Gut Health 101: Microbiome, Probiotics & How to Fix an Unhealthy Gut

“All disease begins in the gut,” proclaimed the “Father of Medicine” Hippocrates centuries ago. Today’s science increasingly confirms Father’s hunch about health issues. Our gut bacteria play a significant role in our overall health. They influence critical human functions, including our mental health, immune system, digestive functions, skin health, and weight 1. The key to a healthy gut is maintaining a delicate balance of good bacteria and bad. Gut Health 101 covers everything you need to know about gut health, probiotics, and getting rid of harmful bacteria that may be causing you symptoms.

Why Gut Health Is Important

In Gut Health 101, we are going to break down all the complexities that make up up the microbiome. We’ll discuss probiotics, health-related conditions associated with poor gut health, and ways to fix your gut health naturally.

Most of us are born with a clean slate. We develop from a zygote into a fetus into a kicking and screaming little baby all within the safe environment of a mother’s womb.

This environment nurtures the development of the gut microbiome. Once we enter the world, we are greeted by a plethora of different germs that we’ve never encountered before.

Some of these foreign bodies will cause us to get sick but, ultimately, boost our immune system. In other instances, these invaders can cause chronic inflammation that may result in a number of different conditions and diseases.

What Leads to Poor Gut Health?

The biggest takeaway of Gut Health 101? Whatever the problem is, chronic inflammation started it!

Foreign bodies inside our system are known to trigger immune responses. When the responses become reoccurring and constant, inflammation can become chronic.

Pathogens enter our system in many ways, including:

• Eating Foods Contaminated with Pesticides or Bad Bacteria
• Continuously Poor Food Choices like Sugar and Trans Fat
• Eating Foods That Trigger Food Allergies, Celiac Disease, etc.
• Nutrient Deficiency Caused By Poor Diet or Illness
• Toxins Re-Entering Our Bloodstream From Our Waste
• Wearing Cosmetics Made with Synthetic Ingredients
• Long-Term Use of Medications
• Breathing in Toxic Chemicals and Heavy Metals
• Underlying Stress like Bills, Work, Relationships
• Catching an Illness From Another Person

There are many ways to enter the body, but there is one way out. As pathogens enter the system, gravity takes over. These pathogens enter from pores, your mouth, or the respiratory tract. Inevitably, they drop down into the gut, where they can either get flushed out or eventually ignite inflammation.

Chronic Inflammation and an Unhealthy Gut

Just as all disease begins in the gut, inflammation is the root of all disease. All germs, viruses, or food that comes into the body ends up entering the digestive tract. Our body is either trying to get all the nutrients out of this potential energy source or attempting to get it out of the system.

Our immune system has a “better safe than sorry” approach. Its innate immune function is to cause inflammation. The innate immune system rids the body of the potential issue, and then curtails the inflammation when the threat goes away 2.

Unfortunately, threats become more common as we age. The once-booming metabolism we used to enjoy starts to slow down. Eventually, poor dietary choices, inflammatory foods, and other toxins begin to have a cumulative effect on the system.

Chronic Diseases Associated with Chronic Inflammation

The over-arching lesson Gut Health 101 is that leaving your gut unhealthy is a precursor for many illnesses. Over time, our digestive issues may begin to worsen. They’ll start to coincide with other symptoms of an unhealthy gut.

Inevitably, you may develop issues pertaining to:

• Immune System (Allergies, Food Intolerances, Colds, Flu)
• Leaky Gut Syndrome
• Irritable Bowel Syndrome (IBS)/Small Intestinal Bacterial Overgrowth (SIBO)
• Other Digestive Issues (Inflammatory Bowel Disease IBD, Heartburn, Bloating, Constipation)
• Weight Gain
• Skin Conditions (Acne, Rosacea, Psoriasis)
• Autoimmune Diseases
• Mental Health (Depression, Anxiety, Mood Swings)
• Poor Sleep

The reason for these issues is that your immune system becomes overworked by chronic inflammation. That leaves your body more susceptible to pathogenic overgrowth. Plus, chronic inflammation starts to destroy healthy gut bacteria. This battle for survival all takes place in an internal community known as the microbiome.

What Is The Gut Microbiome?

Your stomach is home to trillions of microscopic living beings known as microbes. There are thousands of different microbes identified by science and probably will be more discovered for centuries to come 3.

However, the most common types of gut microbiota are:

• Yeast
• Fungi
• Bacteria
• Archaea
• Protists

Of the bunch, gut bacteria are the most abundant and studied. Science has confirmed that there are hundreds of bacteria strains. Each plays a specific role in the internal ecosystem that is the gut microbiome.

Common Gut Flora in the Microbiome

The dominant bacteria phylums typically found in the body fall within the following groups:

Around 90% generally fall specifically within the Firmicutes and Bacteroidetes phyla.

All of these commensal bacteria work together for optimal health of its host — you! They all work in unison, applying the crafts that are their specialties.

The Importance of Gut Bacteria Diversity

It seems like every bacteria has a role. Even Staphylococcus aureus, the bacteria strain behind the potentially life-threatening staph infection, can help keep other opportunistic Staphylococcus strains from becoming unruly 4. Unfortunately, if probiotic bacteria can’t check Staphylococcus aureus, it can become overgrown and result in deadly consequences.

The most beneficial gut bacteria will create metabolites that help prevent other bacteria from overgrowing. For instance, many bacteria strains produce short-chain fatty acids 5. These serve as electrical currency for our gut cells to rejuvenate, divide, and strengthen the intestinal barrier. In particular, probiotics create the short chain fatty acid, butyrate, which is vital in repairing the gut lining and promoting probiotic bacteria growth.

When everything is going smoothly in the microbiome, then you shouldn’t notice any signs of an unhealthy gut. Things go smoothest when gut flora communities remain in balance. As we age and our cumulative life choices start catching up to us, it might begin to cause a deficit in beneficial bacteria opening up room for harmful bacteria to overtake the system.

As harmful bacteria spread, your immune response ignites inflammation. Unfortunately, most harmful bacteria species thrive in these sorts of environments. It’s your probiotic bacteria that suffer.

In the end, this microbial imbalance kickstarts a chain of health-related events that can impede your quality of life. That’s why it’s important to boost your immune system with probiotics and a healthy gut diet plan.

What Are The Symptoms of Poor Gut Health?

There is strong evidence that our gut bacteria pretty much run the ship. Different types of live bacteria play unique roles in countless physiological processes. When the diversity of bacterial cells becomes compromised, key aspects of our overall wellness can be jeopardized, too. Here are some of the most vital ways gut issues can impede our day-to-day life.

Weak Immune System

Our gut bacteria and immune cells are besties. They go back to the womb. Live bacteria live within the vaginal microbiome inside of our mother’s amniotic sac and placenta.

These beings helped shape our first immune cells 6. As we formed, what would become our skin traps in our immune cells and gut bacteria to create our gut microbiome.

Over 80% of immune system cells reside in the gut 7. That’s because everything we ingest ends up there. Our innate immune system kicks in and creates inflammation to eliminate threats and then turns off the fire hose when the danger is a goner.

Unfortunately, our innate immune system gets a bit overworked. We’re always feeding our gut with processed foods, breathing in polluted indoor air, and smearing on gut biome-disruptive cosmetics.

In simple terms, our immune cells are always on duty, working on the messes we make! These actions undoubtedly compromise our immune health. Eventually, they’re going to miss a significant threat, like an opportunistic gut bacteria.

Additionally, an overworked innate immune system causes chronic inflammation. Inevitably, that will start to destroy epithelial cells that make up the gut lining.

Leaky Gut Syndrome

According to one Harvard paper, “we all have some degree of leaky gut 8.” That’s due to the design of our gut lining. There are porous holes along the barrier that allows for ventilation in the intestines. More importantly, it will enable nutrients from our food to permeate into our bloodstream.

Our gastrointestinal tract starts the food breakdown process as soon as we smell our food 9. We then chew the food so we can swallow it and allow our stomach acids, digestive enzymes, and organs to break these food sources down to the simplest particles.

These compounds enter the small intestine, where they get sorted out as nutrients or waste. Waste enters the large intestine, where water is siphoned out, and toxins are expelled from our backside. Meanwhile, the small intestine allows nutrients from our foods to be distributed throughout the entire body.

The small intestine plays a vital role in nutrient absorption. It relies on a barricade of 40 different proteins known as tight junctions 10. Tight junctions protect the epithelial cells that line our gut.

However, tight junctions are always under attack from chronic inflammation happening on the other side of the gut barrier. Eventually, their tightly-wound structure starts to break down. They become loose, which allows for gut bacteria and other toxins in your intestines to enter the bloodstream.

Also, certain foods can trigger tight junctions to move. For instance, gluten contains a protein known as zonulin. Zonulin can activate the tight junctions to open up 11. Therefore, toxins, bacteria, and food particles in your intestines can leak into your bloodstream. This preemptive opening may disrupt the appropriate absorption of food nutrients and trigger inflammation.

Leaky gut develops over time. It can become a precursor to many life-threatening illnesses. It’s vital to repair the gut barrier by removing inflammatory foods, eating probiotic foods, antiviral foods, and foods rich in collagen, like bone broth.

Irritable Bowel Syndrome (IBS)/Small Intestinal Bacterial Overgrowth (SIBO)

Irritable Bowel Syndrome (IBS) and Small Intestinal Bacterial Overgrowth (SIBO) are two common GI conditions that people may experience simultaneously. Many of the symptoms of IBS and SIBO overlap one another. However, fixing them are two completely different processes.

IBS is a condition that impacts the large intestine. Chronic inflammation messes up metabolic functions that affect muscle contraction. So, bathroom frequency can be thrown off.

Most common signs of IBS are abdominal pain, bloating, and frequent trips to the bathroom. Here, they may experience either diarrhea or constipation.

People with SIBO experience many of these symptoms. However, the cause isn’t muscle contractions. It’s due to a bacterial overgrowth from the small intestine.

When you have SIBO, your gut bacteria are severely impacted. You must take a particular test to diagnose SIBO. From there, you have to eliminate potential foods that trigger inflammation, kill the bacteria with either antibiotics or a high-quality supplement recommendation from a naturopath. You must then reinoculate your gut with a probiotic supplement and feed that bacteria a healthy dietary fiber diet.

Other Digestive Issues

Many chronic illnesses can be caused by poor gut health. A few of the more common ones include Inflammatory Bowel Disease (IBD). IBD is actually a blanket term to describe two digestive illnesses — Ulcerative Colitis (UC) and Crohn’s Disease.

UC is caused by inflammation of the cells within the large intestine 11. In addition to bloody stools and intense abdominal pain, those with UC are at an increased risk of developing colorectal cancer.

Crohn’s Disease is an inflammation of the gastrointestinal tract 12. That means it can spark anywhere from the esophagus to the anus. Treating these conditions will require a doctor’s care.

Another common GI condition associated with poor gut health is acid reflux/GERD. When you experience GERD, food particles can backtrack up your esophagus. You can experience severe heartburn and may cause long-term damage to your throat and gut lining.

Weight Gain

It’s not shocking that poor gut health can cause weight gain. After all, many of the reasons for an unhealthy gut are dietary choices. However, our gut bacteria play a role in this, too.

We rely on our gut bacteria to help with food breakdown. So, if less probiotic bacteria are working, there’s less productivity going on in the GI tract. Many of these foods can sit around the belly. Eventually, this can cause long-term inflammation. Scientific evidence shows that there is a strong connection between obesity and a lack of gut diversity 13.

Also, gut bacteria can manipulate us. When pathogenic bacteria infest us, we’ll start to crave sugars and other food additives actively. These unhealthy foods make it easier for them to survive and for beneficial bacteria to die.

The best way to lose weight is to change your diet habits. You might want to consider intermittent fasting for gut health a few times a week. Also, increase your physical activity. Cut down on foods rich in animal fats and opt for leaner proteins, like fish, legumes, and whole grains.

Skin Issues

If you’re inflamed on the inside, it’s going to show on the outside. Your body becomes a pressure cooker, and it’s burning off healthy skin cells. In turn, these dead or dying cells clog up the skin barrier. This backup will manifest as itchy, red, or blotchy skin.

An unhealthy gut, leaky gut, has been strongly tied to many skin conditions, including:

• Rosacea
• Psoriasis
• Eczema
• Acne
• Allergic Reactions
• Arthritis

Furthermore, our skin also protects our gut biome from infestations. There are many viruses, fungi, and opportunistic bacteria on other people and surfaces trying to find a new home in your stomach. So, your body relies on your own skin bacteria as the first line of defense.

In fact, our skin has its own microbiome. This microbiome communicates with cells on the inside via the gut-skin axis to ensure its host’s overall health. Unfortunately, we destroy these healthy bacteria with toxic beauty ingredients. The average woman puts 515 synthetic chemicals on her face every day 15. So, our skin microbiome is always on high alert!

Mental Health Problems

Our gut is the second brain…or is it? The gut-brain connection is more than a metaphorical statement or declaration of being hangry. These two are joined at the hip…or at least by a series of nerves.

At the bottom of the brainstem is our vagus nerve. This barometer-of-sorts relies on information from the gut up through the central nervous system 16. It can influence and collect information from every essential organ along the way!

When harmful bacteria overtake our gut, your vagus nerve lets the brain know. In turn, we can develop many symptoms of neurological disorders, including depression, anxiety, and hyperactivity.

Like most things, the key to regulating the gut-brain axis is balance. A diverse gut is essential for mental health. Actually, one meta-analysis on gut diversity and Autism Spectrum Disorder (ASD) found that children diagnosed with ASD had lower levels of Veillonellaceae, Coprococcus, and Prevotella bacterial cells 17.

Even more notably, these children also lacked bacterial species, Bifidobacterium and Blautia. These two are essential for making tryptophan, the precursor to our joy molecule, serotonin. In fact, up to 90% of our serotonin neurotransmitters are derived from the gut 18.

Furthermore, a recent study found that a few microbial species, particularly Bacteroides, produce the neurotransmitter, gamma-aminobutyric acid (GABA) 19. GABA is known as our inhibitory neurotransmitter. It helps calm our racing thoughts, which lowers our cortisol levels.

Cortisol is one of our stress hormones. When we endure stress on a daily basis, it can cause chronic inflammation. As we’ve discussed, chronic inflammation is the root of all life-threatening conditions that compromise human health.

How to Improve Your Gut Health Naturally

You didn’t ruin your gut overnight. In fact, many unexpected things ruined your gut health. So, fixing it isn’t going to happen in a day, either. Taking care of your gut is an ever-evolving process. Make little changes that ease common digestive symptoms and then slowly chip away at the bigger picture items. Here’s how!

Get Your Gut Tested

The first step to fixing your gut health is to know what you’re working with. A surgeon wouldn’t operate without an x-ray. You can’t reintroduce good gut bacteria into your body until you know the bad ones you’re dealing with.

We send you everything you need to take a gut test safely in your own bathroom. Just bring the kit in when you do #2. Wipe like normal with toilet paper. Then use one of the sterile swabs to collect a small sample from the toilet paper.

Dip the swab into the vial with a preservative liquid that’s provided. After 20-30 seconds, the liquid will change colors, meaning your DNA is secure. Seal the bottle and dispose of the swab like you would a newborn’s diaper.

Mail your vial to us in the pre-addressed envelope we provide. In just a few weeks, we will give you in-depth insights into your gut health. Most importantly, we tell you which gut bacteria are overstaying their welcome. Based on that info, we can give you a bunch of actionable plans to repair your gut.

For one, we can tell you which foods are causing you digestive issues. Different microbes have a penchant for different foods. So, if you have a surplus of one type of bacteria, there’s a high likelihood that specific foods caused that overgrowth.

Furthermore, our gut health program offers you hundreds of recipes that can help you grow the bacteria you need. As we will discuss later, specific foods will give beneficial bacteria the energy necessary to reclaim your gut health.

Order A Custom Probiotic Supplement

However, you don’t want to take a generic probiotic supplement because it might be laden with gut bacteria that you already have plenty of. With our gut health test, we can determine which stomach bacteria your gut biome truly needs.

Our custom probiotic supplement is a delivery service. You can easily manage your subscription in our database to change your delivery date or hold your service. You can also get retested in a few months and compare your recommendations and results!

Cut Out Inflammatory Foods

While you wait for your custom probiotic supplement to come in the mail, there are plenty of actionable things you can do in the meantime. For one, you should cut many of the “usual” suspects.”

From there, try alternating some your diet choices. Opt for a different meal plan, like going keto or paleo vegan. In the meantime, try eliminating these foods.

Gluten

Gluten is the top inflammatory food in the world. It’s in everything from baked goods to cosmetics. While many think that gluten is an issue for people solely with Celiac Disease, that is not the case. Celiac Disease only accounts for about 1% of the population.

Many of us are sensitive to products that commonly contain gluten, such as bread. Many whole grains grown in Western agriculture are made with genetically-modified organisms (GMOs). Research indicates that GMOs might have the ability to alter DNA 20. They also change microbial communities in soil 21. So, what’s to say GMOs won’t do the same to our microbes?

Also, we mentioned earlier, the protein zonulin increased by consumption of gluten products, relaxes our tight junctions. Therefore, gluten increases intestinal permeability for people who don’t even have severe gluten sensitivity.

Lactose/Dairy

Approximately 65% of us lose the ability to digest lactose after infancy properly. 22 Therefore, many of us are lactose intolerant and are probably unaware of it.

Symptoms of lactose intolerance include:

• Diarrhea
• Nausea
• Abdominal Pain
• Cramping
• Bloating
• Constipation

Many of these lactose intolerance symptoms also mirror the common signs of an unhealthy gut. We’re the only mammals to drink milk past infancy. Plus, we’re the only mammals to drink another mammal’s milk. These might be clear indicators that we should limit our dairy intake.

Not to mention, many dairy cows are preemptively treated with antibiotics. That’s because female calves are milked mechanically. These machines can cause the udders to rupture and get infected by bacteria. So, they’re given antibiotics to stop this inevitable occurrence. Unfortunately, we drink that milk and those antibiotics 23.

The purpose of antibiotics is to wipe out bacteria — good and bad. So, consuming antibiotic-rich milk can play a major role in depleting your probiotic bacteria levels.

Soy

Soy is a very protein-heavy plant-based protein. Unfortunately, it’s a common food allergen. For those with a soy allergy, their immune system sees its proteins as a potential threat. Therefore, it will cause inflammation.

There are many soy products, including some you might not be aware of, like:

• Edamame
• Tofu
• Tempeh
• Soy Sauce
• Soy Milk
• Miso

It is not uncommon for people with a soy allergy to also have an allergy to legumes. So, you might want to stay away from chickpeas, peanuts, and peas.

Lectins

Speaking of legumes, some people are sensitive to plant-based compounds known as lectins. Lectins are deemed “anti-nutrients 24.” They latch on the vitamins and minerals our bodies rely on for energy. In turn, we are left bloated and with depleted energy levels.

Some of the foods that contain lectins include:

• Dairy (Casein in Cheese, Milk, Yogurt)
• Legumes (Black Beans, Chickpeas, Lentils, Peanuts, Soybeans)
• Nightshades (Eggplants, Goji Berries, Peppers, Potatoes, Squash, Tomatoes)
• Whole Grains (Baked Goods, Bread, Corn, Crackers)

Start Eating Prebiotic-Rich Foods

After you eliminate foods that are causing digestive issues, you need to replenish the good gut bacteria that you have. The best way to do this is to feed them dietary fiber.

Our gastrointestinal tract can’t break down all dietary fibers. So, our probiotic bacteria eat these carbohydrates for energy. These food sources are known as prebiotics. Feeding stomach bacteria prebiotics allows these microbes to also create short-chain fatty acids that help repair the gut lining, such as butyrate.

Prebiotic-rich foods include:

• Bananas
  
• Jerusalem Artichokes
• Onions
• Garlic
• Leeks
• Apples
• Chicory Root/Inulin
• Barley
• Kefir

When eating fiber, start off slow. Going overboard can cause serious cramping. Also, some people have allergies to members of the allium family (onions, garlic, scallions). If you notice issues when you consume these prebiotics, cut back on your intake.

Ombre has food recommends tailored to feed bacteria we’re attempting to grow in your gut. We don’t leave you alone in the kitchen to fend for yourself. Our database provides you with countless recipes to tailor weeks worth of healthy gut meal plans.

Eat Probiotic Foods

As your first probiotic supplement are on their way to you, you can get ahead of the game by eating probiotic foods. Many foods have live bacteria in them that can help get your digestive juices flowing. Even better, they’re derived from whole foods that are rich in antioxidants that help repair your gut.

Some of the best sources of probiotic foods include:

• Pickles
• Kraut
• Kimchi
• Yogurt
• Kombucha
• Tempeh
• Natto
• Miso