What is the Microbiome?

Overview of the Microbiome 

Sally V. Irwin, May 2023

What is the Human Microbiome and why is it important? 

Humans have been interested in the microorganisms that live in and on them since the late 1600’s when Antonie van Leeuwenhoek (The Father of Microbiology) first discovered their presence throughout all life and the environment.  The ability of bacteria, viruses and fungi to cause disease in humans was established in both the research and medical communities in the late 1800’s. However, research into their role in sustaining health wasn't significant until the early 2000’s. Since that time there have been over 124,000 published peer reviewed scientific research articles on the topic.  The connections to health and disease include significant links to our immune system, digestion, depression, autism, cancer, obesity and Irritable Bowel Disease (IBD) to name a few .  Although we are still a long way from understanding all of the implications of this significant part of each of us, there are several important findings that most Microbiome research agrees with, that are useful for improving individual health (1,2). 

What is it made up of and where is it found in humans?

The microbiome is made up of trillions of bacteria, viruses, archaea, fungi and protists. Bacterial cells are found in about a 1:1 ratio to human cells and are by far the most abundant microorganism in the microbiome.  Most of the research that has been done to date has been on the bacteria that live in and on us and they will be the topic of this discussion. 

There are approximately 1000 different bacterial species that inhabit our bodies with certain species appearing in specific locations around the body. There have been numerous associations found between the numbers and types of certain bacteria found during health and disease that seems to be consistent throughout the world. However your environment, illnesses, medications, what you eat and your genetics will also influence the make up of your microbiota. 

The vast majority of the microbiome is found in the colon, small intestine, stomach and mouth.  The skin is also home to a vast number of bacteria but significantly fewer types than found in the digestive system.  The vagina, breast milk, mucus membranes of the nose and eyes, lungs and urogenital tract have smaller populations of bacteria and have not been as extensively studied as the gut microbiome (3,4). 

Where and when do we acquire our Microbiome?

Humans acquire the Microbiome first when they pass through the birth canal. The microbiome of the vagina is known to change to serve as “seeds” for the baby’s initial gut and skin microbiome as they are born. After birth a baby’s environment of human touch, food, pets and plants all contribute to their microbiomes and their developing immune system. By about 3 years old, it is thought that a child's microbiome will normally resemble that of an adult (5). 

What is the most important in shaping the microbiome?

Nutrition/Diet: Diets that are plant based, not overly processed, free of most preservatives and additives and low in saturated fats and sugar are the most beneficial to the gut microbiome. Studies have consistently shown that our diet is crucial to the gut microbiome which in turn is crucial to our metabolism, digestion, brain health and immune response (6-11)

Environment: It has been suggested that a child's early environment has a significant impact on the composition of their microbiome and development of their immune system. Children who live in rural areas with exposure to animals, plants and soil on a regular basis have more exposure to diverse microbes. Subsequently they generally develop both a more diverse microbiome and a stronger immune system. They have fewer allergies and later in life fewer autoimmune disorders than children who live their first several years in more urban environments (12,13).  Beyond childhood the impacts of the environment continues to help maintain a healthy, diverse microbiome through diet, sleep, exercise, limiting stress and increasing contact with the natural world (14)

Genetics: It has been found that our own gene function can be shaped by the microbiome and in turn shape the function of the microbiome. This is a complex area of study that is a key area of Individualized Medicine. Connections between your personal inherited traits, your microbiome’s genome (which outnumbers our genes by about 100:1) and our environment have been discovered and the impact of those connections on our health is starting to unfold (15)

What is most impacted by a disrupted microbiome (dysbiosis)?

Digestion and disorders of the digestive tract:  Food travels from the mouth through the stomach, into the small and large intestine (colon) before the waste products are expelled. Approximately 80% of the digestive process takes place in the small and large intestines where most of the gut microbiota resides. Depending on the composition of meals, food spends 2–6 hours being absorbed in the small intestine and 10–59 hours in the colon before elimination as feces (16). The gastrointestinal tract of humans is colonized by about 800 different species of bacteria. The mouth microbiome has been shown to have approximately six different phyla of bacteria. Research has shown these bacteria to be involved in many metabolic processes resulting in biosynthesis of molecules which act on the gut and throughout the body (1,4,16). Some bacterial species produce neurotransmitters which act on the brain and affect mood. S. thermophilus generates serotonin while some Lactobacillus produce acetylcholine and gamma aminobutyric acid (GABA) (10). Lactobacillus and Streptococcus species are also known to produce several B vitamins including B1 (thiamine), B2 (riboflavin), B9 (folic acid) and B12 (cobalamin). Lactobacillus plantarum is known to synthesize B2 in abundance. Lactobacillus casei is known to bind and carry thiamine, which S. thermophilus has been found to produce small amounts of, as well as pyridoxine (B6). S. thermophilus and L. plantarum synthesize folate (B9), a molecule used in cell division and construction of DNA and other genetic material (10). Noted to encourage homeostasis of the intestines, the gut microbiota also has a strong influence on development of intestinal microvilli and contributes to the strength and resilience of the overall host immune defense (1,17). 

Mental Health: There are many diseases and disorders of the digestive tract that have increased in incidence over the past 25 years including IBS, Chrons, Metabolic disorders and Obesity (1,18, 19).  Subsequently chemical signals connecting the makeup of the microbiome to the brain have been identified that show links to mental health conditions including depression, anxiety, autism, ADHD and more (6,8,20,21).

Immune System: A healthy immune response to disease and toxins is developed to a large extent by the presence of the microbiome at an early age and exposure to environmental microbes and other antigens. Antibiotic use, cesarean section delivery of babies, urban lifestyles, ultra processed food diets of mother and/or child have all been found to have a negative effect on the composition of the microbiome and subsequently both the innate and adaptive immune systems. This has been linked to chronic inflammation (which is in turn, linked to almost all diseases known) allergies, metabolic disorders, auto-immune disease and cancer as we age (1,4,22).

Summary

The importance of the microbiome to human health cannot be overstated. Scientists around the world have only scratched the surface of this exciting area of research but already its impact on diagnosis and treatment of disease is being felt at the patient level. Maybe even more importantly, the understanding that our microbiome, although not made up of human cells, is a significant, necessary part of the human body, and its ability to function, is changing our understanding of how we need to live our lives for optimal health.