What is the Microbiome and Why Does it Matter for My Health?

Reviewed by Dr. Jonathan Bonnet, MD, MPH and Judy Singer, RD

There has been a rapid expansion of information collected on the human microbiome in recent years. Data continues to be collected and analyzed to determine how exactly the microbiome influences health and disease.

But for non-researchers hearing the word “microbiome” used more frequently in wellness spaces, many questions remain, like: “What is the microbiome and why does it matter?”

Here, we explain the microbiome’s role in the body and gut, how it may impact disease, immunity, and other important health factors, and whether or not you can actually improve your unique network of microbiota.

What is the “microbiome”?

The human microbiome is an internal network of trillions of microorganisms or microbes that live in our bodies. This living ecosystem of bacteria, archaea, viruses, and eukaryotic microbes reside in and on our bodies (don’t forget the skin!), but most live in the intestines. For this reason, you may hear references to the microbiome in discussions about the gut and gut health.

The gut microbiome is host to microbes that are both beneficial and potentially harmful to the body, but the key is in the balance between the two.

When there is a healthy balance between symbiotic and pathogenic (disease promoting) bacteria, the microbiome can help the body in many ways, including:

  • Regulating the immune system

  • Breaking down potentially toxic food compounds or foods that are not as easily digestible

  • Protecting the body from the entrance of pathogenic organisms

  • Preventing overgrowth of harmful bacteria

  • Producing essential vitamins

Each person’s microbiome is unique to them and originally determined by one’s DNA (even identical twins don’t share identical microbial composition).

However, as years progress, environmental exposures, diet, and lifestyle can change the microbiome.

Which factors can weaken the microbiome?

There are several factors that can disturb the balance between symbiotic and pathogenic microbiota in the body and potentially weaken the microbicrobiome, including:

  • Infectious illness

  • Poor diet

  • Poor hygiene

  • Sedentary lifestyle

  • Prolonged use of antibiotics or other bacteria-destroying medication

When this happens, dysbiosis (or an imbalance between the types of organisms) occurs, which can leave the body more susceptible to disease.

How does my microbiome impact my health?

The microbiome is essential for human development, immunity, and nutrition. When in balance, the microbiome helps us to digest our food, support our immune system, protect us against potentially harmful bacteria, and produce vitamins essential for blood coagulation and more.

But when there’s a dysfunction in the microbiome and an imbalance between harmful and beneficial organisms, there are several possible ramifications, including:

  • Metabolic dysfunction: Research suggests that the gut microbiome may play an important role in metabolic health. Specifically, the health of the gut microbiome may impact weight gain, levels of insulin resistance, and metabolic outcomes, including diabetes.

  • Autoimmune diseases: Dysfunction in the microbiome is also associated with autoimmune diseases including rheumatoid arthritis, muscular dystrophy, multiple sclerosis (MS), and fibromyalgia.

  • Gastrointestinal disease: Inflammatory bowel diseases (IBD), including Crohn’s disease (CD) and others may also be influenced by the gut microbiome.

  • Mental health: The gut-brain connection has been of significant interest in recent years and there’s a wealth of research demonstrating how dysbiosis of the gut can cause several mental health conditions, including depression and anxiety.

Should I be testing my gut microbiome?

Whether or not to test your gut microbiome is an excellent question to ask your provider when discussing your health goals and any symptoms you may or may not be experiencing.

Because each person’s microbiome is unique and the symptoms you may be experiencing could indicate another concern, working with your provider to determine if and how to test your gut microbiome is the best way to get optimal care.

Part of this is because many of the experts in the field are divided on whether microbiome testing is useful and which methods are best for getting reliable results.

Stool samples may be one of the more accurate ways to test the microbiome, but even then multiple tests may be required to get a better picture of overall gut health.

Ultimately, the microbiome is like a complex orchestra—there are many components that work in harmony together to support its optimal functioning. While there are ways the microbiome can be manipulated with probiotics and supplements, there are more questions than answers in this young field in terms of what to prescribe and when. However, it is clear that diet and lifestyle exert powerful influences on the microbiome. Regardless of what initial microbiome testing shows, eating whole, unprocessed and nutritious foods is guaranteed to have positive impacts on your microbiome and overall health.

Can I improve my microbiome?

Scientists are continuing to explore the many factors that may impact the gut microbiome. Above all, diet remains one of the clear drivers of gut health or dysbiosis.

Specifically, the Western diet—or one that’s high in packaged and processed foods, especially processed meat—is associated with high incidences of chronic disease.

There are several ways in which a change in diet can affect one’s gut microbiome, but these changes may be especially beneficial:

  • A high-fiber diet: One of the dietary changes that may have a bigger impact on microbiome and overall health is eating a diet high in plant-based fiber and low in processed carbohydrates and meats. This is because a high-fiber diet supports a large amount of beneficial microbiota while preventing the growth of pathogenic bacteria.

  • Prebiotic foods: Raw foods like garlic, onions, leeks or asparagus or prebiotic supplements may help to lower the pH of the colon and limit the growth of some harmful bacteria, including Clostridium difficile (C. diff).

  • Probiotic foods: Foods like yogurt, kombucha, miso, and sauerkraut or probiotic supplements may help beneficial bacteria and microbiota in the body to thrive.

  • A diet low in artificial foods or ingredients: Artificial foods and ingredients, like maltodextrin, have been linked to gut dysbiosis.

  • Intermittent fasting: Intermittent fasting, longer multi-day fasts, and fasting-mimicking diets have been shown to improve gut barrier function (in animal models), increase microbial diversity and even reverse intestinal inflammation in those with IBD.

Factors which may adversely influence the gut microbiome include:

  • Smoking

  • Stress

  • Lack of exercise

  • Geography (most likely an indicator of dietary differences)

  • Infectious diseases (particularly those contracted when traveling)

  • Poor sanitary conditions

  • Poor personal hygiene

  • Circadian disorganization (either because of travel or frequently changing work shifts)

The bottom line

The gut microbiome is complicated, but it’s clear that it plays an essential role in disease prevention and overall health. Understanding how your gut microbiome may be affected by diet and other lifestyle factors can help you find the right strategies for naturally improving your microbiome. If you’re unsure about where to start, Forfend can help. Our whole person wellness exams can help you optimize your approach to whole body health.


Current understanding of the human microbiome. (2020).

Fast Facts About the Human Microbiome.

Gut Microbiome: Profound Implications for Diet and Disease. (2019).

Gut microbiota’s effect on mental health: The gut-brain axis. (2017).

Impact of Physical Exercise on Gut Microbiome, Inflammation, and the Pathobiology of Metabolic Disorders. (2019).

Interactions between host genetics and gut microbiome in diabetes and metabolic syndrome. (2016).

Nutrition and Immunity. (n.d.).

The gut microbiome in health and in disease. (2016).

The impact of Diet and Lifestyle on Gut Microbiota and Human Health. (2015).

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