The human intestinal microbiota is composed of 10(13) to 10(14) microorganisms whose collective genome ("microbiome") contains at least 100 times as many genes as our own genome. We analyzed approximately 78 million base pairs of unique DNA sequence and 2062 polymerase chain reaction-amplified 16S ribosomal DNA sequences obtained from the fecal DNAs of two healthy adults. Using metabolic function analyses of identified genes, we compared our human genome with the average content of previously sequenced microbial genomes. Our microbiome has significantly enriched metabolism of glycans, amino acids, and xenobiotics; methanogenesis; and 2-methyl-d-erythritol 4-phosphate pathway-mediated biosynthesis of vitamins and isoprenoids. Thus, humans are superorganisms whose metabolism represents an amalgamation of microbial and human attributes.

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Metagenomic Analysis of the Human Distal Gut Microbiome

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Food, Nutrition, Physical Activity, and the Prevention of Cancer : a Global Perspective : 食物、栄養、身体活動とがんの予防 : 世界的展望(後篇)

Accumulating evidence suggests that the human intestinal microbiota contributes to the aetiology of colorectal cancer (CRC), not only via the pro-carcinogenic activities of specific pathogens but also via the influence of the wider microbial community, particularly its metabolome. Recent data have shown that the short-chain fatty acids acetate, propionate and butyrate function in the suppression of inflammation and cancer, whereas other microbial metabolites, such as secondary bile acids, promote carcinogenesis. In this Review, we discuss the relationship between diet, microbial metabolism and CRC and argue that the cumulative effects of microbial metabolites should be considered in order to better predict and prevent cancer progression.

The gut microbiota, bacterial metabolites and colorectal cancer

The importance of the gut-brain axis in maintaining homeostasis has long been appreciated. However, the past 15 yr have seen the emergence of the microbiota (the trillions of microorganisms within ...

The Microbiota-Gut-Brain Axis

The microbial communities that colonize different regions of the human gut influence many aspects of health. In the healthy state, they contribute nutrients and energy to the host via the fermentation of nondigestible dietary components in the large intestine, and a balance is maintained with the host's metabolism and immune system. Negative consequences, however, can include acting as sources of inflammation and infection, involvement in gastrointestinal diseases, and possible contributions to diabetes mellitus and obesity. Major progress has been made in defining some of the dominant members of the microbial community in the healthy large intestine, and in identifying their roles in gut metabolism. Furthermore, it has become clear that diet can have a major influence on microbial community composition both in the short and long term, which should open up new possibilities for health manipulation via diet. Achieving better definition of those dominant commensal bacteria, community profiles and system characteristics that produce stable gut communities beneficial to health is important. The extent of interindividual variation in microbiota composition within the population has also become apparent, and probably influences individual responses to drug administration and dietary manipulation. This Review considers the complex interplay between the gut microbiota, diet and health.

The role of the gut microbiota in nutrition and health

A comparison of five methods for extraction of bacterial DNA from human faecal samples.

Butyrate and other SCFA produced by bacterial fermentation of resistant starch (RS) or nonstarch polysaccharides (NSP) promote human colonic health To examine variation in fecal variables, especially butyrate, among individuals and the response to these fibers, a randomized cross-over study was conducted that compared the effects of foods supplying 25 g of NSP or 25 g of NSP plus 22 g of RS/d over 4 wk in 46 healthy adults (16 males, 30 females; age 31-66 y) Fecal SCFA levels varied widely among participants at entry (butyrate concentrations: 35-326 mmol/kg; butyrate excretions: 03-182 mmol/48 h) BMI explained 27% of inter-individual butyrate variation, whereas protein, starch, carbohydrate, fiber, and fat intake explained up to 16, 6, 2, 4, and 2% of butyrate variation, respectively Overall, acetate, butyrate, and total SCFA concentrations were higher when participants consumed RS compared with entry and NSP diets, but individual responses varied Individual and total fecal SCFA excretion, weight, and moisture were higher than those for habitual diets when either fiber diet was consumed SCFA concentrations (except butyrate) and excretions were higher for males than for females Butyrate levels increased in response to RS in most individuals but often decreased when entry levels were high Fecal butyrate and ammonia excretions were positively associated ((2) = 076; P < 0001) In conclusion, fecal butyrate levels vary widely among individuals but consuming a diet high in RS usually increases levels and may help maintain colorectal health

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Fecal Butyrate Levels Vary Widely among Individuals but Are Usually Increased by a Diet High in Resistant Starch

Phylotypes related to Ruminococcus bromii are abundant in the large bowel of humans and increase in response to a diet high in resistant starch

Fermentation products, SCFA, particularly butyrate, are considered a sign of 'good' bowel health but the influence of bacterial population composition and diet on inter-individual difference in metabolites and colonic health is poorly understood. Faecal specimens were collected weekly from eight healthy human volunteers over 12 weeks. Dietary intake was self-reported and ten macronutrient factors were analysed at selected weekly periods. Faecal weight, pH and moisture were recorded, and SCFA concentrations were measured in all samples. From each specimen, DNA was prepared and eubacterial 16S rRNA gene PCR performed. Bacterial population profiles were captured by denaturing gradient gel electrophoresis (DGGE) of PCR products, and multivariate statistical analysis was performed. Faecal weight, pH and moisture varied widely within and between individuals. Average total SCFA concentrations over 12 weeks ranged from 36.9 to 144.4 mmol/kg in 48 h specimens and faecal butyrate concentrations ranged from 1.8 to 48.5 mmol/kg. Two individuals with butyrate concentrations below 10 mmol/kg were considered to be 'low butyrate types' and may represent an at-risk population for bowel health. Dietary fat, sugar and carbohydrate showed weak correlation with SCFA (R - 0.612, P = 0.015; R 0.607, P = 0.016; R 0.610, P = 0.016, respectively) and butyrate concentrations (R - 0.593, P = 0.02; R 0.504, P = 0.054; R 0.528, P = 0.043, respectively). Multivariate analysis of DGGE bacterial profiles demonstrated concise and repeated grouping of intra-individual samples, but these were combined with distinct inter-individual differences (analysis of similarities P or = 0.99) The exact relationship of these SCFA values to the overall bacterial profiles and SCFA-producer bacterial groups was not direct nor linear.

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Alexandra L. McOrist

Papers

A comparison of five methods for extraction of bacterial DNA from human faecal samples.

Fecal Butyrate Levels Vary Widely among Individuals but Are Usually Increased by a Diet High in Resistant Starch

Phylotypes related to Ruminococcus bromii are abundant in the large bowel of humans and increase in response to a diet high in resistant starch

Bacterial population dynamics and faecal short-chain fatty acid (SCFA) concentrations in healthy humans.

Comparison of two selective media for the detection and enumeration of Lactobacilli in human faeces.