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The Ultimate Guide to Gut Health and the Microbiome


There’s a lot of talk going around the fitness realm lately about “gut health.” Don’t get this confused with your abs, though. Researchers are discovering that there is a whole world inside us, almost another organ, that has a huge effect on our body and mind. This is known as the microbiome and getting it in order can help you take control of everything from your weight to your mental health. And maybe if you do take care of your gut, your abs will follow suit.

What is the microbiome?

The collection of microbes that live in and on your body are known as the microbiota. The microbiome are the genes that live inside these microbes. These genes influence how your body operates in a big way and even outnumbers human genes by an incredible ration of 100:1. Every one of us has a unique microbiota and a unique microbiome. They are like snowflakes. The ones that live in your body are determined by what you are exposed to and therefore change constantly. Your geography, health, stress, diet, age, gender, every surface you touch all impact the makeup of your microbiota.

Ok, let’s talk gut facts now. The microbiota is made up of a lot of microorganisms, as in trillions. Bacteria are the main substance with between 30 and 50 trillion cells. Our human bodies contain about 37 trillion human cells, for comparison. Don’t freak out though – this is only by numbers. By weight, the microbes are much smaller than human cells.

Scientists estimate that we carry roughly three pounds of bacteria in our intestines. Our individual microbiome is as special as our fingerprints and has hundreds of different types of bacteria. The exact number of bacteria changes throughout the day though and is always turning over.

Have you had a cold virus yet this year? Most times, that’s what we think of when we hear virus. It’s a literal dirty word. (Your coworker who is always sick because his kid is in daycare is your least favorite person.) However, the most plentiful thing in our microbiota are viruses but the good kind. The ones in our gut are bacteriophages, which mean they infect gut bacteria cells but don’t harm them. They have a symbiotic relationship where the viruses transfer beneficial genes.

When new bacteria are introduced into your gut through diet or probiotics, the viral cells help the bacteria survive by transferring genetic code.

The different things in the body that gut health impacts

Research is beginning to show how important the microbiome is to our overall health and it is so central to our operations that is essentially operating like an organ. It impacts aging, digestion, our immune system, mood, and cognitive function.

Bacteria in our guts produce enzymes that support digestion, especially the healthy and complex sugars that are found in plant foods. They also provide B vitamins, vitamin K, and short chain fatty acids. The microbiota also influences metabolic rate. Now do we have your attention? Who doesn’t want to improve their metabolic rate?

The foundation of your immune system is a strong microbiome. When you are born, your gut is a clean slate. Exposure to microbes gives education to train the immune system on how to respond to different organisms. This is the way the immune system balances the relationship of the body and the microbes in it. Harmful organisms are taken care of and helpful organisms exist in harmony and provide good overall health.

The makeup of the mother’s vaginal microbiota changes during pregnancy and is very influential to a baby. Babies born vaginally are exposed to different bacteria than babies who are born via Caesarean section. Likewise, babies born at home have different exposures than babies born in hospitals. As the baby grows, their microbiome changes. Only about 100 microbes exist during the first few months of life. By the time they reach age 3, a child’s microbiota is closer to 1,000 species of microbes and is close to adult microbiota. Puberty has a significant impact on the change in the composition of the microbiota.

History and current relevance of gut health

You may have only recently heard of “gut health,” but scientist have known about microorganisms for hundreds of years, beginning in 1673 when Antony van Leeuwenhoek informed the Royal Society of London about the discovery of “animalcules.” Leeuwenhoek found microbes everywhere with the help of his microscope but no one else paid attention until about 1870 when scientists realized their role in the cause and spread of disease. Before that, doctors thought that bad air caused disease. Then Robert Koch proved that tiny microorganisms were to blame and his discovery solidified that germ theory was valid – certain microbes cause specific diseases.

People then began to realize that cleanliness was super important for public health and started bathing daily, soap became a basic household necessity, and doctors and surgeons began washing their hands and sanitizing their instruments. That seems wild now, but before the discovery of “germs,” people just didn’t wash things and neither did doctors. This also led to public health initiatives to limit the spread of disease and save lives.

Until recently, scientists have focused on how pathogenic microbes affect humans in a negative way. Now there is the realization that some microorganisms are actually beneficial, enter gut health. More attention is being given to the microbiome and its role in overall health and immunity.

The gut-brain connection

More than just an ill-advised late-night trip to get fast food tacos, did you know that your gut health could affect your mood and behavior?

Scientists have known there is some connection between gut health and mental health since the early 1900s. Scientists and doctors emphasized the relationship between the two but by 1930, opinions reversed and it was thought that mental health disorders influenced gastrointestinal disorders. The renewed interest in gut health has revealed that there is a close relation between behavioral issues, mood, and a bacterial imbalance.

Even though there are a number of factors that influence the condition of your gut microbiota and its environment, your diet is a major one. Immune system health is a close second. Just more “disappointing” news to eat better, right?

Let’s get a little science-y for a bit here. Your gut is connected to your brain in three ways: the vagus nerve, the enteric nervous system, and the gut-brain axis.

  • The vagus nerve runs from your brain stem down into the neck, thorax, and abdomen and supplies motor parasympathetic fibers to all the organs except the adrenal glands. It helps regulate heart rate, speech, sweating, and various gastrointestinal functions.
  • The enteric nervous system connects with the central nervous system (CNS) and has local and central sensory neurons in the gut wall that monitor the conditions. There are other local circuit neurons that integrate the information and make it so the motor neurons regulate the activity of the smooth muscles in your gut wall as well as glandular secretions like digestive enzymes, mucus, stomach acid, and bile. It is referred to as the “second brain” because it can operate by itself and communicate with the CNS.
  • The gut-brain axis links the emotional and cognitive centers of the brain with the peripheral intestinal functions. Evidence from animal studies suggest that gut microorganisms can activate the vagus nerve and has a critical role in mediating effects on the brain and your behavior.

Bacteria and anxiety and depression have interactions that go both ways. A 2009 study found that male pup rats’ microbiota was altered when they were stressed from being separated from their mother. While they were only separated for three hours a day for 11 days, it was enough for researchers to conclude that it might make them more vulnerable to disease later in life, like depression or irritable bowel syndrome.

Your gut microbiota influences serotonin and dopamine production – your “feel good” chemicals. Did you know that over 90 percent of your serotonin is found in your gut? Well, it is, and it is a key regulator of gastrointestinal motility. The enteric nervous system (from above) uses more than 30 neurotransmitters, including serotonin, dopamine, and acetylcholine.

Some depressed rats were used in a 2014 study and given a strain of probiotics which resulted in a reversal of negative behavior and balance of the immune system. The probiotics had a positive therapeutic effect on the anxiety and depression symptoms of the rats.

How your gut impacts your sleep

How you sleep and your microbiome co-exist on a two-way street – the microbiota has an effect on how we sleep and sleep and circadian rhythms appear to have an effect on the gut bacteria. It’s still being researched, but it looks like not enough sleep quickly has an adverse effect on your microbiome.

Swedish and German scientists conducted an experiment in 2016 using nine healthy and normal-weight young men.  After just two nights of partial sleep deprivation, they found a significant decrease in the type of beneficial bacteria, changes to the composition of microorganisms in the microbiome that are specifically linked to obesity and type 2 diabetes, and a significant decrease in insulin sensitivity. After only TWO nights. Whoa.

Kent State researchers did another study in 2017 to investigate the link between relationship between poor sleep and age-related cognitive decline and the role of the microbiome. A group of adults ages 50 to 85 were studied and they found strong connections between higher sleep quality, better cognitive function, and higher levels of beneficial gut microbes.

We should be paying attention to our brain function for sure, but for vanity’s sake let’s also talk about how fragmented sleep affects the microbiome and your metabolic health. Research indicates that fragmented sleep plays a part in the microbiome effects on metabolic health by triggering inflammation that leads to metabolic dysfunction. It’s a complicated relationship but there is growing evidence that sleep and the microbiome are intertwined. If you can take steps now to sleep better and address issues of poor sleep, you can help protect your metabolic health and reduce risks for weight gain and diabetes.

Warning signs of an unhealthy gut

So, how will you know if you have an unhealthy gut environment brewing in there? There are a wide range of signs, such as:

  • Bloating, gas, or diarrhea – These occur mostly due to the number and diversity of the bacteria living in your gut, stomach, intestines, and colon. Gas is a particular sign that food is fermenting in your gut and you don’t have enough acid or there is an imbalance of bacteria to break down the food
  • Sugar cravings – Gut bacteria secrete proteins that are similar to leptin and ghrelin, which are hunger-regulating hormones. They also affect mood and food cravings. The bacteria try to trick you into eating the foods they thrive on so if you eat a lot of sugar, you feed the unhelpful bacteria and then they secrete proteins to make you crave more sugar. Vicious little buggers.
  • Bad breath – Halitosis, or chronic bad breath, comes from the microbes that live in between your teeth and gums and on your tongue and can also be caused by bacteria that are linked to gum disease.
  • Food allergies and sensitivities – Food intolerances to gluten or dairy are almost always due to “leaky gut.” The gut is a sealed passageway from mouth to colon and anything that goes in the mouth and isn’t digested gets passed out the colon. One of the most important jobs of the gut is to prevent foreign substances from entering the body and when the intestinal barrier is permeable, protein molecules can escape and enter the bloodstream. Your body will mount an attack on them and the immune response shows up as food intolerance.
  • Moodiness, anxiety, and depression – Most of your serotonin and roughly half of your dopamine is made in your gut so if you have a “leaky gut” your body may lose those. Your gut won’t be able to absorb the right nutrition or micronutrients if it’s all leaking out. Treating gut issues can be a critical part of managing mental health.
  • Skin issues like eczema – Food intolerance can be visible through the presence of eczema.
  • Diabetes – Russian researchers were able to link the level of glucose intolerance with the presence of three types of microbiota: Blautia, Serratia, and Akkermansia bacteria. All three are found in healthy people but people with diabetes have greatly increased numbers of them.
  • Autoimmune disease and suppressed immunity – some clinicians have seen a link between thyroid disease and a leaky gut and particularly an intolerance to gluten. For those people removing gluten helped heal their gut and reversed their disease. If you suffer from frequent illness and infections you may also have issues with your microbiome.

What foods are bad for your gut

There are certain foods you should eat when you are trying to make gains, foods to eat when you’re trying to cut, and foods that help your athletic performance. That means there are also foods to avoid when you are trying to have a healthy gut, which is going to affect all those things.

  • Sugar – sugar of any kind is bad for your gut health and participants in a study were found to have increased constipation on a high-sugar diet
  • Processed foods – emulsifiers used in processed foods disturb gut microbiota
  • Soy – high levels of processing of today’s soy change how it effects the body and has even been shown to reduce two key strains that are crucial for a balanced gut
  • Dairy – consumption changes the bacterial makeup within days and allows strains linked to intestinal disease and inflammation to grow
  • Red meat – similar to dairy, red meat encourages the growth of certain strains that negatively affect your gut
  • Gluten – even if you don’t have Celiac disease, gluten can lead to stomach pain, bloating, and fatigue
  • Eggs – a certain protein in eggs encourages the growth of a gut bacteria that produces a chemical compound that causes clotting and raises the risk of heart attack and stroke
  • GMOs – traits that help these crops resist disease can also reduce the beneficial bacteria in the gut. Common GMO products in the U.S. are wheat, soybeans, and corn.
  • Corn – again, corn is one of the most common GMO products in the U.S. and can reduce beneficial bacteria
  • Farmed fish – antibiotics used in farmed fish can be passed along if you eat these fish and antibiotics kill all bacteria, good or bad
  • Nightshades – this includes tomatoes, eggplant, potatoes, and bell peppers. Glycoalkaloids found in these have been shown to lead to intestinal inflammation
  • Tap water – some research has found that chlorinated water can alter gut microbiota and even lead to colorectal cancer
  • Artificial sweeteners – more research shows these cause changes in microbial composition, increased gluten intolerance, and higher rates of metabolic disease.

What foods are good for your gut

Probiotics are making their way into mainstream supplements now. What are they? Glad you asked. They are the beneficial forms of gut bacteria that help to stimulate natural enzymes and the processes that keep your digestive organs functioning properly. In order to keep yourself healthy, you have to keep these bacteria healthy. You can do this by taking a probiotic supplement or eating foods that have probiotics.

Breakfast food. Croissants on table with fresh fruit

Live-cultured yogurt is one of the best forms of probiotic food, especially if you can make it yourself. If you buy it, look for brands that are made from goat milk and are infused with extra probiotics such as lactobacillus or acidophilus. They suggest goat milk because it is a rich source or proteins, vitamins, and minerals and has better digestibility and lower rate of allergies than cow milk. It’s also high in probiotics like thermophilus, bifidus, and bulgaricus.

If you use yogurt, be sure to check the labels. Many are filled with high fructose corn syrup and artificial sweeteners which can make them nutritionally equivalent to ice cream. Yikes.

Kefir is similar to yogurt and is a combination of goat milk and fermented kefir grains. It’s high in lactobacilli and bifidus bacteria as well as antioxidants.

Sauerkraut is made from fermented cabbage and some other vegetables, and is really high in healthy live cultures and could also help reduce allergy symptoms. It’s also rich in vitamins A, B, C, and K.

It doesn’t contain probiotics itself, but dark chocolate is a highly effective carrier for probiotics. It helps them survive the pHs of the digestive tract and make it to the colon. This protective ability of probiotics can be added to the high-quality dark chocolate.

Microalgae is a superfood ocean-based plant like spirulina, chlorella, and blue-green algae. These aren’t probiotics but are prebiotics, which mean they feed and nourish the probiotics that are already in your gut. They have been shown to increase good bacteria and improve overall gastrointestinal health. They have also been shown to have the most amount of energetic return per ounce for the system.

It’s an appetizer before Japanese meals for a reason, miso soup is commonly used in macrobiotic cooking as a digestive regulator. It’s made from fermented rye, beans, rice or barley. Adding just a tablespoon of miso to hot water makes an easy and quick probiotic-rich soup full of good bacteria. Miso is also nutrient-dense and it is believed to help neutralize the effects of environmental pollution, alkalinize the body, and stop the effects of carcinogens.

Pickles aren’t just for weird pregnant women – the traditional cucumber stored in brine has a ton of probiotics. Really, any vegetable can be pickled though.

If you are going meat-free, tempeh is a good substitute for animal protein or tofu. It is a fermented grain made from soybeans and a great source of vitamin B12. It can be sautéed, baked, or crumbled on salads. Prepare it correctly and it is also really low in sodium.

Spicy, pickled sauerkraut is known as kimchi in Korea. It is also sour and full of good bacteria, vitamin C, B vitamins, beta-carotene, calcium, iron, potassium, and fiber. If you can handle the spice it’s one of the best things to add to your diet.

Kombucha tea can be found at your neighborhood grocery store now and has a high amount of good gut bacteria. It’s been around for centuries and it’s believed to increase your energy, improve well-being, and might even help you lose weight. It might not work for those with issues with candida and be on the lookout for ones with too much sugar.

How you can learn about what is in your gut

You can use the list of symptoms to tell if you might have issues with your gut, but how do you really know what’s going on in there? Well, quite frankly, you can send your poop to be tested by scientists.

There are a few companies who have jumped at this new way early, like uBiome and Viome, to make it easier for you to get tested without going through your doctor. These tests give you a precise and complete picture of what is going on so you can alter and adjust your diet and lifestyle to get into optimal health condition.

Things you will learn:

  • how to maximize beneficial microbial species that boost gut health
  • which missing probiotics your gut needs
  • whether you are lacking good metabolites and which undesirable ones are present
  • which prebiotics you need for the foundation of gut health
  • the ideal ratio of proteins, carbs, and fats you need in your individualized diet
  • dietary recommendations for achieving healthy weight, energy, focus, and well-being
  • ways to optimize digestion and absorption of nutrients in your gut

The costs range generally from $100 to about $400, depending on the level of detail and support they offer.

Biohacks for improved gut health

We’ve already talked a lot about your diet, and that’s an obvious “easy” change, but there are a couple other things you can do to improve your gut health.

Researchers have found that consistent exercise provides an improvement in gut health. A six-week study sampled microbiomes at the end of six weeks of exercise and found an increase in the gut microbes that assist in the production of short-chain fatty acids. These reduce the risk of inflammatory disease and type 2 diabetes, obesity, and heart disease. Participants were then asked to be sedentary for another six weeks and their microbiomes went back to how they were before the period of exercise. Regular exercise is needed and more research is needed to determine if longer periods of exercise will cause greater changes.

An overall lifestyle shift is usually needed to improve gut health for most of us. A combination of diet, exercise, meditation, and stress management is helpful for the treatment of gastroenterological problems.

Who is this right for?

Do you have a gut? Do you want to be healthy? You, this is for you, and also:

  • Anyone who wants to learn what is in their gut – you can’t fix it if you don’t know what’s in it
  • Anyone who feels themselves going through a health change – if you have been feeling sluggish or foggy lately or just “off,” then your gut may have something to do with it
  • Men in their 30s – tweak your current regimen by tuning into your gut health
  • Men in their 40s – train harder and smarter and get the benefits by balancing your microbiome
  • Men in their 50s and 60s – get ahead of any concerns with the effects of aging on your mental state by paying attention to how your diet effects your gut health
  • Men in their 70s and beyond – be here for the long haul and be mentally agile by making your gut health a priority

Now what?

Gut health and microbiome research are becoming more popular and modifications made to one’s diet can achieve remarkable results. Mental clarity, overall improved mental health, and physical symptoms caused by bad bacteria and inflammation can see drastic improvements by managing your gut health.

The information on this website has not been evaluated by the Food & Drug Administration or any other medical body. Information is provided for educational purposes. You should consult your doctor before acting on any content on this website.

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