‘Long COVID’ risk tied to composition of gut microbiome

Could the severity and length of a COVID-19 infection hinge on the health of a patient’s gut? A recent study suggests that “profiling” the gut microbiome (the environment where bacteria, viruses, and fungi live in the intestines) will help to determine who might develop post-acute COVID-19 syndrome, or “long Covid.”  

Lingering Symptoms and the Gut

A significant number of people who were infected with COVID-19 reported persistent complications and symptoms as long as six months after “recovery.” The most commonly noted issues were fatigue, muscle weakness, and insomnia. 

With about 75% of the immune system living in the gut, any disruption to the microbiome can lead to a difficult and long recovery, especially from a severe infection that attacks major organs. The researchers suggest that this may have a role in long COVID even though it’s not completely clear what the cause is or why only some patients will develop it. More and more research is indicating that a damaged gut microbiome plays a major role in how severe COVID-19 infection is. 

More and more research is indicating that a damaged gut microbiome plays a major role in how severe COVID-19 infection is.  (Photo by Fusion Medical Animation on Unsplash)

The Study

Over a six month period, the researchers analyzed stool samples and the aerobic capacity and endurance of 106 patients with various levels of severity of COVID-19 to track any changes in their microbiomes. The team compared the findings with a group of 68 people who were not infected with the virus.

After checks at three and six months, around 80% of the infected patients showed symptoms of long COVID. Further study of the data showed that those patients with long COVID had much more disruption in the gut. Those who did not have long COVID had similar microbiomes to those who had not had the COVID-19 infection.  

Some of the significant findings in this study were based on the specific bacterial levels found in the patients. As the study progressed, those with long COVID had significantly more “unfriendly” bacteria and more changes in the gut microbiome. Additionally, the “good” bacteria known to boost immunity was completely gone from the long COVID patients at the six month check. 

Because this was an observational study, it doesn’t establish cause. However, researchers say that their findings support previously proven theories that identify a disrupted gut microbiome as the cause of a variety of long-term health issues. 

“In summary, altered gut microbiome composition is strongly associated with persistent symptoms in patients with COVID-19 up to 6 months after clearance of SARS-CoV-2 virus. 

“Considering the millions of people infected during the ongoing pandemic, our findings are a strong impetus for consideration of microbiota modulation to facilitate timely recovery and reduce the burden of post-acute COVID-19 syndrome,” conclude the researchers in a statement

The study can be found in the journal Gut.

58 thoughts on “‘Long COVID’ risk tied to composition of gut microbiome”




  2. If the good bacteria mentioned in your article,where depleted or no longer existed,what is the course for replacing those bacteria that are needed to rebalance the micrombe.I have gut dysbiosis for years with no answer from a doctor for the course of treatment to replace the good bacteria,Iwent on a probiotic prebiotic hunt across the globe to find the way to replace the lost good bacteria,Do they have prescripted probiotics to give or do i just keep chasing probiotics and trying them out which is very challenging.When i think i have my gut issues under somewhat normalcy,flareups occur and a step backward again.No help from doctors,just watch your diet,etc etc.Do the good bacteria exist that??/ can be supplemented to return the gut to balance? Wher do you purchase these bacteria,if at all.?

    • just eat fermented foods, every day…. don’t rely on expensive pills

      Kimchi, Sauerkraut, Pickles, fermented yogurts……anything aged in Brine water

      • My husband eats Greek yogurt and pickles, daily. Sauerkraut from time to time. He still has taste/smell issues, two years out. Beef tastes odd/bad and barely tolerable. He can smell very little, despite trying smell therapy.

        • Parasites should be removed – garlic, ginger, honey… and once or twice a year the re-discovered natural no-adverse-effects antibiotic… Ivermectin: removes more than 70 found parasites.
          If the Greek yogourt is clean, meaning to see no notice of “probiotics” or “active bacteria” – is fine; there is a good natural help.
          Do not use other probiotics or “active bacteria”: is human feces under the religious Hindi belief of superior karma being.
          They destroy the defending function of the body Physiology – auto-imune diseases, cancer and more.

      • I found out post surgery as well as helping my wife with a bowl issue that using a yogurt drink fortified with gut bacteria helped. Took the stuff every day or two for a few weeks reset me. Then added on fresh fruits veggies and more fiber. Not a magic fix but it’s helped me twice as well as my wife

    • A good diet including milk based proteins and yogurt is a great start. Regular eating that flushes the intestinal tract is important and if you are still having issues, a probiotic supplement can help.

      • I’d stay away from milk-based proteins unless they have the enzymes that help digestion. Raw yogurt and raw cheeses should be okay. –As opposed to pasteurized milk or protein bars with calcium caseinate which are hard on the digestive system.

      • To start: tangy tangerine at high levels to flush and fill body with vitamins and pre/probiotics, etc….do that a month and back down on tangy to affordable price…i drank 1 container every 2 weeks….$$$

        Nascent iodine every morning on empty stomach…i do 1800-3600 mcg, but!!!! I dont have any issues! Consult a dr and read up…my sleep improved after 2 months of 1800 mcg a day! Baby sleep

        Vit d3/k2

        Men: dr groups testosterone booster works…global healing health center? Especially with iodine , vit d, and tangy! A good stack!

        Think itd b good for covid!

      • Kimchi, raw sauerkraut, probiotic supplements, coconut yogurt, Tempeh, apple cider vinegar. No processed foods. No McDonalds. Good foods that do not cause inflammation. No donuts. Only fresh, ripened foods. Green tomatoes, potatoes, and onions are bad! A good D3 supplement and 30 minute walks on sunny days.

    • Best to start with a gut detox, using either activated charcoal or medicinal healing (bentonite) clay, for 2-3 weeks, which will help to eliminate most pathogenic bacteria and the toxins which promote their overgrowth. Take perhaps a teaspoon per day on an empty stomach, best just before bed, thus providing many hours overnight to maximize their detoxification efficiency…while avoiding taking any meds within two hours of the charcoal or clay. As for taking healthy probiotics to replace the good bacteria, be sure to take them also on an empty stomach, best first thing in the am (not at the same time as the charcoal or clay), and then drink only liquids but do NOT eat anything solid for at least a half hour, or even better an hour…then the probiotics bypass the stomach (and its high acid environment that kills most microbes) to enter the intestinal gut, where the healthy microbes can then flourish (doubling naturally every 1/2 hour – 2 hours). Thus, you do not need to take high volumes of expensive probiotics, but rather you could take just a few sips daily of a liquid probiotic like kombucha or a tablespoon of raw organic apple cider vinegar (ACV) with the mother, yet have an outsize positive effect on gut microbiota. Also consider eating a small amount of solid fermented food-based probiotics with every meal, such as pickles (without vinegar), kimchi, miso, etc. Add in some prebiotic fiber to your diet, which should plant-based as much as possible, to help maintain the alkalinity and resources that promote healthy microbes, while simultaneously inhibiting pathogenic microbes. God bless!

      • The addition of (labelled) “probiotics” are human feces bacteria with different DNA and are fighting own bacteria because own cells are hunting to kill them; therefore, is a belief, a bad one – it actually demolished the good, natural strength of the Physiology.

      • Yes! Yes! Yes! and Yes!
        What you’ve written is material I learned about 50-plus years ago. I’ve practiced a vegetarian now plant-based lifestyle since my 20s. It’s all about eating alkaline foods rather than acid forming foods = meat, dairy, eggs, etc. are all acid forming. I’m in my 70’s and many of my peers say “I wish I could eat the way you do.” They could and should. Also, the same people who say such things have experienced long COVID. I’ve had it, too, but it was extremely mild. Bless you!

    • Get a kefir grain culture online and grow it on your kitchen counter. Their are approximately 30 different bacteria in a home cultured kefir. Don’t take my word for it. Do some research and then ask what good is your doctor doing for you. Eating raw, organic or wild fruits and vegetables will help also.

    • I get good gut bacteria down on skid row in LA. Comes from organic homeless people poop, right off the sidewalk. Best thing is, it is free!

    • Well, to get a good gut biome in my case…. I don’t use soap of any kind in the shower, just good ole hot water! (But I shower daily religiously)(Also, there is a good exterior SKIN biome of bacteria! Overcleaning and sanitizing your exterior is just as detrimental to your health as doing harm to your gut biome!) I don’t use todays common chemical cocktail deodorants and such (And no I’m not dirty and don’t smell, I’m very clean and odor free, cleaner than most who SAY they practice good hygiene but are only full off ****) I shun most commercial chemicals and avoid all that I possibly can. I embrace natural cotton! I only wash my hands before meals if they are visibly grimy, and even then maybe not. I don’t use antibacterial ANYTHING. I don’t use bandaids unless the bleeding gets in the way of doing something (usually, I’ll just suck on it until it stops!) I bite my fingernails (Bad lifelong anxiety habit and not good for the teeth but good for the immune system anyhow), I’ve rarely been to a doctor in 44 years… maybe 10 times total. I get downright dirty in the dirt. I take good care of my teeth but avoid fluoride like the plague. I eat a large variety of things in balance. Yogurts (Greek preferably) is good for gut health. Fermented foods/beverages as well. Raw fruits and veggies the ones without nasty pesticide and chemical fertilizer use…. “dirty”, unwashed, and right off the plant with “Dirty” hands!

      I’m not perfect…. I do like junkfoods and processed nightmares and I can’t avoid EVERYTHING chemical and bad for the body…. But I do my best to try to keep everything balanced.

      I’ve lived all my life this way…. Now, for someone that has lived their whole life sanitizing everything and embracing all kinds of chemicals, a sudden switch to this lifestyle would probably kill them because of their weak immune and other systems and total dependency on a chemical lifestyle…. so go with a gradual approach!

      I did get a mild to moderate case of COVID and made it through just fine…. It took forever to get my sense of taste and smell back and even to this day it’s not quite right but at least it’s there! Not have taste or smell is worse than it sounds!… lol… I have not gotten a second case even though I have mingled with people who have gotten it (Could just have been lucky so far as well)…. and of course… I will never get the “Vaccine” even with a gun to my head and threat of death…. I’m not afraid of dying… when it’s my time, it’s my time!

    • There is a solution: gut microflora replacement therapy – general name. Essentially it consists of swallowing a capsule with dried out fecal matter from a healthy person. Planting a correct bacteria in the gut and then making sure that you feed it the right foods. 🙂

      • One last thing that helped me:
        Foods helping the good bacteria in the gut:
        Whole milk organic kefir, European style
        Steel cut oatmeal (cooked of course :))
        Fresh pineapple
        Fresh beets

        ** Avoid surgar and any processed foods

      • If you believe the feces are good… stop eating the normal food.
        The “flora” has different DNA and is harming your Physiology.
        You believe they’re smarter than the “inventor” of the human being…

    • I found out post surgery as well as helping my wife with a bowl issue that using a yogurt drink fortified with gut bacteria helped. Took the stuff every day or two for a few weeks reset me. Then added on fresh fruits veggies and more fiber. Not a magic fix but it’s helped me twice as well as my wife

    • I suffered from severe gut issues for years with short-lived success trying numerous solutions. Trying to stay as all-natural as possible I finally gave Plexus Probio5 a try and after going thru a few levels of detox (which is normal) I no longer struggle with these issues. It along with a couple other products changed my life so much!!

  3. The obvious question is which caused which. Did damaged gut microbiome cause COVID to be worse in these people. Or did the bad case of COVID cause damage to the gut microbiome?

  4. Can’t talk about COVID if you do not understand what SARS is…
    The so-called virus SARS… was designed and spread starting 2018 as “no-consent-required” administered… “vaccine”; is bacterial contamination, biologic contamination…. poison.
    Any addition by inoculation is supplemental poisoning damaging the Physiology, defence function being harmed for illusory “scientific” selection, eugenicist known project.

  5. Ciprofloxin for 20 days in 2007 destroyed my gut Flora for years. I knew where every outhouse, portapotty, restroom,
    woods and forest was in a 50 mile radius. Persistence with a good multistrain probiotic along with greens and veggies helped a lot. Avoid carbs and sugars along with alcohol and tobacco like the plague. 5 months after a medium case of Covid my smell/taste comes and goes. When I do the ivermectin paste (cause Iam cheap, $12.00 at tractor supply) the next day I can smell and taste a bit better. Ginger, garlic, medicinal mushrooms, black seed oil and oregano oil are all Gods miracle foods for a healthy gut. Mastic gum is good if your suffering with helicobacter pylori. Also a huge benefit comes from intermittent fasting. You’ll feel better and stronger.
    Patience with prayer along with melatonin and guinea hen weed tea (not bad tasting and a real immune booster) before bed will help make a difference. Hang in there, if I got whipped it you can too.

  6. Sense of smell and not having any is sign of Zinc Deficiency.
    Also in winter combination of heating air and drying it on top
    of dry cold air makes air as good as death valley for humidity level.
    Put a pot of water on your counter or wood burning stove, as if
    certain places would let you install them these days.

  7. I’m surprised the author didn’t ask whether having a subpar gut microbiome might make a person more likely to contract Covid in the first place.

  8. One of the problems with our modern diet is that we ignore grains. I make bread from home ground wheat berries and find it a big help.

  9. I eat plant based and am 76 years old.
    COVID was kind to me and it lasted about 3-4 days feeling horrid then weeks of a cough. I used Tylenol, Elderberry Syrup, Vick’s Vaporub, and a product to help with mucous….I also drank hot water, lemon, and honey, plus gallons of orange juice. Among my peers who eat a lot of meat and dairy they have experienced long term illness from the virus, some have passed away. These are individuals who base their meals around meat, diary, and eggs with a tiny bit of vegetable and few leafy greens or salads. It has been proven that type of diet contributes to an unhealthy gut. Also, many in my age group still smoke and get very little exercise. I walk every single day with my dogs in fresh mountain air, do yard work, and am very active. I didn’t allow partisan politics to keep me from getting vaccinated and a booster. No side effects.

  10. Any insights on “Apple Cider Vinegar”?
    I had just started taking “goli” gummies when I contracted covid.
    Didn’t go too badly, gone in a week.
    Now restarting the goli gummies, and suddenly feeling the same early symptoms.


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