Can Covid-19 infection disrupt the balance of the gut’s microbiome?

A study [1] published in the Molecular Biomedicine Journal reports that the virus causing Covid-19 infection caused severe acute respiratory conditions and disrupted the balance in the gut’s microbiota. The balance was tipped to the overgrowth of harmful bacteria in the gut, especially when those infected with Covid-19 also received antibiotic treatment. 

What is the gut microbiome? 

The microbiome is a collective term for all microorganisms that reside on the skin and in the human body’s gut. The microbiome, which includes the gut microbiota, plays a critical role in the gut’s overall health and the individual’s health.

On the other hand, gut microbiota refers to all types of bacteria residing in the colon. Do you know that the gut houses at least hundreds of trillions of bacteria? Interestingly, microbiota has many roles, as suggested by current research. These roles extend to providing additional immunity against infections and even certain forms of cancer, such as colon cancer. 

Researchers have also established a gut-brain connection. For example, have you ever felt nauseous or experienced butterflies in your stomach? In other instances, you might even label your experience as a ‘gut-wrenching’ experience. We use all these expressions for a reason. Scientifically, the gut is sensitive to emotions such as sadness, anxiety, anger and joy. All these emotions can trigger symptoms in the gut. 

Similarly, the brain directly affects the stomach and intestines. Thinking about food can release juices in the stomach even before the food reaches the stomach. 

Apart from the gut-brain connections, the gut microbiota is also responsible for producing the following: 

  • Short-chain fatty acids 
  • Neurotransmitters such as serotonin and dopamine 
  • Hormones involved in the metabolism of human energy such as gherlin, glucose-dependent insulinotropic polypeptide (GIP) and GILP-1. All these hormones are released in response to the ingestion of food [2]. 

The gut microbiota enables the production of short-chain fatty acids following fermentation and digestion of fibre in the colon. These short-chain fatty acids are essential in maintaining gut health and promoting overall metabolic health. These acids are absorbed into the body and boost the immune system. 

Meanwhile, the neurotransmitters serotonin and dopamine are crucial for communication between nerves and are responsible for body functions such as: 

  • Digestion
  • Mood 
  • Sleep 
  • Wound healing 
  • Bone health 
  • Blood clotting 
  • Movement 
  • Memory 
  • Pleasurable reward and motivation 

What does the latest study by Yin and colleagues say about gut health during Covid 19 infection? 

The study, led by Yin and other researchers from Rutgers University’s Center for Advanced Biotechnology and Medicine, examined the interaction between the severity and progression of Covid-19 and the gut microbiome. The authors aimed to understand the interaction between the host and the microbiota during acute Covid-19. Yin and colleagues characterised the patients’ intestinal microbiome with active infection against those who had just recovered from Covid-19 and controls who are individuals not infected by Covid-19. 

What does the latest study by Yin and colleagues say about gut health during Covid 19 infection?

The findings of the new work may lead to the development of supplements such as probiotics that can restore balance in the gut for patients in the future. Published in the Molecular Biomedicine journal, researchers described the study’s results that examined the gut microbiome of patients and volunteers. All participants were recruited from the Robert Wood Johnson University Hospital in New Brunswick. 

Investigators reported that many of the patients during the early part of the pandemic complained of gastrointestinal issues during the acute phase of the illness and while they were recuperating. One of the authors of the study, Martin Blaser, who is the chair of the human microbiome at Rutgers University, stated that the research team wanted to gain a better and more in-depth understanding of the gut microbiome during Covid-19 by examining specimens that would determine the state of the gut’s health. 

Results of the study indicated that while there were differences in the health of the gut microbiome between those who had active Covid-19, those who had just recuperated and healthy volunteers, the most significant difference was seen in those who received antibiotics during Covid-19 illness. 

In the early days of the pandemic, it was common for patients to receive antibiotics to combat secondary bacterial infections. This was before the availability of vaccines and other antiviral medications to treat Covid-19 infections. 

Blaser, one of the authors, explained that humans host a diverse and large population of microbes. These microorganisms live in the skin, gastrointestinal tract and other organs. However, most of the bacteria live in the colon. 

Scientists have shown in the past decades that the microbiome has a critical role in human health. The microbiome interacts with the central nervous system, immune system and metabolism. According to the study’s authors, the microbiome plays a pivotal role in protecting the body against pathogens. 

What is dysbiosis? 

When the balance between pathogenic and beneficial bacteria is disrupted, this gives rise to the phenomenon called dysbiosis. 

In the study, the authors examined the microbiomes by measuring microorganism populations in the stool samples of the 60 volunteers. The study group consisted of the following: 

  • Covid-19 recovered subjects (n=20)
  • Healthy donors (n=20) 
  • Covid-19 patients (n=20)

Investigators examined 55 species of bacteria in the stools and compared their populations in the three groups of participants. 

The study showed a decrease in the diversity of bacteria in Covid-19 positive patients. Further, Covid-19 patients who received antimicrobials had a further reduction in the abundance of different bacteria genera. 

The researchers concluded that acute infection with Covid-19 and treatment with antimicrobials heightened the depletion of specific populations of good or commensal bacteria. The gut microbiota dysbiosis, however, did not appear to persist in patients who recovered from Covid-19. 

What is dysbiosis? 

Interestingly, the investigators also found that the microbiota of patients who recovered from Covid-19 had similar gut microbiomes as healthy controls. Further, the gut microbiota of these two groups of participants was distinct from those with acute Covid-19. 

Investigators planned to continue tracking and testing patients’ microbiomes in the study to determine the long-term effects of Covid-19 infection on the microbiomes of individuals infected with Covid-19. 

Blaser, one of the study authors, expressed that “further investigation of patients will enhance understanding of the role of the gut microbiome in Covid-19 disease progression and recovery. These findings may help identify microbial targets and probiotic supplements for improving Covid-19 treatment.” 

The National Institute of Health and Danone funded the study. 

What were the bacterial populations depleted in patients with acute Covid-19 infection? 

Covid-19 patients demonstrated depletion of families of bacteria found in healthy adult gut microbiota. These include the following bacteria families: 

  • Lachnospiraceae 
  • Ruminococcaceae
  • Bacteroidaceae 

A study [3] demonstrated that populations of these commensals were reduced in patients suffering from immune-mediated inflammatory diseases such as inflammatory bowel disease, ankylosing spondylitis and multiple sclerosis. 

Loss of these commensal organisms may lead to poor defences against respiratory pathogens, suggesting an interaction with Covid-19 infection. Further, short-chain fatty acids-producing bacteria such as Lachnospiraceae and Ruminococcaceae were also depleted in patients with Covid-19 disease. 

It should be noted that short-chain fatty acids are associated with solid anti-inflammatory activities. These fatty acids modulate responses of the immune system during viral infection. Hence, when the number of short-chain fatty acids is reduced, this could interfere with individuals’ immune responses against Covid-19 infection. 

Limitations of the study 

The study has some significant limitations that should be considered when interpreting the results. First, antibiotics were recognised as substantial disruptors of gut microbiota. Results suggested that those who received antibiotics had lesser populations of good bacteria. However, participants with acute Covid-19 infections had varying degrees of antibiotic regimen and intake. 

Although there were differences in the exposure of the Covid-19 participants to antibiotics, the investigation offered the authors an opportunity to study the gut microbiome in Covid-19 patients with antibiotics and those without antibiotics. 

Potential in identifying probiotics that could address gut imbalance during Covid-19 infection 

The study’s findings have essential contributions to the field of nutrition and immunity. First, the study showed potential microbial targets for supplementation with probiotics. For example, the results revealed that commensal bacteria are most likely to be depleted during acute Covid-19 infection. Researchers can then identify potential probiotics that would help restore the balance of the commensal bacteria. 

Although there have been great strides in Covid-19 treatment, which include antivirals and the use of vaccines to lessen the severity of the disease, probiotic supplements could further enhance the treatment of the infection. 

What are probiotics? 

Probiotics are described as live yeasts and bacteria that could boost gut health and restore gut microbiome balance [4]. It can boost the immune system and digestive health when consumed in adequate amounts. These probiotics can be found in fermented foods, yoghurt and dietary supplements. 

Probiotics can contain different groups of microorganisms. However, the most common bacteria belong to the following: 

  • Lactobacillus 
  • Bifidobacterium 

Probiotics can do the following: 

  • Influence the immune response of the body 
  • Produce substances that have positive effects and benefits on the gut
  • It helps the body restore the balance of good bacteria in the gut or helps the gut maintain healthy microorganisms
  • Prevent antibiotic-associated diarrhoea 

What is the best probiotic supplement for me? 

Probiotics dietary supplements have many benefits. You can begin talking to your doctor when selecting the most appropriate probiotics. Further, these probiotics may also be associated with increased lifespan or longevity, making them an ideal dietary supplement for those who want to live more healthily. 


The information included in this article is for informational purposes only. The purpose of this webpage is to promote broad consumer understanding and knowledge of various health topics. It is not intended to be a substitute for professional medical advice, diagnosis or treatment. Always seek the advice of your physician or other qualified health care provider with any questions you may have regarding a medical condition or treatment and before undertaking a new health care regimen, and never disregard professional medical advice or delay in seeking it because of something you have read on this website.