Most people believe that the bacteria in the body are a cause of illness or the development of certain diseases, but did you know that at any given moment there are actually billions of beneficial bacteria present in all of us? In fact, bacteria make up our microbiome, an integral internal ecosystem that benefits gut health and the immune system.
Recently, the scientific community has truly accepted the important role that bacteria play in stimulating a strong immune system and maintaining a healthy body. Not only do all bacteria not harm our health, but some are actually essential for boosting immunity, maintaining the digestive system to function without issues, balancing hormone levels, and ensuring proper brain function.
What is the human microbiome?
Each of us has a complex internal ecosystem of bacteria, which we call the microbiome. The microbiome is defined as a community of microbes. The vast majority of bacterial species that make up our microbiome live in our digestive systems.
According to the Department of Chemistry and Biochemistry at the University of Colorado, USA, the human microbiota consists of 10-100 trillion symbiotic microbial cells hosted by each person, primarily intestinal bacteria. The human microbiome is made up of the genes that these cells harbor.
Our individual microbiomes are sometimes referred to as our genetic fingerprints, as they help determine our unique DNA, hereditary factors, disease predisposition, body type or weight set point, and much more. The bacteria that make up our microbiome can be found everywhere, even outside the body, on almost every surface we touch and in every part of the environment we come into contact with.
The microbiome can be confusing, as it differs from other organs in that it is not just localized in one place and does not have very large dimensions, plus it has very extensive roles that are related to many different bodily functions. Even the word microbiome says a lot about how it works and the importance of its roles, as “micro” means small, and “biome” means a habitat of living organisms.
Some researchers have stated that up to 90% of all diseases can be traced back in some way to the gut and the health of the microbiome. Believe it or not, your microbiome hosts trillions of microbes, diverse organisms that help govern almost every function of the human body in one way or another. The importance of our gut microbiome cannot be overstated: poor gut health can contribute to leaky gut syndrome and autoimmune diseases and disorders such as arthritis, dementia, heart disease, and cancer, while our health, fertility, and longevity also depend on the balance of creatures living in our intestines.
Throughout life, we help shape our own microbiomes, and they adapt to changes in our environment. For example, the foods you consume, how you sleep, the amount of bacteria you are exposed to daily, and the level of stress you experience all help establish the state of your microbiota.
Diet
Your diet plays an important role in establishing gut health and supporting the good bacteria of your microbiome. Research over the past few decades has revealed evidence of an inextricable link between the microbiota, digestion, body weight, and a person’s metabolism. In an analysis of humans and 59 additional species of mammals, it was shown that the microbiome varies dramatically depending on the species’ diet.
The reverse is also true: gut health can influence how your body extracts nutrients from your diet and stores fat. The intestinal microbiota appears to play an important role in obesity, and changes in bacterial strains in the gut have been shown to lead to significant changes in health and body weight after just a few days. For example, when germ-free mice receive a gut microbiota transplant from conventional/fat mice, they gain more body fat rapidly without even increasing their food intake, as their gut microbes influence hormone production (such as insulin), nutrient extraction, and fat storage (adipose tissue).
Now that you can see why it is essential to reduce inflammation and support gut health, let’s take a look at how you can proceed in this regard.
Foods that promote inflammation include:
Refined vegetable oils (such as canola, corn, and soybean oils, which are high in pro-inflammatory omega-6 fatty acids)
Pasteurized dairy products (common allergens)
Refined carbohydrates and processed grain products
Conventional meat, poultry, and eggs (high in omega-6 due to feeding animals corn and cheap ingredients that negatively affect the microbiome)
Added sugars (found in most packaged snacks, sauces, condiments, canned goods, cereals, etc.)
Trans fats/hydrogenated fats (used in packaged/processed foods and often for frying)
On the other hand, many natural foods can reduce inflammation and help increase the good bacteria in the gut. Foods rich in antioxidants help reduce intestinal damage caused by oxidative stress and reduce an overactive immune system while simultaneously protecting healthy cells.
Anti-inflammatory foods that should form the basis of your diet include:
Fresh vegetables (all types): packed with phytonutrients, which have been shown to lower cholesterol, triglycerides, and symptoms of rheumatoid arthritis, Alzheimer’s disease, cancer, cardiovascular diseases, and diabetes. Aim for variety and a minimum of four to five servings per day. Some of the best include beets; carrots; cruciferous vegetables (broccoli, cabbage, cauliflower, and Brussels sprouts); dark leafy greens (kale, spinach); onions; peas; lettuce; sea vegetables; and zucchini.
Whole fruits (not juice): Fruits contain various antioxidants, such as resveratrol and flavonoids, which are linked to cancer prevention and brain health. Three to four servings per day is a good amount for most people, especially apples, blackberries, blueberries, cherries, nectarines, oranges, pears, pink grapefruit, plums, pomegranates, or grapes.
Herbs, spices, and teas: turmeric, ginger, basil, oregano, thyme, etc., plus green tea and organic coffee in moderation.
Probiotics: Probiotic foods contain good bacteria that populate your gut and fight against harmful bacterial strains. Try to include probiotic foods such as yogurt, kombucha, kvass, kefir, or fermented vegetables in your daily diet.
Wild-caught fish, pasture-raised eggs, and grass-fed meat: richer in omega-3 fatty acids than meat from conventionally raised animals and excellent sources of protein, healthy fats, and essential nutrients such as zinc, selenium, and B vitamins.
Healthy fats: butter from grass-fed cow’s milk, coconut oil, extra virgin olive oil, nuts/seeds.
Ancient grains and legumes/beans: best when sprouted and 100% unrefined/whole. Two to three servings per day or less is ideal, especially Anasazi beans, adzuki beans, black beans, chickpeas, lentils, black rice, amaranth, millet, quinoa.
Red wine and dark chocolate/cocoa in moderation: a few times a week or a small amount daily.
How to Support the Microbiome
1. Avoid antibiotics as much as possible
Antibiotics have been commonly prescribed for over 80 years, but the problem is that they eliminate good bacteria along with killing harmful germs, which means they can decrease immune function and increase the risk of infections, allergies, and diseases. While antibiotics can save lives when truly necessary, they are often over-prescribed and misused.
Over time, harmful bacteria can become resistant to antibiotics, making serious infections harder to eliminate. Before taking antibiotics or giving them to your children, discuss alternative options and the unwanted consequences on the microbiome that may result from taking antibiotics too frequently and when they are not necessary.
2. Reduce stress and exercise more
Stress impairs immune function, as your body uses energy to fight infections—this is one of the reasons chronic stress can destroy quality of life. When your body believes it is facing immediate danger, you become more susceptible to infections and experience more severe symptoms, also developing higher levels of inflammation.
Stress causes immune compounds known as cytokines to contribute to the inflammatory response that harms healthy cells. Physical exercise is a natural stress reliever, can help reduce inflammation, balance hormones, and strengthen the immune system.
3. Add supplements
Coenzyme Q10, carotenoids, omega-3 fish oil, selenium, and antioxidants (vitamins C, D, and E) can help mitigate free radical damage to gut health and the microbiota.
Problems with the Microbiome
The microbiome is much like the ecosystems of the Earth, meaning that as its conditions change, so do the organisms that inhabit it. Microbes interact with each other within the community they inhabit (our intestines), and their concentration changes based on the surrounding environment, which means that diet, lifestyle, medication/antibiotic use, and environment truly affect gut health. At the forefront of how your gut microbiome determines whether you will face various diseases is inflammation.
Inflammation is the root of most diseases. Studies show that an anti-inflammatory lifestyle protects brain neurons, balances hormones, fights tumor formation, and has mood-enhancing benefits. While you might not believe that gut health greatly affects your mood and energy, think again. Friendly gut bacteria can help manage neurotransmitter activity, making them natural antidepressants and anti-anxiety agents. Instead of relying on anti-inflammatory medications to manage diseases like arthritis or heart disease, it is much better to reduce inflammation in the body.
Poor gut health is linked to dozens of diseases, particularly:
Autoimmune diseases (arthritis, inflammatory bowel disease, Hashimoto’s disease, etc.): Autoimmune disorders develop when the body’s immune system malfunctions and attacks its own healthy tissue. Inflammation and autoimmune reactions largely stem from an overactive immune system and poor gut health. Leaky gut syndrome can develop, resulting in small openings in the intestinal lining, releasing particles into the bloodstream and triggering an autoimmune cascade.
Brain disorders/cognitive decline (Alzheimer’s, dementia, etc.): Inflammation is highly correlated with cognitive decline, while an anti-inflammatory lifestyle has been shown to lead to better memory, longevity, and brain health. We now know that there are multiple neurochemical and neuro-metabolic connections between the central nervous system/brain and the microbiome/digestive tract that send signals to each other, affecting our memory, thought patterns, and reasoning. Differences in our microbial communities may be one of the most important factors in determining whether we face cognitive disorders in old age. A 2017 study from the University of Pennsylvania found a link between the gut microbiome and the formation of cerebral cavernous malformations (CCM), which can cause strokes and seizures. Researchers observed that in mice, TLR4 activation, a receptor for lipopolysaccharides (LPS)—a bacterial molecule—on the endothelial cells of the brain by LPS greatly accelerated CCM formation. When mice were observed in a germ-free environment, CCM formation decreased significantly, illustrating the effects of harmful bacteria and the microbiome on cerebral cavernous malformations.
Cancer: Many studies have shown a link between gut health and better protection against free radicals, which cause cancer in the brain, skin, colon, pancreas, prostate, and stomach. Microbes influence our genes, meaning they can either promote inflammation and tumor growth or enhance immune function and act as a natural treatment for cancer. An anti-inflammatory lifestyle can also help reduce the severe side effects of cancer treatments (such as chemotherapy).
Fatigue and joint pain: Certain bacteria in our digestive tract contribute to joint and tissue deterioration. Research shows that a healthier gut environment helps reduce the risk of joint pain, swelling, and mobility issues in people with osteoarthritis and inflamed joints. Some studies have found that patients with psoriatic arthritis (an autoimmune joint disease) have significantly lower levels of certain types of gut bacteria, and that patients with rheumatoid arthritis are more likely to have other strains present.
Mood disorders (depression, anxiety): Have you ever heard of the gut-brain connection? Well, here’s how it works: your diet affects the microbiome and neurotransmitter activity, and therefore how you feel, your ability to manage stress, and your energy levels. Dietary changes over the last century—including industrial agriculture, pesticide and herbicide use, and nutrient degradation in foods—are major forces behind the rising mental health issues such as depression. Low nutrient availability, inflammation, and oxidative stress affect the neurotransmitters dopamine, norepinephrine, and serotonin, which control your mood, ease tension, and enhance alertness. It is also a two-way street when it comes to the gut and your mood: poor gut health contributes to mood issues, and high levels of stress harm both gut and hormonal balance. A 2017 study illustrated the correlation between gut health and depression. Researchers studied 44 adults with irritable bowel syndrome and mild to moderate anxiety or depression. Half of the group took the probiotic Bifidobacterium longum NCC3001, while the other half received a placebo. At six weeks after taking probiotics daily, 64% of patients who took the probiotic reported a decrease in depression. Among patients who took the placebo, only 32% reported a decrease in depression.
Learning disorders (ADHD, autism): Our bodies are interconnected systems, and everything we put into them affects the whole person, including growth, development, and mental capabilities. ADHD and other learning difficulties have been linked to poor gut health, especially in infants and children. We continue to learn how neurodevelopment, cognition, personality, mood, sleep, and eating behavior are all affected by the bacteria residing in our intestines. There appears to be an association between diet and mental disorders due to the metabolism of dietary components and the enzymes encoded in our human genome that reside in our intestines. One of the most important factors seems to be establishing a healthy microbiome from birth, including a vaginal birth, ideally, and breastfeeding, which populates the newborn’s gut with the mother’s healthy bacteria.
How It Works
Microbes reside both inside and outside our bodies, especially in the intestines, digestive tract, genital organs, mouth, and nasal areas. What determines whether someone’s microbiome is in good shape or not? It comes down to the balance between harmful bacteria versus good bacteria.
Essentially, we need a higher ratio of friendly gut bacteria to outnumber the harmful ones to remain resilient and symptom-free. Unfortunately, due to factors such as a poor diet, high levels of stress, and exposure to environmental toxins, the microbiome of most people hosts many billions of potentially harmful bacteria, fungi, and pathogens.
The human microbiome hosts more than just bacteria. It also hosts various human cells, viral strains, fungi—but bacteria seem to be the most important when it comes to controlling immune function and inflammation. To date, researchers have identified over 10,000 different species of microbes living in the human body, each with its own set of DNA and specific functions. There is still much to learn about how each strain of bacteria affects different aspects of the body and how each can protect us or contribute to conditions such as obesity, autoimmune disorders, cognitive decline, and inflammation.
The Microbiome and Genes
Researchers often talk about the microbiota as the complete collection of genes and microbes living in a community, in this case, the community that resides in our intestines. According to the Center for Genetic Science at the University of Utah in the USA, the human microbiome (all the genes of our microbes) can be considered a counterpart to the human genome (all our genes). The genes in our microbiome outnumber the genes in our genome by about 100 to 1.
You may have learned in school that all human beings actually have very closely related genetic codes, even though we all look so different as a species. What is amazing is that each of our intestinal microbiomes is very different. One of the most astonishing things about the microbiome is how different it can be from one person to another.
Estimates of the human gene catalog show that we have about 22,000 genes (as we normally think of them), but a staggering 3.3 million non-redundant genes in the human intestinal microbiome! The diversity among individuals’ microbiomes is phenomenal: humans are about 99.9% identical to each other in terms of host genome, but usually differ by 80% to 90% in terms of microbiome.
Today, researchers are rapidly working to better understand the microbiome to help prevent, heal, or treat symptoms of all kinds of diseases. DNA sequencing tools help us discover various bacterial strains and how they might hinder or help the immune system.
While some bacteria contribute to diseases, many are beneficial. In fact, there are many very beneficial bacterial strains. At the same time, having certain diseases can negatively affect the microbiome, although we still have much to learn about how exactly this happens. The more we can understand how the bacteria in the microbiome affect our genes and predispose us to diseases, the better we can personalize treatment approaches and prevent and manage diseases before they put lives at risk.
Conclusion
The microbiota consists of trillions of bacterial organisms living in our bodies. The entire community of these bacteria is called the microbiome.
Our intestines are a central location of the microbiome, where the vast majority of bacteria reside.
Poor gut health is linked in some way to almost all existing diseases, as a large part of our immune system resides here and where inflammation often begins.
By improving your diet, consuming many anti-inflammatory and probiotic foods, reducing stress, and engaging in regular physical exercise, you can support your body’s microbiome.
