Healthy microbial communities that exist in the body can alter the state of the body’s systems. Microbial communities differ by site and have site-specificity. Dysbiosis in one site will affect the particulars site but might also disequilibrate the function of other sites. In this way, systemic eubiosis is established by all sites being in eubiosis.
However, our biggest microbial community exists in the gut because it is the most exposed to the outside world. The microbiome comes in contact with food and this produces other energy bi-products useful to the whole body. Cell proliferation, endocrine neuron firing, and immune system activation is linked to gut microbiota products. Bi-products of the gut microbiome could access the brain through blood flow. There could be endocrine or vagus nerve activation. An unhealthy microbiome can influence the most powerful protecting mechanism for our brain: the immune system. If the immune system is not working properly, and inflammation in the brain can’t occur.
The above picture shows the gut-brain axis; this is the term for the connection between the brain and microbiome. Some connections of disease influencing the brain have been made directly from the state of the microbiome. For example, depression has been linked to the use of antibiotics (antibiotics alter the microbiome). Parkinson’s and Alzheimer’s are linked to less diverse microbiomes and certain bacterial species being present. On the other hand, the connection can first affect the brain than the microbiome. For example, stress can disrupt the microbiome by the secretion of excess hormones. Environmental stressors and emotions are also linked to the changes in the microbiome.
Image and Source: Al-Asmakh, Maha et al. “Gut microbial communities modulating brain development and function.” Gut microbes vol. 3,4 (2012): 366-73. doi:10.4161/gmic.21287