A Crash Course in the Gut Microbiome: What it is + How to use it to your advantage


The average adult has somewhere between 2-4 pounds (0.9-1.8 kg) of bacteria in their gut [1].

That’s a little bit heavier than a quart of milk.

That’s a lot of bacteria

Far from making you feel gross, this should make you feel incredibly lucky to have so many tiny little inhabitants inside your intestines because they can do some great things for our health if we know how to take care of them. 

Quick anatomy lesson

The lymphatic system is the less commonly acknowledged circulatory system in our bodies. Everyone is familiar with the cardiovascular system. Looks a little something like this:

Our powerful heart muscles contract and pump blood throughout this system that reaches every organ and tissue in our bodies. The lymphatic system (LS), has a similarly far-reaching effect. This system is made up of an extensive network of over 600 lymph nodes connected by vessels [2] and looks a little something like this:

The function of the LS is to play a key role in the immune system and digestion. It facilitates the absorption of essential fats and fat-soluble vitamins in the gut tissue. The vessels also collect fluids, bacteria, and other “foreign materials” that should not be in our tissues and transports it to lymph nodes where it is checked out by immune cells. If the immune system gives the signal and recognize there is a threat in the body, they send in the immune cell soldiers to try and destroy it. Obviously our lymphatic system’s ability to properly identify, transport, and react to invading infections in our bodies plays an enormous role in our overall health. 

As you can see from the photo, a large proportion of these lymph nodes reside in and around the gut tissue. Studies have also shown that these lymph vessels are connected to the brain [3], so you can imagine how vital it is to do the best we can to keep the risk of bacterial infection in our gut low. More on that later. 

What are probiotics? 

Pro – meaning positive, and bio, meaning living or life form = a positive or beneficial lifeform. Basically, they are the living bacteria the long food tube we call a “gastrointestinal system” that have the potential to facilitate positive health. Our microbiome refers to the populations of all of the different kinds of bacteria that are living in one place (i.e. our intestines). 

What do probiotics do for us? 

Those bacteria aren’t just a bunch of freeloaders hitching a ride in our gut. Our microbiome is totally unique to each of us, kind of like a bacteria fingerprint inside our intestines. No two microbiomes are exactly the same. 

The majority of the probiotics that we have identified and studied fall under two genera: Lactobacillus and Bifidobacterium

They are named by genus followed by species – Examples: “Genus: Lactobacillus, Species: acidophilus (L. acidophilus) and Bifidobacteria lactis (B. lactis). The genus and species together are considered to be the “strain” and there are thousands upon thousands of just these two genera alone. They can all function in different, but similar, ways that science is still working on figuring out. 

Lactobacillus and Bifidobacterium are lactic acid forming bacteria [4], meaning lactic acid is a byproduct of them munching on the foods we provide them. This lactic acid has a large variety of functions, from killing other harmful bacteria [5] to stimulating immune activity in our gut’s lining ( we will discuss this again later on). The outside of these bacteria are often covered in a sticky “polysaccharide” coating that allows them to adhere to the lining of our intestinal cells as sort of an additional barrier between the potentially harmful bacteria that our food may carry (think food poisoning bacteria) and the sensitive skin of our gut lining that would allow that harmful bacteria access to our blood stream. 

On top of actively producing byproducts that defend our immune system, a lot of a probiotic’s benefit also comes from just taking up space. The more space taken up by these “helpful” bacteria, the less room there is for “pathogenic” (meaning: disease causing) bacteria to establish themselves. It hangs up a “No Vacancy” sign for all of these potentially harmful bacteria and uses up the resources that they would otherwise take advantage of to wreak havoc. 


What are prebiotics? 

To put it simply: Fiber. Probiotics are bacteria, they’re living things. And like all living things, they have to eat. It’s not quite as black and white as “good and bad” bacteria when it comes to your microbiome. The good bacteria can potentially become problematic if they grow out of control, but for the sake of simplicity I will be referring to the generally “good” bacteria here. The “good” bacteria need to work a little harder for their food, and they put in the time to break down that fiber and get their nutrients that way. The “bad” bacteria really proliferate best when they’re fed a diet of simple, refined sugars. They’re looking to make a quick buck by taking the easy way and breaking down the most easily digestible food source to give them the energy to grow out of control. Think of fiber as a way to teach your gut bacteria patience and the value of a hard-earned dollar. Make them earn their keep. 

I like to use the analogy of planting seeds to stress the importance of eating a fiber-rich diet along with your probiotic foods. The bacteria are like the seeds, they’re organisms that are ready to grow given the right conditions. Taking probiotics without eating any fiber is kind of like scattering those seeds on a sidewalk.

 Sure, some seeds might take hold in one of the sidewalk cracks, some might find a way to make it work, but unfortunately most of them will be washed away with the next rain before they get a chance to take hold and flower.

But eating your probiotics in combination with fiber is like throwing those flower seeds on soil. Now they have something to feed off of. (Are you still following?) 

The seeds are the bacteria, the soil is the fiber, and you are the gardener that gets to enjoy the beautiful garden while the plants get to enjoy the great soil you’ve provided for them. It’s a win-win, or what we call in biology “symbiotic relationship” (both parties benefit from interacting with each other). 

Sources of fiber: 

Fiber is a carbohydrate – a “complex” carbohydrate (think complex carb vs. simple sugars). There are two different types of fiber: soluble and insoluble fiber. Insoluble fiber has sort of a crunchy texture (no, not potato chips, but nice try) and soluble fiber (soluble or “dissolvable” in water) forms sort of a gel, like what you find in your cooked oatmeal. Resistant starches are a really great type of prebiotic for your bacteria, they are formed when a starch is cooked and then allowed to cool and its structure crystallizes, for example when you cook your whole grain pasta and then eat it cooled to room temperature in a pasta salad. 

Other sources of fiber:

  • Whole grains
  • Non-starchy vegetables
  • Beans and legumes
  • Fruits
  • Nuts and seeds
    • You will notice that there is quite a bit of overlap between the sources of fiber and the sources of complementary proteins! One of the many benefits of getting your protein from plant-based sources.


What is the hygiene hypothesis?

It is hypothesized that an increased use of antibiotics for common, non-life threatening infections and sterilization methods in our everyday lives may be the culprit behind the increasing incidence of allergic and autoimmune conditions in our society [6]. This hypothesis, termed the “hygiene hypothesis,” is the proposed explanation that we have waged an unnatural war with the bacteria that we spent so long being blissfully unaware that they were there (for the most part) and playing such a vital role in our digestion and immune systems. It is theorized that when certain bacteria were first discovered and labeled as the culprits of infection and disease, it gave a bad reputation to all bacteria in general. As a result we started wiping them out completely at the first sign of mild illnesses, sterilizing every surface we touched, and decreasing the amount of time we spent outside interacting with the bacteria that once thrived on and inside of us. 

Bacteria have gotten a bad reputation from a few bad apples


While the CDC does encourage doctors to use more discretion when prescribing antibiotics nowadays [7], it is better to be safe than sorry. If there is ever any doubt that an illness could have a long-term effect on your health, take the antibiotic. BUT if it is a matter of convenience or getting over your sickness just a little bit faster, as long as you are a healthy adult with no other pre-existing condition that would make this a risk to your health, talk with your doctor about the option of letting your body and your immune system do the work and take care of the bacterial infection rather than taking an antibiotic that wipes out the vast majority of your microbiome just to target the few bacteria that are causing issues. 

Absolutely, if you do take an antibiotic, take the entire prescription. Do not stop when you start feeling better. The bacteria that were exposed to the antibiotic but not destroyed can develop defenses against that antibiotic so that the next time it grows out of control causing an infection, you won’t be able to get rid of it with that antibiotic anymore. This can cause major health issues for you or whoever else you transfer that bacteria to. 

So, you’ve taken a round of antibiotics, what now? Some studies have shown that it can take up to 4 years for your GI microbiome to return back to a similar state as it was before the antibiotics, and often it will never go back to the exact same as it was before [8]. Luckily, there are plenty of ways that you can start to reintroduce probiotics back into your diet and re-establish  new, healthy community of gut bacteria. Keep reading to find out how. 


Sources of probiotics in foods: 

Bacteria is naturally found on the surface of, well, everything – but especially on our food. Fermentation is the process through which those food components are broken down by the bacteria – either naturally occurring or sometimes added in – so the end product is that the food is altered from its original state, and the bacteria are often still present and have now reproduced to create much more of them. 

Our bodies have a natural defense mechanism against bacteria – our stomach acid. The reason we have harsh stomach acid is to try and kill harmful bacteria before it can make it to the sensitive, lymph-filled tissue of our intestines. Unfortunately this can also work against probiotics, too, since stomach acid doesn’t really differentiate. There is power in numbers, though, so eating the following foods regularly can help give those little guys a fighting chance to make it to the intestines. 

  1. Yogurt (can be from dairy or non-dairy sources, which are increasingly prevalent in today’s grocery stores)
  2. Kefir
  3. Sauerkraut (unpasteurized)
  4. Kimchi (unpasteurized – spicy!)
  5. Kombucha 
  6. Tempeh – fermented soybeans 
  7. Miso 
  8. Pickles
  9. Certain cheeses

Please note that as living things, probiotics are killed by heat. This can’t be avoided in some cases, but if you have the choice, make sure not to cook your food above 115 degrees fahrenheit to try and preserve as many bacteria as possible. Choose foods that specifically say that they have not been pasteurized or have been heated to destroy the bacteria. 

When choosing sweets like kombucha, yogurt, and kefir take a look at the label and try to choose brands and flavors that don’t load up on added sugar. It’s a bit counterintuitive to take all of these great probiotics along with tons of refined sugars. 

Remember those strains we talked about before, Lactobacillus and Bifidobacterium? The more the merrier, so take a look at the label to see how many different active strains are in the product. The label will also list “CFU” which stands for “Colony Forming Units”, or the amount of bacteria alive to grow colonies on a petri dish. This is tested at the time of packaging, so it’s not always guaranteed that by the time you pick it up on the shelf that there are still that many alive in there, but there should still be enough to benefit from. 

Be aware that some of these take time to develop a taste for. You don’t need to polish off an entire jar of sauerkraut to get the benefits, just taking a couple of bites sometime throughout the day can be very beneficial. Sometimes in life we eat stuff not just because it tastes good, but because we appreciate what it can do for our health. If you are ready to move on to advanced mode, you can even try fermenting your own foods, but this is definitely a more advanced practice and brings with it its own set of food safety concerns so I definitely recommend learning more about it before jumping in. 


Probiotics in supplement form: 

I wouldn’t necessarily recommend probiotic supplements to the average person. Like with most nutrients, I would recommend trying to get them through a healthy, varied diet first. If you are still interested in taking a probiotic supplement my advice would be to find a trustworthy company with quality packaging. Bacteria can be somewhat fragile and during the packaging process a lot of them can die, and even more can be lost during the time they sit on the shelves if they are not properly packaged. Using a company like labdoor.com or some other third-party supplement testing site can help you to find a probiotic that’s more likely to contain all of the bacteria in the amounts it claims it contains. While more research needs to be done in this area, it has been suggested that the best packaging for preserving and maintaining active probiotics in supplements are in airtight, refrigerated bottles and blister packs. 


Major takeaways:

  1. Don’t be grossed out, be grateful! Gut Bacteria are a great thing, embrace it
  2. Eat fermented foods regularly (sorry, win doesn’t count as a probiotic – now matter how much we all wish it did)
  3. Fiber matters 


If there were any questions I didn’t address or any topics you didn’t quite understand please feel free to leave me a comment or message and I will do my best to get back to you. Otherwise, I really hoped this was helpful and gave you information you can use to improve your everyday life. Thank you so much for taking the time to read my crash course lesson in your gut microbiota. I hope to see you again for my next post!


Remember to follow me on my other social media to stay apprised of my upcoming content:




[1] “Gut Microbiota Info.” Gut Microbiota for Health, https://www.gutmicrobiotaforhealth.com/en/about-gut-microbiota-info/.

[2] Macgill, Marcus. “Lymphatic System: Definition, Anatomy, Function, and Diseases.” Reviewed by Elaine K Luo, MD, Medical News Today, MediLexicon International, 23 Feb. 2018, https://www.medicalnewstoday.com/articles/303087.php 

[3] Absinta, Martina et al. “Human and nonhuman primate meninges harbor lymphatic vessels that can be visualized noninvasively by MRI.” eLife vol. 6 e29738. 3 Oct. 2017, doi:10.7554/eLife.29738 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5626482/

[4] Bifidobacteria: Uses, Side Effects, Interactions, Dosage, and Warning https://www.webmd.com/vitamins/ai/ingredientmono-891/bifidobacteria

[5] 2014, Dr. Eric Johansen. “Twelve Reasons You Need to Read about Lactic Acid Bacteria.” BioMed Central, 4 Dec. 2014, https://blogs.biomedcentral.com/on-biology/2014/08/29/twelve-reasons-you-need-to-read-about-lactic-acid-bacteria/ 

[6] Okada, H et al. “The ‘hygiene hypothesis’ for autoimmune and allergic diseases: an update.” Clinical and experimental immunology vol. 160,1 (2010): 1-9. doi:10.1111/j.1365-2249.2010.04139.x https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2841828/

[7] “CDC Encourages Safe Antibiotic Prescribing and Use.” CDC Newsroom, Centers for Disease Control and Prevention, https://www.cdc.gov/media/releases/2017/safe-antibiotic-prescribing.html 

[8] Yoon, Mi Young, and Sang Sun Yoon. “Disruption of the Gut Ecosystem by Antibiotics.” Yonsei medical journal vol. 59,1 (2018): 4-12. doi:10.3349/ymj.2018.59.1.4 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5725362/


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