Introduction to the Microbiome
What is the microbiome?
The microbiome has become a buzz word in the health community in recent years, and its hype is not only justified, but long-overdue. When we refer to a microbiome, we are referring to the microbial genes in a particular environment. In regards to human health, we are usually referring to the gut microbiome. The gut microbiome contains millions of microbial genes. In fact, it contains 150-200x more genes than our own human genome.¹ Acknowledging how massive of an influence these microbial genes have on our health and behavior calls into question just how genetically “human” we are.
Humans are covered in microbes, not only in our gut, but on our skin, in the vagina, in our nostrils, in our mouths, and more. Microbes are inescapable. Our microbiota communities consist of bacteria, fungi, and viruses, and they confer positive health benefits when in a symbiotic relationship with their host (us). In your large intestine alone, there are trillions of bacterial cells- 10x more bacterial cells than human cells in your body.¹ The gut microbiome has even come to be considered its own organ, weighing up to five pounds and interacting bidirectionally with a wide variety of other physiological systems.
The gut microbiome is considered to be in a state of eubiosis when it is has a stable, resilient microbiota composition. Dybiosis is the state of the microbiome when it is out of balance, when “bad” bacteria have overtaken the populations of “good” bacteria. But the bacteria inhabiting the gut cannot be easily categorized into “good” and “bad”; they interact with one another, as well as the environment they are in, to be beneficial in some circumstances and combinations and less beneficial in others. For instance, although some strains are pathogenic and can cause infections, most people have E. coli normally living in their guts. This is why microbiome research is so overwhelming and exciting!
Why should I care about the microbiome?
Most disease results from inflammation. The microbiome is highly associated with inflammatory pathways; it possesses the power to inhibit or stimulate these pathways (often by microbiota-derived metabolites). Therefore, it is logical that the microbiome is linked to immune-mediated, inflammatory illnesses. Although research is still revealing just how intricately the gut microbiota is linked to these various illnesses, the current data indicates mechanisms of interaction and communication between the microbiome and…
mental health
The gut-brain axis has gained much-deserved popularity as the bidirectional pathway between the central nervous system and gastrointestinal tract.² Not only does the brain affect the functioning of the gut, the gut can also communicate with the brain to affect mood and cognition.² In fact, the gut - the place where 95% of the body’s serotonin is produced - is often referred to as our “second brain”.² The gut microbiota play a large role in this communication, as seen in depression, anxiety, autism, and more.
digestion
Microbes in your gut can synthesize vitamin K, B vitamins, and short-chain fatty acids (i.e. butyrate, known for its anti-inflammatory actions), amongst other metabolites.³ They also have enzymes that help us break down food that is otherwise indigestible to human enzymes.³
obesity
Gut microbial diversity has been shown to be preventative in the onset of obesity.⁴ Obese patients show gut microbiota changes, and antibiotics increase the risk of weight gain.⁴ Conversely, probiotics have the potential to increase weight loss.⁴ Studies using germ-free mice that are then transplanted with the microbiota of either lean or obese mice demonstrate the microbiota’s ability to induce weight gain or loss, through a variety of mechanisms (inflammation, nutrient availability/energy harvest, neurotransmitter and hormone secretion, etc.).⁴
diabetes
Poor glucoregulation and the increased incidence of type 2 diabetes are linked to obesity and inflammation, all of which are associated with microbiota changes. Recent research indicates type 2 diabetes might also be immune-mediated, meaning the microbiota could be impacting type 2 diabetes by its effects on the immune system. Probiotics have been shown to reduce fasting blood glucose and insulin resistance.⁵
immune system functioning & autoimmunity
70-80% of your immune system is located in your gut, so it makes sense that the microbiome affects immune homeostasis. There is a bidirectional communication between the microbiota and both the innate and adaptive immune systems.⁶ Immune dysregulation can result from microbiome disturbances and instability.⁶ IBD, eczema, celiac, lupus, type 1 diabetes, rheumatoid arthritis, and more are all considered autoimmune diseases, which might be resulting from prolonged T-cell activation and dysreguation of apoptosis.
Future blog posts will dive deeper into these topics, especially autoimmunity and intestinal permeability’s role in its development. Fecal transplants as a solution to diseases of dysbiosis will also be discussed.
What is a good microbiome? How do I improve my microbiome?
Diversity is essential for a healthy gut microbiome. A diverse microbiome is more stable and resilient. Although more research is needed to determine the best ways to improve an individual’s microbiota composition, broad, nonmaleficent suggestions include:
Avoid antibiotics, unless necessary
Their undiscriminated destruction of bacterial cells can kill the beneficial bacteria in the gut, reducing diversity and creating unstable dysbiotic conditions that increase risk of infection by modifying immune homeostasis.
Heal leaky gut through supplementation and dietary changes
Leaky gut is a term for increased intestinal permeability, which is thought to be regulated by the protein zonulin. High levels of zonulin are associated with obesity, autoimmunity, poor glucoregulation, inflammation, etc.
Increase fiber in your diet
Fiber acts a prebiotic for gut bacteria to feed on, so they can grow their populations. High fiber diets are linked to greater microbial diversity in the gut.
Consume more probiotics
Fermented foods, like yogurt, kimchi, kefir, cottage cheese, and sauerkraut containing live and active cultures, may improve the gut microbiota composition.
Get dirty!
It is thought that society’s increase in sanitization is what has led to the overall decrease in gut microbial diversity and thus, increased rates of autoimmunity, allergies, obesity, etc. Strengthen that immune system!
Prioritize stress reduction & mental health
The brain communicates with the entire body. Psychological factors can have systemic downstream effects on physiology.
The amount of information emerging on the microbiome is mind-blowing and dense. This serves only as an introduction to the complicated field of microbiome research, which I hope to elaborate on further in future blog posts.
References
Zhu B, Wang X, Li L. Human gut microbiome: the second genome of human body. Protein Cell [Internet]. 2010 [cited 2023 Feb 9];1(8):718–25. Available from: https://pubmed.ncbi.nlm.nih.gov/21203913/
Appleton J. The gut-brain axis: Influence of Microbiota on mood and mental health. Integr Med (Encinitas). 2018;17(4):28–32.
Hansen NW, Sams A. The microbiotic highway to health-new perspective on food structure, gut Microbiota, and host inflammation. Nutrients [Internet]. 2018 [cited 2023 Feb 9];10(11):1590. Available from: http://dx.doi.org/10.3390/nu10111590
Aoun A, Darwish F, Hamod N. The influence of the gut microbiome on obesity in adults and the role of probiotics, prebiotics, and synbiotics for weight loss. Prev Nutr Food Sci [Internet]. 2020 [cited 2023 Feb 9];25(2):113–23. Available from: http://dx.doi.org/10.3746/pnf.2020.25.2.113
Zhou Z, Sun B, Yu D, Zhu C. Gut Microbiota: An important player in type 2 diabetes mellitus. Front Cell Infect Microbiol [Internet]. 2022;12:834485. Available from: http://dx.doi.org/10.3389/fcimb.2022.834485
Zheng D, Liwinski T, Elinav E. Interaction between microbiota and immunity in health and disease. Cell Res [Internet]. 2020 [cited 2023 Feb 9];30(6):492–506. Available from: https://www.nature.com/articles/s41422-020-0332-7