The human microbiome represents the diverse collection of microbial species living on us and in us. It is said that the adult human body contains 1 X 1014 cells – that’s 100,000,000,000,000 cells, fewer that 10% of which belong to you! The rest are microbial in origin, including bacteria, yeasts, fungi, and potentially parasites. These cells are much smaller than our cells, but they are incredibly diverse and far more numerous.
Though we are all born sterile, soon after birth we start to be colonized with microbes, as acquired from our mother, as well as from the surrounding environment and in what we eat and drink. Within the first year of life many complex ecosystems have been established in the body, including those on the skin, intestines and genitourinary tract. Our intestines contain the largest biomass, or collection of organisms. By 3 years of age a diverse and complex set of ecosystems has developed. These microbial communities continue to shift and adapt over our lifetime, influenced by our diet, general health, surrounding environment, and also by mediations that we take, including antibiotics and drugs that may alter the immune and digestive systems.
The bulk of species in the intestines are obligately anaerobic, meaning they can’t grow and survive in the presence of air, which contains approximately 20% oxygen (O2). Additional species are facultatively anaerobic, meaning they can grow in the presence or absence of oxygen, while others are microaerophilic – able to grow in low percentages of O2, commonly 2-5%. A smaller number still are obligate aerobes, meaning they need O2 to survive. In contrast, for the skin and other exposed bodily surfaces, many – though not all, species are better able to tolerate O2. Other factors including how moist or dry a location is (consider your mouth vs. your elbow), acidity or pH, and types of nutrients an organism could eat all impact the composition of local communities and how dense they are.
These organisms provide many benefits, from key micronutrients such as vitamin K, needed for us to adequately clot our blood, to vitamin B12 – something our bodies can’t produce but is needed by every cell in the body to copy its DNA and carry out other necessary processes. Microbes are also essential to mature the immune system, a form of “training” to insure our defenses are ready to attack infections but be tolerant of our own tissues and of foodstuffs that we eat. Microbes also produce mimics of hormonal factors which, locally, can influence gut motility and replenishment of the gut’s lining, and increasingly are being found to have effects outside of the intestine, including on organs as far away as the brain.
The small intestine is the primary site of digestion and absorption of what we eat. Here enzymes from your stomach, liver, pancreas and from the lining of your gut break down foodstuffs into smaller molecules that make it easier to absorb. Microbes in this location also have the opportunity to feast on the diet and can start digesting things that our bodies can’t, such as complex carbohydrates and other complex molecules.
The small intestine is also an active site for immune surveillance of what’s coming through. You have the largest population of immune cells within your intestines. The immune defenses serve to protect us against infection-causing organisms that may get through, from viruses to disease-causing bacteria or parasites, and to monitor for things we ingest that may be toxic. When things are running smoothly, the partnership among microbes, the gut and immune system works to our advantage. However, cases of dysbiosis – or disruptions in the gut microbiota, can pre-dispose to the development of diseases. Human food allergies are increasingly believed to arise from states of dysbiosis where the communities of organisms in the intestines alter the behavior of the immune system and of other organ systems.
In humans, the large intestine – cecum and colon – contains the largest biomass of organisms in the microbiota. The cecum, in particular has the largest biomass of metabolically active organisms. Within our bodies, the cecum and right-side, or proximal colon, is where the body resorbs fluids and electrolytes released to help with digestion. For every quart of material you ingest, your body will secrete 5-6 quarts that need to be brought back in, else you will rapidly become dehydrated. The colon pulls in the remaining 1-2 quarts of fluids that make it past the small intestine.
Though not a primary site for our body’s digestion, the colon is the primary site of microbial digestion where microbes tackle the complex carbohydrates and fibers that could not be digested and absorbed in the small intestine. A by-product of this action is the release of short chain fatty acids (SCFAs) which include acetate (vinegar), proprionate and butyrate – which smell like rancid butter or worse, but provide a source of energy to other microbes and also to our cells that line the colon. Eating fiber not only helps your gut function but also helps your gut microbial communities function to your benefit.
The right side of the colon also has an active immune system that continues to sense and interact with the microbial communities at this location.
The left side of the colon (transverse, sigmoid colon, rectum and anus) focuses on compacting the remaining undigested materials into feces so they can be excreted from the body. 40% of the wet weight of fecal material is made up of microbes so our body is constantly regenerating and shedding our microbioal ecosystems.