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Can Omicron Disrupt Your Gut Bacteria? Here’s What We Know So Far.

January 25, 2022 4 min read

Can Omicron Disrupt Your Gut Bacteria? Here’s What We Know So Far. - Layer Origin Nutrition

As the Omicron variant of the novel coronavirus continues to sweep its way throughout the world, there are still more questions than answers, regarding its severity, transmissibility, and several other aspects.

But one key question those who catch Omicron may be wondering is whether it could impact their gut health?

This is a key consideration, given that 70 to 80 percent of the immune system is housed in the gut microbiome.

Covid is primarily known as presenting via symptoms in the upper respiratory tract, but could it also wreak havoc on the delicate balance of bacteria in your gut?


For example, if you are suffering from vomiting, nausea and abdominal pain (even without fever) it could be due to an Omicron infection. It’s important to get tested for Covid if you have these abdominal complaints even if you don’t have any respiratory symptoms or fever.

"The symptoms of Omicron are not significantly different than with Delta," said Dr. Anthony Fauci, the chief medical advisor to the President and the director of the National Institute of Allergy and Infectious Diseases.

"There are some reports that need to be verified, that there is less of a loss of taste and smell and more of an upper respiratory mild symptom, very reminiscent of an upper respiratory infection. But you see that with other variants, including Delta." 


  • You may have cold-like symptoms especially if you are vaccinated (mild fatigue, fever, aches)
  • Fever or chills
  • Cough
  • Shortness of breath, difficulty breathing
  • Severe fatigue
  • Headache
  • Muscle aches
  • New loss of taste or smell
  • Sore throat and congestion or runny nose
  • Nausea, vomiting and diarrhea

Did you see that last line of symptoms there? Gut-related issues.

"The people may initially present with abdominal symptoms without any respiratory complaints. The presenting complaints could be back ache, abdominal ache, nausea, vomiting, loss of appetite and diarrhea. This could be due to Omicron infecting the gut mucosa and the resulting inflammation," says Dr Manoj Goel, Director, Pulmonology, Fortis Memorial Research Institute, Gurugram.


According to Bloomberg, SARS-CoV-2 infects a wide variety of human tissues along with the lungs, including the gut, and is frequently excreted by infected people. Dutch researchers reported in March 2020 that they were able to find genetic material from the virus in wastewater before Covid-19 cases were reported in the population.

The technique “gives you a heads-up because people may not want to pick up the phone for surveys, but everybody poops,” said Gigi Gronvall, an immunologist at the John Hopkins Center for Health Security. “And it’s so unbiased because everybody uses the same sewer system.” 


Dr. Jonathan Eisen is director of the UC Davis Microbiome Special Research Program and is an expert on microbes—organisms such as bacteria, fungi and viruses. He holds degrees from Harvard and Stanford, and previously held appointments at Johns Hopkins University and The Institute for Genomic Research. He is currently a professor at UC Davis with appointments in the department of medical microbiology and immunology, the department of evolution and ecology, and the Genome Center.    

He spoke recently with Sac Town Magazine (Sacramento, CA) about the Omicron variant and how the vaccine is far from a complete protection against contracting the virus.

“I think that’s part of why it’s spreading so fast—people who have been vaccinated and/or boosted have mistakenly thought they were not going to get infected, and so they were going maskless everywhere. But if you have five times as many people infected, that’s going to create havoc, and that’s what is happening in New York and the Northeast, where the hospitals are full,” said Dr. Eisen.

Eisen states that being vaccinated is still beneficial though and reduces the likelihood of hospitalization from COVID-19.


A recent randomized clinical trial from the United States (US) shows how daily use of Lactobacillus Rhamnosus GG (LGG) probiotic may protect against symptom development as it pertains to respiratory illnesses. 

These results support the notion that our symbiotic microorganisms, our own gut microflora, can be viewed as indispensable partners in the fight against COVID-19, but also against potentially other pandemic diseases in the future.

Therefore, it's crucial to consider anything we can do to build or bolster our gut microbiome. How can we find the perfect blend of bacteria for offering protection? 

The first place to begin is with your day to day diet: what are you eating? One might also look at when they are eating (what time of day or night?), how much they are eating, and how fast they are eating (and whether they are chewing each bite of food enough). All of these factors can impact gut health, which in turn, can have drastic effects on overall wellbeing and immunity. 


Garlic, ginger and chilli are all strong and fiery flavors which can improve your dining experience.

But these ingredients also have immune-boosting benefits: garlic and ginger are both known to be anti-inflammatory, and ginger can also treat nausea. Chilli contains many vitamins and has even been credited with pain-relieving qualities.

The Bottom Line: many of us think of COVID-19 as something that presents as an upper-respiratory illness but it could also manifest as issues surrounding the gut.

Paying attention to diet, supplementation, and overall gut microbiome health can help us to block Omicron or recover more quickly once it is contracted.



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