The more research that is done on the human microbiome the clearer it becomes that its malfunction can lead to disease. The range of diseases linked to an out-of-sorts microbiome (especially in terms of the gut) includes: autoimmune diseases (diabetes, rheumatoid arthritis, muscular dystrophy, multiple sclerosis, and fibromyalgia); metabolic diseases (obesity, chronic fatigue syndrome, cancer); infections (bacterial vaginosis, Clostridioides difficile infection); and gut-brain axis perturbations (anxiety, depression, autism).
The increasing incidence of atopic diseases (eczema, asthma and food allergies) where the immune system goes into overdrive against harmless microbes or proteins from things such as pollen or food have been linked to an overabundance of hygiene in our modern, urban, industrialised societies. Lack of early-life exposure to microbial antigens in hygienic developed countries retards the microbial evolution of the infant gut, which in turn disrupts immune development. Species such as Bacteroides fragilis reportedly induce immunological tolerance through immune receptor signalling pathways and can be considered teachers of our immune system. When the right bugs such as B. fragilis are not present shortly after birth and during infancy, the immune system lacks these vital tutors to mould it and begins to behave oddly. The infant gut microbiota is affected in a positive sense by factors equated with a “dirtier” environment: being brought up with pets, residing in rural settings, and having many siblings have been shown to have protective effects against asthma and allergies. There is also a higher prevalence of atopic diseases in infants delivered by caesarean sections, formula fed infants* and those exposed to antibiotics. Cleanliness is not always next to godliness!
The technical term for a microbiome gone bad – a movement away from the “ideal” mix of microbes – is “dysbiosis!**”, and this has been linked to disease. Dysbiosis can be caused by a short, sharp shock such as the taking of a course of antibiotics or by gradual insults such as a high-fat diet, alcohol abuse or even stress. In general, high diversity of a microbiome can be equated to a healthy state, and low diversity to sickness. A rich and diverse gut microbiome is now recognised as being essential to our health and associated with resilience. Sometimes it is not the absolute numbers of certain bugs which equates to health but their ratio to other bugs. For example, a high fat diet (not to be recommended, obviously) reduces the proportion of phylum Bacteroidetes and increases the proportions of phylum Proteobacteria. A high-fibre diet***, increases the proportion of Firmicutes bacteria, and in many studies, a high level of these has been associated with a healthy gut.
The structure and composition of the gut microbiome is complex and, once matured at around three years of age, prevents the proliferation of potentially harmful bacteria from the environment. This is known as a “barrier function”, which also benefits from a rich and diverse microbiome. Bacteria are swallowed every day, but they are transitive in our gut ecosystem: pathogenic bacteria are eliminated, or chaperoned by the good bugs so that they cause no harm.
Finally, it is important to remember that the microbiome can be damaged by the disease process, leading to further disease symptoms.
*Entire books have been written on the importance of mother’s milk to the development of the gut microbiome. My advice to anyone having doubts about breastfeeding is to think of the bugs in the gut!
**Even bad breath seems to be caused by a perturbation of the mouth’s “ideal” mix of bugs!
***Any gut microbiome dude or dudes is practically Talibanic as regards believing that a high-fibre diet is essential, not only for a healthy gut, but for the health, both physical and mental, of the entire organism.
The Bug Hunter 