Person: Carmody, Rachel
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Carmody
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Carmody, Rachel
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Publication Cooking shapes the structure and function of the gut microbiome(Springer Science and Business Media LLC, 2019-09-30) Carmody, Rachel; Bisanz, Jordan E.; Bowen, Benjamin P.; Maurice, Corinne F.; Lyalina, Svetlana; Louie, Katherine B.; Treen, Daniel; Chadaideh, Katia; Maini Rekdal, Vayu; Bess, Elizabeth N.; Spanogiannopoulos, Peter; Ang, Qi Yan; Bauer, Kylynda C.; Balon, Thomas W.; Pollard, Katherine S.; Northen, Trent R.; Turnbaugh, Peter J.; TurnbaughDiet is a critical determinant of variation in gut microbial structure and function, outweighing even host genetics. Numerous microbiome studies have compared diets with divergent ingredients, but the everyday practice of cooking remains unclear. Here, we show that a plant diet served raw versus cooked reshapes the murine gut microbiome, with effects attributable to improvements in starch digestibility and degradation of plant-derived compounds. Shifts in the gut microbiota modulated host energy status, applied across multiple starch-rich plants, and were detectable in humans. Thus, diet-driven host-microbial interactions depend on the food as well as its form. Since cooking is human-specific, ubiquitous and ancient, our results prompt the hypothesis that humans and our microbiomes co-evolved under unique cooking-related pressures.Publication Energetic Consequences of Thermal and Non-Thermal Food Processing(2013-03-06) Carmody, Rachel; Wrangham, Richard W.; Lieberman, Daniel; Ellison, Peter; Secor, StephenAll human societies process their food extensively by thermal and non-thermal means. This feature distinguishes us from other species, and may even be compulsory given that humans are biologically committed to an energy-rich diet that is easy to chew and digest. Yet the energetic consequences of food processing remain largely unknown. This dissertation tests the fundamental hypothesis that thermal and non-thermal processing lead to biologically relevant increases in energy gain from protein-rich meat and starch-rich tubers, two major caloric resources for modern and ancestral humans that present divergent structural and macronutrient profiles. The energetic consequences of food processing are evaluated using three indices of energy gain, each of which account for costs not currently captured by conventional biochemical assessments of dietary energy value. Chapter 2 investigates the effects of cooking and pounding on net energy gain as indexed by changes in body mass, controlling for differences in food intake and activity level. Chapter 3 examines the effect of cooking and pounding on diet-induced thermogenesis, the metabolic cost of food digestion. Chapter 4 considers the effort required to engage in food processing, arguing that the advantageous ratio of benefit to cost has likely had important effects on human life history. By each of these definitions of energy gain, food processing is shown to have substantial energetic significance. Overall, energetic gains due to thermal processing exceeded those of non-thermal processing, consistent with recent proposals that the adoption of cooking had a particularly important influence on human biology. Gains due to food processing were observed in both meat and tuber substrates, supporting a transformative role for habitual food processing in the evolution and maintenance of the human energy budget.Publication Diet rapidly and reproducibly alters the human gut microbiome(2013) David, Lawrence A.; Maurice, Corinne F.; Carmody, Rachel; Gootenberg, David; Button, Julie E.; Wolfe, Benjamin; Ling, Alisha; Devlin, A. Sloan; Varma, Yug; Fischbach, Michael A.; Biddinger, Sudha; Dutton, Rachel Janelle; Turnbaugh, Peter J.Long-term diet influences the structure and activity of the trillions of microorganisms residing in the human gut1–5, but it remains unclear how rapidly and reproducibly the human gut microbiome responds to short-term macronutrient change. Here, we show that the short-term consumption of diets composed entirely of animal or plant products alters microbial community structure and overwhelms inter-individual differences in microbial gene expression. The animal-based diet increased the abundance of bile-tolerant microorganisms (Alistipes, Bilophila, and Bacteroides) and decreased the levels of Firmicutes that metabolize dietary plant polysaccharides (Roseburia, Eubacterium rectale, and Ruminococcus bromii). Microbial activity mirrored differences between herbivorous and carnivorous mammals2, reflecting trade-offs between carbohydrate and protein fermentation. Foodborne microbes from both diets transiently colonized the gut, including bacteria, fungi, and even viruses. Finally, increases in the abundance and activity of Bilophila wadsworthia on the animal-based diet support a link between dietary fat, bile acids, and the outgrowth of microorganisms capable of triggering inflammatory bowel disease6. In concert, these results demonstrate that the gut microbiome can rapidly respond to altered diet, potentially facilitating the diversity of human dietary lifestyles.Publication Cooking and the Human Commitment to a High-quality Diet(Cold Spring Harbor Laboratory Press, 2009) Carmody, Rachel; Wrangham, RichardFor our body size, humans exhibit higher energy use yet reduced structures for mastication and digestion of food compared to chimpanzees, our closest living relatives. This suite of features suggests that humans are adapted to a high-quality diet. Although increased consumption of meat during human evolution certainly contributed to dietary quality, meat-eating alone appears to be insufficient to support the evolution of these traits, because modern humans fare poorly on raw diets that include meat. Here, we suggest that cooking confers physical and chemical benefits to food that are consistent with observed human dietary adaptations. We review evidence showing that cooking facilitates mastication, increases digestibility, and otherwise improves the net energy value of plant and animal foods regularly consumed by humans. We also address the likelihood that cooking was adopted more than 250,000 years ago (kya), a period that we believe is sufficient in length for the proposed adaptations to have occurred. Additional experimental work is needed to help discriminate the relative contributions of cooking, meat eating, and other innovations such as nonthermal food processing in supporting the human transition toward dietary quality.Publication Genetic Evidence of Human Adaptation to a Cooked Diet(Oxford University Press, 2016) Carmody, Rachel; Dannemann, Michael; Briggs, Adrian; Nickel, Birgit; Groopman, Emily E.; Wrangham, Richard; Kelso, JanetHumans have been argued to be biologically adapted to a cooked diet, but this hypothesis has not been tested at the molecular level. Here, we combine controlled feeding experiments in mice with comparative primate genomics to show that consumption of a cooked diet influences gene expression and that affected genes bear signals of positive selection in the human lineage. Liver gene expression profiles in mice fed standardized diets of meat or tuber were affected by food type and cooking, but not by caloric intake or consumer energy balance. Genes affected by cooking were highly correlated with genes known to be differentially expressed in liver between humans and other primates, and more genes in this overlap set show signals of positive selection in humans than would be expected by chance. Sequence changes in the genes under selection appear before the split between modern humans and two archaic human groups, Neandertals and Denisovans, supporting the idea that human adaptation to a cooked diet had begun by at least 275,000 years ago.Publication Human Adaptation to the Control of Fire(Wiley-Blackwell, 2010) Wrangham, Richard; Carmody, RachelCharles Darwin attributed human evolutionary success to three traits. Our social habits and anatomy were important, he said, but the critical feature was our intelligence, because it led to so much else, including such traits as language, weapons, tools, boats, and the control of fire. Among these, he opined, the control of fire was “probably the greatest ever [discovery] made by man, excepting language.” Despite this early suggestion that the control of fire was even more important than tool use for human success, recent anthropologists have made only sporadic efforts to assess its evolutionary significance. Here we use recent developments in understanding the role of cooked food in human diets to support the spirit of Darwin's offhand remark. We first consider the role of fire in increasing the net caloric value of cooked foods compared to raw foods, and hence in accounting for the unique pattern of human digestion. We then review the compelling evidence that humans are biologically adapted to diets that include cooked food, and that humans have a long evolutionary history of an obligate dependence on fire. Accordingly, we end by considering the influence of fire on various aspects of human biology. We pay particular attention to life history, and also briefly discuss effects on anatomy, behavior, and cognition.Publication The Energetic Significance of Cooking(Wiley-Blackwell, 2009) Carmody, Rachel; Wrangham, RichardWhile cooking has long been argued to improve the diet, the nature of the improvement has not been well defined. As a result, the evolutionary significance of cooking has variously been proposed as being substantial or relatively trivial. In this paper, we evaluate the hypothesis that an important and consistent effect of cooking food is a rise in its net energy value. The pathways by which cooking influences net energy value differ for starch, protein and lipid, and we therefore consider plant and animal foods separately. Evidence of compromised physiological performance among individuals on raw diets supports the hypothesis that cooked diets tend to provide energy. Mechanisms contributing to energy being gained from cooking include increased digestibility of starch and protein, reduced costs of digestion for cooked versus raw meat, and reduced energetic costs of detoxification and defense against pathogens. If cooking indeed consistently improves the energetic value of foods through such mechanisms, its evolutionary impact depends partly on the relative energetic benefits of non-thermal processing methods used prior to cooking. We suggest that if non-thermal processing methods, such as pounding, were used by Lower Paleolithic Homo, they likely provided an important increase in energy gain over unprocessed raw diets. However, cooking has critical effects not easily achievable by non-thermal processing, including the relatively complete gelatinization of starch, efficient denaturing of proteins, and killing of foodborne pathogens. This means that however sophisticated the non-thermal processing methods were, cooking would have conferred incremental energetic benefits. While much remains to be discovered, we conclude that the adoption of cooking would have led to an important rise in energy availability. For this reason, we predict that cooking had substantial evolutionary significance.