Studies on intestinal microbiota raise questions as to whether consuming a modern diet that is hyperhygienic and highly processed results in reduction of microbial functional maturity by preventing the exchange of beneficial genes between gut microbiota and microbes from the diet and environment. In addition, the increasing use of sanitization and antibiotics in food processing may contribute to a profound impact on the gut microbiome . The activity and composition of the gut microbiome is also affected by an individual’s attitudes, taste preference, and dietary habits that are likewise influenced by culture, the global food industry, and media. Furthermore, there is growing evidence that the human diet has undergone profound simplification since industrialization, which has occurred too recently on an evolutionary time scale for the human genome to adapt.This maladaption to the modern diet has been hypothesized to be the underlying evolutionary origin of “civilization diseases,” such as cardiovascular disease, in the 21st century.The gut microbiome is remarkably stable and shares a high degree of functional capability across all human healthy individuals; however, intestinal bacterial communities are diverse and variable from person to person.For example,vertical plant tower intraindividual variability of the fecal microbiota is consistently lower than between-subject variability.

Recent discoveries of greater similarities in gut microbiota between monozygotic and dizygotic twin adults or between family members versus unrelated individuals highlight the powerful impact of shared environment, lifestyle, and diet as a whole on intestinal microbial configuration.Interestingly, in mice, genetics was shown to play less of a role than diet on the gut microbial community.Age and health are also associated with alterations to the intestinal microbiota that might explain inter individual differences as well.In general, dietary effects on the intestinal microbiota can occur on short and long time frames. An acute influx of energy and nutrients is assumed to induce bacterial blooms in a short time frame. As expected, short-term dietary modulation in a humanized gnotobiotic mouse model resulted in a significant shift within the microbiome in a single day.A similar change in fecal microbiome within a day of a dietary change was confirmed in a controlled-feeding study of 10 healthy volunteers.Likewise, in as short as 3 days, dramatic changes in the community composition of the gut microbiome occurred with alterations in calorie content of the diet for several individuals.Long-term, diet-driven structural and functional differences in the microbial community are apparent in populations from different geographic areas with very distinct dietary patterns. Studies employing culture-based and culture-independent methods found significant global differences in the fecal microbiota from individuals in different cultures.For example, children from Burkino Faso practice a diet with high fiber and low animal protein and fat, consisting mainly of cereals, legumes, and vegetables.

Italian children practice a typical Western-style diet characterized by high animal protein, simple sugars, starch, and fat with less vegetables and fiber than the diet in Burkina Faso. The microbial composition of children from Burkina Faso revealed higher levels of Prevotella and Xylanibacter , Treponema , and Butyrivibrio , which were absent in the Italian children.A similar observation was reported in a comparison of Bangladeshi and American children. Bangladeshi children, who consumed a diet similar to that of children from BurkinoFaso, exhibited a significantly greater bacterial diversity and distinct microbial community composition enriched in Prevotella, Butyrivibrio, and Oscillospira and depleted in Bacteroides in comparison with American children.Both children and adults from the United States have very different microbiota from rural communities in Malawi and Venezuela. A typical U.S. diet that is rich in protein differs from the diets of Malawians and Venezuelan populations that are dominated by maize, cassava, and other plant-derived polysaccharides. The major change in macronutrient composition may contribute to the higher bacterial diversity of those in Malawi and Venezuela compared to adults living in U.S. metropolitan areas.Comparative studies between different geographic regions have been challenged with multiple dependent factors such as socioeconomic status, genetics, dietary habits, age, hygiene, food quality, pathogen exposure, history of antibiotic use, body composition , stress, physical activity, and other environmental conditions. Despite ethnic and geographical variation, both comparative and controlled feeding studies conducted in the United States and Africa revealed similar patterns of the Bacteroides−Prevotella balance based on diet.

Global macronutrient profiles are recognized to modulate the intestinal microbial community. In a study charactering human fecal samples from 98 individuals, Wu et al. found that saturated fat and animal protein decreased microbial diversity and enriched the abundance of Bacteroidetes and Actinobacteria, whereas a plant-based diet with high carbohydrates increased microbial diversity and was linked with Firmicutes and Proteobacteria abundance.In a recent study, gnotobiotic mice colonized with 10 human intestinal bacterial species were provided diets containing various percentages of protein , fat , polysaccharides , and sucrose.Intriguingly, the authors were able to explain over half of the variation in species abundance in the fecal microbiome depending on the food ingested, even when the mice were fed more complex diets.Recent evidence suggests that extreme changes in carbohydrate intake will lead to a shift in the composition of human gut microbiota. Although reports of the relative proportion of Bacteroidetes and Firmicutes with respect to carbohydrate intake are contradictory in several studies, certain genera and bacterial families are associated with levels of carbohydrate consumption. For example, in human obese subjects, a declining carbohydrate intake induced a marked progressive decrease of a butyrate-producing subgroup of Clostridial cluster XIVa as well as bifidobacteria. A reduced-carbohydrate, high-protein diet resulted in decreased proportions of butyrate and total shortchain fatty acid by reducing butyrate-producing bacteria such as the Roseburia/Eubacterium rectale group.Likewise, Bifidobacterium levels decreased in mice fed a low-carbohydrate, high-fat “Atkin’s style diet” compared with their counterparts consuming a high-carbohydrate, high-fiber, and low-fat diet.More detailed documentation of diet-induced specific changes on the gut microbial relative abundance was reviewed by Krajmalnik-Brown et al.Although many inconsistent results have been observed regarding the impact of diet on phylumwide changes in gut microbiota composition and energy harvesting capacity, many have suggested that the complex relationship might involve the severity of obesity, microbial adaptation to diet over time and perhaps an age−microbial interaction. Notably, the high-fat, low-fiber diet has also been recognized as a well-established model of obesity; thus, the impact of differences in caloric consumption and subsequent response from host metabolic perturbations through weight change needs to be considered. Studies on experimental animals need to control for body mass and composition, which will allow a better comparison of the gut microbiota without the confounding effects of weight/ adiposity.Although it appears that the overall macro-nutrient profile affects general patterns of fecal microbiota, understanding the responses of intestinal microbial communities to major dietary composition presents an additional set of challenges. For example, a carbohydrate-rich diet is often accompanied with elevated dietary fiber intake and a low percentage of protein and fat; hence, the microbial composition should respond to the complex profile of the dietary structure instead of the shifting of a single dietary component. If not specifically controlled, dietary factors will affect the gut microbiome in both energy intake and relative proportion of macronutrients in the diet. Recently, interest in microbial response to major dietary composition has re-emerged in many reviews. In this section, we will explore the complex influence of dietary structure on the gut microbiome including gluten-free diet, vegetarian/vegan diet, and food restriction. Gluten-free Diet. To determine the effect of a gluten-free diet on the gut microbiome, a crossover study involving 10 healthy subjects consuming a conventional diet without any restriction, except for gluten-containing products,growing strawberries vertically resulted in a reduction in bacterial populations that are generally regarded as beneficial for human health such as Bifidobacterium and Lactobacillus, as well as an increase in opportunistic pathogens such as Escherichia coli and total Enterobacteriaceae.

The observed changes might be explained by the associated reduction in polysaccharide intake that may have prebiotic action for certain bacteria. Provision of a gluten-free but polysaccharide- and probiotic-rich food intake could avoid this situation and provide better support to balance gut microbiota.Several small-scale culturebased studies examined the effect of a vegetarian diet on the composition of the human gut microbiota.However, results from these studies offer no clear consensus.A crossover study reported that a Western-style diet high in meat facilitates the growth of Bacteroides, Bifidobacterium, Peptostreptococcus, and Lactobacillus spp. compared to a vegetarian diet.Similarly, elevated Bacteroides spp. levels were observed in a 4 week high beef diet.Dietary modulation of 12 healthy male subjects with either mixed Western, lacto-ovo vegetarian, or vegan diet in a 20 day crossover study revealed significantly lower fecal lactobacilli and enterococci in the vegetarian diet than in the other two diets.Hayashi et al. reported a predominance of bacteria from the Clostridium cluster XVIII, in addition to high levels of bacteria from Clostridium clusters IV and XIVa in the fecal microbiome of a strict vegetarian woman.However, Liszt et al.and Kabeerdoss et al.report that the proportions of Clostridium clusters IV and XIVa are lower in vegetarians. The inconsistent findings from these studies might be due to the use of different experimental methods, the limited number of individuals in these studies, or poorly matched control groups.The stool pH was lower among 250 subjects on strict vegan or vegetarian diets with equal numbers of age- and gender-matched control subjects compared to individuals consuming ordinary omnivorous diets, and this likely inhibited the growth of E. coli and Enterobacteriaceae in vegetarian/vegan subjects.Furthermore, it has been established that microbial− mammalian co-metabolites may be measured in urine that may provide information concerning intestinal microbial metabolic activities.Clear metabolic differences in urine associated with the vegetarian and omnivorous diets have been observed, with creatine, carnitine, acetylacarnitine, and trimethylamine-N-oxide being elevated in a high meat diet and p-hydroxyphenylacetate increased in a vegetarian diet.A 40% calorie restriction in mice for 9 weeks revealed small changes in fecal anaerobic populations using fluorescent in situ hybridization and denaturing gradient gel electrophoresis .Similarly, using conventional anaerobic culture of rat feces,small changes in fecal anaerobic bacterial populations with no significant difference in the bacterial cellular fatty acid profile were observed after caloric restriction.Patients with rheumatoid arthritis who participated in an intermittent modified 8-day fasting therapy also exhibited no changes in the fecal bacterial counts of clostridia, bifidobacteria, Candida, E. coli, Enterococcus, or Lactobacillus. Interestingly, the Lactobacillus spp. and archaeon Methanobrevibacter smithii counts were elevated in anorexia patients compared with healthy controls, and this difference was associated with the increased efficiency in removal of excess H2 from the human GI tract.In hibernating ground squirrels, the relative proportion of Firmicutes was decreased relative to Verrucomicrobia and Bacteroidetes after several months of fasting.Follow-up studies need to address the impact of food restriction in both the short- and long-term scale and the global significance of these changes in the intestinal microbiota.In normal healthy individuals, the large intestine receives contents that escape from the terminal ileum, which are subsequently mixed and retained for 20−140 h to provide an opportunity for microbes to ferment a range of undigested dietary substances. The transition time through the colon strongly influences the gut microbial community, which has been correlated with stool weight and excretion of bacterial dry matter. Although few data exist on the nutrients that enter the colon from the small intestine, generally, about 85−90% of dietary sugar and starch, 66−95% of protein, and almost all fat are absorbed before entering the large intestine depending on genetics and other dietary factors. It is well established that dietary intake of non-digestible material, in combination with host-derived peptides,bile acids,and mucin,influences microbial anaerobic fermentation activity and microbial population in the colon. Increasing evidence supports that shifts in the microbial composition occur in response to changes in the content of the diet. Such changes can be expected to result from differential effects of substrates on stimulating or inhibiting microbial growth. Perhaps one of the greatest challenges in nutrition is to interrogate the interaction between the complex food matrices that integrate a wide range of biologically active compounds. This raises the question of whether there are specific dietary ingredients that have stronger selective forces on microbial diversity and configuration of functional communities than others. Dietary Fiber. Dietary fiber and complex carbohydrates consist of non-starch polysaccharides, such as resistant starch and oligosaccharides, as well as edible indigestible plant components that are resistant to digestion by endogenous enzymes in the small intestine and become the primary source of microbial fermentation, particularly in the large intestine.