Diet and the Intestinal Microbiome: Associations, Functions, and Implications for Health and Disease

In the paper

“The initial intestinal colonization pattern depends upon mode of delivery1.”

What the sources say

• Not checked yetcites [1] Dominguez-Bello, 2011, Development of the human gastrointestinal microbiota and insights from high-throughput sequencing, Gastroenterology source

In the paper

“The mutual relationship between the intestinal microbiota and its mammalian host is influenced by diet.”

In the paper

“MOS are indigestible glycans that remain whole as they travel through the intestinal tract to the colon, where they nourish specific colonic bacteria.”

In the paper

“A healthy human fetus develops in an environment that is thought to be largely sterile1.”

What the sources say

• Not checked yetcites [1] Dominguez-Bello, 2011, Development of the human gastrointestinal microbiota and insights from high-throughput sequencing, Gastroenterology source

In the paper

“There was also a shift towards a more stable, adult-like microbiota with weaning3.”

What the sources say

• Not checked yetcites [3] Koenig, 2011, Succession of microbial consortia in the developing infant gut microbiome, Proc Natl Acad Sci U S A source

In the paper

“Multiple studies have established differences in the composition of the intestinal microbiota based on whether infants are breast- or formula-fed5-7.”

What the sources say

• Not checked yetcites [5] Penders, 2006, Factors influencing the composition of the intestinal microbiota in early infancy, Pediatrics source
• Not checked yetcites [6] Stark, 1982, The microbial ecology of the large bowel of breast-fed and formula-fed infants during the first year of life, J Med Microbiol source
• Not checked yetcites [7] Yoshioka, 1983, Development and differences of intestinal flora in the neonatal period in breast-fed and bottle-fed infants, Pediatrics source

In the paper

“Similarities among individual infants can be attributed to the major taxonomic groups associated with the infant diet.”

In the paper

“Ultimately, the intestinal microbiota of the young resemble that of the adult by approximately the age of 34 (Figure 1).”

What the sources say

• Not checked yetcites [4] Yatsunenko, 2012, Human gut microbiome viewed across age and geography, Nature source

In the paper

“It is believed that MOS benefit the infant by functioning as prebiotics and selectively promoting growth of members of the genus Bifidobacterium.”

In the paper

“The microbiota can produce small molecules that are absorbed by the host and affect many important physiological processes.”

In the paper

“Recent studies have shown that select strains of Bifidobacteria possess specialized enzymes capable of metabolizing MOS glycans15-17.”

What the sources say

• Not checked yetcites [15] LoCascio, 2007, Glycoprofiling of bifidobacterial consumption of human milk oligosaccharides demonstrates strain specific, preferential consumption of small chain glycans secreted in early human lactation, J Agric Food Chem source
• Not checked yetcites [16] Marcobal, 2010, Consumption of human milk oligosaccharides by gut-related microbes, J Agric Food Chem source
• Not checked yetcites [17] Sela, 2011, An infant-associated bacterial commensal utilizes breast milk sialyloligosaccharides, J Biol Chem source

In the paper

“there are important bioactive compounds in human milk that contribute to physiologic functions such as absorption and digestion of nutrients, immune protection, and defense against potentially pathogenic gut microbes8, 9.”

What the sources say

• Not checked yetcites [8] Le Huerou-Luron, 2010, Breast- v. formula-feeding: impacts on the digestive tract and immediate and long-term health effects, Nutr Res Rev source
• Not checked yetcites [9] Hernell, 2011, Human milk vs. cow's milk and the evolution of infant formulas, Nestle Nutr Workshop Ser Pediatr Program

In the paper

“Characterization of the intestinal microbiota in a single infant, over a period of 2.5 years, showed how the bacterial taxa changed with life events such as illnesses, dietary changes, and antibiotic treatment.”

What the sources say

• Not checked yetcites [3] Koenig, 2011, Succession of microbial consortia in the developing infant gut microbiome, Proc Natl Acad Sci U S A source

In the paper

“Age-dependent and societal differences in the intestinal microbiota could result from differences in diet.”

In the paper

“Interestingly, the greatest change in the composition of the infant's intestinal microbiota occurred with the introduction of solid foods.”

What the sources say

• Not checked yetcites [3] Koenig, 2011, Succession of microbial consortia in the developing infant gut microbiome, Proc Natl Acad Sci U S A source

In the paper

“these bacteria have been linked to fortification of the gut mucosal protection through activities against pathogens12, 13.”

What the sources say

• Not checked yetcites [12] Lievin, 2000, Bifidobacterium strains from resident infant human gastrointestinal microflora exert antimicrobial activity, Gut source
• Not checked yetcites [13] Fukuda, 2011, Bifidobacteria can protect from enteropathogenic infection through production of acetate, Nature source

In the paper

“In controlled dietary experiments in humans, variations in intake of resistant starch or non-starch polysaccharide altered levels of specific bacterial taxa such as Ruminococuccus bromii and Eubacterium rectale32.”

What the sources say

• Not checked yetcites [32] Walker, 2011, Dominant and diet-responsive groups of bacteria within the human colonic microbiota, ISME J source

In the paper

“Oligosaccharide-enriched formulas have been developed, and infants fed these specialized formulas have been shown to harbor greater numbers of bifidobacteria in the feces 5,23.”

What the sources say

• Not checked yetcites [5] Penders, 2006, Factors influencing the composition of the intestinal microbiota in early infancy, Pediatrics source
• Not checked yetcites [23] Veereman-Wauters, 2011, Physiological and bifidogenic effects of prebiotic supplements in infant formulae, J Pediatr Gastroenterol Nutr source

In the paper

“significant and meaningful alterations in the intestinal microbiota have been associated with alterations in diet, primarily influenced by the consumption of dietary fiber from fruits, vegetables, and other plants.”

In the paper

“These taxa were shown to selectively metabolize specific insoluble carbohydrate substrates, based on in vitro analyses of human fecal samples33.”

What the sources say

• Not checked yetcites [33] Leitch, 2007, Selective colonization of insoluble substrates by human faecal bacteria, Environ Microbiol source

In the paper

“a formula that was more similar to breast milk, in terms of protein composition and amount of phosphate, was found to increase proportions of Bifidobacterium similar to a formula that was supplemented with these bacteria24.”

What the sources say

• Not checked yetcites [24] Hascoet, 2011, Effect of formula composition on the development of infant gut microbiota, J Pediatr Gastroenterol Nutr source

In the paper

“Detection of enterotypes depends upon the computational approach used to analyze datasets40.”

What the sources say

• Not checked yetcites [40] Koren, 2013, A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets, PLoS Comput Biol source

In the paper

“A comparison of the intestinal microbiota between different primates and mammals found that humans clustered more closely with other primates than non-primates.”

What the sources say

• Not checked yetcites [28] Ley, 2008, Evolution of mammals and their gut microbes, Science source

In the paper

“the abundant intestinal bacterium Bacteroides thetaiotaomicron, undergoes changes in gene expression that allow it to predominantly metabolize host-derived glycans when dietary sources of these molecules are unavailable35.”

What the sources say

• Not checked yetcites [35] Sonnenburg, 2005, Glycan foraging in vivo by an intestine-adapted bacterial symbiont, Science source

In the paper

“Associations between diet and bacterial taxonomy, based on answers to dietary questionnaires collected over long periods of time, indicate that diet affects the proportions of Prevotella vs Bacteroides in U.S. populations30.”

What the sources say

• Not checked yetcites [30] Wu, 2011, Linking long-term dietary patterns with gut microbial enterotypes, Science source

In the paper

“multiple studies have shown a decrease in Clostridia colonization of breast-fed infants19, 20 including colonization with Clostridium difficile 21.”

What the sources say

• Not checked yetcites [19] Stark, 1982, Clostridia isolated from the feces of infants during the first year of life, J Pediatr source
• Not checked yetcites [20] Harmsen, 2000, Analysis of intestinal flora development in breast-fed and formula-fed infants by using molecular identification and detection methods, J Pediatr Gastroenterol Nutr
• Not checked yetcites [21] Stark, 1982, Colonization of the large bowel by Clostridium difficile in healthy infants: quantitative study, Infect Immun source

In the paper

“Model systems have demonstrated that an important function of the intestinal microbiome is its ability to metabolize complex carbohydrates and polysaccharides, collectively termed glycans, which leads to production of short-chain fatty acids through fermentation34.”

What the sources say

• Not checked yetcites [34] Koropatkin, 2012, How glycan metabolism shapes the human gut microbiota, Nat Rev Microbiol source

In the paper

“An analysis of the NIH-sponsored Human Microbiome Project dataset revealed that organisms that are phylogenetically related and functionally similar tend to co-exist within the same environment, consistent with niche-driven community structures.”

In the paper

“A number of studies have associated increased microbial richness, at either the taxonomic or gene level, with diets higher in fruits, vegetables, and fiber42-44.”

What the sources say

• Not checked yetcites [42] Claesson, 2012, Gut microbiota composition correlates with diet and health in the elderly, Nature source
• Not checked yetcites [43] Cotillard, 2013, Dietary intervention impact on gut microbial gene richness, Nature source
• Not checked yetcites [44] Le Chatelier, 2013, Richness of human gut microbiome correlates with metabolic markers, Nature source

In the paper

“Bacteroides are also present in a lower concentration in breast-fed infants7, 20.”

What the sources say

• Not checked yetcites [7] Yoshioka, 1983, Development and differences of intestinal flora in the neonatal period in breast-fed and bottle-fed infants, Pediatrics source
• Not checked yetcites [20] Harmsen, 2000, Analysis of intestinal flora development in breast-fed and formula-fed infants by using molecular identification and detection methods, J Pediatr Gastroenterol Nutr

In the paper

“extreme short-term diets, such as those devoid of any carbohydrates, have been shown to have a more-pronounced effect on the human microbiota31.”

What the sources say

• Not checked yetcites [31] David, 2014, Diet rapidly and reproducibly alters the human gut microbiome, Nature source

In the paper

“diet was the most important determinant where human microbiota samples were most similar to samples from omnivorous primate species28.”

What the sources say

• Not checked yetcites [28] Ley, 2008, Evolution of mammals and their gut microbes, Science source

In the paper

“De Fillipo et al. demonstrated that the composition of the intestinal microbiota differs significantly between children living in a rural African village in Burkina Faso and those living in Europe36.”

What the sources say

• Not checked yetcites [36] De 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 source

In the paper

“Sources of glycans for intestinal microbiome metabolism are derived not only from diet but also from mucus produced by the host.”

In the paper

“Genome sequencing of numerous strains, particularly Bifidobacterium longum subsp. Infantis, has confirmed the presence of genes that allow these organisms to metabolize mammalian carbohydrates 18.”

What the sources say

• Not checked yetcites [18] Zivkovic, 2011, Human milk glycobiome and its impact on the infant gastrointestinal microbiota, Proc Natl Acad Sci U S A source

In the paper

“The inverse relationship between Prevotella and Bacteroides has been reproduced in studies comparing the intestinal microbiota of residents of agrarian societies in South America and Bangladesh with residents of industrialized societies4, 37.”

What the sources say

• Not checked yetcites [4] Yatsunenko, 2012, Human gut microbiome viewed across age and geography, Nature source
• Not checked yetcites [37] Lin, 2013, Distinct distal gut microbiome diversity and composition in healthy children from Bangladesh and the United States, PLoS One source

In the paper

“At a minimum, the intestinal microbiome might be a useful biomarker of long-term consumption of healthy or unhealthy diets.”

In the paper

“Diet-associated bacterial clades, called “co-abundance groups”, included Bacteroides and Prevotella (Figure 2).”

What the sources say

• Not checked yetcites [42] Claesson, 2012, Gut microbiota composition correlates with diet and health in the elderly, Nature source

In the paper

“The association was much stronger for red and processed meats than for other meats.”

What the sources say

• Not checked yetcites [66] Jowett SL SC, Pearce MS, et al. nfluence of dietary factors on the clinical course of ulcerative colitis: a prospective cohort study. Gut 2004;53:1479–1484. source

In the paper

“studies in Japanese populations have shown that following consumption of seaweeds, genes that encode enzymes that metabolize marine red algae are transferred from marine-associated bacteria to specific bacterial taxa in the intestinal microbiome52.”

What the sources say

• Not checked yetcites [52] Hehemann, 2010, Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota, Nature source

In the paper

“Wang et al. identified a novel pathway linking dietary lipid intake, the intestinal microbiota, and atherosclerosis (Figure 3)57, 58.”

What the sources say

• Not checked yetcites [57] Wang, 2011, Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease, Nature source
• Not checked yetcites [58] Tang, 2013, Intestinal microbial metabolism of phosphatidylcholine and cardiovascular risk, N Engl J Med source

In the paper

“The intestinal microbiota may also contribute to development of atherosclerosis by producing metabolites of the dietary lipid phosphatidylcholine that are associated with the risk for coronary vascular disease.”

What the sources say

• Not checked yetcites [57] Wang, 2011, Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease, Nature source
• Not checked yetcites [58] Tang, 2013, Intestinal microbial metabolism of phosphatidylcholine and cardiovascular risk, N Engl J Med source

In the paper

“The composition of the intestinal microbiota is thought to be an important factor in pathogenesis, because patients with IBD and healthy individuals have been reported to have differences in intestinal microbiota63.”

What the sources say

• Not checked yetcites [63] Peterson, 2008, Metagenomic approaches for defining the pathogenesis of inflammatory bowel diseases, Cell Host Microbe source

In the paper

“production of short-chain fatty acids by the intestinal microbiome increases mucosal immune tolerance through the activation of G-protein coupled receptors (GPCRs) and the subsequent activation of T regulatory cells61 (Figure 3).”

What the sources say

• Not checked yetcites [61] Tremaroli, 2012, Functional interactions between the gut microbiota and host metabolism, Nature source

In the paper

“intestinal microbiome-dependent effects of diet have been associated with risk of coronary vascular disease and intestinal inflammation.”

In the paper

“Diet has also been associated with other types of microbes in the gut, such as archaea, fungi, and bacteriophage (Figure 2)45-47.”

What the sources say

• Not checked yetcites [45] Dollive, 2012, A tool kit for quantifying eukaryotic rRNA gene sequences from human microbiome samples, Genome Biol source
• Not checked yetcites [46] Hoffmann, 2013, Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents, PLoS One source
• Not checked yetcites [47] Minot, 2011, The human gut virome: inter-individual variation and dynamic response to diet, Genome Res source

In the paper

“a polymorphism in the gene encoding Dectin1 (CLEC7A) was associated with a severe form of ulcerative colitis in humans49.”

What the sources say

• Not checked yetcites [49] Iliev, 2012, Interactions between commensal fungi and the C-type lectin receptor Dectin-1 influence colitis, Science source

In the paper

“In a prospective study, Jowett et al. found that patients who reported consuming higher amounts of meat, eggs, protein, and alcohol were more likely to experience a relapse of UC66.”

What the sources say

• Not checked yetcites [66] Jowett SL SC, Pearce MS, et al. nfluence of dietary factors on the clinical course of ulcerative colitis: a prospective cohort study. Gut 2004;53:1479–1484. source

In the paper

“A recent study49 demonstrated that mice lacking Dectin1 had increased susceptibility to chemically induced colitis, due to their altered responses to indigenous fungi.”

What the sources say

• Not checked yetcites [49] Iliev, 2012, Interactions between commensal fungi and the C-type lectin receptor Dectin-1 influence colitis, Science source

In the paper

“Most of the nonpathogenic bacterial taxa that express genes encoding these lyases are found in 3 of the 4 major phyla of the human intestinal microbiome.”

What the sources say

• Not checked yetcites [60] Craciun, 2012, Microbial conversion of choline to trimethylamine requires a glycyl radical enzyme, Proc Natl Acad Sci U S A source

In the paper

“The pathogenesis of IBD involves an abnormal immune response, likely to environmental factors, in genetically susceptible individuals62.”

What the sources say

• Not checked yetcites [62] Abraham, 2009, Inflammatory bowel disease, N Engl J Med source

In the paper

“Methanobrevibacter can increase the production of short-chain fatty acids by metabolizing hydrogen, a byproduct of bacterial carbohydrate fermentation 48.”

What the sources say

• Not checked yetcites [48] Samuel, 2006, A humanized gnotobiotic mouse model of host-archaeal-bacterial mutualism, Proc Natl Acad Sci U S A source

In the paper

“Together with the well-described health benefits of plant-based diets typical of vegetarians and vegans50, 51, it is likely that the intestinal microbiome associated with residence in industrialized areas results from the Western diet.”

What the sources say

• Not checked yetcites [50] Craig, 2010, Nutrition concerns and health effects of vegetarian diets, Nutr Clin Pract source
• Not checked yetcites [51] Craig, 2009, Health effects of vegan diets, Am J Clin Nutr source

In the paper

“A similar pathway has been identified for conversion of dietary carnitine, which is high in red meat, into TMAO59.”

What the sources say

• Not checked yetcites [59] Koeth, 2013, Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis, Nat Med source

In the paper

“many molecules in foods are substrates for the intestinal microbiota, which then produce small molecules that, after metabolism in the liver, affect host physiology (Figure 2)53.”

What the sources say

• Not checked yetcites [53] Holmes, 2012, Gut microbiota composition and activity in relation to host metabolic phenotype and disease risk, Cell Metab source

In the paper

“Researchers have identified the bacterial gene family responsible for the conversion of choline into TMA; these are called choline TMA lyases60.”

What the sources say

• Not checked yetcites [60] Craciun, 2012, Microbial conversion of choline to trimethylamine requires a glycyl radical enzyme, Proc Natl Acad Sci U S A source

In the paper

“The features of the intestinal microbiome of people on Western diets are associated with the increasing incidence of diseases such as obesity, coronary vascular disease, metabolic syndrome, and certain malignancies.”

In the paper

“carbohydrate consumption is associated with the proportion of the archaeon, Methanobrevibacter,46 in the intestinal microbiota.”

What the sources say

• Not checked yetcites [46] Hoffmann, 2013, Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents, PLoS One source

In the paper

“only long-term alterations in environment and diet were associated with the composition of the microbiota, supporting observations previously made in studies performed with dietary questionnaires30.”

What the sources say

• Not checked yetcites [30] Wu, 2011, Linking long-term dietary patterns with gut microbial enterotypes, Science source

In the paper

“omnivorous subjects produced more TMAO than vegans or vegetarians following ingestion of L-carnitine, via an intestinal microbiota-dependent mechanism59.”

What the sources say

• Not checked yetcites [59] Koeth, 2013, Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis, Nat Med source

In the paper

“Diet can alter the functional metabolism of the intestinal microbiome at a genomic level.”

In the paper

“A Cochrane meta-analysis found similar efficacy of formulas with variable degrees of protein hydrolysis in treating CD79.”

What the sources say

• Not checked yetcites [79] Zachos, 2001, Enteral nutritional therapy for inducing remission of Crohn's disease, Cochrane Database Syst Rev

In the paper

“These diets are also effective in maintaining remission78.”

What the sources say

• Not checked yetcites [78] Takagi, 2006, Effectiveness of an ‘half elemental diet’ as maintenance therapy for Crohn's disease: a randomized-controlled trial, Aliment Pharmacol Ther source

In the paper

“As for non-intestinal diseases, it was recently shown that mice fed high fiber diets are protected from allergic inflammation in the lung through a mechanism involving production of propionate and the activation of GPR4171.”

What the sources say

• Not checked yetcites [71] Trompette, 2014, Gut microbiota metabolism of dietary fiber influences allergic airway disease and hematopoiesis, Nat Med source

In the paper

“A large amount of data indicate the importance of the diet in establishing the composition and metabolome of the human intestinal microbiome.”

In the paper

“A subsequent randomized controlled trial evaluating various nutritional interventions for patients with CD showed that bowel rest was not a major factor in achieving remission74.”

What the sources say

• Not checked yetcites [74] Greenberg, 1988, Controlled trial of bowel rest and nutritional support in the management of Crohn's disease, Gut source

In the paper

“Although IBD does not develop through an allergic disease process, this study demonstrates that diet can alter immune responsiveness by modifying the metabolome of the intestinal microbiota.”

In the paper

“Literature on this subject suggests that there is a profound change in the fecal microbiota following EEN therapy80, 81.”

What the sources say

• Not checked yetcites [80] Leach, 2008, Sustained modulation of intestinal bacteria by exclusive enteral nutrition used to treat children with Crohn's disease, Aliment Pharmacol Ther source
• Not checked yetcites [81] Lionetti, 2005, Enteral nutrition and microflora in pediatric Crohn's disease, JPEN J Parenter Enteral Nutr source

In the paper

“Despite the conflicting evidence, bowel rest with TPN may improve symptoms, at least in the short-term, in patients presenting with a severe exacerbation of CD.”

In the paper

“fasting has been shown to have an effect on the gut microbiota in mice75”

What the sources say

• Not checked yetcites [75] Crawford, 2009, Regulation of myocardial ketone body metabolism by the gut microbiota during nutrient deprivation, Proc Natl Acad Sci U S A source

In the paper

“The results of these studies are broadly consistent with those from epidemiology studies associating IBD with industrialized nations67, 68 and the consumption of a Western diet.”

What the sources say

• Not checked yetcites [67] Molodecky, 2012, Increasing incidence and prevalence of the inflammatory bowel diseases with time, based on systematic review, Gastroenterology source
• Not checked yetcites [68] Lashner, 1995, Epidemiology of inflammatory bowel disease, Gastroenterol Clin North Am source

In the paper

“Functional studies in animal models, together with descriptive association studies in humans, provide evidence for the role of diet in disease pathogenesis, through its effects on intestinal microbes.”

In the paper

“Interestingly, there does not appear to be major differences in efficacy of EEN based on the composition of the formula.”

What the sources say

• Not checked yetcites [79] Zachos, 2001, Enteral nutritional therapy for inducing remission of Crohn's disease, Cochrane Database Syst Rev