Link between COVID-19 severity and microbiome of saliva and nasopharynx
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In a current examine posted to the bioRxiv* preprint server, researchers profiled the salivary and nasopharyngeal microbiomes of coronavirus illness 2019 (COVID-19) sufferers and decided the affiliation between the microbiomes and COVID-19 severity.

Study: The salivary and nasopharyngeal microbiomes are related to SARS-CoV-2 an infection and illness severity. ​​​​​​​Image Credit: Kateryna Kon / Shutterstock

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections trigger delicate or no signs in a number of people, whereas extreme pulmonary damage or dying within the others. Due to such assorted medical presentation, figuring out biomarkers of COVID-19 severity would extremely profit COVID-19 sufferers is important.

Factors needed for SARS-CoV-2 invasion into the host embody transmembrane serine protease 2 and 4 (TMPRSS 2, 4) and angiotensin-converting enzyme 2 (ACE2) are expressed in excessive quantities in salivary glands and cells of the oral epithelium. Furthermore, the microbiome of the nasopharynx bears additional exploration on account of the truth that the mucosa of the nasopharynx is the first web site of an infection, multiplication, and dissemination of SARS-CoV-2 in host tissues and organs.

About the examine

In the current examine, researchers explored the position of salivary and nasopharyngeal microbiomes within the severity of SARS-CoV-2 infections.

Saliva (oral) samples and nasopharyngeal swab samples had been obtained from 60 and 54 SARS-CoV-2-positive sufferers, respectively, who had been symptomatic, and their COVID-19 analysis was confirmed by polymerase chain response (PCR). Most of the samples had been obtained inside two weeks of COVID-19 symptom onset. For comparability, 18 and 12 salivary and nasopharyngeal swab samples had been obtained from SARS-CoV-2-negative people, respectively.

Microbial deoxyribonucleic acid (DNA) extracted from the samples was subjected to 16S ribosomal ribonucleic acid (RNA) gene sequencing for microbiome characterization. Additionally, the affiliation between nasopharyngeal and salivary microbiomes, plasma cytokine ranges, and age was assessed.

The affiliation between community-level alterations in oral and nasopharyngeal microbiomes and COVID-19 signs was assessed by evaluating the alpha range and beta range amongst symptomatic COVID-19 and non-COVID-19 members. COVID-19 signs assessed had been fever, shortness of breath, coughing, nausea/vomiting, and diarrhea. COVID-19 severity was decided based mostly on the standing of intensive care unit (ICU) admissions.

Furthermore, differential abundance evaluation was carried out for the salivary and nasopharyngeal microbiomes of ICU, and non-ICU COVID-19 sufferers for genus stage evaluation of microbial variations on the taxa stage amongst sufferers with extreme COVID-19 and non-severe COVID-19. The correlation between microbial findings and systemic immune responses was decided based mostly on the associations between the relative abundances of every genus and plasma cytokine ranges.  


In the gene sequencing evaluation, for oral samples and nasopharyngeal swab samples, the typical reads per participant had been 17,820 and eight,543, respectively. The 5 phyla most ample within the oral microbiome had been Actinobacteria, Firmicutes, Bacteroidetes, Fusobacteria, and Proteobacteria. SARS-CoV-2-positive sufferers demonstrated a decrease abundance of Fusobacteria and Proteobacteria within the oral microbiome.

Associations between salivary and nasopharyngeal microbiomes of SARS-CoV-2-positive sufferers and COVID-19 signs and age. (A) Alpha range, represented by richness, in saliva (pink) and nasopharyngeal swab (blue) samples, for sufferers with a given symptom (darkish pink or darkish blue) or with out (mild pink or mild blue). Age versus alpha range represented by Shannon index and richness of salivary (B) and nasopharyngeal (C) microbial communities. Principal coordinates (PC) evaluation of weighted (D, E, left) and unweighted (D, E, proper) UniFrac distances for salivary (D) and nasopharyngeal (E) microbial communities with age. The shaded areas in panels B and C point out the 95% confidence intervals. Statistical significance was assessed utilizing the Wilcoxon signed-rank check for panel A, linear regression for panels B and C, and PERMANOVA for panels D and E. *, P < 0.05.

The high 5 phyla within the microbiome of the nasopharynx had been Actinobacteria, Firmicutes, Fusobacteria, Proteobacteria, and Bacteroidetes, and their abundances didn’t considerably differ between COVID-19 sufferers and non-COVID-19 sufferers. In comparability to non-severe COVID-19 sufferers, oral Bifidobacterium, Solobacterium, and Lactobacillus had been depleted in sufferers with extreme COVID-19. In addition, nasopharyngeal microbes akin to Proteus, Cupravidus, and Lactobacillus had been elevated, whereas Paracoccus was depleted in sufferers with extreme COVID-19.

The abundance of Bifidobacterium within the salivary microbiome was negatively related to plasma ranges of COVID-19 biomarkers akin to monocyte chemoattractant protein-1 (MCP-1) and interleukin 17F (IL-17F). SARS-CoV-2 an infection standing however not the an infection severity was related to community-level alterations within the oral and nasopharyngeal microbiomes.

Alpha range of oral and nasopharyngeal microbiomes was considerably decreased amongst COVID-19 sufferers in comparison with non-COVID-19 sufferers. However, no vital variations had been noticed in alpha range between ICU and non-ICU sufferers for the salivary and nasopharyngeal microbiomes. Salivary and nasopharyngeal microbiome alpha range demonstrated a detrimental correlation with age and had been related to diarrhea and fever.

In saliva samples, Bifidobacterium, Lactobacillus, and Solobacterium had been extra ample within the non-ICU sufferers. A larger abundance of oral Bifidobacterium was related to decrease MCP-1 and IL-17F ranges. In nasopharyngeal samples, Proteus, Cupravidus, and Lactobacillus had been extra ample within the ICU group, whereas Paracoccus was extra ample within the non-ICU group.

To summarize, the examine findings demonstrated the oral and nasopharyngeal microbial profiles of COVID-19 sufferers and confirmed that COVID-19 severity was related to the relative abundance of sure bacterial taxa.

*Important discover

bioRxiv publishes preliminary scientific studies that aren’t peer-reviewed and, due to this fact, shouldn’t be considered conclusive, information medical apply/health-related habits, or handled as established info.

Journal reference:

  • The salivary and nasopharyngeal microbiomes are related to SARS-CoV-2 an infection and illness severity. Josh G. Kim, Ai Zhang, Adriana M. Rauseo, Charles W. Goss, Philip A. Mudd, Jane A. O’Halloran, Leyao Wang. bioRxiv preprint 2022, DOI:, material/10.1101/2022.05.31.494162v1

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