SARS-CoV-2 infection and severity are strongly associated with nasal microbiota

Nasal microbiota diversity and respiratory tract infections are differentially related. The microbiota is known to influence the immune response, as species richness in an individual’s nasal microbiota is correlated to milder symptoms when infected with the rhinovirus.

Study: Alteration in Nasopharyngeal Microbiota Profile in Aged Patients with COVID-19. Image Credit: goa novi /

In a recent study, researchers conducted a nasopharyngeal microbiota profiling parallelism in an effort to analyze microbiota variations in elderly coronavirus disease 2019 (COVID-19) patients. The findings of this study distinguish distinct patterns in the nasal microbiota of COVID-19 patients, with and without symptoms, as compared to those present in individuals who are negative for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).


SARS-CoV-2, which is the etiological agent of COVID-19, is transmitted mainly through respiratory droplets and aerosols. SARS-CoV-2 is associated with a wide range of presentations from asymptomatic to symptomatic involving fever, cough, and respiratory distress.

Symptomatic COVID-19 patients may experience mild cold-like symptoms to severe disease that require hospitalization or intensive care unit (ICU) admission in some cases. To date, over 4.8 million worldwide have succumbed to COVID-19.

Despite research on understanding COVID-19 in terms of its pathology, prognosis, and prevention, and treatment, current knowledge is still limited on explaining the variations in its clinical manifestations. Thus, the most striking feature of COVID-19 is the wide clinical spectrum observed in patients with no distinct/specific aspect that influences the nature of the disease progression in an individual.

Since the microbiota plays a significant role in diverse diseases, some of which including chronic inflammatory bowel syndrome, peptic ulcers, and viral diseases, the current study aimed to document changes in the diversity and composition of the nasal bacteriome between the three cohorts. These cohorts included patients with severe COVID-19, asymptomatic COVID-19 individuals, and healthy individuals.

About the study

The current study cohort included 84 age-matched individuals between the ages of 48 and 70, of which 27 were negative for SARS-CoV-2, 30 were asymptomatic, and positive for SARS-CoV-2, and 27 were positive for SARS-CoV-2 and experienced moderate symptoms that did not require hospitalization. The researchers collected the patients’ nasopharyngeal (NPS) clinical specimens in either healthcare or community settings, which were subsequently tested for SARS-CoV-2. Microbial Community Profiling using 16S ribosomal ribonucleic acid (rRNA) Amplicon Sequencing was also performed on the NPS samples.

The researchers found a significant difference in the bacterial population between each cohort. More specifically, a low level of the bacterial population was detected in COVID-19 positive symptomatic (PSY) individuals as compared to the asymptomatic or healthy individuals.

While this could be due to the frequent wash-offs because of a runny nose and sneezing that is prominent in COVID-19 symptomatic patients, the researchers also suggest the low microbiota in these patients might put them at high risk for disease severity. Taken together, the researchers were not sure if the microorganisms are responsible for the risk for disease severity or if SARS-CoV-2 was responsible for the alteration in the microbiota profile.

Upon identification of the nasal bacteria associated with SARS-CoV-2 infection, the researchers found high levels of Cyanobacteria, also called the blue-green algae. This bacteria is known to cause pneumonia and liver damage and is suspected to have a role in regulating the immune response. The symptomatic patients had twice as much of these bacteria present in their NPS samples as compared to the asymptomatic cohort.

The researchers also observed an upward trend in the population of Bacteroidota, Litoricola, Amylibacter, Balneola, and Aeromonas as compared to the COVID-negative groups.


The findings from this study reaffirm the increasing trend in the population of these bacteria. Comparing the COVID-19-symptomatic and -asymptomatic patients, the study revealed that the symptomatic (PSY) patients were enriched with the signatures of two bacteria Cutibacterium and Lentimonas. The researchers also noted a range of microorganisms that were significantly low in COVID-19-positive symptomatic patients.

Thus, based on this study, it can be inferred that alterations in the microbiota in COVID-19 positive symptomatic patients might regulate the immune response to the severity of the infections.

“Dysbiosis of the nasal microbiota might be one of the reasons for the increased susceptibility and severity of COVID-19 infection.”

Notably, this study demonstrates a strong association between the profile of the nasal microbiota and SARS-CoV-2 infection and severity, which is variably manifested in COVID-19 patients. Limitations of the study include a small sample size that included patients of an older age. The researchers call for further studies in large-scale samples and with a focus to correlate immune response and nasal microbiota to identify the underlying mechanisms.

“Our preliminary results show that the nasal microbiota profile of the patients affected with COVID-19 provides a piece of insightful information that can help in developing both biomarkers to assess the severity of disease and new therapeutic strategies to mitigate negative outcomes for patients.”

Journal reference:
Dr. Ramya Dwivedi

Written by

Dr. Ramya Dwivedi

Ramya has a Ph.D. in Biotechnology from the National Chemical Laboratories (CSIR-NCL), in Pune. Her work consisted of functionalizing nanoparticles with different molecules of biological interest, studying the reaction system and establishing useful applications.


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  1. Boulcherab Samir Boulcherab Samir Algeria says:

    I do not think that there is anything more powerful than onions in killing nose germs... What if we made a spray of onion extract to eliminate Covid in the nose before it escalated

The opinions expressed here are the views of the writer and do not necessarily reflect the views and opinions of News Medical.
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