Long Covid Symptoms and Your Gut Bacteria, is there a connection?

Up to 1 in 3 people who recover from an initial Covid-19 illness go on to develop lingering symptoms like fatigue, insomnia, and muscle weakness that can sometimes last for months. While researchers are still working to determine what exactly causes the collection of symptoms known as "long Covid," there is evidence to suggest that the gut microbiome may play a big role. As early as 2020, studies have shown that people with long Covid symptoms have higher levels of gut barrier permeability, and different gut microbiota composition compared to those who have fully recovered.

The exact cause of long Covid may still remain a mystery, but today we'll shed light on possible mechanisms involving the gut immune system that explain why some people experience these lingering symptoms, and others go on to recover completely.

Do you have or suspect symptoms of long Covid? Heal with the help of functional medicine today.

Symptoms of long Covid

Common symptoms of post acute Covid-19 syndrome, also called long Covid, or Covid long hauler syndrome, are characterized by generalized feelings of fatigue, neurological complaints such as brain fog, and other symptoms.

Between 10 to 30 percent of Covid-19 patients experience either persistent, recurrent, or even new symptoms up to 6 months later, including (1,2): 

  • Fatigue
  • Fever
  • Trouble completing physically challenging tasks
  • Shortness of breath
  • Cough
  • Chest pain
  • Pounding heartbeat or palpitations
  • Brain fog
  • Headache
  • Sleep problems
  • Dizziness upon standing
  • Pins-and-needles feelings
  • Change in smell or taste
  • Depression or anxiety
  • Gastrointestinal symptoms
  • Joint or muscle pain
  • Rashes
  • Changes in menstrual cycles

It's worth noting that even if you have long Covid, medical tests may appear normal, leaving little to no obvious explanation for these persistent symptoms.

Read: Is Epstein-Barr Reactivation the Cause of Your Chronic Fatigue?

How does the microbiome help combat illness & disease?

Microbiota are powerful immunomodulatory factors in various diseases, such as cancers, Crohn’s and colitis, diabetes, and viral infections. These beneficial bacteria work with your body's immune system to fight off potential threats, and extend beyond just the gut microbiome.

We know that good bacteria in the body help fight illness and disease by (3): 

And because the respiratory tract (the nose, mouth, lungs, etc.) are also home to beneficial microbes, they can help prevent pathogens from establishing infections and spreading on the mucosal surfaces (4). 

Because of this, the microbiome within the respiratory tract might help inhibit Covid-19 infection to a certain degree by preventing the virus from replicating on sensitive mucosal surfaces in the nose and respiratory system.

Related: How to Strengthen Your Immune System After Covid-19

Want to learn more?

Understanding what causes long Covid

As early as 2020, researchers at the Center for Gut Microbiota Research in Hong Kong, found a clue. They discovered that people with Covid-19 had significantly altered gut microbiota compared with healthy controls (5).

Fast forward to 2022, and a growing body of evidence has now implicated the gut microbiome—the trillions of bacteria, fungi, and other microbes that inhabit the gut, lungs, and elsewhere—in Covid-19 severity the development of long Covid (6). 

So far, here’s what we know about Covid-19 and gut bacteria:

  • After 6 months, people with long Covid had significantly less of the friendly species Faecalibacterium prausnitzii and Blautia obeum in their gut.
  • They also had a greater abundance of the “unfriendly” species Ruminococcus gnavus and Bacteroides vulgatus.
  • Friendly bacteria that produce the beneficial fatty acid butyrate, such as Bifidobacterium pseudocatenulatum and F. prausnitzii, were the most likely species to be depleted in people with long Covid.

For people who did not develop long Covid, bacteria in their gut microbiome had returned to normal.

Read more: Heal Your Gut to Boost Immune Function & More

Leaky gut allows bacteria to escape and flare cytokines

One of the potential mechanisms causing long Covid symptoms is something called microbial translocation.

Microbial translocation is when microbes move (or translocate) through the epithelial barrier of an organ and go from where they should be to where they should not be (I.e. from the gut or lungs to the blood). This is a process similar to that which happens with a leaky gut. 

Here’s how researchers believe this happens (7):

  • First, an infection or injury in the lung, like from Covid-19, triggers inflammation in the body and the release of molecules called cytokines. 
  • Then, cytokines disrupt the gut’s barrier, allowing microbes such as fungus or bacteria to move from the gut to the blood. 
  • After, the immune system in the blood sees these microbes that should not be there, and it reacts by increasing inflammation even more.

Inflammation can then worsen the original Covid-19 infection, which puts the immune system in a vicious cycle. This could cause dysfunctional immune responses where this cycle of higher inflammation and lower immune function lead to the persistent symptoms of long Covid.

Read: How to Heal a Leaky Gut

Individuals with long Covid have higher markers of gut barrier permeability

Individuals with long Covid have higher levels of markers of gut barrier permeability and gut dysbiosis compared to individuals who are fully recovered (8). Covid-19 not only increases gut permeability, but also elevates levels of inflammation throughout the body (9). 

To measure this permeability, researchers can look at a specific type of polysaccharide (sugar molecule) called β-glucan on the surface of the bacteria that was found in the blood. Patients with long Covid had higher levels of β-glucan than people who were fully recovered, or who never got Covid-19 (10).

Shop: GI Defend | Nutritional Support for Healthy Gut Barrier Function

The microbiome isn’t the only factor in long Covid syndrome

Long Covid is likely not only caused by microbial translocation. This is probably one out of several mechanisms that contribute to symptoms. It is likely that long Covid involves multiple processes that vary between each person.

An exaggerated immune system response, cell damage, or the physiological effects of a critical illness may also contribute to the development of long Covid.

Be proactive against viral illness with a stronger, healthier gut

You can’t completely eliminate the risk of developing lingering Covid symptoms, but you can take steps to make sure your gut microbiome is as healthy as possible. A strong and healthy gut will be better equipped to fight off viral illness and reduce the chance of developing severe illness.

Eat a diet rich in fiber, take probiotics and/or eat fermented foods, reduce stress, and exercise. For more, learn how to improve the health of your gut here.

If you are struggling with long Covid symptoms, it is important to talk to your doctor about what might be causing them and what treatments are available. Remember, you are not alone–there is a growing community of people who understand what you are going through.

What to remember

The gut microbiome is recognized as a very important contributor to overall health, and conversely, in association with many diseases. Persistent and recurrent symptoms can happen after many different viral infections, including Covid-19. Understanding how the gut regulates immune function, and how changing the gut microbiota can influence long Covid is an important factor moving forward. 


  1. https://www.gao.gov/products/gao-22-105666
  2. https://www.cdc.gov/coronavirus/2019-ncov/long-term-effects/index.html
  3. https://www.frontiersin.org/articles/10.3389/fmicb.2020.01877/full
  4. https://pubmed.ncbi.nlm.nih.gov/28316330/
  5. https://www.gastrojournal.org/article/S0016-5085(20)34701-6/
  6. https://gut.bmj.com/lookup/doi/10.1136/gutjnl-2021-325989
  7. https://wistar.org/news/blog/looking-inside-gut-answers-long-covid
  8. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9280735/
  9. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9409329/
  10. https://insight.jci.org/articles/view/160989


COVID, gut health, Holistic Medicine

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