Updated: Sep 28, 2022
The human gut microbiome is a pretty hot topic these days, especially in the world of functional medicine. In this article, we will start with some basic definitions and then discuss some numbers, regarding bacterial cells and species within the digestive or gastrointestinal tract (GIT). We will then summarize other bodily systems that the gut microbiome communicates with, and what diseases, in general, may manifest as a result of altered microbial populations within the gut (aka gut dysbiosis, a concept that we will revisit in a few minutes).
So let's start from the beginning with a most basic question, what is the gut microbiome? The first important point is that "gut" mostly refers to the small and large intestines. The microbiomes of the remaining GIT are obviously significant, however, the microbial numbers are comparatively much more highly concentrated in the intestines and the functions of the microbes in this region of the GIT are incredibly diverse. There will be additional articles that explore the differences between the microbiomes throughout the GIT---mouth, esophagus, stomach, duodenum, jejunum, ileum, colon, and rectum. For now, just know that there are differences in both the quantity and the species of bacteria throughout each section of the GIT.
The second thing to point out is the definition of "ome". In science, one of the meanings of the suffix --ome is "the complete or collective set of"... something.  The genome is the collective set of DNA and associated genes within a cell. The transcriptome is the collective set of all known RNA transcripts (i.e. the intermediate biochemistry in going from DNA to protein) within a cell. The proteome is the collective set of all known proteins within a cell.  The translation of the word biome would be the collective set of life.
The gut microbiome is then defined as the collective set of all microbes--bacteria, archaea, fungi, viruses, and parasites--that reside within the gut, and their associated genomes.  The term microbiota is often interchanged with microbiome, but microbiota is referring to the taxonomical classification (genus, species, etc.) of the microbes, without taking the microbial genome into account.  Some of the more common terminology that you may have heard in relation to the gut microbiome include gut flora, normal flora, or microflora.
While the technical definition of gut microbiome includes all microbial species, by far, the gut bacteriome (bacterial species and associated genomes) has been the primary focus of research, to date. Microbiome research, in general, is still in its infancy stages. However, the gut mycobiome (fungal species and associated genomes), the gut virome (viruses and associated genomes), and the gut parasitome (parasitic species and associated genomes) are less researched and documented than the gut bacteriome.  This article will remain limited to gut bacteria, since they are the most heavily researched, but look out for future articles with relevant research regarding the other gut "-omes" involving viruses, parasites, and fungi.
Let's move on and review some quick numbers. According to one research group, the ratio of bacterial cells to human cells is 1:1, if you include non-nucleated cells (e.g. red blood cells), and approximately 10:1, if you exclude non-nucleated cells. Put another way, the average human body has approximately 3 trillion nucleated cells and it is estimated that we are covered by ~38 trillion bacterial cells, inside and out. Speaking in terms of genetics, it is estimated that humans have 20,000 genes, while the number of non-redundant bacterial genes within our body's equals approximately 3~ 4 million.  In other words, according to total cell count and genetic ratios, we are way more bacteria than we are human.
Now that we covered what the gut microbiome is, the follow-up question is what purpose does the human gut microbiome serve? This is a loaded question, but here are a few of the critical physiological roles of the gut microbiome, and we will do a deeper dive on each in future articles:
Participates in immune system activity
Assists with host metabolism and production of important metabolites
Maintains healthy gut epithelial cells
Assists with host energy homeostasis
Supports neurobehavioral development
Communicates with and supports other bodily systems
The GIT is not the only human system harboring microbiomes. Our bodies have microbial ecosystems throughout, including the respiratory microbiome, urinary microbiome, integumentary microbiome, ocular microbiome, nasal microbiome, vaginal microbiome, among others. [7-10] There are still microbiomes that have yet to be discovered and scientists are beginning to realize that we may have microbiomes in anatomical locations once thought to be sterile, including brain / central nervous system microbiomes, circulatory system microbiomes, and placental microbiomes. [11-13]
Evidence exists that the gut microbiome is involved, in one way or another, with all of the systems of the body. There are 12 organ systems of the body, and the gut microbiome interacts with all 12 systems.
Gut---->Skeletal Axis 
Gut---->Muscular Axis 
Gut---->Nervous Axis 
Gut---->Cardiovascular Axis 
Gut---->Respiratory Axis 
Gut---->Endocrine Axis 
Gut---->Digestive Axis 
Gut---->Immune Axis 
Gut---->Integumentary Axis 
Gut---->Urinary Axis 
Gut---->Lymphatic Axis 
Gut---->Reproductive Axis [25-26]
As a result of these connections to the gut, many chronic diseases, involving every bodily system, have been associated with an altered gut microbiome--an imbalanced gut microbial ecosystem known as gut dysbiosis. In general, dysbiosis of the gut results from poor gut health, and poor gut health may occur from multiple environmental factors and circumstances, often in various combinations, including:
Birthing procedures that prevent delivery through the vaginal canal (i.e. Cesarean section) [27-28]
Being formula-fed instead of breast-fed or not being breast-fed for long enough [29-30]
Pharmaceutical drugs (both antibiotic and non-antibiotic drugs) [31-33]
Other chemical exposures to the gut (this may include, but is not limited to, household products, pesticides, and herbicides) [34-39]
Prolonged exposures to radiation, for example, during cancer treatments  (and possibly long-term direct exposure to wireless EMF, although I could not yet find studies to support this)
Emotional stress 
And last, certainly not least, suboptimal dietary and nutrition habits [42-43]
Health conditions that have been associated with gut dysbiosis are truly too many to list here, but at some point, I hope to create and link to an exhaustive list of diseases with associated references. In general, however, associations have been made between gut dysbiosis and cardio- and cerebrovascular diseases (i.e. heart attack and stroke); the cancer spectrum; autoimmune diseases (there are over 150 potential autoimmune conditions the last time I checked); diabetes and other hormonal-metabolic diseases (e.g. PCOS, NAFLD, etc.); neurodegenerative conditions (Alzheimer's, Parkinson's, etc.); mental-emotional conditions (depression, anxiety, bipolar, etc.); neurological conditions (ADHD, autism, etc.); and many more. [44-52]
Maintaining good gut health truly is of critical importance to overall health and, sadly, most people do not realize this fact. Although association is not causation, with continued research it is becoming more and more unambiguous that the gut is a key player in the manifestation of these diseases. If you can learn what you're gut needs to be happy, you're mind, body, and soul will reward you with a better quality of life. If you're not sure how or where to begin, then don't hesitate to reach out to your local functional medicine practitioner!
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Disclaimer: The information within this blog is for educational purposes only and is not meant to be interpreted as medical advice, or to diagnose, treat, or cure any disease. The articles within this blog are simply a sharing of knowledge and information based on research and / or experience. If you feel the need to see a doctor for your condition, then you should definitely follow your instincts and do just that. Please do not alter your dose of any prescribed medications without the direct supervision of your healthcare practitioner. The information contained herein is not intended to replace a one-on-one relationship with a qualified healthcare practitioner. These statements have not been evaluated by the FDA.