Dietary Selection Pressures and Their Impact on the Gut Microbiome

Rodríguez, 2015, The composition of the gut microbiota throughout life, with an emphasis on early life, Microb Ecol Health Dis, 26, 26050 Bergström, 2014, Establishment of intestinal microbiota during early life: a longitudinal, explorative study of a large cohort of Danish infants, Appl Environ Microbiol, 80, 2889, 10.1128/AEM.00342-14 Koenig, 2011, Succession of microbial consortia in the developing infant gut microbiome, Proc Natl Acad Sci U S A, 108, 4578, 10.1073/pnas.1000081107 Zmora, 2019, You are what you eat: diet, health and the gut microbiota, Nat Rev Gastroenterol Hepatol, 16, 35, 10.1038/s41575-018-0061-2 Gilbert, 2018, Current understanding of the human microbiome, Nat Med, 24, 392, 10.1038/nm.4517 Gentile, 2018, The gut microbiota at the intersection of diet and human health, Science, 362, 776, 10.1126/science.aau5812 Yatsunenko, 2012, Human gut microbiome viewed across age and geography, Nature, 486, 222, 10.1038/nature11053 Wu, 2019, Interactions between food and gut microbiota: impact on human health, Annu Rev Food Sci Technol, 10, 389, 10.1146/annurev-food-032818-121303 Albenberg, 2014, Diet and the intestinal microbiome: associations, functions, and implications for health and disease, Gastroenterology, 146, 1564, 10.1053/j.gastro.2014.01.058 Carmody, 2019, Cooking shapes the structure and function of the gut microbiome, Nat Microbiol, 4, 2052, 10.1038/s41564-019-0569-4 Wu, 2011, Linking long-term dietary patterns with gut microbial enterotypes, Science, 334, 105, 10.1126/science.1208344 Schnorr, 2014, Gut microbiome of the Hadza hunter-gatherers, Nat Commun, 5, 3654, 10.1038/ncomms4654 Sonnenburg, 2016, Diet-induced extinction in the gut microbiota compounds over generations, Nature, 529, 212, 10.1038/nature16504 Deehan, 2016, The fiber gap and the disappearing gut microbiome: implications for human nutrition, Trends Endocrinol Metab, 27, 239, 10.1016/j.tem.2016.03.001 Johnson, 2019, Personalized Microbiome Class Students, Walter J, Menon R, Koecher K, Knights D. Daily sampling reveals personalized diet-microbiome associations in humans, Cell Host Microbe, 25, 789, 10.1016/j.chom.2019.05.005 David, 2014, Diet rapidly and reproducibly alters the human gut microbiome, Nature, 505, 559, 10.1038/nature12820 Zeevi, 2015, Personalized nutrition by prediction of glycemic responses, Cell, 163, 1079, 10.1016/j.cell.2015.11.001 Filippo, 2010, Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa, Proc Natl Acad Sci U S A, 107, 14691, 10.1073/pnas.1005963107 Gomez, 2016, Gut microbiome of coexisting BaAka pygmies and Bantu reflects gradients of traditional subsistence patterns, Cell Rep, 14, 2142, 10.1016/j.celrep.2016.02.013 Jha, 2018, Gut microbiome transition across a lifestyle gradient in Himalaya, PLOS Biol, 16, 10.1371/journal.pbio.2005396 Mancabelli, 2017, Meta-analysis of the human gut microbiome from urbanized and pre-agricultural populations, Environ Microbiol, 19, 1379, 10.1111/1462-2920.13692 Brito, 2016, Mobile genes in the human microbiome are structured from global to individual scales, Nature, 535, 435, 10.1038/nature18927 Clemente, 2012, The impact of the gut microbiota on human health: an integrative view, Cell, 148, 1258, 10.1016/j.cell.2012.01.035 Obregon-Tito, 2015, Subsistence strategies in traditional societies distinguish gut microbiomes, Nat Commun, 6, 6505, 10.1038/ncomms7505 Keohane, 2020, Microbiome and health implications for ethnic minorities after enforced lifestyle changes, Nat Med, 26, 1089, 10.1038/s41591-020-0963-8 Fragiadakis, 2019, Links between environment, diet, and the hunter-gatherer microbiome, Gut Microbes, 10, 216, 10.1080/19490976.2018.1494103 Pasolli, 2019, Extensive unexplored human microbiome diversity revealed by over 150,000 genomes from metagenomes spanning age, geography, and lifestyle, Cell, 176, 649, 10.1016/j.cell.2019.01.001 Sonnenburg, 2019, Vulnerability of the industrialized microbiota, Science, 366, 10.1126/science.aaw9255 Rampelli, 2015, Metagenome sequencing of the Hadza hunter-gatherer gut microbiota, Curr Biol, 25, 1682, 10.1016/j.cub.2015.04.055 Zupancic, 2012, Analysis of the gut microbiota in the Old Order Amish and its relation to the metabolic syndrome, PLoS One, 7, 10.1371/journal.pone.0043052 Turroni, 2016, Fecal metabolome of the Hadza hunter-gatherers: a host-microbiome integrative view, Sci Rep, 6, 32826, 10.1038/srep32826 Smits, 2017, Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania, Science, 357, 802, 10.1126/science.aan4834 Davenport, 2014, Seasonal variation in human gut microbiome composition, PLoS One, 9, 10.1371/journal.pone.0090731 Liu, 2016, Unique features of ethnic Mongolian gut microbiome revealed by metagenomic analysis, Sci Rep, 6, 34826, 10.1038/srep34826 Zhang, 2014, Mongolians core gut microbiota and its correlation with seasonal dietary changes, Sci Rep, 4, 5001, 10.1038/srep05001 Hisada, 2015, Inter- and intra-individual variations in seasonal and daily stabilities of the human gut microbiota in Japanese, Arch Microbiol, 197, 919, 10.1007/s00203-015-1125-0 Koliada, 2020, Seasonal variation in gut microbiota composition: cross-sectional evidence from Ukrainian population, BMC Microbiol, 20, 100, 10.1186/s12866-020-01786-8 Dubois, 2017, The Inuit gut microbiome is dynamic over time and shaped by traditional foods, Microbiome, 5, 151, 10.1186/s40168-017-0370-7 Gómez-Gallego, 2019, The microbiota and malnutrition: impact of nutritional status during early life, Annu Rev Nutr, 39, 267, 10.1146/annurev-nutr-082117-051716 Million, 2017, Gut microbiota and malnutrition, Microb Pathog, 106, 127, 10.1016/j.micpath.2016.02.003 Trehan, 2013, Antibiotics as part of the management of severe acute malnutrition, N Engl J Med, 368, 425, 10.1056/NEJMoa1202851 Selber-Hnatiw, 2017, Human gut microbiota: toward an ecology of disease, Front Microbiol, 8, 1265, 10.3389/fmicb.2017.01265 Tidjani Alou, 2017, Gut bacteria missing in severe acute malnutrition, can we identify potential probiotics by culturomics?, Front Microbiol, 8, 899, 10.3389/fmicb.2017.00899 Goyal, 2015, Feeding the brain and nurturing the mind: Linking nutrition and the gut microbiota to brain development, Proc Natl Acad Sci U S A, 112, 14105, 10.1073/pnas.1511465112 Ahmed, 2014, An evolving perspective about the origins of childhood undernutrition and nutritional interventions that includes the gut microbiome, Ann N Y Acad Sci, 1332, 22, 10.1111/nyas.12487 Smith, 2013, Gut microbiomes of Malawian twin pairs discordant for kwashiorkor, Science, 339, 548, 10.1126/science.1229000 Gordon, 2012, The human gut microbiota and undernutrition, Sci Transl Med, 4, 137ps12, 10.1126/scitranslmed.3004347 Blanton, 2016, Gut bacteria that prevent growth impairments transmitted by microbiota from malnourished children, Science, 351, 10.1126/science.aad3311 Pekmez, 2019, Gut microbiota alterations and dietary modulation in childhood malnutrition – the role of short chain fatty acids, Clin Nutr, 38, 615, 10.1016/j.clnu.2018.02.014 Monira, 2011, Gut microbiota of healthy and malnourished children in Bangladesh, Front Microbiol, 2, 228, 10.3389/fmicb.2011.00228 Ghosh, 2014, Gut microbiomes of Indian children of varying nutritional status, PloS One, 9, 10.1371/journal.pone.0095547 Subramanian, 2014, Persistent gut microbiota immaturity in malnourished Bangladeshi children, Nature, 510, 417, 10.1038/nature13421 Kau, 2015, Functional characterization of IgA-targeted bacterial taxa from undernourished Malawian children that produce diet-dependent enteropathy, Sci Transl Med, 7, 10.1126/scitranslmed.aaa4877 Million, 2016, Increased gut redox and depletion of anaerobic and methanogenic prokaryotes in severe acute malnutrition, Sci Rep, 6, 26051, 10.1038/srep26051 Pham, 2019, Gut microbiota alteration is characterized by a proteobacteria and fusobacteria bloom in Kwashiorkor and a Bacteroidetes paucity in marasmus, Sci Rep, 9, 9084, 10.1038/s41598-019-45611-3 Kristensen, 2016, Gut microbiota in children hospitalized with oedematous and non-oedematous severe acute malnutrition in Uganda, PLoS Negl Trop Dis, 10, 10.1371/journal.pntd.0004369 Patnode, 2019, Interspecies competition impacts targeted manipulation of human gut bacteria by fiber-derived glycans, Cell, 179, 59, 10.1016/j.cell.2019.08.011 Barratt, 2017, The gut microbiota, food science and human nutrition; a timely marriage, Cell Host Microbe, 22, 134, 10.1016/j.chom.2017.07.006 Blanton, 2016, Childhood undernutrition, the gut microbiota, and microbiota-directed therapeutics, Science, 352, 10.1126/science.aad9359 Gehrig, 2019, Effects of microbiota-directed foods in gnotobiotic animals and undernourished children, Science, 365, 10.1126/science.aau4732 Raman, 2019, A sparse covarying unit that describes healthy and impaired human gut microbiota development, Science, 365, eaau4735, 10.1126/science.aau4735 Chen, 2021, A Microbiota-directed food intervention for undernourished children, N Engl J Med, 384, 1517, 10.1056/NEJMoa2023294 Garrett, 2021, Microbial nourishment for undernutrition, N Engl J Med, 384, 1566, 10.1056/NEJMe2104212 Gérard, 2019, Impact of gut microbiota on host glycemic control, Front Endocrinol, 10, 29, 10.3389/fendo.2019.00029 Cuevas-Sierra, 2019, Diet, Gut microbiota, and obesity: links with host genetics and epigenetics and potential applications, Adv Nutr, 10, S17, 10.1093/advances/nmy078 Gérard, 2017, Gut microbiome and obesity. How to prove causality?, Ann Am Thorac Soc, 14, S354, 10.1513/AnnalsATS.201702-117AW Ng, 2014, Global, regional, and national prevalence of overweight and obesity in children and adults during 1980-2013: a systematic analysis for the Global Burden of Disease Study 2013, Lancet, 384, 766, 10.1016/S0140-6736(14)60460-8 Myles, 2014, Fast food fever: reviewing the impacts of the Western diet on immunity, Nutr J, 13, 61, 10.1186/1475-2891-13-61 Zhao, 2013, The gut microbiota and obesity: from correlation to causality, Nat Rev Microbiol, 11, 639, 10.1038/nrmicro3089 Wostmann, 1983, Dietary intake, energy metabolism, and excretory losses of adult male germfree Wistar rats, Lab Anim Sci, 33, 46 Bäckhed, 2004, The gut microbiota as an environmental factor that regulates fat storage, Proc Natl Acad Sci U S A, 101, 15718, 10.1073/pnas.0407076101 Ley, 2005, Obesity alters gut microbial ecology, Proc Natl Acad Sci U S A, 102, 11070, 10.1073/pnas.0504978102 Ridaura, 2013, Gut microbiota from twins discordant for obesity modulate metabolism in mice, Science, 341, 1241214, 10.1126/science.1241214 Turnbaugh, 2006, An obesity-associated gut microbiome with increased capacity for energy harvest, Nature, 444, 1027, 10.1038/nature05414 Riva, 2017, Pediatric obesity is associated with an altered gut microbiota and discordant shifts in F irmicutes populations, Environ Microbiol, 19, 95, 10.1111/1462-2920.13463 Bervoets, 2013, Differences in gut microbiota composition between obese and lean children: a cross-sectional study, Gut Pathog, 5, 10, 10.1186/1757-4749-5-10 Hildebrandt, 2009, High-fat diet determines the composition of the murine gut microbiome independently of obesity, Gastroenterology, 137, 1716, 10.1053/j.gastro.2009.08.042 Turnbaugh, 2009, A core gut microbiome in obese and lean twins, Nature, 457, 480, 10.1038/nature07540 Turnbaugh, 2008, Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome, Cell Host Microbe, 3, 213, 10.1016/j.chom.2008.02.015 Sze, 2016, Looking for a signal in the noise: revisiting obesity and the microbiome, mBio, 7, 10.1128/mBio.01018-16 Walters, 2014, Meta-analyses of human gut microbes associated with obesity and IBD, FEBS Lett, 588, 4223, 10.1016/j.febslet.2014.09.039 Payne, 2011, The metabolic activity of gut microbiota in obese children is increased compared with normal-weight children and exhibits more exhaustive substrate utilization, Nutr Diabetes, 1, e12, 10.1038/nutd.2011.8 Schwiertz, 2010, Microbiota and SCFA in lean and overweight healthy subjects, Obesity (Silver Spring), 18, 190, 10.1038/oby.2009.167 Zhang, 2009, Human gut microbiota in obesity and after gastric bypass, Proc Natl Acad Sci U S A, 106, 2365, 10.1073/pnas.0812600106 Finucane, 2014, A taxonomic signature of obesity in the microbiome? Getting to the guts of the matter, PLoS One, 9, 10.1371/journal.pone.0084689 Stanislawski, 2019, Gut microbiota phenotypes of obesity, NPJ Biofilms Microbiomes, 5, 18, 10.1038/s41522-019-0091-8 Tims, 2013, Microbiota conservation and BMI signatures in adult monozygotic twins, ISME J, 7, 707, 10.1038/ismej.2012.146 Gophna, 2017, Oscillospira and related bacteria – From metagenomic species to metabolic features, Environ Microbiol, 19, 835, 10.1111/1462-2920.13658 Everard, 2013, Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity, Proc Natl Acad Sci U S A, 110, 9066, 10.1073/pnas.1219451110 Depommier, 2019, Supplementation with Akkermansia muciniphila in overweight and obese human volunteers: a proof-of-concept exploratory study, Nat Med, 25, 1096, 10.1038/s41591-019-0495-2 Liu, 2017, Gut microbiome and serum metabolome alterations in obesity and after weight-loss intervention, Nat Med, 23, 859, 10.1038/nm.4358 Byrne, 2015, The role of short chain fatty acids in appetite regulation and energy homeostasis, Int J Obes 2005, 39, 1331 Kimura, 2013, The gut microbiota suppresses insulin-mediated fat accumulation via the short-chain fatty acid receptor GPR43, Nat Commun, 4, 1829, 10.1038/ncomms2852 López, 2017, EJE PRIZE 2017: Hypothalamic AMPK: a golden target against obesity?, Eur J Endocrinol, 176, R235, 10.1530/EJE-16-0927 Wang, 2017, The intestinal microbiota regulates body composition through NFIL3 and the circadian clock, Science, 357, 912, 10.1126/science.aan0677 Semova, 2012, Microbiota regulate intestinal absorption and metabolism of fatty acids in the zebrafish, Cell Host Microbe, 12, 277, 10.1016/j.chom.2012.08.003 Martinez-Guryn, 2018, Small intestine microbiota regulate host digestive and absorptive adaptive responses to dietary lipids, Cell Host Microbe, 23, 458, 10.1016/j.chom.2018.03.011 Cani, 2007, Metabolic endotoxemia initiates obesity and insulin resistance, Diabetes, 56, 1761, 10.2337/db06-1491 Kootte, 2017, Improvement of insulin sensitivity after lean donor feces in metabolic syndrome is driven by baseline intestinal microbiota composition, Cell Metab, 26, 611, 10.1016/j.cmet.2017.09.008 Vrieze, 2012, Transfer of intestinal microbiota from lean donors increases insulin sensitivity in individuals with metabolic syndrome, Gastroenterology, 143, 913, 10.1053/j.gastro.2012.06.031 Mendes-Soares, 2019, Model of personalized postprandial glycemic response to food developed for an Israeli cohort predicts responses in MidWestern American individuals, Am J Clin Nutr, 110, 63, 10.1093/ajcn/nqz028 Korem, 2017, Bread affects clinical parameters and induces gut microbiome-associated personal glycemic responses, Cell Metab, 25, 1243, 10.1016/j.cmet.2017.05.002 Berry, 2020, Human postprandial responses to food and potential for precision nutrition, Nat Med, 26, 964, 10.1038/s41591-020-0934-0