Our long term goal for the Microbiome Rules project  is to combine knowledge from humans and animal model systems to define what are the rules of microbiome and symbiosis variation within and between host species. We seek to answer three main questions: (1) What human features (genes, diet, sociality, etc) robustly impact the microbiome, metabolome, virome, mycobiome, and disease risk phenome? (2) What animal genes affect colonization, replication, and maternal transmission of microbes such as the inherited Wolbachia endosymbiont in arthropods? (3) What is the degree of phylogenetic signal on animal-associated microbiomes (aka, phylosymbiosis); simply put, do phylogenetically-related species have more similar microbiomes? If the answer is yes, then is phylosymbiosis consequential to host biology?

Human Microbiome Variation

• Van Syoc, E.P., E.R. Davenport, and S.R. Bordenstein (2025) Gut fungi are associated with human genetic variation and disease risk. PLOS Biology 23(9): e3003339.
  • Penn State News 09.03.25. Connections among gut fungi, genetics, and disease risk in humans identified
• Mallott, E.K., A.R. Sitarik, L.D. Leve, C. Cioffi, C.A. Camargo, K. Hasegawa, S.R. Bordenstein (2023) Human microbiome variation associated with race and ethnicity emerges as early as three months of age. PLOS Bioloygy 21(8): e3002230
• Markowitz, R.H.G., A.L. LaBella, M. Shi, A. Rokas, J.A. Capra, J.F. Ferguson, J.D. Mosley, and S.R. Bordenstein (2022) Microbiome-associated human genetic variants impact phenome-wide disease risk. Proceedings of the National Academy of Sciences 119(26):e2200551119.
• Li, J., R.H.G. Markowitz, A.W. Brooks, E.K. Mallott, B.A. Leigh, T. Olszewski, H. Zare, M. Bagheri, H.M. Smith, K.A. Friese, I. Habibi, W.M. Lawrence, C.L. Rost, A. Ledeczi, A.M. Eeds, J.F. Ferguson, H.J. Silver, and S.R. Bordenstein (2022) Individuality and ethnicity eclipse a short-term dietary intervention in shaping microbiomes and viruses. PLOS Biology 20(8): e3001758.
• Brooks, A.W., S. Priya, R. Blekhman, and S.R. Bordenstein (2018) Gut microbiota diversity across ethnicities in the United States. PLOS Biology 16(12): e2006842. https://doi.org/10.1371/journal.pbio.2006842

Phylosymbiosis

• Van Syoc, E.P., A. Gomez, E.R. Davenport, and S.R. Bordenstein (2025) Gut fungal profiles reveal phylosymbiosis and codiversification across humans and nonhuman primates. PLoS Biology 23(9): e3003390
• Leigh, B.A., S.R. Bordenstein, A.W. Brooks, A. Mikaelyan, and S.R. Bordenstein (2018) Finer-scale phylosymbiosis: Insights from insect viromes. mSystems 3(6) e00131-18; DOI: 10.1128/mSystems.00131-18
• Brooks AW, Kohl KD, Brucker RM, Van Opstal EJ, and Bordenstein SR (2016) Phylosymbiosis: Relationships and functional effects of microbial communities across host evolutionary history. PLOS Biology

Insect Suppression of Endosymbionts

• Funkhouser, L.J., E.J. van Opstal, A. Sharma, and S.R. Bordenstein (2018) The maternal effect gene Wds controls Wolbachia titer in Nasonia. Current Biology 28(11):1692-1702 .