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OMED Health

Exploring the Human Gut Microbiome and Its Functions

Trillions of microbes inhabit your gut, collectively known as the gut microbiome. Learn more about the role of the gut microbiome in human health and disease.

Did you know that 99.9% of your DNA is identical to everyone else’s (1)? Although human genetic make-up is similar, vast differences exist between the microbes that inhabit our bodies – termed the microbiome. A particularly diverse community of microbes inhabit your intestines and are known as the gut microbiome. Shaped by biological, genetic, and environmental factors, the microorganisms that inhabit our guts differentiate us from others and have many roles in both health and disease. This blog will discuss the human gut microbiome, and some of the ways in which it helps and hinders us.

So, what is the gut microbiome?

Living within your gut is an intricate and extensive community of microbes, including bacteria, viruses, archaea, fungi, and protozoans (2). You may have heard the terms ‘microbiota’ and ‘microbiome’ used interchangeably, but they actually have slightly different meanings.

  • Microbiota – this term refers to the entire population of microorganisms present in your gut. You can think of this as ‘who is there?’ (3).
  • Microbiome – this term refers to the microbiota (who is there?) as well as their genetic material (what can they do?) and metabolic functions (what are they doing?) (3).
Image of a human outline with a magnifying glass over the gut. In the callout, there are graphics explainign that the 'gut microbiota' refer to who is there, and the 'gut microbiome' refers to who is there, what they can do, and what they are doing.

We’ll use the term ‘gut microbiome’ throughout this blog, and will primarily discuss gut bacteria, the largest and best studied component of your gut microbiome. Rough estimates suggest that your gut may contain up to 1000 bacterial species and 2 million bacterial genes – that’s 100 times the number of genes you have (around 20,000) (4).  Despite your high genetic similarity to other humans, your gut microbiome is more unique and can be 80-90% different from someone else’s (4).

What does the gut microbiome do?

Despite its microscopic constituents, your gut microbiome is one of your biggest supporters, with a diverse set of roles as a result of human and microbial co-evolution. Your gut microbiome contributes to food breakdown, micronutrient production, protection from invading bacteria, and even helps to shape your immune system. Let’s explore these roles in a little more depth!

Food breakdown

Your body is responsible for most digestive processes, producing enzymes to break down fats, carbohydrates, and proteins. However, one component of foods – fiber – cannot be broken down by your enzymes and needs input from your gut microbes (2). In the large intestine, your gut bacteria work to digest the fiber you consume, using their own arsenal of enzymes (2). Fiber acts as food for your gut microbes, so it’s important that you consume the recommended intake (~30g per day) to ensure that you are providing them with the fuel they need to thrive.

Micronutrient and beneficial molecule production

In the process of breaking down fiber, your gut microbes produce an array of bioactive molecules. Short-chain fatty acids (SCFAs; propionate, butyrate, and acetate) are one such class of molecules. SCFAs can benefit your gut in many ways, including reducing inflammation, providing fuel for cells in your colon, and impacting the speed at which food travels through your intestine (5)

Your gut bacteria can also synthesize essential vitamins, notably vitamin K and B group vitamins such as biotin, folate, and thiamine. In fact, for several B group vitamins (cobalamin, folate, niacin, pyridoxine), gut bacteria are estimated to contribute more than 25% of your daily recommended intake (6).

Protection from harmful bacteria and immune system support

In addition to synthesizing valuable compounds and vitamins, bacteria in your gut can also provide protection against invading pathogens that might be harmful to our health like E. coli, Salmonella, and Campylobacter species (7).  By producing specific metabolites, gut bacteria induce the synthesis of antimicrobial proteins by gut cells to help stop microbial infections from taking hold. Additionally, the presence of a normal, healthy gut microbiome can hinder the establishment of intestinal pathogens – a phenomenon called ‘colonization resistance’ (7).

Gut microbes also have roles in shaping and regulating your immune system, especially during infancy. Interactions between your gut microbiome and your immune system are complex and dynamic, and much of the research exploring this connection is carried out in germ-free mice (mice without gut microbes) (8). In germ-free mice, a lack of gut microbiome has resulted in intestinal tissue defects, reduced levels of immune cells, and reduced immune function (8), highlighting the important of the gut microbiome in supporting the immune system.

Outline of a human body with microbe graphics on the gut. Around the body are the various roles of the gut microbiome, including food breakdown, vitamin synthesis, protection from pathogens, bioactive molecule production, and immune system support.

The gut microbiome in health and disease

There are numerous reports of the gut microbiome being involved in disease states. Although much of the research in this area is promising, many of the relationships between gut microbes and human disease are associative, meaning that we don’t know if the gut microbiome is driving the disease state or if the disease causes changes to the gut microbiome (9).  Nevertheless, a growing body of literature has identified relationships between gut microbes and obesity, mental health, nutrition-related diseases, cancer, and cardiometabolic diseases. We will explore the connections between the gut, its microbial inhabitants, and human disease further in future blogs.

Is it important to know what’s in your gut microbiome?

Discussing the role of gut microbiome poses a question – do we need to know ‘who is there’? Although results from gut microbiome tests can be interesting, research hasn’t yet identified strong causative links between gut microbes and disease, so it can be challenging to make useful inferences from gut microbiome testing.

Additionally, knowing about the community structure at a single time point (what many microbiome testing kits offer) provides very little practical insight, given that the gut microbiota can change substantially in response to diet in as little as 24 hours (10). For most people, focusing on habits that promote gut microbiome health, such as eating a diversity of plant foods, reducing stress, getting plenty of sleep, and exercising regularly, is the best way to support your gut microbiome, so they can support you in return.

We can help you to take control of your gut health

If you are living with uncomfortable digestive symptoms, taking a simple at-home breath test can help to identify whether your gut microbiome is hindering rather than helping you. We offer breath tests for small intestinal bacterial overgrowth (SIBO) and carbohydrate malabsorption. You can learn more about the tests we offer here.

You can also now join the waitlist have priority access to our OMED Health Breath Analyzer device and App which can help to monitor symptoms, triggers, and whether your treatment pathway is working.

If you are interested in learning more about how breath can provide insights into the gut microbiome, you can watch our webinar here: Functional Assessment of the Microbiome


  1. Genetics vs. Genomics Fact Sheet. Genome.gov. Published September 14, 2022. Accessed May 15, 2023. https://www.genome.gov/about-genomics/fact-sheets/Genetics-vs-Genomics
  2. Jandhyala SM, Talukdar R, Subramanyam C, Vuyyuru H, Sasikala M, Reddy DN. Role of the normal gut microbiota. World J Gastroenterol. 2015;21(29):8787-8803. doi:10.3748/wjg.v21.i29.8787
  3. Berg G, Rybakova D, Fischer D, et al. Microbiome definition re-visited: old concepts and new challenges. Microbiome. 2020;8(1):103. doi:10.1186/s40168-020-00875-0
  4. Gilbert JA, Blaser MJ, Caporaso JG, Jansson JK, Lynch SV, Knight R. Current understanding of the human microbiome. Nat Med. 2018;24(4):392-400. doi:10.1038/nm.4517
  5. Blaak EE, Canfora EE, Theis S, et al. Short chain fatty acids in human gut and metabolic health. Benef Microbes. 2020;11(5):411-455. doi:10.3920/BM2020.0057
  6. Rowland I, Gibson G, Heinken A, et al. Gut microbiota functions: metabolism of nutrients and other food components. Eur J Nutr. 2018;57(1):1-24. doi:10.1007/s00394-017-1445-8
  7. Iacob S, Iacob DG, Luminos LM. Intestinal Microbiota as a Host Defense Mechanism to Infectious Threats. Frontiers in Microbiology. 2019;9. Accessed May 15, 2023. https://www.frontiersin.org/articles/10.3389/fmicb.2018.03328
  8. Zheng D, Liwinski T, Elinav E. Interaction between microbiota and immunity in health and disease. Cell Res. 2020;30(6):492-506. doi:10.1038/s41422-020-0332-7
  9. Witkowski M, Weeks TL, Hazen SL. Gut Microbiota and Cardiovascular Disease. Circulation Research. 2020;127(4):553-570. doi:10.1161/CIRCRESAHA.120.316242
  10. Sonnenburg JL, Bäckhed F. Diet–microbiota interactions as moderators of human metabolism. Nature. 2016;535(7610):56-64. doi:10.1038/nature18846