets for novel therapeutics. Our lab is making microbiome engineering quantitative by combining mathematical models and high throughput experiments. We are also broadly interested in the physics of living systems and synthetic biology.
Using microbiology experiments, metabolomics, metagenomics, and mathematical modeling, we build theoretical and experimental tools to dissect complex communities with focus on the human gut microbiota:
1. Metabolomic profiles of individual gut bacterial species allowed us to predict community dynamics in vitro (Ho et al, Nat Microbiol 2024). We are applying this approach to investigate microbial interactions in complex environments and during evolution.
2. Antibiotic activity can affect the resource competition landscape and vice versa, and this interplay can result in synergism or antagonism among multiple antibiotics (Newton, Ho# et al, Nat Commun 2023). We are testing these predictions using high-throughput screens and leveraging them to engineer community dynamics.
3. A highly diverse yet defined model community reproducibly colonizes mice gut, and mice colonized by either the model community or human fecal communities are phenotypically similar (Cheng*, Ho* et al, Cell 2022). We are quantifying microbial interactions in this model system.
4. Diverse microbiotas exhibit special statistics of fluctuations in species abundances, and these fluctuations can be reproduced by a mathematical model of resource competition (Ho et al, eLife 2022). We are using this link to infer the ecological parameters of various microbiotas.
