The microbiome is a group of microorganisms living in a particular environment (for example, the human gut). These microorganisms are not just limited to bacteria: viruses, fungi, and archaea can also be present. Microbiomes are not limited to humans or even to mammals–insects and plants have microbiomes that are crucial for their health. Microbiomes are involved with processes such as energy homeostasis, metabolism, and immune function.
The microbiome is thought to be acquired by a combination of maternal contact and contact with the external environment. Newborn babies can have different microbiome makeups depending on if they were delivered vaginally or via Cesarean section. Vaginally delivered infants dominantly harbor genera that are also found in the vaginal canal—infants delivered via Cesarean section dominantly harbor genera that are commonly found on skin. However, if Cesarean section-delivered babies are exposed to vaginal fluids after birth, their makeup can shift to that which is more similar to the microbial makeup of vaginally-delivered babies. Even in the first moments of life, the microbiome is hard at work getting established! As babies grow and develop, the microbiome continues shifting and changing, especially after certain intense events, such as the transition to solid food. The microbiome also produces essential nutrients for human life, like vitamin K.
In terms of the immune system, the microbiome can directs its programming, development, and function. In fact, some evidence suggests that the early microbiome is involved in the pathogenesis of some diseases, for example, allergies, autoimmunity, and inflammation.
The immune system has a crucial role to play for the microbiome: the immune system must work feverishly (no pun intended!) to identify which microbes are OK and which, if any, are potentially harmful threats. For this herculean task, the gut-associated lymphoid tissue (GALT) is key. GALT aids the immune system in routine surveillance of microbes to determine who is a friend or foe, as well as defense from potentially harmful microbes. T cell tolerance is a key part of regulating the relationship between immunity and the microbiota of the gut. Dysbiosis of the intestinal microbiome can lead to adverse health consequences such as increased risk for asthma and rheumatoid arthritis. The microbiome may also be altered by exposure to certain compounds, such as toxicants, and these effects can even be seen in fish! There may also be shifts in the microbiome due to stress, trauma, and after medical procedures. Clearly the microbiome is a key component in a healthy life, and we have only begun scratching the surface of its importance and contributions.
If you’re reading this, fortunately (or perhaps unfortunately) your six critical windows of microbiome development have long passed. The first window was the compatibility between the microbiomes of your ancestors and their immune systems. The second window was during pregnancy when microbiome of the uterus is tested against the embryo—pregnancy can be naturally terminated if there’s a disruption. Next comes the window surrounding birth (vaginal delivery vs. Cesarean section), and then the recruitment of regulatory T cells to the skin. This recruitment and migration is thought to help establish immune tolerance to the skin microbiome. Finally, food sources played a role in the development and grooming of your microbiome: breast milk adds additional microbes to the microbiome.
Can dysregulated microbiomes be restored, even after the critical developmental windows? Yes! One way to attempt to restore a healthy microbiome is through the use of probiotics. Though probiotics are now a buzzword, these clever medicines got their start a very long time ago. In 1909, a study described an improvement of autoimmune arthritis via supplementation with live cultures of both Streptococcus lacticus and Bacillus bulgaricus (seriously—this manuscript is entitled The toxemic factor in rheumatoid arthritis and you can find it here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1653048/?page=1). Many studies have examined the role of probiotics in the treatment of an array of other conditions since then, and some of the results are promising. There have even been studies in our beloved companion animals suggesting that certain probiotics may also aid in some of their ailments.
So, are you in good health? Maybe you should thank your microbiome!