Microbiome refers to the collective genomes of the micro-organisms in a particular environment, and microbiota is the community of micro-organisms themselves. The complex communities of microorganisms that colonize the human gastrointestinal tract play an important role in human health. The intestinal microbiota plays a role in metabolic, nutritional, physiological and immunological processes in the human body. It exerts important metabolic activities by extracting energy from otherwise indigestible dietary polysaccharides such as resistant starch and dietary fibers. These metabolic activities also lead to the production of important nutrients, such as short-chain fatty acids, vitamins and amino acids, which humans are unable to produce. In addition, the intestinal microbiota participates in the defense against pathogens by mechanisms such as colonization resistance and the production of antimicrobial compounds. Furthermore, the intestinal microbiota is involved in the development, maturation and maintenance of the GI sensory and motoric functions, the intestinal barrier and the mucosal immune system. These are just a few examples of the functional contributions of the intestinal microbiota to human health, a subject that is regularly reviewed.

 Microbiota diversity and health

Lower bacterial diversity has been reproducibly observed in people with inflammatory bowel disease, psoriatic arthritis, type 1 diabetes, atopic eczema, celiac disease, obesity, type 2 diabetes, and arterial stiffness than in healthy controls. In Crohn’s disease smokers have even lower gut microbiome diversity. The association between reduced diversity and disease indicates that a species-rich gut ecosystem is more robust against environmental influences, as functionally related microbes in an intact ecosystem can compensate for the function of other missing species. Consequently, diversity seems to be a generally good indicator of a “healthy gut.” But recent interventional studies indicate that major increases in dietary fiber can temporarily reduce diversity, like the microbes that digest fiber become specifically enriched, leading to a change in composition and, through competitive interactions, reduced diversity. 

The gut microbiota and obesity

The gut microbiota seems to play a role in the development and progression of obesity. Most studies of overweight and obese people show a dysbiosis characterized by a lower diversity. Germ-free mice that receive fecal microbes from obese humans gain more weight than mice that received microbes from healthy weight humans. A large study of UK twins found that a genus was rare in overweight people and when given to germ-free mice, preventing weight gain. This microbe and others correlate with lower visceral fat deposits. Although much of the confirmatory evidence comes from mouse models, long term weight gain (over 10 years) in humans correlates with low microbiota diversity, and this association is exacerbated by low dietary fiber intake. Gut microbiota dysbiosis probably promotes diet-induced obesity and metabolic complications by a variety of mechanisms including immune dysregulation, altered energy regulation, altered gut hormone regulation, and proinflammatory mechanisms. 

Effects of food on the gut microbiota

Specific foods and dietary patterns can all influence the abundance of different types of bacteria in the gut, which in turn can affect health. Examples of foods, nutrients, and dietary patterns that influence human health linked to their effect on the gut microbiota. 

High-intensity sweeteners on the gut microbiota

They are commonly used as sugar alternatives, being many times sweeter than sugar with minimal calories. Despite being “generally recognized as safe” by regulatory agencies, some animal studies have shown that these sugar substitutes may have negative effects on the gut microbiota. Sucralose, aspartame, and saccharin have been shown to disrupt the balance and diversity of gut microbiota. Mice given sucralose for six months had an increase in the expression in the gut of bacterial pro-inflammatory genes and disrupted fecal metabolites.

 Food additives on the gut microbiota

Food additives, such as emulsifiers, which are ubiquitous in processed foods, have also been shown to affect the gut microbiota in animals. Mice fed relatively low concentrations of two commonly used emulsifiers showed reduced microbial diversity compared with mice not fed with emulsifiers. 

Restrictive diets on the gut microbiota

Other areas of concern include the side effects of popular restrictive diets on gut health. These include some strict vegan diets, raw food or “clean eating” diets, gluten-free diets, and low FODMAP (fermentable oligosaccharides, disaccharides, monosaccharides, and polyols) diets used to treat irritable bowel syndrome. Vegans are viewed by some as healthier than omnivores. A study of 15 vegans and 16 omnivores found striking differences in serum metabolites generated by the gut microbes but very modest differences in gut bacterial communities. 

Animal and in vitro studies indicate that gluten-free bread reduces the microbiota dysbiosis seen in people with gluten sensitivity or celiac disease. But most people who avoid gluten do not have celiac disease or proved intolerance, and a recent large observational study showed an increased risk of heart disease in gluten avoiders, potentially because of the reduced consumption of whole grains.

One study showed that 21 healthy people had substantially different gut microbiota profiles after four weeks on a gluten-free diet. Most people showed a lower abundance of several key beneficial microbe species. 

Medication on the gut microbiota

In addition to diet, medication is a key modulator of the gut microbiota composition. A large Dutch-Belgian population study showed that had the largest explanatory power on microbiota composition. Other studies have shown major effects of commonly prescribed proton pump inhibitors on the microbial community, which could explain higher rates of gastrointestinal infection in people taking these drugs. Antibiotics clearly have an effect on gut microbes, and low doses are routinely given to livestock to increase their growth and weight.

A large proportion of antibiotic use in many countries is for agriculture—particularly intensive farming of poultry and beef. Several observational human studies as well as many rodent studies have pointed to an obeso-genic effect of antibiotics in humans even in tiny doses found in food. But humans have very variable responses to antibiotics, and intervention studies have not shown consistent metabolic consequences. 

Pesticides and other chemicals are commonly sprayed on foods, but, although levels can be high, solid evidence for their harm on gut health and the effects of organic food is currently lacking. 

Insufficient clinical evidence exists to draw clear conclusions or recommendations for these or other dietary preferences based on gut microbiota. But future studies of food additives, drugs, and the safety and efficacy of dietary modifications must take into account these advances and their effect on the gut microbiota.