Research

Our lab studies Patescibacteria (also known as the Candidate Phyla Radiation, CPR), a large group of bacteria that is widespread in nature and prevalent in human oral microbiomes, where its members have been linked to both oral health and disease. These ultrasmall bacteria have streamlined genomes and limited metabolic capability (generally lacking biosynthetic pathways for nucleotides, amino acids, and fatty acids) and live as obligate epibionts on host bacteria. Their unique biology and phylogenetic distance from well-studied model bacteria make Patescibacteria a reservoir of unexplored biological mechanisms with bioengineering and pharmaceutical potential.

We combine genetic, biochemical, structural, and bioinformatic approaches to study these enigmatic bacteria and their interactions with hosts. Current projects include: 1) characterizing the molecular mechanisms governing Patescibacteria–host attachment and host-binding specificity; 2) investigating how host bacteria defend themselves against Patescibacteria; and 3) discovering novel enzymes, pathways, and molecular machines in Patescibacteria using modern high-throughput techniques.

Beyond Patescibacteria, we are broadly interested in exploring mechanisms underlying intermicrobial interactions, especially those that are medically relevant or associated with human microbiomes. Our goal is to understand how these interactions shape microbiomes and impact human health, and to address pressing medical and environmental challenges by harnessing the diverse biological conflict systems that microbes have evolved over billions of years.

Selected Publications

Wang Y, Colautti J, Gallagher LA, Lee J, Tan Y, Farrell S, Farrell C, Bor B, Whitney JC, Zhang D, Peterson SB, Mougous JD. Oral Actinobacteria sense and defend against parasitic epibionts. bioRxiv (2026). doi

Humphreys IR*, Zhang J*, Baek M*, Wang Y*, Krishnakumar A, Pei J, Anishchenko I, Tower CA, Jackson BA, Warrier T, Hung DT, Peterson SB, Mougous JD, Cong Q, Baker D. Protein interactions in human pathogens revealed through deep learning. Nature Microbiology (2024). doi (*equal contribution)

Wang Y*, Gallagher LA*, Andrade PA, Liu A, Humphreys IR, Turkarslan S, Cutler KJ, Arrieta-Ortiz ML, Li Y, Radey MC, McLean JS, Cong Q, Baker D, Baliga NS, Peterson SB, Mougous JD. Genetic manipulation of Patescibacteria provides mechanistic insights into microbial dark matter and the epibiotic lifestyle. Cell (2023). doi (*equal contribution)

Wang Y, Ledvina HE, Tower CA, Kambarev S, Liu E, Charity JC, Kreuk LSM, Tang Q, Chen Q, Gallagher LA, Radey MC, Rerolle GF, Li Y, Penewit KM, Turkarslan S, Skerrett SJ, Salipante SJ, Baliga NS, Woodward JJ, Dove SL, Peterson SB, Celli J, Mougous JD. Discovery of a glutathione utilization pathway in Francisella that shows functional divergence between environmental and pathogenic species. Cell Host & Microbe (2023). doi

Wang Y, Yuan P, Grabon A, Tripathi A, Lee D, Rodriguez M, Lönnfors M, Eisenberg-Bord M, Wang Z, Lam SM, Schuldiner M, Bankaitis VA. Noncanonical regulation of phosphatidylserine metabolism by a Sec14-like protein and a lipid kinase. Journal of Cell Biology (2020). doi

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