The gut microbiota regulates many aspects of host physiology, including immunity. This has long been emphasised by germ-free (i.e. microbiota-free) mice, which have a grossly underdeveloped immune system and enhanced susceptibility to infection, among other physiological deficits. More recent research is gradually showing how gut microbes influence every major immune cell type, from their birth in bone marrow (i.e. haematopoiesis), to the differentiation and functional activity/priming of immune cells throughout the body (e.g. gut, blood, spleen, nervous system, etc.).
Gut microbiota regulation of host immunity occurs via two main mechanisms:
- Microbes and their components (e.g. PAMPs) directly stimulate specific immune receptors (e.g. PRRs). This happens both within the gut mucosa and via the constant low-level translocation of PAMPs (e.g. LPS and peptidoglycan) from gut to bloodstream 7.
- Microbes release metabolites such as short-chain fatty acids (SCFAs) which also regulate the immune system. SCFAs (e.g. acetate, propionate and butyrate) are produced via bacterial metabolism of indigestible carbohydrates (i.e. resistant starch and fibre) and are absorbed into systemic circulation. SCFAs modulate energy metabolism, activate specific G-protein coupled receptors, and act as histone deacetylase inhibitors (HDIs) which modulate epigenetics 14,21.
Given the gut microbiota consists of trillions of microbes from hundreds of species, all of which can stimulate the immune system in specific ways, the diversity and balance of the gut microbiota is probably important for a balanced immune system! This may be emphasised by several basic observations. Firstly, as mentioned above, germ-free mice have profound immunodeficiencies. Similarly, mammalian newborns take several years to acquire an adult gut microbiota, and this is paralleled by initial immunodeficiency and reliance upon breast milk for passive immunity. Many animal studies have also shown that antibiotics deplete gut microbiota populations, induce inflammation, disrupt systemic immunity and increase vulnerability to allergy 12 and infection 5–7 (e.g. seasonal influenza 19,22).
When it comes to chronic diseases, varied microbial changes and lower diversity are often reported, which might skew the immune system in complex ways. This could result from many internal and environmental factors which shape the gut microbiota. Intriguingly, the increasing prevalence of many chronic diseases in developed countries is paralleled by practices which negatively impact the gut microbiota, such as C-section, formula feed, antibiotic use, extreme hygiene and processed foods 23,24. On the other hand, the gut microbiome of modern hunter-gatherer societies, largely untouched by modern practices, has greater microbial diversity (e.g. Hadza 25 and Yanomami 26). This suggests modernization may be gradually shrinking the core microbiome and altering our physiology 23. The new field of paleomicrobiology should gradually reveal the evolutionary significance of all this 24. So far it is clear that we have coevolved with our microbiota, it is deeply entwined within our physiology, and we depend upon it for health 24.
Could the gut microbiota influence the immunology and course of ME/CFS? Perhaps there are some initial clues. For instance, ME/CFS can be preceded by allergies/asthma 27 and triggered by many different infections; even in the course of the disease there is evidence for chronic infections and immunodeficiency 28. There is also increased translocation of LPS from gut bacteria 29,30, which correlates immune activation 31, autoimmunity 32 and even remission of CFS 33,34. Furthermore, a clinical trial with B. Infantis (a Treg-stimulating probiotic 18) lowered blood inflammatory markers in CFS 35.
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