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

In the paper

“Bifidobacteria are also thought to modulate the intestinal immune system and have been shown to increase the production of immunoglobulin A14.”

What the sources say

• Not checked yetcites [14] Ouwehand, 2002, The role of the intestinal microflora for the development of the immune system in early childhood, Eur J Nutr

In the paper

“Infants born vaginally are initially colonized by bacterial taxa found in the vagina, such as Lactobacillus and Prevotella, whereas infants who are born by Cesarean section are initially colonized by bacteria found in the skin microbiota2.”

What the sources say

• Not checked yetcites [2] Dominguez-Bello, 2010, Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns, Proc Natl Acad Sci U S A source

In the paper

“Human milk oligosaccharides (MOS) are bioactive compounds that are the third largest component of human milk10.”

What the sources say

• Not checked yetcites [10] LoCascio, 2010, Broad conservation of milk utilization genes in Bifidobacterium longum subsp. infantis as revealed by comparative genomic hybridization, Appl Environ Microbiol source

In the paper

“Within the first year of life, there are significant inter-individual differences in the composition of the intestinal microbiota, yet some similarities exist.”

In the paper

“Significant colonization of the gut begins immediately after delivery although, remarkably, bacteria can be found in an infant's first meconium2.”

What the sources say

• Not checked yetcites [2] Dominguez-Bello, 2010, Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns, Proc Natl Acad Sci U S A source

In the paper

“Some of the differences in the composition of the intestinal microbiota in breast-fed vs formula-fed infants are thought to be secondary to the effects of MOS on these bacteria—many studies have shown an increased proportion of Bifidobacteria in breast-fed infants 6, 7, 11 compared to formula-fed infants.”

What the sources say

• 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
• Not checked yetcites [11] Balmer, 1989, Diet and faecal flora in the newborn: breast milk and infant formula, Arch Dis Child source

In the paper

“differences in microbial richness in individuals consuming an agrarian plant-based vs a Western diet, which is high in meat and fat.”

In the paper

“After this primary inoculation, infants are regularly exposed to microbes, and diversity increases rapidly3.”

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

“Consumption of various nutrients affects the structure of the microbial community and provides substrates for microbial metabolism.”

In the paper

“a greater proportion of Prevotella in the human intestinal microbiota is a marker of residence in an agrarian culture, whereas a greater proportion of Bacteroides is associated with residence in more-industrialized regions38.”

What the sources say

• Not checked yetcites [38] Arumugam, 2011, Enterotypes of the human gut microbiome, Nature source

In the paper

“differences in the taxonomy of the intestinal microbiota were associated with residence in different environments. The most extreme differences were observed in community residence vs long-term residential care, attributed to differences in diet—community residents typically consume diets higher in fiber and lower in fat42.”

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

“Short-term dietary interventions in healthy humans lead to statistically significant and rapid alterations in the composition of the intestinal microbiota, but the magnitude of the effect is modest relative to inter-subject variability in the intestinal microbiota, and changes in taxonomy are not consistent among individuals30.”

What the sources say

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

In the paper

“aerobic organisms seem to be more prevalent in the feces of breast-fed infants, whereas anaerobic and facultatively anaerobic organisms, which preferentially use anerobic glycolysis, are more commonly found in the feces of formula-fed infants6.”

What the sources say

• 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

In the paper

“The MetaHit consortium has proposed that individuals can be classified as having intestinal microbiota predominantly composed of Prevotella or Bacteroides; a third group has higher proportions of Ruminococcus, compared with the others. These categories have been named “enterotypes”38.”

What the sources say

• Not checked yetcites [38] Arumugam, 2011, Enterotypes of the human gut microbiome, Nature source

In the paper

“certain Bacteroides strains are able to digest MOS,22 suggesting a potential competitive relationship between Bifidobacterium and Bacteroides in breast-fed infants.”

What the sources say

• Not checked yetcites [22] Marcobal, 2011, Bacteroides in the infant gut consume milk oligosaccharides via mucus-utilization pathways, Cell Host Microbe source

In the paper

“A better term might be enterogradient, based on whether Bacteroides or Prevotella dominate the intestinal microbial community—it appears that these 2 genera generally do not exist in equal proportions in the human intestine 41.”

What the sources say

• Not checked yetcites [41] Faust, 2012, Microbial co-occurrence relationships in the human microbiome, PLoS Comput Biol source

In the paper

“However, Bacteroides and Prevotella are taxonomically and functionally similar genera, yet do not co-exist in the intestine; this is an exception to the model, possibly resulting from competition within the same niche41.”

What the sources say

• Not checked yetcites [41] Faust, 2012, Microbial co-occurrence relationships in the human microbiome, PLoS Comput Biol source

In the paper

“The microbiota of children in Burkina Faso had greater amounts of Prevotella, lower amounts of Bacteroides, overall greater microbial richness, and produced higher levels of short-chain fatty acids than the microbiota of European children.”

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

“Foods rich in phosphatidylcholine are a major source of choline.”

In the paper

“Because of the effects that diet can have on the structure and function of the intestinal microbiome, it is reasonable to suspect that diet may be involved in the pathogenesis of IBD, or even a potential therapeutic target.”

In the paper

“In composite, studies associating diet with the intestinal microbiome have consistently associated agrarian-based diets (high in fruits, vegetables, and fiber) with distinct bacterial taxa, an increase in bacterial richness at the taxonomic and gene level, and better health, compared with Western diets.”

In the paper

“Co-abundance groups were associated with the health status of elderly individuals—diets higher in fruits, vegetable, and fiber (associated with community residence) were linked to lower levels of frailty.”

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

“Catabolism of choline by the intestinal microbiota results in the formation of the gas, trimethylamine (TMA), which is metabolized by the liver into trimethylamine oxide (TMAO)—a small molecule that is strongly associated with the increased risk for coronary vascular disease in humans.”

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

“increased consumption of fruits and vegetables in higher-fiber diets and energy-restricted diets were both associated with increased bacterial gene richness (Figure 2)43, 44.”

What the sources say

• 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

“TMAO was also found to promote the development of atherosclerosis in animal models, providing the first link between dietary lipid intake, the intestinal microbiota, and the risk for the development of atherosclerosis57.”

What the sources say

• Not checked yetcites [57] Wang, 2011, Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease, Nature source

In the paper

“A systematic review concluded that diets with high levels of total fats, polyunsaturated fatty acids, omega-6 fatty acids, and meat were associated with an increased risk of CD and UC; high fiber and high fruit intake were associated with a decreased risk of CD, whereas high vegetable intake was associated with a decreased for UC65.”

What the sources say

• Not checked yetcites [65] Hou, 2011, Dietary intake and risk of developing inflammatory bowel disease: a systematic review of the literature, Am J Gastroenterol source

In the paper

“diet might also affect intestinal fungal communities, which have been associated with pathogenesis of inflammatory bowel diseases (IBD)49.”

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

“indigestible carbohydrates in the diet are fermented by the intestinal microbiota to produce short-chain fatty acids, which regulate immune function54, 55, intestinal hormone production, and lipogenesis56.”

What the sources say

• Not checked yetcites [54] Maslowski, 2009, Regulation of inflammatory responses by gut microbiota and chemoattractant receptor GPR43, Nature source
• Not checked yetcites [55] Smith, 2013, The microbial metabolites, short-chain fatty acids, regulate colonic Treg cell homeostasis, Science source
• Not checked yetcites [56] Samuel, 2008, Effects of the gut microbiota on host adiposity are modulated by the short-chain fatty-acid binding G protein-coupled receptor, Gpr41, Proc Natl Acad Sci U S A source

In the paper

“increased bacterial gene richness was also associated with human health, whereas lower bacterial richness was associated with obesity, insulin resistance, dylipidemia, and inflammatory disorders.”

What the sources say

• 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

“These findings support the effects of diet on the structure and metabolome of the gut microbiome and its importance in disease pathogenesis.”

In the paper

“Because dietary antigens can stimulate the mucosal immune system, bowel rest with total parenteral nutrition (TPN) has been used to treat certain patients with IBD72.”

What the sources say

• Not checked yetcites [72] Graham, 2002, Nutritional factors in inflammatory bowel disease, Gastroenterol Clin North Am source

In the paper

“In this model system, the exacerbation of colitis may involve a direct effect of Bilophila wadsworthia, which promote a T helper 1 cell-mediated immune response and/or the production of hydrogen sulfide, a toxic small molecule that disrupts intestinal epithelial barrier function70.”

What the sources say

• Not checked yetcites [70] Sartor, 2012, Gut microbiota: Diet promotes dysbiosis and colitis in susceptible hosts, Nat Rev Gastroenterol Hepatol source

In the paper

“It is possible that bowel rest alters the gut microbiota in a way that reduces symptoms of IBD, because 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

“In a prospective study of 30 patients with CD treated with bowel rest and TPN, 25 (83%) achieved initial remission, but relapse was common73.”

What the sources say

• Not checked yetcites [73] Muller, 1983, Total parenteral nutrition as the sole therapy in Crohn's disease—a prospective study, Br J Surg source

In the paper

“Consumption of milk fat has been shown to alter bile acid composition, promoting expansion of the sulphite-reducing pathobiont Bilophila wadsworthia and exacerbating colitis in IL10 knockout mice69.”

What the sources say

• Not checked yetcites [69] Devkota, 2012, Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il10-/- mice, Nature source

In the paper

“However, nutritional therapy has been shown to be effective for patients with CD, although its mechanism of action has not been characterized.”

In the paper

“Exclusive enteral nutrition (EEN) with elemental, semi-elemental, and defined formula diets have been widely studied for their ability to induce remission in patients with CD and are considered first-line therapy in certain parts of the world76, 77.”

What the sources say

• Not checked yetcites [76] Sandhu, 2010, Guidelines for the management of inflammatory bowel disease in children in the United Kingdom, J Pediatr Gastroenterol Nutr
• Not checked yetcites [77] Caprilli, 2006, European evidence based consensus on the diagnosis and management of Crohn's disease: special situations, Gut source