Long-term dietary intake influences the structure and activity of the trillions of microorganisms residing in the human gut, but it remains unclear how rapidly and reproducibly the human gut microbiome responds to short-term macronutrient change. Here we show that the short-term consumption of diets composed entirely of animal or plant products alters microbial community structure and overwhelms inter-individual differences in microbial gene expression. The animal-based diet increased the abundance of bile-tolerant microorganisms (Alistipes, Bilophila and Bacteroides) and decreased the levels of Firmicutes that metabolize dietary plant polysaccharides (Roseburia, Eubacterium rectale and Ruminococcus bromii). Microbial activity mirrored differences between herbivorous and carnivorous mammals, reflecting trade-offs between carbohydrate and protein fermentation. Foodborne microbes from both diets transiently colonized the gut, including bacteria, fungi and even viruses. Finally, increases in the abundance and activity of Bilophila wadsworthia on the animal-based diet support a link between dietary fat, bile acids and the outgrowth of microorganisms capable of triggering inflammatory bowel disease. In concert, these results demonstrate that the gut microbiome can rapidly respond to altered diet, potentially facilitating the diversity of human dietary lifestyles.

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Diet rapidly and reproducibly alters the human gut microbiome

Indigenous Bacteria from the Gut Microbiota Regulate Host Serotonin Biosynthesis

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 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

Animals assemble and maintain a diverse but host-specific gut microbial community. In addition to characteristic microbial compositions along the longitudinal axis of the intestines, discrete bacterial communities form in microhabitats, such as the gut lumen, colonic mucus layers and colonic crypts. In this Review, we examine how the spatial distribution of symbiotic bacteria among physical niches in the gut affects the development and maintenance of a resilient microbial ecosystem. We consider novel hypotheses for how nutrient selection, immune activation and other mechanisms control the biogeography of bacteria in the gut, and we discuss the relevance of this spatial heterogeneity to health and disease.

/pdf/gut-biogeography-of-the-bacterial-microbiota-3n30t8tim5.pdf

Gut biogeography of the bacterial microbiota

https://www.gastrojournal.org/article/S0016-5085(11)01081-X/pdf

Bile acid is a host factor that regulates the composition of the cecal microbiota in rats

To improve the sensitivity of a kit, ESPLINE INFLUENZA A&B for rapid diagnosis of influenza by detecting influenza A or B virus specific nucleoproteins (NP), the ESPLINE INFLUENZA A&B-N was developed by using newly established monoclonal antibodies (MAbs) to the respective NP molecule. MAbs FVA2-11 and FrB1-03 recognize the epitope on the amino acid region 59-130aa of the NP molecule of influenza A virus, and that on the region 72-191aa of the NP of influenza B virus, respectively. The new kit detected influenza A and B virus antigens with a detection limit of 10(2.0)-10 (2.7) pfu/test, which is 4-1000 times higher than that of the original kit. Importantly, this kit detected each of influenza A viruses of the known hemagglutinin (HA) subtypes (H1-H15) including the H5N1 viruses recently isolated from human and avian sources in Asia. The kit also detected all of the 15 representative influenza B virus strains tested. The ESPLINE INFLUENZA A&B-N is thus a rapid and highly sensitive and specific kit for the diagnosis of either influenza A or B virus infections.

Improvement of a rapid diagnosis kit to detect either influenza A or B virus infections.

Ingestion of a high-fat (HF) diet is known to enhance bile acid (BA) secretion, but precise information about the BA molecular species is lacking, especially information on the conjugated BAs in enterohepatic circulation. As cholesterol is the precursor of BAs, we analyzed alterations of the entire BA metabolic pathway in response to a HF diet without the addition of cholesterol and BA in the diet. Additionally, we evaluated the relationships between BA metabolism and some disorders, such as plasma transaminase activities and glucose intolerance induced by the HF diet. Acclimated WKAH/HkmSlc male rats (3 wk old) were divided into two groups fed a control or the HF diet for 22 wk. Fasting blood glucose was measured during the experimental period, and an intraperitoneal glucose tolerance test was performed at week 21. As a result, ingestion of the HF diet selectively increased the concentration of taurocholic acid in the bile and small intestinal contents as well as deoxycholic acid in the large intestinal contents and feces. These results indicated a selective increase of 12α-hydroxylated BA concentrations in response to the HF diet. Moreover, fecal 12α-hydroxylated BA concentration was positively correlated with cumulative energy intake, visceral adipose tissue weight, and glucose intolerance. The present study suggests that fecal 12α-hydroxylated BA is a non-invasive marker that can detect the early phase of glucose intolerance.

Alteration of Bile Acid Metabolism by a High-Fat Diet Is Associated with Plasma Transaminase Activities and Glucose Intolerance in Rats.

A method of immunoassay of H5 subtype influenza A virus by which the virus can be accurately assayed even in cases where a certain level of mutation has occurred in the H5 subtype influenza A virus, and a kit therefor, and a novel anti-H5 subtype influenza A virus monoclonal antibody which can be used for the immunoassay are disclosed. The antibody or an antigen-binding fragment thereof of the present invention undergoes antigen-antibody reaction with hemagglutinin of H5 subtype influenza A virus, and the corresponding epitope of the antibody or an antigen-binding fragment thereof is located in a region other than the receptor subdomain (excluding C-terminal region thereof consisting of 11 amino acids), which antibody or an antigen-binding fragment thereof does not have neutralizing activity against the influenza A virus.

Anti-(influenza a virus subtype h5 hemagglutinin) monoclonal antibody

A novel severe acute respiratory syndrome-associated coronavirus (SARS-CoV) has been discovered. The detection of both antigens and antibodies in SARS-CoV from human specimens with suspected SARS plays an important role in preventing infection. We developed a novel rapid immunochromatographic test (RICT) based on the sandwich format enzyme immunoassay (EIA) with an all-in-one device for detecting the native nucleocapsid antigen (N-Ag) of SARS-CoV using monoclonal antibodies (MoAbs), which we produced by immunizing recombinant N-Ag to mice. RICT is a qualitative assay for respiratory aspirates and serum specimens. With this assay, a positive result can be judged subjectively by the appearance of a blue line on the device 15 min after the sample is applied. RICT with several pairs of MoAbs showed a high sensitivity for the detection of recombinant N-Ag as well as viral N-Ag of SARS-CoV. rSN122 and rSN21-2 were the best MoAbs for immobilized antibody and enzyme labeling, respectively. With regard to analytical sensitivity, RICT detected N-Ag at 31 pg/mL for recombinant N-Ag, and at 1.99 x 10(2) TCID(50)/mL for SARS-CoV. The specificity of RICT was 100% when 150 human sera and 50 nasopharyngeal aspirates (NSPs) were used. RICT based on an EIA using the rSN122/rSN21-2 pair is a sensitive, specific, and reliable rapid assay for detecting N-Ag in SARS-CoV treated with either heat or Triton X-100.

https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcla.20070

Nobuyuki Fujii

Papers

Bile acid is a host factor that regulates the composition of the cecal microbiota in rats

Improvement of a rapid diagnosis kit to detect either influenza A or B virus infections.

Alteration of Bile Acid Metabolism by a High-Fat Diet Is Associated with Plasma Transaminase Activities and Glucose Intolerance in Rats.

Anti-(influenza a virus subtype h5 hemagglutinin) monoclonal antibody

Novel rapid immunochromatographic test based on an enzyme immunoassay for detecting nucleocapsid antigen in SARS‐associated coronavirus