Diversity is the theme of World Microbiome day this year. A microbiome are the microorganisms in a particular environment (1). The gut microbiome is the community of microbes in the gastrointestinal (GI) tract and can be beneficial to the human host; the benefits are dependent on the composition of the collection of microbes in the gut. For example, a diverse collection of bacteria that maintains proper functioning of physiological systems is beneficial.

The diversity of a gut microbiome can be a predictor of general health – particularly the Firmicutes to Bacteroidetes ratio. However, the environment, lifestyle and diet can both play a major role in gut microbiome diversity (2).

What are the benefits of the gut microbiome?

Bacterial diversity is one way that gut health is monitored and addressed. In order to understand the benefits of diversity in the gut microbiome, first we need to understand the impact an imbalanced gut microbiome can have. A lack of diversity can lead to proliferation of unhelpful or harmful bacteria, known as dysbiosis. Dysbiosis of the gut microbiome can lead to compositional changes that can derail the functionality of the gut microbiome and is associated with some disease states.

Dysbiosis can happen for many reasons such as the use of broad-spectrum antibiotics, liver malfunctionor a sudden lifestyle change (3). After the gut microbiome has developed and matured, typically at 2-3 years of age in humans, the gut microbiome composition stays relatively stable. The change in diversity caused by repeated use of antibiotics, a sudden change in diet or lifestyle, or an acute case of gastroenteritis are reported to have associations with gastroentestinal pathophysiologies. Essentially, a high level of bacterial diversity is protective against instability in the gut microbiome of adults and therefore diversity is important for health (4).

In populations and communities that reflect the hunter-gatherer lifestyle and diet of the Western world’s ancestors, the higher diversity of species in the gut microbiome is thought to provide a greater stability and flexibility to withstand pathogens. Their gut microbiome responds to fluctuations in diet due to the seasonal food supply (5).

A gut microbiome that is more resilient can return to equilibrium after physical, chemical and microbial influences, and is often associated with higher microbial diversity. It is difficult to define a healthy gut microbiome, due to the differences in composition seen between individuals, as the gut microbiome is as unique as one’s fingerprint.

However, patterns have been recognised between the gut microbiome and immune function, as well as brain and cognitive health, nerve system function and bioaccessability of nutrients. The patterns in good health can be associated with short chain fatty-acid (SCFA) production by gut microbes. In the future, specific markers need to be established to indicate a healthy gut microbiome (6).

What is happening to gut microbiome diversity?

By means of example, the Hadza hunter-gatherers of Tanzania have a high dietary diversity, eating approximately 600 species of plants and animals throughout the year. This results in high gut microbiome diversity that differs significantly from a Western or urban diet. Additionally, the Hadza people have no exposure to commercial antibiotics and pesticides.

Aspects of Western culture should be taken into consideration when tackling the public health issue of decreasing intestinal diversity (7). It may not be that 600 species a year are recommended – instead a small increase in the types of plants consumed weekly would be a step forward for many.

In rural populations such as in the Himalayas, the change in lifestyle through farming industrialisation has changed the gut microbiome composition in those communities. Although a change in diversity was not reported, the change in composition suggests that the industrialisation of lifestyles is what begins the initial change in gut microbiome composition to later cause a fall in gut microbial diversity (8).

In another example, a cohort of people who immigrated to the United States, dietary variation was a contributor to the gut microbiome changes observed. There was a significant shift in the dominant taxa of the gut microbiome away from Prevotella abundance and a greater Bacteroides proportion. Displacement of the immigrant’s dominant native bacteria   with European and United States  bacteria occurred at varying rates and even a short residence in the US reduced bacterial diversity and changed the gut microbiome composition (9).

It is likely that the displacement of native bacteria are due to multiple factors associated with Western lifestyles, such as stress, altered exercise patterns and medication use, excessive hygiene, as well as dietary changes. The lack of dietary fibre causes a reduction in Prevotella and enzymes required to break down dietary fibre. These changes are then passed on through generations living in the United States and Europe (9).

It is also probable that a combination of lifestyle changes has caused a more general loss in diversity of the gut microbiome over time. This has happened through less exposure to microbes as a result of more time spent inside, as well as cleaner environments with increased use of antibiotics and excessive hygiene.

Additionally, dietary patterns in Western countries have become less abundant in fibre. This provides fewer carbohydrates for microbes to feed on in the gut, which has led to a reduction in some beneficial bacteria over several generations (10).

How can we support diversity in the gut microbiome?

From birth (and perhaps even earlier), various factors are known to affect the development of the gut microbiome and its diversity later in life. Children born by caesarean section have been found to demonstrate a less favourable composition of their microbiome than children born vaginally (11).

After this, recurring intake of antibiotics is known to reduce diversity and extend the time the bacterial ecosystem takes to recover. Exposure to microorganisms and reducing interruptions to the developing gut microbiome in the first 3 years of life is important for building diversity in the gut microbiome (11).

There may be a decrease in gut microbiome diversity in Western countries, however there are lifestyle choices that can be made to help our diversity thrive:

  1. Breastmilk influences the development of the gut microbiome in infants and there is a continued benefit after the introduction of solid food. Breastfeeding is associated with bacteria that decrease the risk of allergy development in infants. This highlights the importance of breastfeeding and the early development of the gut microbiome (12).
  2. Exercise is associated with positive effects on gut microbiome diversity. Cardiorespiratory fitness is linked with better microbial diversity, suggesting that both fitness and microbial diversity are benefits gained from exercise. The improvement is thought to be caused by the resulting increase in abundance of butyrate producing bacteria from higher levels of physical activity (13).
  3. Dietary intake is one of the main environmental factors that can shape the intestinal microbial community. The type, amount and balance of the three macronutrients – carbohydrates, protein and fat – have a large impact on the composition of the gut microbiome. A diet high in plant-based foods, particularly complex carbohydrates, and lower in fat and animal proteins, is protective against inflammation and leads to a preferable composition of bacteria in the gut (14).
  4. The changes in food manufacturing due to industrialisation, alongside pressures for greater food production, has led to a decreased agrobiodiversity. As a result, dietary diversity has decreased over generations. Dietary diversity contributes to feeding a diverse microbial community in the gut (15). Increasing the variety of foods included in a weekly dietary pattern can feed and promote a greater diversity of beneficial microbes in the gut.
  5. Supplementing the diet with prebiotic and probiotic foods can improve gut microbiome composition and, in some cases, using supplements is recommended, where prebiotics cannot be obtained from diet alone. Probiotics are live microorganisms consumed for their health promoting benefits. Supplementing a diet with probiotics after a course of antibiotics has been reported to reduce the proliferation of opportunistic pathogens in the gut and restore diversity (16).
  6. Prebiotics, ‘a substrate that is selectively utilised by the host microorganisms conferring a health benefit’ (17), can promote growth of beneficial bacteria. Consuming a variety of foods in a dietary pattern that is rich in complex carbohydrates and plant-based foods can provide naturally occurring prebiotics. However, there is notably a fibre gap, with only 9% of UK adults consuming the recommended daily intake of fibre (18). In cases where it may be difficult for people to increase their fibre intake significantly, a prebiotic supplement could be recommended, such as Bimunoâ.

Diversity is hugely important in microbial communities for the general health of the public. Lifestyle recommendations can be used to encourage diversity within the gut microbiome for a composition that promotes health. In adults, maintaining dietary diversity and physical activity are arguably the most important factors to support the gut microbiome.