Gut Health

Understanding Probiotics and the Human Microbiome

Understanding Probiotics and the Human Microbiome

Armed with the latest microbial research, we now know how important gut health is for our long-term vitality. It supports our immune system, our metabolism, and even how we think and feel.

But with complicated names like Bifidobacterium bifidum and biological concepts that seem confusing at first glance, you might be left with more questions than answers when it comes to probiotics—aka the beneficial bacteria that reside within our bodies.

Still, the science is clear: probiotics can positively support overall health and day-to-day well-being. So, here’s a simplified introduction to probiotics and why they’re so important for your long-term health.

A Peek Into the Past: The Human Microbiome

Ever wonder how our ancestors fared without personal medicine cabinets to ease every ailment? While the centuries leading up to our current era were filled with their own set of challenges and many practices were quite different, some used then actually led to better gut health than we have today.

You see, each person has their own unique microbiome, which houses nearly 100 trillion bacteria that outnumber our human cells by a factor of around 10 to 1. Being mostly composed of bacteria might sound a little odd, but that’s just because many people only think of bacteria as germs that can make us sick. However, that’s actually not the case at all!

Your body is comprised of all kinds of bacteria that have different jobs within your body, and most of them are probiotics that serve a beneficial purposethey can help your body produce vitamins, help you absorb nutrients from your food, and even support your mood. Probiotic bacteria can also serve as placeholders, taking up room by colonizing within your digestive tract so that other bacteria can’t settle in, multiply, and create chaos for your system.

Our ancestors had fantastically diverse microbiomes. Instead of obsessively cleaning their hands with sanitizer, they spent much of their time outdoors working in soil filled with beneficial microorganisms. Rather than popping antibiotics every time they felt under the weather, they used natural healing methods to improve their overall health. They also enjoyed unprocessed and unrefined diets rich in prebiotic foods, one of nature’s ultimate gifts. We are starting to realize that our ancestors’ more natural lifestyles and diets might be big contributors to their more diverse, healthy microbiomes.

Prebiotics are the natural dietary fibers that nourish our probiotic bacteria, and they occur in a plethora of fruits and vegetables that our ancestors likely consumed in large quantities.

We know that the key to any thriving ecosystem is the biodiversity of its residents. Jeff Leach, the founder of the Human Food Project, takes a deep dive into how our microbes keep us well with his pioneering research into the human gut microbiome.

In studying the Hadza hunter-gatherers that live in East Africa (who live outside nearly 24-7 and eat a similar diet to our ancestors), Leach found that the Hadza harbor nearly twice as many gut microbes of those living in westernized areas. The Hadza are exposed to a diversity of microbes from the soil, water, air, animals, and plants, making them incredibly healthy individuals.1 And because these healthy hunter-gatherers aren’t exposed to the same diet, lifestyle, and medicinal factors used in today's Western society, many scientists posit that the reduced diversity in our gut microbiomes is indeed attributed to modern culture and that we’re steadily weakening our natural defenses.

Our Modern Lifestyle vs. the Microbiome


But here’s the rub: we might enjoy modern-day inventions like electricity and the Internet and benefit from advances in science and medicine, but our current hygienic habits and lifestyle choices are depleting our microbiomes at a breakneck speed.

Our industrialized, modern culture isn’t very conducive to maintaining a healthy microbiome. A study published in April of 2015 in Science Advances found the highest human microbiome diversity ever seen in an isolated Yanomami tribe that had no contact with the industrialized world, similar to the Hadza hunter-gatherers of Africa.2

When comparing three different groups (Amazonian hunter-gatherers, Andean farmers, and an industrialized population in the U.S.), they found, yet again, that the Americans had significantly less diversity in their microbiomes than the other two groups—which really shows how life after the Industrial Revolution is changing the foundation of our health.

To be fair, we only recently discovered that this world beneath the microscope was so paramount for our health and well-being. In fact, this information was non-existent when we developed our microbiome-depleting cultural habits.

Instead of eating fermented and whole foods with healthy prebiotics and spending time outdoors (naturally repopulating our digestive tracts), many of us eat a diet high in processed foods, spend too much time indoors at home or at work, and live a high-stress lifestyle. Even if we don’t take antibiotics while we’re sick, both antibiotics and antimicrobials are often unavoidable due to their presence in our food and water.

We are only beginning to understand the long-term impact that these cultural habits have on our health. The good news is that your microbiome is malleable—meaning that you can improve your gut health with a few simple changes in your daily routine.

Support With Probiotics

When it comes to giving your gut a helping hand, probiotics are the best place to start. Probiotics help to encourage balance in your microbiome, which helps keep your body healthy. When your microbiome is in out of balance, it means that the bad guys could gain a foothold if you’re not careful.

That’s why, if you must take antibiotics, it’s a good idea to take probiotics as well so that you’re repopulating your GI tract with the good bacteria that may have been indiscriminately wiped out.

There are several ways to boost your probiotic consumption. First, some foods are natural probiotics that you can incorporate into your diet. Plain yogurt often contains probiotics, but make sure you get a brand that is marked with “Live and Active Cultures.” This phrase specifically distinguishes yogurts claiming to contain probiotics from those with actual cultures benefiting your gut. At the same time, be mindful with yogurt purchased from the store as it can have hidden additives and sugars incorporated—which aren’t so good for your gut.

Fermented foods also provide plenty of probiotics. And you can ferment just about anything! Pineapple and turmeric are favorites around here, but some classic staples include sauerkraut, kombucha, kimchi, and strong, aged cheese. These are just a few examples of probiotic-rich foods that can help you get the beneficial you need for overall health.

The thing is, it can be difficult to obtain a healthy amount of probiotics in your diet alone, especially if you are replenishing your gut environment after a round of antibiotics. Many of the probiotic bacteria you consume through food are destroyed when they reach your stomach acids and never make it through your intestinal tract to colonize.

An excellent way to replenish your microbiome with probiotics is to take them in supplement form. But with thousands of different formulas available on the market, how can you decipher what is best? Here are some basic guidelines that can help you make your choice:

  • Number of strains. Research has demonstrated that bacteria prefer to colonize in different parts of your digestive tract, where there are various ecological niches.3 The more probiotic strains you ingest, the more coverage you’ll provide for each of these niches. Each strain of bacteria also has its own different purpose, so choosing a formula with many different strains gives you that many more benefits.

  • Delivery method. Many probiotic supplements are in the form of veggie capsules with probiotic powder inside, which can actually be detrimental to the living flora. You see, the freeze-dried probiotic powder wicks moisture away from the capsule shell, causing many of the bacteria to die off before they even have a chance to support you.

  • Protection. If you want the benefits of probiotic supplementation, you need to make sure that the probiotic bacteria will be protected from your stomach acids on their way to your gut. Otherwise, many of the bacteria will never make it there alive.

  • Resident strains. Quite a few probiotics on the market contain things like active yeasts or soil based organisms. While these ingredients may be helpful for some people, for optimal gut health, it's important to look for strains that are resident to the human gut like those from the Lactobacillus, Bifidobacterium, and Streptococcus families.

  • Shelf stability. Many probiotics sold today are available solely in the refrigerated section of your health food store, or are shipped via icepack. Unfortunately, because of temperature fluctuations during shipment, many of the bacteria in these formulas will not be alive when you consume the product. Choosing a shelf-stable formula that can withstand temperature changes will help ensure you get a viable dose of probiotics into your system.

Whether you decide to get your probiotics from food or from a supplement (or both!), it’s critical to understand what you’re ingesting. When you look at a food or supplement label, you will probably notice a list of bacterial strains included in the product. This tells you exactly what type of bacteria you are taking and is where you want to look for an abundance of strains, especially from the important Lactobacillus, Bifidobacterium, and Streptococcus families.

Incredibly, the human body houses more than 500 different strains (with more being discovered all the time). A higher variety of strains leads to better colonization, which is why you want to look for a probiotic with at least seven unique strains. Make sure you research which strains you are consuming, as they each help support your body in different ways.

The Best Place to Start

A great place to start is with a premium supplement like our flagship formula, Hyperbiotics PRO-15

PRO-15 includes 15 different strains of bacteria to offer a variety of targeted probiotics for whole-body support. We also utilize the patented manufacturing process, LiveBac®, which ensures our probiotics are protected from the heat with zero refrigeration—without being freeze-dried or coated in any way. BIO-tract®, our patented delivery method, protects probiotics from your stomach acids and releases them deep within your GI tract where they can really get to work supporting your health.

Even if you haven't had the time to keep track of all the current medical research, the good news is that scientists are consistently demonstrating that a healthy microbiome is the foundation for overall health.

Learning just a little about how you can support your microbiome, and taking the time to implement that knowledge through probiotic supplementation, could make all the difference for you and your family in the long run.


1. Schnorr, S. L., Candela, M., Rampelli, S., Centanni, M., Consolandi, C., Basaglia, G., . . . Crittenden, A. N. (2014). Gut microbiome of the Hadza hunter-gatherers. Nature Communications, 5, 3654. doi:10.1038/ncomms4654

2. Clemente, J. C., Pehrsson, E. C., Blaser, M. J., Sandhu, K., Gao, Z., Wang, B., . . . Dominguez-Bello, M. G. (2015). The microbiome of uncontacted Amerindians. Science Advances,1(3). doi:10.1126/sciadv.1500183

3. Hao, W.L., Lee, Y.K. (2004). Microflora of the gastrointestinal tract: a review. Methods in Molecular Biology, 268, 491-502.


Julie Hays is the Communications Director here at Hyperbiotics. Health writer and mama of two little girls, Julie's on a mission to empower others to live lives free of the microbial depletion many of us face today. For more ideas on how you can maximize wellness and benefit from the power of probiotics, be sure to subscribe to our newsletter.