Kerri Waldron
Walker, A. W. & Hoyles, L. Human microbiome myths and misconceptions. Nat. Microbiol. 8, 1392–1396 (2023).
Google Scholar
Lundgren, S. N. et al. Maternal diet during pregnancy is related with the infant stool microbiome in a delivery mode-dependent manner. Microbiome 6, 109 (2018).
Google Scholar
Singh, R. K. et al. Influence of diet on the gut microbiome and implications for human health. J. Transl. Med. 15, 73 (2017).
Google Scholar
David, L. A. et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature 505, 559–563 (2014).
Google Scholar
Ghosh, T. S. et al. Mediterranean diet intervention alters the gut microbiome in older people reducing frailty and improving health status: the NU-AGE 1-year dietary intervention across five European countries. Gut 69, 1218–1228 (2020). This paper demonstrates that a 1-year Mediterranean dietary intervention in elderly individuals can positively alter the gut microbiota, leading to improved markers of lower frailty, cognitive function and reduced inflammation.
Google Scholar
Bourdeau-Julien, I. et al. The diet rapidly and differentially affects the gut microbiota and host lipid mediators in a healthy population. Microbiome 11, 26 (2023).
Google Scholar
Heinken, A. et al. Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine. Nat. Biotechnol. 41, 1320–1331 (2023).
Google Scholar
Zampieri, G., Vijayakumar, S., Yaneske, E. & Angione, C. Machine and deep learning meet genome-scale metabolic modeling. PLoS Comput. Biol. 15, e1007084 (2019).
Google Scholar
Valls-Pedret, C. et al. Mediterranean diet and age-related cognitive decline. JAMA Intern. Med. 175, 1094 (2015).
Google Scholar
Sánchez-Villegas, A. et al. Mediterranean dietary pattern and depression: the PREDIMED randomized trial. BMC Med. 11, 208 (2013).
Google Scholar
Martinez-Gonzalez, M. A. & Martin-Calvo, N. Mediterranean diet and life expectancy; beyond olive oil, fruits, and vegetables. Curr. Opin. Clin. Nutr. Metab. Care 19, 401–407 (2016).
Google Scholar
Berry, S. E. et al. Human postprandial responses to food and potential for precision nutrition. Nat. Med. 26, 964–973 (2020).
Google Scholar
Johnson, A. J. et al. Daily sampling reveals personalized diet-microbiome associations in humans. Cell Host Microbe 25, 789–802.e5 (2019).
Google Scholar
Kopp, W. How Western diet and lifestyle drive the pandemic of obesity and civilization diseases. Diabetes Metab. Syndr. Obes. 12, 2221–2236 (2019).
Google Scholar
Shanahan, F., Ghosh, T. S. & O’Toole, P. W. The healthy microbiome — what is the definition of a healthy gut microbiome? Gastroenterology 160, 483–494 (2021).
Google Scholar
Abdelsalam, N. A., Hegazy, S. M. & Aziz, R. K. The curious case of Prevotella copri. Gut Microbes 15, 2249152 (2023).
Google Scholar
Pasolli, E. et al. Accessible, curated metagenomic data through experimentHub. Nat. Methods 14, 1023–1024 (2017).
Google Scholar
De Filippis, F. et al. Distinct genetic and functional traits of human intestinal Prevotella copri strains are associated with different habitual diets. Cell Host Microbe 25, 444–453.e3 (2019).
Google Scholar
Hippe, B. et al. Faecalibacterium prausnitzii phylotypes in type two diabetic, obese, and lean control subjects. Benef. Microbes 7, 511–517 (2016).
Google Scholar
Armet, A. M. et al. Rethinking healthy eating in light of the gut microbiome. Cell Host Microbe 30, 764–785 (2022).
Google Scholar
KEYS, A. et al. The diet and 15-year death rate in the seven countries study. Am. J. Epidemiol. 124, 903–915 (1986).
Google Scholar
Muralidharan, J. et al. Effect on gut microbiota of a 1-y lifestyle intervention with Mediterranean diet compared with energy-reduced Mediterranean diet and physical activity promotion: PREDIMED-plus study. Am. J. Clin. Nutr. 114, 1148–1158 (2021).
Google Scholar
Meslier, V. et al. Mediterranean diet intervention in overweight and obese subjects lowers plasma cholesterol and causes changes in the gut microbiome and metabolome independently of energy intake. Gut 69, 1258–1268 (2020).
Google Scholar
Gómez-Pérez, A. M. et al. Gut microbiota in nonalcoholic fatty liver disease: a PREDIMED-Plus trial sub analysis. Gut Microbes 15, 2223339 (2023).
Google Scholar
Wang, D. D. et al. The gut microbiome modulates the protective association between a Mediterranean diet and cardiometabolic disease risk. Nat. Med. 27, 333–343 (2021).
Google Scholar
Rinott, E. et al. The effects of the green-Mediterranean diet on cardiometabolic health are linked to gut microbiome modifications: a randomized controlled trial. Genome Med. 14, 29 (2022).
Google Scholar
Waddell, I. S. & Orfila, C. Dietary fiber in the prevention of obesity and obesity-related chronic diseases: from epidemiological evidence to potential molecular mechanisms. Crit. Rev. Food Sci. Nutr. 63, 8752–8767 (2022).
Google Scholar
Oliver, A. et al. High-fiber, whole-food dietary intervention alters the human gut microbiome but not fecal short-chain fatty acids. mSystems 6, e00115–e00121 (2021).
Google Scholar
Coker, J. K., Moyne, O., Rodionov, D. A. & Zengler, K. Carbohydrates great and small, from dietary fiber to sialic acids: how glycans influence the gut microbiome and affect human health. Gut Microbes https://doi.org/10.1080/19490976.2020.1869502 (2021).
Benítez-Páez, A. et al. A multi-omics approach to unraveling the microbiome-mediated effects of arabinoxylan oligosaccharides in overweight humans. mSystems 4, e00209–e00219 (2019).
Google Scholar
Costabile, A. et al. Whole-grain wheat breakfast cereal has a prebiotic effect on the human gut microbiota: a double-blind, placebo-controlled, crossover study. Br. J. Nutr. 99, 110–120 (2008).
Google Scholar
Wang, Y. et al. High molecular weight barley β-glucan alters gut microbiota toward reduced cardiovascular disease risk. Front. Microbiol. 7, 129 (2016).
Google Scholar
Deehan, E. C. et al. Precision microbiome modulation with discrete dietary fiber structures directs short-chain fatty acid production. Cell Host Microbe 27, 389–404.e6 (2020).
Google Scholar
Vangay, P. et al. US immigration westernizes the human gut microbiome. Cell 175, 962–972.e10 (2018).
Google Scholar
den Besten, G. et al. The role of short-chain fatty acids in the interplay between diet, gut microbiota, and host energy metabolism. J. Lipid Res. 54, 2325–2340 (2013).
Google Scholar
Smith, P. M. et al. The microbial metabolites, short-chain fatty acids, regulate colonic Treg cell homeostasis. Science 341, 569–573 (2013).
Google Scholar
Siddiqui, M. T. & Cresci, G. A. The immunomodulatory functions of butyrate. J. Inflamm. Res. 14, 6025–6041 (2021).
Google Scholar
van der Hee, B. & Wells, J. M. Microbial regulation of host physiology by short-chain fatty acids. Trends Microbiol. 29, 700–712 (2021).
Google Scholar
Roager, H. M. et al. Whole grain-rich diet reduces body weight and systemic low-grade inflammation without inducing major changes of the gut microbiome: a randomised cross-over trial. Gut 68, 83–93 (2019).
Google Scholar
Procházková, N. et al. Advancing human gut microbiota research by considering gut transit time. Gut 72, 180–191 (2023).
Google Scholar
Muegge, B. D. et al. Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science 332, 970–974 (2011).
Google Scholar
Trefflich, I. et al. Is a vegan or a vegetarian diet associated with the microbiota composition in the gut? Results of a new cross-sectional study and systematic review. Crit. Rev. Food Sci. Nutr. 60, 2990–3004 (2020).
Google Scholar
Losno, E. A., Sieferle, K., Perez-Cueto, F. J. A. & Ritz, C. Vegan diet and the gut microbiota composition in healthy adults. Nutrients 13, 2402 (2021).
Google Scholar
Miao, Z. et al. Gut microbiota signatures of long-term and short-term plant-based dietary pattern and cardiometabolic health: a prospective cohort study. BMC Med. 20, 204 (2022).
Google Scholar
Cheng, H. et al. Interactions between gut microbiota and polyphenols: a mechanistic and metabolomic review. Phytomedicine 119, 154979 (2023).
Google Scholar
Corrêa, T. A. F., Rogero, M. M., Hassimotto, N. M. A. & Lajolo, F. M. The two-way polyphenols-microbiota interactions and their effects on obesity and related metabolic diseases. Front Nutr. 6, 188 (2019).
Google Scholar
Ross, F. C. et al. Potential of dietary polyphenols for protection from age-related decline and neurodegeneration: a role for gut microbiota? Nutr. Neurosci. https://doi.org/10.1080/1028415X.2023.2298098 (2024).
Selinger, E. et al. Evidence of a vegan diet for health benefits and risks — an umbrella review of meta-analyses of observational and clinical studies. Crit. Rev. Food Sci. Nutr. 63, 9926–9936 (2022).
Google Scholar
Espín, J. C., González-Sarrías, A. & Tomás-Barberán, F. A. The gut microbiota: a key factor in the therapeutic effects of (poly)phenols. Biochem. Pharmacol. 139, 82–93 (2017).
Google Scholar
Sesso, H. D. et al. Effect of cocoa flavanol supplementation for the prevention of cardiovascular disease events: the COcoa Supplement and Multivitamin Outcomes Study (COSMOS) randomized clinical trial. Am. J. Clin. Nutr. 115, 1490–1500 (2022).
Google Scholar
Stapleton, P. D., Shah, S., Ehlert, K., Hara, Y. & Taylor, P. W. The β-lactam-resistance modifier (−)-epicatechin gallate alters the architecture of the cell wall of Staphylococcus aureus. Microbiology 153, 2093–2103 (2007).
Google Scholar
Chan, C.-L., Gan, R.-Y., Shah, N. P. & Corke, H. Polyphenols from selected dietary spices and medicinal herbs differentially affect common food-borne pathogenic bacteria and lactic acid bacteria. Food Control 92, 437–443 (2018).
Google Scholar
Santos, C. A., Lima, E. M. F., de Melo Franco, B. D. G. & Pinto, U. M. Exploring phenolic compounds as quorum sensing inhibitors in foodborne bacteria. Front. Microbiol. 12, 735931 (2021).
Google Scholar
Plamada, D. & Vodnar, D. C. Polyphenols — gut microbiota interrelationship: a transition to a new generation of prebiotics. Nutrients 14, 137 (2021).
Google Scholar
Cortés‐Martín, A., Selma, M. V., Tomás‐Barberán, F. A., González‐Sarrías, A. & Espín, J. C. Where to look into the puzzle of polyphenols and health? The postbiotics and gut microbiota associated with human metabotypes. Mol. Nutr. Food Res. 64, 1900952 (2020).
Google Scholar
Prochazkova, M. et al. Vegan diet is associated with favorable effects on the metabolic performance of intestinal microbiota: a cross-sectional multi-omics study. Front. Nutr. 8, 783302 (2022).
Google Scholar
Dingeo, G. et al. Phytochemicals as modifiers of gut microbial communities. Food Funct. 11, 8444–8471 (2020).
Google Scholar
Davila, A.-M. et al. Intestinal luminal nitrogen metabolism: role of the gut microbiota and consequences for the host. Pharmacol. Res. 68, 95–107 (2013).
Google Scholar
Ma, N., Tian, Y., Wu, Y. & Ma, X. Contributions of the interaction between dietary protein and gut microbiota to intestinal health. Curr. Protein Pept. Sci. 18, 795–808 (2017).
Google Scholar
Neis, E., Dejong, C. & Rensen, S. The role of microbial amino acid metabolism in host metabolism. Nutrients 7, 2930–2946 (2015).
Google Scholar
Barreto, F. C. et al. Serum indoxyl sulfate is associated with vascular disease and mortality in chronic kidney disease patients. Clin. J. Am. Soc. Nephrol. 4, 1551–1558 (2009).
Google Scholar
Yue, T. et al. Hydrogen sulfide creates a favorable immune microenvironment for colon cancer. Cancer Res. 83, 595–612 (2023).
Google Scholar
Ang, Q. Y. et al. Ketogenic diets alter the gut microbiome resulting in decreased intestinal Th17 cells. Cell 181, 1263–1275.e16 (2020). This paper shows that a ketogenic diet changes the gut microbiota by depleting bifidobacteria and inhibiting their growth through ketone bodies, leading to a reduction in pro-inflammatory TH17 cells and emphasizing the importance of chemical communication in mediating host responses to dietary interventions.
Google Scholar
Zhu, H. et al. Ketogenic diet for human diseases: the underlying mechanisms and potential for clinical implementations. Signal Transduct. Target. Ther. 7, 11 (2022).
Google Scholar
Bisanz, J. E., Upadhyay, V., Turnbaugh, J. A., Ly, K. & Turnbaugh, P. J. Meta-analysis reveals reproducible gut microbiome alterations in response to a high-fat diet. Cell Host Microbe 26, 265–272.e4 (2019).
Google Scholar
Lindefeldt, M. et al. The ketogenic diet influences taxonomic and functional composition of the gut microbiota in children with severe epilepsy. NPJ Biofilms Microbiomes 5, 5 (2019).
Google Scholar
Olson, C. A. et al. The gut microbiota mediates the anti-seizure effects of the ketogenic diet. Cell 173, 1728–1741.e13 (2018).
Google Scholar
Kong, C. et al. Ketogenic diet alleviates colitis by reduction of colonic group 3 innate lymphoid cells through altering gut microbiome. Signal Transduct. Target. Ther. 6, 154 (2021).
Google Scholar
Ma, D. et al. Ketogenic diet enhances neurovascular function with altered gut microbiome in young healthy mice. Sci. Rep. 8, 6670 (2018).
Google Scholar
Goldberg, E. L. et al. Ketogenesis activates metabolically protective γδ T cells in visceral adipose tissue. Nat. Metab. 2, 50–61 (2020).
Google Scholar
Frioux, C. et al. Enterosignatures define common bacterial guilds in the human gut microbiome. Cell Host Microbe 31, 1111–1125.e6 (2023).
Google Scholar
Schnorr, S. L. et al. Gut microbiome of the Hadza hunter-gatherers. Nat. Commun. 5, 3654 (2014).
Google Scholar
Martínez, I. et al. The gut microbiota of rural Papua New Guineans: composition, diversity patterns, and ecological processes. Cell Rep. 11, 527–538 (2015). This paper compares the gut microbiota of Papua New Guineans and US residents, indicating that variations in microbial diversity and abundance may result from modern lifestyle factors in industrialized societies, limiting bacterial diversity with implications for human health.
Google Scholar
Sun, S. et al. Does geographical variation confound the relationship between host factors and the human gut microbiota: a population-based study in China. BMJ Open 10, e038163 (2020).
Google Scholar
De Filippo, C. et al. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc. Natl Acad. Sci. 107, 14691–14696 (2010).
Google Scholar
De Filippo, C. et al. Diet, environments, and gut microbiota. a preliminary investigation in children living in rural and urban Burkina Faso and Italy. Front. Microbiol. 8, 1979 (2017).
Google Scholar
Zhou, X., Qiao, K., Wu, H. & Zhang, Y. The impact of food additives on the abundance and composition of gut microbiota. Molecules 28, 631 (2023).
Google Scholar
del Pozo, S. et al. Potential effects of sucralose and saccharin on gut microbiota: a review. Nutrients 14, 1682 (2022).
Google Scholar
Wolfson, S. J. et al. Bacterial hydrogen sulfide drives cryptic redox chemistry in gut microbial communities. Nat. Metab. 4, 1260–1270 (2022).
Google Scholar
Naimi, S., Viennois, E., Gewirtz, A. T. & Chassaing, B. Direct impact of commonly used dietary emulsifiers on human gut microbiota. Microbiome 9, 66 (2021).
Google Scholar
Filippou, C. D. et al. Dietary approaches to stop hypertension (DASH) diet and blood pressure reduction in adults with and without hypertension: a systematic review and meta-analysis of randomized controlled trials. Adv. Nutr. 11, 1150–1160 (2020).
Google Scholar
Dwiyanto, J. et al. Ethnicity influences the gut microbiota of individuals sharing a geographical location: a cross-sectional study from a middle-income country. Sci. Rep. 11, 2618 (2021).
Google Scholar
Rampelli, S. et al. Metagenome sequencing of the Hadza hunter-gatherer gut microbiota. Curr. Biol. 25, 1682–1693 (2015).
Google Scholar
Gomez, A. et al. Gut microbiome of coexisting BaAka pygmies and Bantu reflects gradients of traditional subsistence patterns. Cell Rep. 14, 2142–2153 (2016).
Google Scholar
Mancabelli, L. et al. Meta‐analysis of the human gut microbiome from urbanized and pre‐agricultural populations. Env. Microbiol. 19, 1379–1390 (2017).
Google Scholar
Ecklu-Mensah, G. et al. Gut microbiota and fecal short chain fatty acids differ with adiposity and country of origin: the METS-Microbiome study. Nat. Commun. 14, 5160 (2023).
Google Scholar
Jha, A. R. et al. Gut microbiome transition across a lifestyle gradient in Himalaya. PLoS Biol. 16, e2005396 (2018).
Google Scholar
Carter, M. M. et al. Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes. Cell 186, 3111–3124.e13 (2023).
Google Scholar
Huang, Y. et al. Gut microbiota insights into human adaption to high‐plateau diet. iMeta https://doi.org/10.1002/imt2.6 (2022).
Grześkowiak, Ł. et al. Distinct gut microbiota in Southeastern African and Northern European infants. J. Pediatr. Gastroenterol. Nutr. 54, 812–816 (2012).
Google Scholar
Hansen, M. E. B. et al. Population structure of human gut bacteria in a diverse cohort from rural Tanzania and Botswana. Genome Biol. 20, 16 (2019).
Google Scholar
Tett, A. et al. The Prevotella copri complex comprises four distinct clades underrepresented in westernized populations. Cell Host Microbe 26, 666–679.e7 (2019). This paper reveals that the gut microorganism P. copri includes a P. copri complex with four distinct clades, predominantly found in non-Western populations, wherein individuals commonly exhibit co-presence of all clades.
Google Scholar
Pedersen, H. K. et al. Human gut microbes impact host serum metabolome and insulin sensitivity. Nature 535, 376–381 (2016).
Google Scholar
Dhakan, D. B. et al. The unique composition of Indian gut microbiome, gene catalogue, and associated fecal metabolome deciphered using multi-omics approaches. Gigascience 8, giz004 (2019).
Google Scholar
Dehingia, M. et al. Gut bacterial diversity of the tribes of India and comparison with the worldwide data. Sci. Rep. 5, 18563 (2015).
Google Scholar
Keohane, D. M. et al. Microbiome and health implications for ethnic minorities after enforced lifestyle changes. Nat. Med. 26, 1089–1095 (2020). This paper shows that Irish Travellers retain similar human gut microbiomes to that of non-industrialized populations, indicating that microbiota composition is associated with non-dietary factors and may be linked to the risk of microbiome-related metabolic diseases.
Google Scholar
Vatanen, T. et al. Mobile genetic elements from the maternal microbiome shape infant gut microbial assembly and metabolism. Cell 185, 4921–4936.e15 (2022).
Google Scholar
Ennis, D., Shmorak, S., Jantscher-Krenn, E. & Yassour, M. Longitudinal quantification of Bifidobacterium longum subsp. infantis reveals late colonization in the infant gut independent of maternal milk HMO composition. Nat. Commun. 15, 894 (2024).
Google Scholar
Walsh, C., Lane, J. A., van Sinderen, D. & Hickey, R. M. Human milk oligosaccharides: shaping the infant gut microbiota and supporting health. J. Funct. Foods 72, 104074 (2020).
Google Scholar
Ma, J. et al. Comparison of gut microbiota in exclusively breast-fed and formula-fed babies: a study of 91 term infants. Sci. Rep. 10, 15792 (2020).
Google Scholar
Ho, N. T. et al. Meta-analysis of effects of exclusive breastfeeding on infant gut microbiota across populations. Nat. Commun. 9, 4169 (2018).
Google Scholar
van den Elsen, L. W. J., Garssen, J., Burcelin, R. & Verhasselt, V. Shaping the gut microbiota by breastfeeding: the gateway to allergy prevention? Front. Pediatr. 7, 47 (2019).
Google Scholar
Forbes, J. D. et al. A comparative study of the gut microbiota in immune-mediated inflammatory diseases — does a common dysbiosis exist? Microbiome 6, 221 (2018).
Google Scholar
Le Huërou-Luron, I., Blat, S. & Boudry, G. Breast- v. formula-feeding: impacts on the digestive tract and immediate and long-term health effects. Nutr. Res. Rev. 23, 23–36 (2010).
Google Scholar
Taylor, R., Keane, D., Borrego, P. & Arcaro, K. Effect of maternal diet on maternal milk and breastfed infant gut microbiomes: a scoping review. Nutrients 15, 1420 (2023).
Google Scholar
Sindi, A. S. et al. Effect of a reduced fat and sugar maternal dietary intervention during lactation on the infant gut microbiome. Front. Microbiol. 13, 900702 (2022).
Google Scholar
Savage, J. H. et al. Diet during pregnancy and infancy and the infant intestinal microbiome. J. Pediatr. 203, 47–54.e4 (2018).
Google Scholar
Sikder, Md. A. A. et al. Maternal diet modulates the infant microbiome and intestinal Flt3L necessary for dendritic cell development and immunity to respiratory infection. Immunity 56, 1098–1114.e10 (2023).
Google Scholar
Grant, E. T., Boudaud, M., Muller, A., Macpherson, A. J. & Desai, M. S. Maternal diet and gut microbiome composition modulate early‐life immune development. EMBO Mol. Med. 15, e17241 (2023).
Google Scholar
Wang, C. et al. Maternal consumption of a fermented diet protects offspring against intestinal inflammation by regulating the gut microbiota. Gut Microbes 14, 2057779 (2022).
Google Scholar
Turnbaugh, P. J. et al. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444, 1027–1031 (2006).
Google Scholar
Turnbaugh, P. J., Bäckhed, F., Fulton, L. & Gordon, J. I. Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe 3, 213–223 (2008).
Google Scholar
Bäckhed, F., Manchester, J. K., Semenkovich, C. F. & Gordon, J. I. Mechanisms underlying the resistance to diet-induced obesity in germ-free mice. Proc. Natl Acad. Sci. USA 104, 979–984 (2007).
Google Scholar
Moretti, C. H. et al. Germ‐free mice are not protected against diet‐induced obesity and metabolic dysfunction. Acta Physiol. 231, e13581 (2021).
Google Scholar
Rabot, S. et al. High fat diet drives obesity regardless the composition of gut microbiota in mice. Sci. Rep. 6, 32484 (2016).
Google Scholar
Fleissner, C. K. et al. Absence of intestinal microbiota does not protect mice from diet-induced obesity. Br. J. Nutr. 104, 919–929 (2010).
Google Scholar
Ley, R. E. et al. Obesity alters gut microbial ecology. Proc. Natl Acad. Sci. USA 102, 11070–11075 (2005).
Google Scholar
Arumugam, M. et al. Enterotypes of the human gut microbiome. Nature 473, 174–180 (2011).
Google Scholar
Duncan, S. H. et al. Human colonic microbiota associated with diet, obesity and weight loss. Int. J. Obes. 32, 1720–1724 (2008).
Google Scholar
Sze, M. A. & Schloss, P. D. Looking for a signal in the noise: revisiting obesity and the microbiome. mBio 7, e01018–e01116 (2016).
Google Scholar
Dalby, M. J. Questioning the foundations of the gut microbiota and obesity. Philos. Trans. R. Soc. Lond. B Biol. Sci. 378, 20220221 (2023).
Google Scholar
Gurung, M. et al. Role of gut microbiota in type 2 diabetes pathophysiology. EBioMedicine 51, 102590 (2020).
Google Scholar
Ryan, P. M. et al. Metformin and dipeptidyl peptidase-4 inhibitor differentially modulate the intestinal microbiota and plasma metabolome of metabolically dysfunctional mice. Can. J. Diabetes 44, 146–155.e2 (2020).
Google Scholar
Fan, Y. & Pedersen, O. Gut microbiota in human metabolic health and disease. Nat. Rev. Microbiol. 19, 55–71 (2021). This review explores the connection between the gut microbiota, its microbial compounds and their roles in healthy metabolism and in metabolic diseases.
Google Scholar
Pascale, A. et al. Microbiota and metabolic diseases. Endocrine 61, 357–371 (2018).
Google Scholar
Chey, W. D., Kurlander, J. & Eswaran, S. Irritable bowel syndrome. JAMA 313, 949 (2015).
Google Scholar
Vervier, K. et al. Two microbiota subtypes identified in irritable bowel syndrome with distinct responses to the low FODMAP diet. Gut 71, 1821–1830 (2022).
Google Scholar
Bootz-Maoz, H. et al. Diet-induced modifications to human microbiome reshape colonic homeostasis in irritable bowel syndrome. Cell Rep. 41, 111657 (2022).
Google Scholar
Duan, R., Zhu, S., Wang, B. & Duan, L. Alterations of gut microbiota in patients with irritable bowel syndrome based on 16S rRNA-targeted sequencing: a systematic review. Clin. Transl. Gastroenterol. 10, e00012 (2019).
Google Scholar
Serrano-Moreno, C. et al. Diets for inflammatory bowel disease: what do we know so far? Eur. J. Clin. Nutr. 76, 1222–1233 (2022).
Google Scholar
Dong, C. et al. Meat intake is associated with a higher risk of ulcerative colitis in a large European prospective cohort study. J.Crohns Colitis 16, 1187–1196 (2022).
Google Scholar
Rohr, M. W., Narasimhulu, C. A., Rudeski-Rohr, T. A. & Parthasarathy, S. Negative effects of a high-fat diet on intestinal permeability: a review. Adv. Nutr. 11, 77–91 (2020).
Google Scholar
Schmitt, M. & Greten, F. R. The inflammatory pathogenesis of colorectal cancer. Nat. Rev. Immunol. 21, 653–667 (2021).
Google Scholar
O’Keefe, S. J. D. et al. Fat, fibre and cancer risk in African Americans and rural Africans. Nat. Commun. 6, 6342 (2015).
Google Scholar
Zhou, Z., Chen, J., Yao, H. & Hu, H. Fusobacterium and colorectal cancer. Front. Oncol. https://doi.org/10.3389/fonc.2018.00371 (2018).
Tjalsma, H., Boleij, A., Marchesi, J. R. & Dutilh, B. E. A bacterial driver–passenger model for colorectal cancer: beyond the usual suspects. Nat. Rev. Microbiol. 10, 575–582 (2012).
Google Scholar
Estruch, R. et al. Primary prevention of cardiovascular disease with a mediterranean diet supplemented with extra-virgin olive oil or nuts. N. Engl. J. Med. 378, e34 (2018).
Google Scholar
Delgado-Lista, J. et al. Long-term secondary prevention of cardiovascular disease with a Mediterranean diet and a low-fat diet (CORDIOPREV): a randomised controlled trial. Lancet 399, 1876–1885 (2022).
Google Scholar
Sobiecki, J. G. et al. A nutritional biomarker score of the Mediterranean diet and incident type 2 diabetes: integrated analysis of data from the MedLey randomised controlled trial and the EPIC-InterAct case-cohort study. PLoS Med. 20, e1004221 (2023).
Google Scholar
Haskey, N. et al. A Mediterranean diet pattern improves intestinal inflammation concomitant with reshaping of the bacteriome in ulcerative colitis: a randomised controlled trial. J. Crohns Colitis 17, 1569–1578 (2023).
Google Scholar
Staudacher, H. M. et al. Clinical trial: a Mediterranean diet is feasible and improves gastrointestinal and psychological symptoms in irritable bowel syndrome. Aliment. Pharmacol. Ther. 59, 492–503 (2024).
Google Scholar
Barnes, L. L. et al. Trial of the mind diet for prevention of cognitive decline in older persons. N. Engl. J. Med. 389, 602–611 (2023).
Google Scholar
Suskind, D. L. et al. The specific carbohydrate diet and diet modification as induction therapy for pediatric Crohn’s disease: a randomized diet controlled trial. Nutrients 12, 3749 (2020).
Google Scholar
Lewis, J. D. et al. A randomized trial comparing the specific carbohydrate diet to a Mediterranean diet in adults with Crohn’s disease. Gastroenterology 161, 837–852.e9 (2021).
Google Scholar
Wilson, B. et al. Faecal and urine metabolites, but not gut microbiota, may predict response to low FODMAP diet in irritable bowel syndrome. Aliment. Pharmacol. Ther. 58, 404–416 (2023).
Google Scholar
Cox, S. R. et al. Effects of low FODMAP diet on symptoms, fecal microbiome, and markers of inflammation in patients with quiescent inflammatory bowel disease in a randomized trial. Gastroenterology 158, 176–188.e7 (2020).
Google Scholar
Poslt Königová, M., Sebalo Vňuková, M., Řehořková, P., Anders, M. & Ptáček, R. The effectiveness of gluten-free dietary interventions: a systematic review. Front. Psychol. 14, 1107022 (2023).
Google Scholar
Bonder, M. J. et al. The influence of a short-term gluten-free diet on the human gut microbiome. Genome Med. 8, 45 (2016).
Google Scholar
Francavilla, A. et al. Gluten-free diet affects fecal small non-coding RNA profiles and microbiome composition in celiac disease supporting a host-gut microbiota crosstalk. Gut Microbes 15, 2172955 (2023).
Google Scholar
Hahn, D., Hodson, E. M. & Fouque, D. Low protein diets for non-diabetic adults with chronic kidney disease. Cochrane Database Syst. Rev. 10, CD001892 (2020).
Google Scholar
Hsu, C.-K. et al. Effects of low protein diet on modulating gut microbiota in patients with chronic kidney disease: a systematic review and meta-analysis of international studies. Int. J. Med. Sci. 18, 3839–3850 (2021).
Google Scholar
Garcia-Mazcorro, J. F., Mills, D. A., Murphy, K. & Noratto, G. Effect of barley supplementation on the fecal microbiota, caecal biochemistry, and key biomarkers of obesity and inflammation in obese db/db mice. Eur. J. Nutr. 57, 2513–2528 (2018).
Google Scholar
Connolly, M. L., Tuohy, K. M. & Lovegrove, J. A. Wholegrain oat-based cereals have prebiotic potential and low glycaemic index. Br. J. Nutr. 108, 2198–2206 (2012).
Google Scholar
Chen, L. et al. Short- and long-read metagenomics expand individualized structural variations in gut microbiomes. Nat. Commun. 13, 3175 (2022).
Google Scholar
Shalon, D. et al. Profiling the human intestinal environment under physiological conditions. Nature 617, 581–591 (2023).
Google Scholar
Finishing the euchromatic sequence of the human genome. Nature 431, 931–945 (2004).
Abdill, R. J., Adamowicz, E. M. & Blekhman, R. Public human microbiome data are dominated by highly developed countries. PLoS Biol. 20, e3001536 (2022).
Google Scholar
Browne, H. P. et al. Boosting microbiome science worldwide could save millions of children’s lives. Nature 625, 237–240 (2024).
Google Scholar
Schei, K. et al. Early gut mycobiota and mother-offspring transfer. Microbiome 5, 107 (2017).
Google Scholar
Zhang, F., Aschenbrenner, D., Yoo, J. Y. & Zuo, T. The gut mycobiome in health, disease, and clinical applications in association with the gut bacterial microbiome assembly. Lancet Microbe 3, e969–e983 (2022).
Google Scholar
Liang, G. & Bushman, F. D. The human virome: assembly, composition and host interactions. Nat. Rev. Microbiol. 19, 514–527 (2021).
Google Scholar
Schulfer, A. et al. Fecal viral community responses to high-fat diet in mice. mSphere 5, e00833–e00919 (2020).
Google Scholar
Pargin, E. et al. The human gut virome: composition, colonization, interactions, and impacts on human health. Front. Microbiol. 14, 963173 (2023).
Google Scholar
Pärnänen, K. et al. Maternal gut and breast milk microbiota affect infant gut antibiotic resistome and mobile genetic elements. Nat. Commun. 9, 3891 (2018).
Google Scholar
Pärnänen, K. M. et al. Early-life formula feeding is associated with infant gut microbiota alterations and an increased antibiotic resistance load. Am. J. Clin. Nutr. 115, 407–421 (2022).
Google Scholar
Stege, P. B. et al. Impact of long-term dietary habits on the human gut resistome in the Dutch population. Sci. Rep. 12, 1892 (2022).
Google Scholar
Oliver, A. et al. Association of diet and antimicrobial resistance in healthy U.S. adults. mBio 13, e0010122 (2022).
Google Scholar
Jacka, F. N. et al. Correction to: a randomised controlled trial of dietary improvement for adults with major depression (the ‘SMILES’ trial). BMC Med. 16, 236 (2018).
Google Scholar
Parletta, N. et al. A Mediterranean-style dietary intervention supplemented with fish oil improves diet quality and mental health in people with depression: a randomized controlled trial (HELFIMED). Nutr. Neurosci. 22, 474–487 (2019).
Google Scholar
Horn, J., Mayer, D. E., Chen, S. & Mayer, E. A. Role of diet and its effects on the gut microbiome in the pathophysiology of mental disorders. Transl. Psychiatry 12, 164 (2022). This review compiles evidence from preclinical and clinical studies investigating the impact of dietary interventions on various psychiatric and neurological disorders, to highlight the role of diet-induced microbial alterations and potential benefits for brain health.
Google Scholar
Govindpani, K. et al. Vascular dysfunction in Alzheimer’s disease: a prelude to the pathological process or a consequence of it? J. Clin. Med. 8, 651 (2019).
Google Scholar
Kinney, J. W. et al. Inflammation as a central mechanism in Alzheimer’s disease. Alzheimers Dement. 4, 575–590 (2018).
Berding, K. et al. Feed your microbes to deal with stress: a psychobiotic diet impacts microbial stability and perceived stress in a healthy adult population. Mol. Psychiatry 28, 601–610 (2023).
Google Scholar
Adams, J. et al. Comprehensive nutritional and dietary intervention for autism spectrum disorder — a randomized, controlled 12-month trial. Nutrients 10, 369 (2018).
Google Scholar
Ghalichi, F., Ghaemmaghami, J., Malek, A. & Ostadrahimi, A. Effect of gluten free diet on gastrointestinal and behavioral indices for children with autism spectrum disorders: a randomized clinical trial. World J. Pediatr. 12, 436–442 (2016).
Google Scholar
Ross, F. C. et al. Existing and future strategies to manipulate the gut microbiota with diet as a potential adjuvant treatment for psychiatric disorders. Biol. Psychiatry 95, 348–360 (2023).
Google Scholar
Source: nature.com
Add comment