Frequently Asked Questions on the Gut Microbiome

Written by: Kristina Campbell, MSc

Updated: July 11th, 2023

With June 27th being World Microbiome Day, we’ve compiled a list of frequently asked questions on the Microbiome, including the gut microbiome, what negatively impacts it, how it develops, and what the latest research is saying.

1. What is the gut microbiome?

A microbiome (also called a microbiota) is usually defined as a group of microorganisms—bacteria as well as fungi and ancient microbes called archaea—living and interacting with each other in a certain environment. Just as the earth has many different biomes that are shaped by geography and climate, you have different microbiomes associated with different parts of your body. Overall you have about 38 trillion microorganisms in/on your body, approximately equal to the number of human cells[1].

Your gut microbiome is your very own collection of microorganisms that live throughout your digestive tract. Since your digestive tract is sealed off from the rest of your body, whatever you eat doesn’t really become part of you until it gets past the walls of the gut and into the blood circulation. The microorganisms in the gut help act as gatekeepers at the gut wall, working in tandem with your immune system to keep out harmful substances. They constantly work in complex ways to maintain your overall health[2].

Sometimes when people say ‘gut microbiome’ they are specifically referring to the microbiome in the colon, or large intestine—in other words, the microorganisms in your poop. The colon has the richest collection of microorganisms in your entire body.

2. How does it develop?

The microbiome you have in your body at this exact moment is the result of many things in your past as well as your present.

All the action kicks off at birth. Before you were born, your body had no microbes (although it probably talked to microbes through the placental ‘telephone’). During your birth, whether by vaginal delivery or C-section, you had your first microbial bath, setting the stage for what comes later[3].

The next big influence was what you ate in your first few months of life: babies who consume human milk harbour a different gut microbiome than those who consume formula[4].

Your gut microbiome continued to change rapidly in the first three years of life before reaching a more stable state[5]. In adulthood the main factors determining the makeup of your gut microbiome are your health status (i.e. diagnosed diseases) as well as the medications you take[6]. And let’s not forget your diet – although it only accounts for 10% or less of the total microbes in your gut, it’s an important way for you to actively change your gut microbiome and your health in adulthood[7].

Minor (but still potentially important) influences on your gut microbiome include the people and pets you live with, your exercise and sleep habits, and your country of residence. Your microbiome truly bears the imprint of your health and lifestyle, both in the past and in the present.

3. What negatively affects your gut microbiome?

Antibiotics save lives and should be taken when they’re necessary. But they also have the most dramatic effects on your gut microbiome because they actively kill off some of the bugs in your thriving, diverse gut community. While many people’s gut microbiomes bounce back after antibiotics, other people experience changes that can last indefinitely[8]. So it’s worth having a conversation your doctor and being very cautious about the reasons you take antibiotics.

Unnecessary antibiotics are not the only thing that can negatively affect your gut microbiome. Over time, a lack of what the microbes need to thrive can also be a problem. Many beneficial microorganisms require sources of fibre (including prebiotics) in your diet, so if you lack these, you’ll end up with a less-than-ideal microbial community[9]. A diet high in sugary and processed foods, for example, leaves nothing for the beneficial bugs to eat.

Other factors such as constant stress and disrupted sleep (making you feel jet lagged) are also associated with fewer beneficial microorganisms in the gut.

Some scientists have advanced the “missing microbes” theory[10]: with our industrialized way of life, we’re killing off more and more types of microorganisms in our digestive tracts over time. They think this may be linked with the rapid rise in chronic diseases—so it’s important to be proactive in keeping your gut microbiome diverse and happy.

4. How do you improve/restore the gut microbiome?

Because the gut microbiome of each healthy person is slightly different, scientists haven’t yet figured out the ‘ideal’ gut microbiome to aim for. This means that supporting your best health through the gut microbiome probably looks different for you than for anyone else.

But then again, some basic principles are clear. Eating a wide variety of fibre sources – from salads with raw vegetables and seeds, to bean chili and whole grain bread – helps you maintain a diverse and thriving microbial community. Aiming for at least 30 different plant foods per week appears to benefit your gut microbes the most[11].

In addition, emerging evidence shows the benefits of eating fermented foods, especially those containing large quantities of live microorganisms. Yogurt is a great source of live microbes, as are unpasteurized kimchi, sauerkraut, and kefir. Fermented foods are linked with reduced inflammation in the body and various health benefits[12].

Fermented foods can boost the numbers of live microorganisms in your diet, but not all of these live microorganisms actually qualify as probiotics. True probiotics have been measured and tested to prove that they provide a health benefit[13]. So besides fermented foods, you can also consider taking a probiotic supplement as a way to achieve certain digestive or immune health benefits, with or without affecting your gut microbiome.

5. How can you ‘rebuild’ your gut microbiome after a course of antibiotics?

The basic idea seems straightforward: antibiotics deplete your gut microbiome, so probiotics (adding ‘good bugs’) should restore it, right?

It’s not quite so simple. Not every probiotic will help. Only certain probiotics are shown to reduce the unpleasant side-effects of antibiotics (namely, diarrhea), even though the probiotic bugs don’t necessarily stick around in the gut[14]. So if you take antibiotics it’s wise to track down one of these specific probiotics designed to mitigate antibiotic side effects, and make sure you take the probiotics and antibiotics on the exact same days.

This may not completely rebuild your gut microbiome, however. To increase proliferation of beneficial species, you should also focus on consuming many different sources of fibre, according to what your gut can tolerate.

6. Can you test your gut microbiome?

Yes, you can test your gut microbiome by sending a fecal sample to a lab that does microbiome analysis. You’ll get back a list of all the types of microbes in your gut. Keep in mind that each company or lab has different ways of processing the sample, so it’s normal to get slightly different results from different places. Depending on the technology used for the analysis, you might get a list of only the broader categories of microbes, or you might get the exact strains.

Once you have this list of the microbes in your gut, what can you do with the information? Here’s where it gets less clear.

General gut microbiome tests are not useful in a clinical setting, unfortunately. Many companies will give you lists of foods you should or shouldn’t eat based on your gut microbes, but in truth the diet and gut microbe research isn’t advanced enough to guarantee you can improve your health by following a personalized list of foods. The larger, well-designed studies that are needed to prove the health benefits of these diet recommendations will take many more years to complete. Some companies have a test that predicts your blood glucose response to individual foods using a gut microbiome-based algorithm[15]. These are potentially interesting but still lack the connection to specific health benefits.

7. What is the latest in research on mental health and the microbiome?

This is a fascinating (and growing) area of scientific study. More and more research draws a line between the diet you adopt over time and your mental health. (News flash: too many sweet drinks and ultra-processed foods such as hotdogs, chips, and candy are linked with poor mental health[16].) And we know that diet also affects the gut microbes. According to what scientists know so far, your diet can help certain gut microbes thrive or die off, which may contribute to the emergence of mental health disorders. Microbes can ‘talk’ to the brain in at least three known ways: by directly stimulating the nerves that travel to the brain, by putting pressure on your immune system, and by releasing compounds that travel all around the body, including to the brain[17].

There might be certain times of life when you’re more susceptible to suffering mental health consequences from a poor diet[18]. But the good news is that once scientists zero in on the specific microbes involved in these processes, we may learn how to protect ourselves from negative mental health consequences. Watch this space!

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