Mark R. Charbonneau, PhD

Biotechnology Leader and Science Communicator


About

Mark Charbonneau, PhD, is a scientist and biotech leader whose work centers on understanding and harnessing microbial ecosystems to improve human health. Trained at Washington University in St. Louis in the lab of Jeffrey I. Gordon, he uncovered fundamental links between the infant gut microbiome, growth, and undernutrition and published this work in Science, Cell, and Nature. He went on to translate microbiome science into therapeutic applications at Synlogic, where he developed in vitro and computational models that predicted engineered microbial function in patients and supported multiple clinical programs and industry partnerships.

As Vice President of Research & Development at Sōlaria Biō, Mark leads a cross-functional team developing synbiotic medical foods derived from the edible plant microbiome to address chronic disease and promote healthy aging. Under his leadership, Sōlaria launched its flagship medical food synbiotic for postmenopausal bone loss, secured nine issued U.S. patents, and generated compelling evidence supporting microbial solutions for inflammation, bone health, and longevity.

Articles and Media

Publications

Schott EM, Charbonneau MR, Kiel DP, Bukata S, Zuscik MJ, Rosen C, Ballok AE, Toledo GV, Steels E, Huntress H, Rao A, Ebelt P, Travison TG, Soto-Giron MJ, Wolff I, Easson DD, Engelke K, and Vitetta L. A Randomized, Double-Blind, Placebo-Controlled Clinical Study to Evaluate the Efficacy of the Synbiotic Medical Food, SBD111, for the Clinical Dietary Management of Bone Loss in Menopausal Women. Osteoporos Int. 36, 2019-2030 (2025).

Green RS, Roy T, Morales DDI, Morrow C, Neilson R, Schott EM, Charbonneau MR, Ballok AE, Motyl KJ, and Toledo GV. A synbiotic medical food improves gut barrier function, reduces immune responses, and inhibits osteoclast activity in models of postmenopausal bone loss aligned with clinical outcomes. J. Funct. Foods 135, 107114 (2025).

Miller KJ, Wolff IM, Montes de Oca Valeriano LA, Soto-Giron MJ, Jangi S, Schott EM, Charbonneau MR, Ballok AE, Toledo GV. Targeted detection of microbes in synbiotic medical foods SBD111 and SBD121 to evaluate gut persistence: a randomised, open label trial. Beneficial Microbes 9, 1-13 (2026).

Lubkowicz D, Horvath NG, James MJ, Cantarella P, Renaud L, Bergeron CG, Shmueli RB, Anderson C, Gao JR, Kurtz CB, Perreault M, Charbonneau MR, Isabella VM, & Hava DL. An engineered bacterial therapeutic lowers urinary oxalate in preclinical models and in silico simulations of enteric hyperoxaluria. Mol Syst Biol 18(3), e10539 (2022).

Charbonneau MR, Denney WS, Horvath N, Cantarella P, Castillo MJ, Puurunen MK, and Brennan AM. Modeling the impact of an engineered bacterial therapeutic on plasma phenylalanine in healthy subjects and patients with phenylketonuria. Commun Biol 4, 898. (2021).

Puurunen MK, Vockley J, Searle S, Sacharow S, Phillips J, Denney WS, Goodlett B, Wagner DA, Blankstein L, Castillo MJ, Charbonneau MR, Isabella VM, Sethuraman V, Riese R, Kurtz CB, and Brennan AM. Safety and pharmacodynamics of an engineered E. coli Nissle for the treatment of phenylketonuria: a first-in-human study. Nat Metab. 3(8), 1125-1132 (2021).

Nelson MT*, Charbonneau MR*, Coia HG, Castillo MJ, Holt C, Greenwood ES, Robinson PJ, Merrill EA, Lubkowicz D, Mauzy CA. Characterization of an engineered live bacterial therapeutic for the treatment of phenylketonuria in a human gut-on-a-chip. Nat. Comms. 12, 2805. (2021).

Charbonneau MR, Isabella VM, Li N, and Kurtz CB. Developing a new class of engineered live bacterial therapeutics to treat human diseases. Nat. Comms. 11, 1738. (2020).

Kurtz CB, Millet YA, Puurunen MK, Perreault M, Charbonneau MR, Isabella VM, Kotula JW, Antipov E, Dagon Y, Denney WS, Wagner DA, West KA, Degar AJ, Brennan AM, and Miller PF. An engineered E. coli Nissle improves hyperammonemia and survival in mice and shows dose-dependent exposure in healthy humans. Sci. Transl. Med. 11(475), eaau7975. (2019).

Charbonneau MR, Blanton LV, DiGiulio DB, Relman DA, Lebrilla CB, Mills DA, and Gordon JI. A microbial perspective of human developmental biology. Nature 535, 48-55. (2016).

Blanton LV, Barratt MJ, Charbonneau MR, Ahmed T, and Gordon JI. Childhood undernutrition, the gut microbiota, and microbiota-directed therapeutics. Science 352(6293), 1533. (2016).

Charbonneau MR, O’Donnell D, Blanton LV, Totten SM, Davis, JCC, Barratt MJ, Cheng J, Guruge J, Talcott M, Bain JR, Muehlbauer MJ, Ilkayeva O, Wu C, Struckmeyer T, Barile D, Mangani C, Jorgensen J, Fan Y-M, Maleta K, Dewey KG, Ashorn P, Newgard CB, Lebrilla C, Mills DA, and Gordon JI. Sialylated milk glycans promote growth in gnotobiotic mice and pigs with a stunted Malawian infant gut microbiota. Cell 164(5), 859–871 (2016).

Blanton LV, Charbonneau MR, Salih T, Barratt MJ, Venkatesh S, Ilkayeva O, Subramanian S, Manary MJ, Trehan I, Jorgensen JM, Fan Y-M, Henrissat B, Leyn SA, Rodionov DA, Osterman AL, Maleta KM, Newgard CB, Ashorn P, Dewey KG, and Gordon JI. Gut bacteria that prevent growth impairments transmitted by microbiota from malnourished children. Science 351(6275), aad3311. (2016).

Faith JJ, Guruge JL, Charbonneau MR, Subramanian S, Seedorf H, Goodman AL, Clemente JC, Knight R, Heath AC, Leibel RL, Rosenbaum M, and Gordon JI. The long-term stability of the human gut microbiota. Science 341(6141), 1237439 (2013).