Just when we thought scientists found the key to understanding everything there is to know about humans thanks to DNA and its role in genetics, along comes an entirely different element of biology proving to be equally influential in human health.

In fact, some scientists are calling it the “second genome” due to its part in determining how our bodies relate to the environments we live in; such as how each one of us responds to diet, drugs, disease, stress, and more.

Unlike DNA, which is literally part of our cellular structure, the second genome isn’t “us” at all. In fact, it’s a whole bunch of separate organisms living on and in us. Scientists call this collection of organisms our “microbiome,” and they live within pretty much every organ system. However, there’s one place in particular the majority of these little buggers really like to hang out.

The human gut.

Is this a good thing or bad? Read on to find out

The Microbiome: An (Hopefully!) Understandable Overview for Regular People

The human microbiome consists of literally trillions of bacteria and other types of single-celled organisms, all collectively called “microbiota” (you probably known them by their more informal name: “germs”).

In other words, we have a helluva lot of germs living in and on our bodies all the time.

And that’s actually a good thing.

While we most often associate germs with illness, it turns out that some play a very important role in keeping us healthy. In fact, many of them help prevent the very illnesses we’re trying to avoid.

Right now the exact mechanism of microbiota in relation to our health is still under a great deal of study, but there is one thing scientists know for certain: Like a fingerprint, every person’s microbiome is unique. Not a single one of us share the exact same germy types, numbers, or sequences.

That’s because we aren’t born with our microbiomes already in place. In fact, it is believed that humans don’t have a microbiome at all while happily floating around in their mother’s womb. Microbiomes, if you remember, are made entirely of germs, and the amniotic sac surrounding a fetus is a sterile environment.

Quick aside here: There is some speculation that the “sterile womb” may not be entirely true and scientists are exploring the possibility that maybe the microbiome begins prior to birth, though so far evidence of this is sketchy. However, I feel like I need to put it out there in the event Bill Nye the Science Guy is reading this and attempts to one-up my microbiome knowledge. Because, you know, Bill Nye has that kind of time and I’m certain he’s a fan of my blog.

Anyway! It is believed that it is not until we leave the amniotic sack that we become exposed to external microorganisms. The moment a mother’s water breaks, a baby’s microbiome begins to develop. In fact, mothers are the very first to contribute microorganisms via her birth canal and breast milk, providing her baby immunity to harmful pathogens while promoting his or her digestive development.

So I want you to stop right now, call your mom, and thank her for setting your microbiome up for success. At the very least make a note of it in your next Mother’s Day card. I’m sure it’ll make her day.

According to one study by the Baylor College of Medicine, development of the human microbiome doesn’t stabilize until around four years of age. That being said, our microbiomes are not static; they constantly change throughout our lives depending on the various germs, antibacterial agents, foods, and other environmental factors we are exposed to every day.

And this is where gut health becomes important. Healthy humans typically have a balanced community of diverse microbiota, especially in their guts. It’s when this balance is disrupted that problems begin to happen.

Signs that you May Have an Unhealthy Gut

Because each one of us has a unique “gut print” (I just made that up, but in the event it becomes popular this article is evidence that I said it first), it’s pretty much impossible to say what the exact ratio and species of germs we need for ideal gut health. However, what is known is that when our bodies are lacking in or in excess of certain microbes, issues begin to present themselves. This imbalance is formally called “dysbiosis.”

So how do you know if your microbiome may be in dysbiosis? Some common symptoms are:

• Digestive issues like frequent diarrhea, chronic constipation, gas, or bloating
• Unexplained weight loss or gain
• Getting sick easily and often
• Mood concerns like depression and anxiety
• Poor memory or ongoing fatigue

What to do if you Suspect You Have an Unhealthy Gut

While there are several commercial fecal microbiome tests available on the market today, the truth is that scientists are still in the process of developing a clinical tool that accurately identifies the state of an individual’s microbiome. Because our microbiomes may look different from day to day depending on the food we eat and the bacteria we’re exposed to, it would be difficult to capture an accurate picture of the constants found in a microbiome through a single test. Not to mention what a healthy microbiome looks like for one person may not match a healthy microbiome of someone else. So be wary of any commercial product that suggests it can provide anything other than a snapshot of the germs living in our poop for one single day.

That being said, despite there not being a concrete test to confirm the state of one’s gut stability, the following tips are ideas that you might try if experiencing symptoms that cannot be explained by your doctor. Each is relatively inexpensive and safe, and at the very least should not make matters worse. For best results, I encourage you to consistently try one strategy for 30-90 days to see if any health concerns improve. You can also try all of the strategies…all at once, do it up! All are darn natural and we should be doing most of these regularly anyway.

Try a Probiotic Food or Supplement

Probiotics have been around for quite some time, but I feel like they developed their public persona when Activia began promoting it in their products (dare you to try to say “Activia” without singing it). In fact, according to the all-knowing Wikipedia, “Activia pioneered the probiotic spoonable yogurt market.”

Well played, Activia. Well played.

But what are probiotics exactly? Well, in a nutshell, they are a whole bunch of healthy bacteria that naturally develop during the process of fermentation (a form of food preservation). Foods like yogurt, sauerkraut, kombucha, kefir, and even pickles contain probiotics. When we consume these foods, the bacteria they contain find their way to our guts; thus adding to our microbiota content and diversity. Remember, an unhealthy gut means there is some imbalance occurring within the microbiome; probiotics are designed to help stabilize these inequities by introducing a whole bunch of new bacteria into the mix.

However, not all microbiota serve the same purpose. Some sequences may help with diarrhea, others with skin conditions, and yet others allergies, so it’s not as simple as consuming any product containing probiotics when looking to improve issues relating to your “[fill in health issue].” In fact, identifying the different species and communities of microbes and their role in health is the focus of metagenomics – an area of study that is very much still in the research phase.

That being said, preliminary analysis has identified some strains of bacteria showing promise in helping with certain health issues. I encourage you to Google “probiotic strains for [insert your condition]” to find specific bacteria names to look for on any probiotic product you may be considering. Also, while probiotics are thought to be safe, they have not undergone any formal testing by the FDA to confirm this claim. Please consult with your physician before introducing any supplement into your daily diet.

Eat more Plant-Based Foods

Since the microbiota in our guts are a bunch of tiny organisms separate from ourselves, they need to obtain food to survive like any other living thing. So far scientists have determined our microbiomes really love two things in particular: polyphenols and fiber.

Polyphenols are micronutrients found in plant-based foods like seeds, fruits, vegetables, cocoa, soy, and whole grains – pretty much any whole food that doesn’t originate from an animal. While polyphenol content varies depending on the plant from whence it came, a good clue that it’s rich in this particular micronutrient is its color: the more vibrant a plant-derived whole food is, the higher amount of polyphenols it likely contains.

Microbiota are a little more picky when it comes to fiber, however. That’s because they have an appetite for foods specifically containing oligosaccharides.

Yeah, I’m not entirely sure I can pronounce that either.

Oligosaccharides are a special form of carbohydrate that the human body has trouble digesting. Because of this, most oligos escape the wrath of digestion and absorption, instead seeking refuge in the large intestine where they ferment; providing a feast for microbiota to grow and flourish.

Seemingly-random question: Have you heard of “prebiotics” and wondered what they were?

Well it turns out foods containing polyphenols and oligosaccharides are also called “prebiotics.” So there you go, now you know.

I bet manufacturers coined the term “prebiotic” because no one could pronounce the word oligosaccharides. Don’t quote me on that though.

Anyway, prebiotics – or, eh hem, polyphenols and oligosaccharides – are also a great adjunct to probiotic supplements you may decide to try. Prebiotics (whether in food or supplement form) give new bacteria obtained from probiotics a hardy buffet of nutrients that allows them to take root and proliferate (otherwise, your probiotic may just end up dying off after a few days due to lack of sustenance).

Here’s another way of looking at it through a beautifully crafted metaphor: You buy a fish, put it in a bowl full of water, and do nothing more. The fish will survive for awhile, but after a few days you can be certain it’ll be belly up and flushed away via the porcelain portal. However, if you buy a fish, put it in a bowl full of water, then feed it once every day or two, chances are little fishy is going to be a wonderful companion in your life for years to come.

Unless it’s a goldfish. Nothing you do can make those suckers last!

Eat More Fermented Foods

Fermented foods are GREAT for gut health as they take the above two and combine them. Probiotics and veggies all in one. Well kefir is not a veggie but the rest are. A natural source of probiotics can be most beneficial for more diverse strains. Try Kimchi, sauerkraut, miso, kombucha and kefir.

Take L-Glutamine

The human gut is lined by a mucous membrane, which is formed by a wall of cells that contain itsy bitsy spaces between them allowing for nutrient particles to pass from the small intestine into the bloodstream. However, when the microbiome is unbalanced, these tiny spaces in the gut lining can become larger; allowing microbiota and other small particles to pass through. When this happens, the body senses foreign invaders entering the bloodstream, which initiates an inflammatory response and causes a whole host of other problems like diarrhea, depression, fatigue, and auto-immune disorders.

L-Glutamine is an amino acid that helps maintain the integrity of this mucous membrane so those spaces designed exclusively for absorption remain tight. It has also shown to boost immune cell activity in the gut, which helps to prevent infection and reduce inflammation.

Even if your gut is stable, for people who exercise regularly, who are stressed (who isn’t?!), or who have had major infections, trauma, shock, radio/chemo therapy, immune or gastrointestinal disorders (ie: Chrohn’s disease or IBS), or who just plain lack L-Glutamine in the diet should consider using this supplement.

Take about 5 grams per day. For those that really need to focus on gut health, it is suggested to take 5 grams 2-3 times per day for several months and then drop down to 1 time per day.

An additional supplement to consider is colostrum. The hormone insulin-like growth factor (IGF-I) is prevalent in colostrum and, like L-glutamine, studies show that it can help restore the permeability of the gut lining. You can learn more about this and the other benefits of colostrum in my post here.

Finally, if you prefer a more natural source of L-Glutamine, try adding grass-fed organic beef bone broth into your daily diet. Bone broth is also a great source of other amino acids and other essential nutrients that can improve bone and joint health, keep skin looking young, balance hormones, and aid in digestion. You can read more about bone broth, how to make it, or where to buy it in this post: Bone Broth’s Incredible Benefits.

Beware of Antibiotics in Oral Medications and Food

While metagenomics and its role in human health is still in its infancy, there is one thing scientists know for sure: antibiotics negatively impact the human microbiome. In fact, one study reports that after a seven day course of antibiotics, microbiome diversity can decrease up to 25%. How this damage affects humans long-term is still being explored, but one study found it can take up to four weeks for the microbiome to recover, with some microbes remained MIA for up to six months.

That’s not very encouraging.

Currently we are caught in a bit of a Catch-22 when it comes to antibiotic prescriptions. They are the only course of action to fight certain bacterial infections and diseases, so we can’t simply declare we’ll never take them again and hope for the best. Yet, we now know taking them presents the potential for other concerns due to their negative impact on the helpful bacteria found in our guts.

Until scientists discover a way to get around this quandary, the best plan of action is to try to minimize the damaging effects of prescription antibiotics by taking probiotic supplements and being mindful about eating polyphenols and oligosaccharides during and after an antibiotic course of treatment. This will introduce new, healthy bacteria strains to (hopefully!) replace those that may be destroyed while taking your prescription.

While it’s pretty much impossible to avoid antibiotics entirely, one thing you do have more control over is limiting the intake of antibiotics through your diet.

Once upon a time farmers were allowed to provide antibiotics to livestock to promote growth. As a result, antibiotics began to contaminate our food sources, which began a worldwide crisis of antibiotic resistance in humans.

To address this problem, in 2017 the FDA released new rules that banned the use of medically-important antibiotics for the purpose of growth promotion, but they can still be used to “treat, control, and prevent” diseases.

While it’s great that antibiotics are no longer allowed to make livestock beefier (did you see that pun?!), the chances of factory-farmed livestock not needing antibiotics to “treat, control, and prevent” diseases is pretty slim (you can read more about this in my post here).

In other words, it’s likely that standard meat and dairy products have been exposed to antibiotics at some point and you are inadvertently consuming them.

The only way to ensure that animal-based foods are free of antibiotics is to purchase those having the “USDA Certified Organic” symbol. This symbol verifies that a product has not been given antibiotics in any form or for any reason. In fact, livestock on organic farms needing antibiotics for medical concerns are not allowed to be sold as organic following treatment.

We’ve Just Scratched the Surface

While I’ve done my best to provide an understandable overview of the microbiome, the fact remains that this is a very basic look at a very complex subject. Clearly, we still have a lot to learn about the “second genome.” Is it possible that healthy bacteria hold the key to reducing rates of obesity and disease while improving overall wellness? Wouldn’t it be amazing if the solution to some of our greatest health concerns could be as simple as taking a probiotic? I can’t wait to find out.

Until then, if you find the topic of gut health and the microbiome intriguing, I encourage you to dig even deeper through one of the many gut-health-specific podcasts available online. Or, if you are really into scientific data and graphs, check out the Human Microbiome Project put out by the National Institutes of Health.