It's common to think of bacteria in terms of germs that make you sick. But bacteria aren't always harmful. In fact, the human body is full of bacteria and other microorganisms that function to help keep you healthy. The largest population of microorganisms in the human body lives in the gut. Collectively called the gut microbiota, these microorganisms influence everything from digestion to how the body fights off gastrointestinal (GI) infections. 

There are many studies on the gut microbiota, and some research shows an association between certain chronic health conditions and a disturbance in the microorganisms in the gut. Interestingly, recent research shows alterations in bacteria living in the gut in patients with COVID-19.1

It remains unclear, however, if an altered gut microbiota is the root cause of some health conditions or if the health condition leads to alterations in the microbiota. Regardless, there are things you can do to maintain a healthy mix of microbes in your gut. 

The Human Microbiota

The human microbiota includes microorganisms (bacteria, bacteriophages, fungi, protozoa, and viruses) that live inside and on the body in areas like the mouth, skin, GI tract, and lungs. The microbiota on the skin differs from the microbiota in the GI tract, and microbiota differ from person to person.2,3

Your body has a mutually beneficial (symbiotic) relationship with the microorganisms that make up your microbiota – the microorganisms help keep you healthy and your body provides them a home and nutrients.4 These microorganisms help maintain your health in many ways, including building your immune system and fighting off harmful bacteria such as Clostridioides difficile – a common pathogen that causes severe diarrhea and colitis (inflammation of the colon).5,6 

Each microbial niche in the body requires a balance – you need enough beneficial microorganisms to offset the pathogens. Diet choices, medications, illnesses, and genetics can disrupt the balance of microorganisms. These disturbances are associated with several conditions including:7-10

  1. Allergies
  2. Asthma
  3. Autoimmune diseases
  4. Crohn’s disease
  5. Cancer
  6. Mental health issues like anxiety and depression

It's important to note that although an imbalance of microorganisms is associated with certain health conditions, it is not known if the altered microbial composition leads to these diseases.

The Gut Microbiota

The body contains 10-100 trillion microorganisms, and most of these live in the GI  tract.  With just as many bacteria as cells in the human body, the GI tract is a complex bionetwork consisting of 300-500 different species of bacteria called the gut microbiota.2,4,11 

Gut microbiota:12,13

  1. Help digest food and extract nutrients
  2. Produce vitamins the body can’t make on its own
  3. Protect your GI tract from harmful bacteria 
  4. Communicate with your brain and help regulate stress responses

The Gut-Lung Axis: An Information Highway

To function properly, each microbial niche in the body requires a balance of microorganisms. If one niche is out of balance and overrun by pathogens, then it has the potential to affect microbes in other parts of the body as well. One such hypothesis is the "gut-lung axis." 

The gut-lung axis is suggested to be an internal information highway connecting your GI tract to your respiratory system.1,5,14 Disruptions of the gut microbiota might also affect the type and quantity of lung microbiota. This, in turn, might compromise lung immunity and could make it more difficult for the lungs to effectively fight infection.

COVID-19 and Microbiota Changes: Cause or effect?

Although COVID-19 is primarily a respiratory illness, many people who contract COVID-19 also experience GI symptoms like diarrhea, nausea, and vomiting.15 In more severe cases, the virus can cause cardiovascular, central nervous, and other systemic symptoms. 

Scientists are continually studying SARS-CoV-2 (the virus that causes COVID-19) and learning how it affects people differently. It's commonly recognized that chronic conditions like heart disease, diabetes, and asthma make it more likely for an individual to develop severe cases of COVID-19.16

Some recent research shows alterations in the gut microbiota in patients with COVID-19.1  One study documented that patients with less severe COVID-19 had higher levels of a specific type of bacteria, Lactobacillus species. In general, species of Lactobacillus are good for gut health. They help break down food, absorb nutrients, and prevent harmful bacteria from overtaking the GI tract. Whereas, patients with severe COVID-19 had elevated levels of certain other types of bacteria (Klebsiella, Streptococcus, and Ruminococcus gnavus), which are pathogens.17  

In addition, patients with an increased level of Lactobacillus sp. showed higher levels of an anti-inflammatory cytokine called interleukin 10 (IL-10). IL-10 plays a crucial role in balancing the body's inflammatory response. Whereas, the patients who had higher levels of pathogenic bacteria also had elevated levels of proinflammatory cytokines.17 

Although this is an interesting observation, it's not a conclusive one, and more research is needed. It's not clear if COVID-19 leads to an alteration in gut microbiota, or if an imbalance of microbiota leads, in part, to more severe cases of COVID-19. At this time, there is not sufficient evidence to support using Lactobacillus probiotics for COVID-19.

Gut Check: Keep Your Gut Microbiota Healthy 

It is important to maintain a proper balance of microorganisms in the gut. There are several lifestyle choices you can make to help maintain a healthy gut microbiota:18-23

  1. Eat a wide variety of foods, including lots of fruits, vegetables, beans, whole grains, and fermented foods. The more diverse your diet, the more diverse your gut microbiota, which is associated with a healthier microbial composition. Plant-based foods contain fiber, which serve as food for the bacteria in your gut, while fermented foods like yogurt contain beneficial bacteria that can support your gut microbiota (but choose low-sugar yogurt options).
  2. Limit sugar. Diets high in added sugar are linked to increased inflammation and are associated with an unhealthy gut microbiota. 
  3. Only take antibiotics when necessary and prescribed by your doctor. Antibiotics change the composition of the gut microbiota, which can cause diarrhea, nausea, and other GI issues. 

Science is still uncovering the ways in which the intricate set of structures and systems in the human body connect. More research into the gut microbiota and how it impacts overall health could play an important part in the discovery of potential treatments for acute and chronic illnesses.

Information Provided by Thorne

Gut health is a foundation for wellness. Thorne’s Gut Health Test gives you a detailed analysis of your microbiome and a personalized plan that targets your GI discomfort and optimizes wellness. The test combines cutting-edge sequencing with Onegevity’s Health Intelligence to make meaningful changes.


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