The nasopharyngeal microbiome in COVID-19

Abstract

The development of novel culture-independent techniques of microbial identification has allowed a rapid progress in the knowledge of the nasopharyngeal microbiota and its role in health and disease. Thus, it has been demonstrated that the nasopharyngeal microbiota defends the host from invading pathogens that enter the body through the upper airways by participating in the modulation of innate and adaptive immune responses. The current COVID-19 pandemic has created an urgent need for fast-track research, especially to identify and characterize biomarkers to predict the disease severity and outcome. Since the nasopharyngeal microbiota diversity and composition could potentially be used as a prognosis biomarker for COVID-19 patients, which would pave the way for strategies aiming to reduce the disease severity by modifying such microbiota, dozens of research articles have already explored the possible associations between changes in the nasopharyngeal microbiota and the severity or outcome of COVID-19 patients. Unfortunately, results are controversial, as many studies with apparently similar experimental designs have reported contradictory data. Herein we put together, compare, and discuss all the relevant results on this issue reported to date. Even more interesting, we discuss in detail which are the limitations of these studies, that probably are the main sources of the high variability observed. Therefore, this work is useful not only for people interested in current knowledge about the relationship between the nasopharyngeal microbiota and COVID-19, but also for researchers who want to go further in this field while avoiding the limitations and variability of previous works.

Analysis of 16S rRNA Gene Sequence of Nasopharyngeal Exudate Reveals Changes in Key Microbial Communities Associated with Aging

“…Among these different areas, the nasopharynx is anatomically unique because it presents a common meeting place for the ear, nose, and mouth cavities [ 15 ], but has not gained special prominence until the outbreak of the current COVID-19 pandemic [ 16 ]. Importantly, dozens of studies have already detected unquestionable correlations between the composition of the nasopharyngeal microbiota and susceptibility to different viral infections in humans [ 13 ], and some evidence is emerging, although still controversial, that it may be playing a role in the susceptibility to SARS-CoV-2 infection, too [ 17 ]. Elucidating this might shed light on the still unexplained fact that some COVID-19 patients, such as the elderly, are more susceptible and present more severe forms of COVID-19 than others [ 18 ].…”

Alterations in microbiota of patients with COVID‐19: implications for therapeutic interventions

“…Analysis of nasopharyngeal microbiota abundance in hospitalized patients with COVID-19 and healthy controls found that some gut microbiota and nasopharyngeal microbiota participate in the host immune response. [83][84][85] 3. 1.3 Changes in microbiota and immune microenvironment SARS-CoV-2 infection is associated with intestinal inflammation, intestinal barrier disruption, and changes in lipid metabolism.…”

“…Nasopharyngeal microbiota may be associated with SARS‐CoV‐2 infection. Analysis of nasopharyngeal microbiota abundance in hospitalized patients with COVID‐19 and healthy controls found that some gut microbiota and nasopharyngeal microbiota participate in the host immune response 83–85 …”

Age- and disease severity-associated changes in the nasopharyngeal microbiota of COVID-19 patients

“…Even through the respiratory microbiota had not been so studied as that of other anatomical areas, such as the gut, due to the old paradigm that lungs were sterile (13,14), recent studies have demonstrated that changes in the nasopharyngeal microbiota clearly correlate with increased or reduced susceptibility to different viral infections in humans (13). Indeed, focusing on COVID-19 research, dozens of studies have already tried to elucidate whether SARS-CoV-2 infection or the COVID-19 disease severity are associated with changes in the nasopharyngeal microbiota (14). However, unfortunately, the analysis of all these previous studies 3 reveals extremely variable and contradictory results, which prevent solid and reliable conclusions from being drawn (14).…”

“…Indeed, focusing on COVID-19 research, dozens of studies have already tried to elucidate whether SARS-CoV-2 infection or the COVID-19 disease severity are associated with changes in the nasopharyngeal microbiota (14). However, unfortunately, the analysis of all these previous studies 3 reveals extremely variable and contradictory results, which prevent solid and reliable conclusions from being drawn (14).…”