Publications

Peer-reviewed research from the lab

Preprints

Schell LD, Liow YJ, Carmody RN
Fasting and re-feeding independently alter mouse gut microbiota during intermittent fasting.
bioRxiv. 2026.
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Schell LD, Rubin G, Chan E, Carmody RN
Early-life microbiota disruption by antibiotics elicits fitness trade-offs that differ by sex.
bioRxiv. 2025.
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Liow YJ, Eshima S, Talay M, Yeliseyev V, Bry L, Carmody RN
Polyunsaturated fatty acids promote appetite via the microbiome-gut-brain axis.
bioRxiv. 2025.
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2026

Sarkar A, Raulo A, Stothart MR, Ibata NGO, Harty S, Metcalf CJE, Bohannan BJM, Bennett GM, Carmody RN
The island biology of the host microbiome.
Trends in Microbiology. 2026.
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2025

Liow YJ, Sarkar A, Carmody RN
Industrialized diets modulate host eating behavior via the microbiome–gut–brain axis.
Trends in Endocrinology & Metabolism, 36(12). 2025.
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Schell LD, Chadaideh KS, Allen-Blevins CR, Venable EM, Carmody RN
Dietary preservatives alter the gut microbiota in vitro and in vivo with sex-specific consequences for host metabolic development in a mouse model.
American Journal of Clinical Nutrition, 122: 221-234. 2025.
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Schell LD, Carmody RN
An energetic framework for gut microbiome-mediated obesity induced by early-life exposure to antibiotics.
Cell Host & Microbe, 33: 470-483. 2025.
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2024

Venable EM, Carmody RN
Decoupled Nutrient Status: a framework to disentangle host from microbial responses to diets of varying digestibility.
Frontiers in Food Science and Technology, 4: 1469470. 2024.
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Carmody RN, Varady K, Turnbaugh PJ
Digesting the complex metabolic effects of diet on the host and microbiome.
Cell, 187: 3857-3876. 2024.
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Sarkar A, McInroy CJA, Harty S, Raulo A, Ibata NGO, Valles-Colomer M, Johnson KVA, Brito IL, Henrich J, Archie EA, Barreiro LB, Gazzaniga FS, Finlay BB, Koonin EV, Carmody RN*, Moeller AH*
Microbial transmission in the social microbiome and host health and disease.
Cell, 187: 17-43. 2024.
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2023

Lieberman DE, Worthington S, Schell LD, Parkent CM, Devinsky O, Carmody RN
Comparing measured dietary variation within and between tropical hunter-gatherer groups to the Paleo diet.
American Journal of Clinical Nutrition, 118: 549-560. 2023.
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Amato KR, Carmody RN
Gut microbial intersections with human ecology and evolution.
Annual Review of Anthropology, 52: 295-311. 2023.
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Wang K, Mehta RS, Ma W, Nguyen LH, Wang DD, Ghazi AR, Yan Y, Al-Shaar L, Wang Y, Hang D, Fu BC, Ogino S, Rimm EB, Hu FB, Carmody RN, Garrett WS, Sun Q, Chan AT, Huttenhower C, Song M
The gut microbiome modifies the associations of short- and long-term physical activity with body weight changes.
Microbiome, 11: 121. 2023.
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Carmody RN, Bisanz JE
The role of the gut microbiome in weight management.
Nature Reviews Microbiology, 21: 535-550. 2023.
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McNamara MP, Venable EM, Cadney MD, Castro AA, Schmill MP, Kazzazi L, Carmody RN, Garland T
Juvenile microbiome composition of a mouse model selectively bred for high voluntary wheel-running behavior.
Journal of Experimental Biology, 226: jeb.245081. 2023.
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2022

MacArthur MR, Mitchell SJ, Chadaideh KS, Trevino-Villareal JH, Reynolds J, Jung J, Kalafut K, Trocha K, Tao M, Yeliseyev V, Bry L, Ozaki CK, Lewis CA, Carmody RN, Mitchell JR
Multi-omics assessment of dietary protein titration reveals altered hepatic glucose utilization.
Cell Reports, 40: 111187. 2022.
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2021

Sarkar A, Harty S, Moeller AH, Klein SL, Erdman SE, Friston KJ, Carmody RN
The gut microbiome as a biomarker of differential susceptibility to SARS-CoV-2.
Trends in Molecular Medicine, 27: 1115-1134. 2021.
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Chadaideh KS, Carmody RN
Host-microbial interactions in the metabolism of different dietary fats.
Cell Metabolism, 33: 857-872. 2021.
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Carmody RN, Sarkar A, Reese AT
Gut microbiota through an evolutionary lens.
Science, 372: 462-463. 2021.
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Reese AT, Chadaideh KS, Diggins CE, Schell LD, Beckel M, Callahan P, Ryan R, Emery Thompson M, Carmody RN
Effects of domestication on the gut microbiota parallel those of human industrialization.
eLife, 10: e60197. 2021.
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Ma S, Ren B, Mallick H, Moon YS, Schwager E, Maharjan S, Tickle TL, Lu Y, Carmody RN, Franzosa EA, Janson L, Huttenhower C
A statistical model for describing and simulating microbial community profiles.
PLoS Computational Biology, 17: e1008913. 2021.
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Ke S, Mitchell SJ, MacArthur MR, Kane AE, Sinclair DA, Venable EM, Chadaideh KS, Carmody RN, Grodstein F, Mitchell JR, Liu YY
Gut microbiota predicts healthy late-life aging in male mice.
Nutrients, 13: 3290. 2021.
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2020

Reese AT, Phillips-Garcia S, Owens LA, Venable EM, Machanda ZP, Langergraber KE, Mitani JC, Watts DP, Muller MN, Wrangham RW, Goldberg TL, Emery Thompson M, Carmody RN
Age patterning in the wild chimpanzee gut microbiota reveals differences from humans in early life.
Current Biology, 31: 613-620. 2020.
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Sarkar A, Harty S, Johnson KVA, Moeller AH, Archie EA, Schell LD, Carmody RN, Clutton-Brock TH, Dunbar RIM, Burnet PWJ
Microbial transmission in animal social networks and the social microbiome.
Nature Ecology & Evolution, 4: 1020-1035. 2020.
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Sarkar A, Harty S, Johnson KVA, Moeller AH, Carmody RN, Lehto SM, Erdman SE, Dunbar RIM, Burnet PWJ
The role of the microbiome in the neurobiology of social behaviour.
Biological Reviews, 95: 1131-1166. 2020.
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2019

Carmody RN, Bisanz JE, Maurice CF, Lyalina S, Bowen BJ, Chadaideh KS, Maini Rekdal V, Bess EN, Spanogiannopoulos P, Bauer KC, Balon TW, Pollard KS, Northen TR, Turnbaugh PJ
Cooking shapes the structure and function of the gut microbiome.
Nature Microbiology, 4: 2052-2063. 2019.
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Wallace IJ, Bendele AM, Riew G, Hung HH, Frank EH, Holowka NB, Bolze AS, Venable EM, Yegian A, Dingwall HL, Carmody RN, Grodzinsky AJ, Lieberman DE
Physical inactivity and knee osteoarthritis in guinea pigs.
Osteoarthritis and Cartilage, 27: 1721-1728. 2019.
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Carmody RN, Baggish AL
Working out the bugs: microbial modulation of athletic performance.
Nature Metabolism, 1: 658-659. 2019.
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Kip P, Trocha KM, Tao M, O’Leary JJ, Ruske J, Giulietti JM, Trevino-Villareal JH, MacArthur MR, Bolze AS, Burak MF, Patterson S, Ho KJ, Carmody RN, Guzman RJ, Mitchell JR, Ozaki CK
Insights from a short-term protein-caloric restriction exploratory trial in elective carotid endarterectomy patients.
Vascular and Endovascular Surgery, 53: 470-476. 2019.
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2018

Reese AT, Carmody RN
Thinking outside the cereal box: non-carbohydrate routes for dietary manipulation of the gut microbiota.
Applied and Environmental Microbiology, 85: e02246-18. 2018.
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Zhang L, Carmody RN, Kalariya H, Duran RM, Moskal K, Poulev A, Kuhn P, Turnbaugh PJ, Raskin I, Roopchand DE
Grape proanthocyanidin-induced intestinal bloom of Akkermansia muciniphila is dependent on its baseline abundance and precedes activation of host genes related to metabolic health.
Journal of Nutritional Biochemistry, 56: 142-151. 2018.
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2017

Carmody RN
Evolution of the human dietary niche: quest for high-quality.
In Muller MN, Wrangham RW and Pilbeam DR (eds.) Chimpanzees and Human Evolution. Cambridge, MA: Harvard University Press. 2017.
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2016

Carmody RN*, Dannemann M*, Briggs AW, Nickel B, Groopman EE, Wrangham RW and Kelso J
Genetic evidence of human adaptation to a cooked diet.
Genome Biology and Evolution, 8: 1091-1103. 2016.
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Spanogiannopoulos P, Bess EN, Carmody RN and Turnbaugh PJ
The microbial pharmacists within us: a metagenomic view of xenobiotic metabolism.
Nature Reviews Microbiology, 14: 273-287. 2016.
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Wrangham RW and Carmody RN
Influences of the control of fire on the energy value and composition of the human diet.
In Lee-Thorp J and Katzenberg MA (eds.), Oxford Handbook of the Archaeology of Diet. Oxford: Oxford University Press. 2016.
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2015

Roopchand DE, Carmody RN, Kuhn P, Moskal K, Rojas-Silva P, Turnbaugh PJ and Raskin I
Dietary polyphenols promote growth of the gut bacterium Akkermansia muciniphila and attenuate high fat diet-induced metabolic syndrome.
Diabetes, 64: 2847-2858. 2015.
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Smith A, Carmody RN, Dutton RJ and Wrangham RW
The significance of cooking for early hominin scavenging.
Journal of Human Evolution, 84: 62-70. 2015.
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Carmody RN*, Gerber G*, Luevano JM, Somes L, Svenson KL and Turnbaugh PJ
Diet dominates host genotype in shaping the murine gut microbiota.
Cell Host & Microbe, 17: 72-84. 2015.
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Groopman EE, Carmody RN and Wrangham RW
Cooking increases net energy gain from a lipid-rich food.
American Journal of Physical Anthropology, 156: 11-18. 2015.
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Carmody RN
Digestion and human evolution.
In Beaudry MC and Metheny K (eds.), Archaeology of Food: An Encyclopedia. Lanham, MD: Rowman & Littlefield. 2015.
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2014

Carmody RN and Turnbaugh PJ
Host-microbial interactions in the metabolism of therapeutic and diet-derived xenobiotics.
Journal of Clinical Investigation, 124: 4173-4181. 2014.
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David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, Ling AV, Devlin AS, Varma Y, Fischbach M, Biddinger SB, Dutton RJ and Turnbaugh PJ
Diet rapidly and reproducibly alters the human gut microbiome.
Nature, 505: 559-563. 2014.
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2013

Wrangham RW and Carmody RN
What makes us human — is it cooking?
In Jobling MA, Hollox E, Hurles M, Kivisild T and Tyler-Smith C (eds.), Human Evolutionary Genetics: Origins, Peoples and Disease (2nd Edition). New York: Garland Science. 2013.
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2012

Carmody RN and Turnbaugh PJ
Gut microbes make for fattier fish.
Cell Host & Microbe, 12: 259-261. 2012.
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Carmody RN, Weintraub GS and Wrangham RW
Reply to Wollstonecroft et al.: Cooking increases the bioavailability of starch from diverse plant sources.
PNAS, 109: E992. 2012.
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2011

Carmody RN, Weintraub GS and Wrangham RW
Energetic consequences of thermal and nonthermal food processing.
PNAS, 108: 19199-19203. 2011.
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2010

Wrangham R and Carmody R
Human adaptation to the control of fire.
Evolutionary Anthropology, 19: 187-199. 2010.
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2009

Carmody RN and Wrangham RW
Cooking and the human commitment to a high-quality diet.
Cold Spring Harbor Symposia on Quantitative Biology, 74: 427-434. 2009.
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Carmody RN and Wrangham RW
The energetic significance of cooking.
Journal of Human Evolution, 57: 379-391. 2009.
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2007

Boback SM, Cox CL, Ott BD, Carmody R, Wrangham RW and Secor SM
Cooking and grinding reduces the cost of meat digestion.
Comparative Biochemistry & Physiology A, 148: 651-656. 2007.
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Bold denotes Carmody lab members. * denotes equal contributions.