How Can You Improve Your Microbiome?

Mar 11, 2024

The microbiome is the total of all of the microbes (bacteria, viruses and fungi) living in and on us. The area we know the most about and the one I'm referring to in this blog is the "gut microbiome". This refers to the bacteria living in the large bowel or colon. As you will see we have a symbiotic relationship with these tiny creatures. We feed them and in return they make many molecules critical for human health.

In this blog I describe the many ways in which the gut microbiome is essential for human health and share 6 tips to improve the health of your microbiome one bug at a time.

This question — how can you improve your microbiome? — was motivated by a recent presentation by Dr. Brent Williams as part of the NIH ME/CFS roadmap webinar series. Dr. Williams is a member of Dr. Ian Lipkin’s research group, the Center for Infection and Immunity at Columbia University. This group’s research interests me and will likely interest you if you’ve been diagnosed with myalgic encephalomyelitis/ chronic fatigue syndrome (ME/CFS) like I have.

This research group has found that in people with ME, changes to the microbiome correlate with measures of energy metabolism and symptoms like fatigue. They are pulling many threads of the ME experience together.

What makes this research exciting is that there are many ways we can improve the health of our microbiome.


Humans Are More than Half Bacteria

Believe it or not, the bacteria invisible to the naked eye — that live in and on us outnumber human cells in the body by a ratio of 1.3 to 1. The average human female has about 30 trillion cells and the average male up to 40 trillion cells. The number of microbial cells, mostly found in the bowel, are greater than this — over 50 trillion organisms per human.

Bacteria are not the only microbes living in and on us. There are also fungi, protozoa and viruses. And taken together, the number of microbial genes outnumber human genes by 150 to 1. This means that the microbes that live in and on us have far more diversity and metabolic capacity than we have.

They live in a fragile symbiosis with us. We supply them with food in the form of the “human” food we don’t digest or use. In return, they can create many substances (metabolites) that we need but cannot create. Sometimes this win–win relationship goes astray. If we don’t provide them with enough diverse nutrients and fiber, their growth patterns change, and they can contribute to health symptoms and diseases. When it comes to microbial metabolites,

  • some are essential to our health;
  • some are helpful or harmful, depending on the situation;
  • and some are generally associated with disease.

I’d like to share with you some of the most important functions that the bacteria that live in our bowel perform for us. Then I will give you some simple, powerful tips on how to improve the health of your microbiome so that it, in turn, improves your health. You and your microbiome rely on each other, so anything you do to keep your bacteria healthy is a win for them and for you.

The diagram below gives a sense of the incredibly diverse health impacts of our gut microbiome. You may notice that these impacts affect the entire body not only the gastrointestinal system. This is because the bacteria that live in our bowel break down the food we eat but can’t absorb. From that food, the bacteria make substances that are then absorbed into our blood and moved around our body.

Source: Spivak, I., Fluhur, L., & Elinav, E., 2002,
a recent review paper by the Elinav Lab at Tel Aviv University.


Prof. Elinav, one of the co-authors of the paper with this diagram, often collaborates with his colleague Prof. Eran Segal. The two have published numerous game-changing papers about the impact of diet on the microbiome and human health. I described some of their work in “Chapter 3: The Biology of Change” in my new book More Light. You can get a free copy of this chapter by signing up for my monthly newsletter.

Keep in mind that the substances (metabolites) produced by our microbiome are constantly interacting with our genetics, our geographic location, our age, our diet, and other lifestyle factors. Nothing in the human body is simple or linear. As you read through this next section, note that the bacteria in our bowel have the capacity to save you a lot of money and potential side effects. Improving the health of the microbiome may decrease the number of medications you need to take.


7 Important Ways the Microbiome Impacts Our Health

  1. Certain bacteria that produce short chain fatty acids, such as butyrate and propionate, support the integrity of the lining of the gut by providing food for the gut epithelial (lining) cells. A healthy gut barrier prevents things from leaking from the body into the gut and unwanted molecules in the gut from crossing tight junctions into the body. When these tight junctions fail, the result is leaky gut. In leaky gut, unwanted molecules leak from the gut into the body causing chronic inflammation body wide. This smoldering inflammation increases the risk of numerous serious health conditions like heart disease, stroke, diabetes, and even dementia.
  2. Bowel bacteria process bile acids into other molecules that activate an important hormone called glucagon-like protein-1 (GLP-1). GLP-1 increases insulin release from the pancreas, slows emptying of the stomach, and increases a sense of fullness through actions on the fullness centers in the brain. GLP-1 agonist drugs, such as Ozempic® and Victosa®, achieve what our bowel bacteria could do for us if we fed them appropriately. The drugs don’t do as good a job as the bacteria, are more expensive, and have more side effects. Although the world is very taken with this class of drugs as the solution for overweight, note that the weight loss achieved by this class of drugs called GLP-1 agonists is 50% lean muscle and 50% fat. This is not ideal since most overweight diabetics could benefit from building muscle rather than breaking it down.

  3. Bowel bacteria produce short chain fatty acids and tryptamine that increase the contractility — the ability to contract — of the bowel, thereby improving bowel movement regularity and decreasing constipation. Feeding your bacteria could put the laxative industry out of business!

  4. Bowel bacteria influence how much energy we derive from food and how much we store as fat. Two people could eat the same number and type of calories, but one may gain weight and the other lose weight. Weight management is about much more than calories in and calories out. Some evidence suggests that bowel bacteria may even be responsible for yo-yo obesity — the tendency of people who diet to gain back even more weight than they lost when they return to normal eating.

  5. Bacteria in the bowel influence our risk of heart disease. The fatty plaques that block the arteries of the heart and brain contain a molecule called trimethylamine-N-oxide (TMAO) made by gut bacteria from the amino acids in red meat. The bugs living in the bowels of vegetarians don’t make these molecules, and their risk of heart disease and stroke is decreased as a result. But as with most things diet related, it’s not as simple as that. Eating more fiber decreases the risk of heart disease and stroke even in those who eat red meat. Again, the microbiome is involved. Bacteria break down dietary fiber into short chain fatty acids, which are anti-inflammatory and lower the risk of heart disease and stroke.

  6. The gut microbiome can modulate inflammaging (inflammation + aging). The gut lining becomes leakier with age. More molecules leak into the body from the gut, and over time, the body becomes overloaded with foreign molecules. These molecules activate the immune system, causing low-grade chronic inflammation which in turn increases the risk of many types of chronic health conditions such as cardiovascular disease, metabolic syndrome, depression, and dementia. But — good news — the presence of beneficial bacteria can slow down this process.

  7. Bowel bacteria make essential neurotransmitters such as noradrenaline and GABA. Some of these molecules help us feel better, and others cause symptoms of depression and anxiety even when we are not in a stressful situation. It seems that this relationship between the microbiome and mental health is causal because preliminary studies show that changing the microbiome with probiotics (bacterial supplements) and fecal transplants decreases mental health symptoms.

So, why am I writing about the microbiome in a blog for people with complex chronic diseases? Most people with disease diagnoses, including myalgic encephalomyelitis/ chronic fatigue syndrome (ME/CFS) and fibromyalgia (FM), have evidence of dysbiosis — less favorable microbes living in the bowel. The diagram below is an example from research by Dr. Ian Lipkin’s group at Columbia University that specifically looked at people with ME/CFS.

The decrease in the beneficial bacterial species Fecalibacterium prausitzii is associated with lower levels of butyrate production and increased levels of fatigue. This finding remained even when controlling for things that could have impacted it, such as presence of age, race, and the use of pre- and post-biotics and medications. The abnormal findings correlate with the presence of symptoms of irritable bowel syndrome (IBS). So, if you have IBS, keep reading. There are things you can do about it.

Source: Guo, C. et al. 2023.

A recent paper by the Williams lab at Columbia University

We can significantly influence our bowel microbiome through diet. Research shows that measurable changes can be found in the microbiome within a couple days of a diet change. You don’t have to purchase expensive probiotics and supplements to improve the health of your microbiome. Here are some simple things you can do to increase the health of your microbiome (and yourself) within a few days.


6 Ways to Improve Your Health One Bug at a Time

  • Increase naturally occurring dietary fiber. This means eating more plant-based foods, especially those that are a bit harder to chew. Think legumes, seeds, nuts, avocado, artichokes, and whole grains. Fiber that is naturally occurring in food is better than added fiber supplements because the food contains many other healthy nutrients. Added fiber does not.
  • Eat the rainbow. Eat as many different colored plant-based foods as possible. Each food has different nutrients and fiber types that support a wide range of microbes in the bowel. When it comes to the microbiome, diversity is good.
  • Eliminate processed foods. “Processed” is code for “all the fiber and goodness got taken out” creating empty calories for you and your microbiome. Processed foods are smooth and easy to chew — not what you want. When fiber and nutrients are removed from food, the bacteria in your bowel starve. How do you know if food is processed?
    • It has more than five ingredients.
    • It contains ingredients you would never cook with.
    • It has ingredients you can’t pronounce.
    • It comes in a package and doesn’t need to be refrigerated to prevent spoiling.
  • Avoid foods with emulsifiers in them. Emulsifiers are frequently added to liquid and soft foods to make them smoother and to extend shelf life. They do this by preventing the separation of oil and water. The problem is that emulsifiers are like soap. When they get to the large bowel, emulsifiers strip the bowel of its mucous lining causing leaky gut and inflammation. Coconut milk is a prime example of a healthy food that is ruined by the addition of emulsifiers, usually guar gum. As emulsifiers are in virtually all processed foods, they add to the already long list of reasons to eat freshly prepared whole foods.

            Common Chemical Emulsifiers

    1. Polysorbates: Used in ice creams to prevent it from melting too quickly an Common Chemical Emulsifiers d extends the shelf life of baked goods.
    2. Carboxymethylcellulose (CMC): Often used in gluten-free baked goods to improve texture and shelf life.
    3. >Alginate: Used to coat fruits and vegetables for antimicrobial and antiviral protection to thicken and stabilize liquids.
    4. Soy lecithin: Used to prevent the sugar from separating out of chocolate.
    5. Xanthan gum: Used to prevent separation of salad dressing, spreads, and sauces
    6. Mono and diglycerides: Used in a wide range of desserts, bread, processed meat, ice cream, and yoghurt.

  • Avoid added sugar and decrease starches. Sugar feeds the less favorable bacteria and leads to an imbalance, causing all the problems mentioned — fewer needed molecules, less healthy gut lining, leaky gut, and inflammation.
  • Keep a regular sleep schedule. Bacteria have their own internal clocks. They expect to eat during the day and rest at night just like you. If you eat too closely to bedtime or have an erratic eating and sleep schedule, they don’t function as efficiently. If you get 8 hours of sleep each night and keep a regular sleep schedule, your microbiome will thank you with improved health.


Any small step you take to improve your diet using the above tips will improve your health. It is not all or nothing. Baby steps work. Remember: the microbiome changes quickly within a few days of you making changes to your diet. You don’t have to be perfect or implement everything at once. Choose a change that you could make relatively easily and start there.

To learn more, join my live online sessions called Live! with Dr. Stein.  Held every two weeks, these sessions provide some new information and then I open up the session to questions from the attendees. I will also be featuring many guest experts on a variety of topics related to your health.



Feltman, R. (2013). The Gut’s Microbiome Changes Rapidly with Diet [Electronic Version]. Scientific American.

Guo, C., et al. (2023). Deficient butyrate-producing capacity in the gut microbiome is associated with bacterial network disturbances and fatigue symptoms in ME/CFS. Cell Host Microbe, 31(2), 288–304.e288. doi:10.1016/j.chom.2023.01.004

Hofmeister, M., et al. (2021). The effect of interventions targeting gut microbiota on depressive symptoms: a systematic review and meta-analysis. CMAJ Open, 9(4), E1195–E1204.

Santoro, A., Zhao, J., Wu, L., Carru, C., Biagi, E., & Franceschi, C. (2020). Microbiomes other than the gut: Inflammaging and age-related diseases. Seminars in Immunopathology, 42(5), 589–605.

Spivak, I., Fluhr, L., & Elinav, E. (2022). Local and systemic effects of microbiome-derived metabolites. EMBO Rep, 23(10), e55664. doi:10.15252/embr.202255664