Gastrointestinal Health, Nutrition

What the Research Says About How to Support a Healthy Gut Microbiome

Working on a thesis is not what I expected (separate post on this to come). I have been researching the human gut microbiome for some time now, and I feel like the more I learn, the less I know. That is simply because, even with all of the hype around the gut microbiome and all of the research that has come out of it, we still have much to learn. With this blog post, there are two things I aim to point out: 1) what we currently know that constitutes or helps to create a healthy gut microbiome, and 2) why the gut microbiome is so challenging to study.

What makes a healthy gut?

This is a loaded and murky question. To answer truthfully, there is no one-size-fits-all answer, so to speak. A clear definition of a “healthy gut” does not exist. What we do know however, is that microbiome diversity is characteristic of gut health. That means having lots and lots of different kinds of microbes living in your gut is beneficial. The more diversity in microbes themselves, the larger the range of genetic material provided by those microbes which serve functional purposes. Basically, more diversity means the bugs can do more to help us out.

Okay, let’s back up for a second. In case you do not know what the microbiome is, I want to break it down for you. You will hear the term microbiome and microbiota used interchangeably. They are in fact, two different things. The microbiota is the collective of bacteria (and other microorganisms) residing in the gut. The microbiome is all of the bacteria (and other microorganisms) as well as their genetic material. Think of it like a city. The people living in the city make up the microbiota where as the whole, functioning city itself is the microbiome.

Great. So how do we get this diversified community of microorganisms living in our gut? So far what the evidence suggests is that a diet rich in plants, like vegetables, fruits, whole grains and legumes, is the key. These foods are high in many different types of fiber that us humans do not produce the proper enzymes to digest. Therefore, when we eat these foods, the non-digestible fibers travel to our colon untouched, where they can be used by the microbiota for fuel. We call this, fermentation. This process of microbe feasting (fermentation) produces gases and other compounds like short chain fatty acids (SCFA), which are beneficial to our health. The more variety of these types of foods you eat, the more diverse of a microbiota you will likely have in your gut.

It is not to say that you have to be a vegan or a vegetarian in order to support a healthy gut microbiota. Some research investigating meat and animal product consumption is suggesting that a byproduct of eating meat, trimethylamine (TMA), is a marker of cardiovascular disease (CVD) risk. However, we cannot say for certain that TMA is a strong marker of CVD risk because it is a byproduct of all animal protein, including fish, and we know that fish is heart protective. I am not sharing this to scare anyone away from consuming meat or fish. They can absolutely be a part of a healthy, gut supportive diet. For now, more research needs to be done in the field. If anything, choose to eat more plants (very high in fiber) and less meat (which have no fiber), but understand that there is no need to eliminate meat from the diet.

Lastly, there is evidence to support that an active lifestyle does positively impact the gut microbiota by increasing diversity. Exercise supports a healthy gut by promoting the growth of SCFA-producing (especially butyrate) bacteria which confer health benefits to the host (yay, that’s us)! The recommendations for physical activity are three days of moderate cardio (150 minutes per week) and two days of strength training using weights and targeting all muscle groups.

Why is the gut microbiome so hard to study?

There are thousands of microbes living in the human gastrointestinal tract (gut). The gastrointestinal tract is basically a long tube that begins at the mouth and ends at the anus. Bacteria live throughout this long tube, including in the mouth, small intestine and colon (large intestine). Common, non-invasive analysis techniques used in research include stool sampling. The stool is sequenced for DNA which identifies the bacteria (and other microorganisms) present in the stool. Not only is this sample not representative of the entire gut microbiome, but only the most pervasive bugs will be able to be identified. That leaves out any microbes that may be present in smaller numbers but still very important to the function of the microbiome as a whole.

If you think of it as a city again, all of the people in the city are needed for it to run optimally day-to-day. The garbage man is just as important as the mayor. The same goes for the natural world in that, the potentially harmful creatures like mosquitoes, wasps, and snakes, are just as important as the rabbits, birds, and deer. The latter animals may be bigger and easier to identify, but if you leave out the small guys, you are missing the big picture. The stool samples used in microbiome research are mostly representative of the distal colon (part of the colon right before the anus), and not so much the transverse colon, ascending color, or the small intestine. The majority of bacteria likely reside in the distal colon, however it is still not giving us the entire microbial family tree.

Identifying the kinds of microbes present leaves out their associated function(s). The function of the gut microbiome is the part that connects the microbes to our health. What the microbes can do is really where the benefits (or harm) come into play. Part of what they do is transform the fiber we eat into other compounds like the SCFAs mentioned above. It should also be noted that sampling protocols differ vastly from study to study, and that storage temperature and other techniques used in sample analysis can alter results. When studying the gut microbiome and diet, assessing diet becomes imperative. The method used to obtain dietary information from individuals becomes another limitation. Food frequency questionnaires, 24-hour recalls and food diaries all have their own inherent biases and inaccuracy.

With that being said, there are a few things I would like for you to take-away after reading this. You may feel like we know jack about the gut microbiome, and you would not be entirely wrong for feeling that way. The thing is, the field of gut microbiome research is in its infancy. We have to remain curious, open-minded and driven to continue investigation. Based on where we currently stand with research and evidence, it is safe to say that if you desire a thriving, beneficial microbiome you can:

1. Eat more vegetables, fruits & whole grains

2. Be physically active

3. Get adequate sleep and rest


Natalie, future RDN



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