The salivary and nasopharyngeal microbiomes are associated with SARS‐CoV‐2 infection and disease severity

Abstract

Emerging evidence suggests the oral and upper respiratory microbiota may play important roles in modulating host immune responses to viral infection. As the host microbiome may be involved in the pathophysiology of coronavirus disease 2019 , we investigated associations between the oral and nasopharyngeal microbiome and COVID-19 severity. We collected saliva (n = 78) and nasopharyngeal swab (n = 66) samples from a COVID-19 cohort and characterized the microbiomes using 16S ribosomal RNA gene sequencing. We also examined associations between the salivary and nasopharyngeal microbiome and age, COVID-19 symptoms, and blood cytokines. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection status, but not COVID-19 severity, was associated with community-level differences in the oral and nasopharyngeal microbiomes. Salivary and nasopharyngeal microbiome alpha diversity negatively correlated with age and were associated with fever and diarrhea. Oral Bifidobacterium, Lactobacillus, and Solobacterium were depleted in patients with severe COVID-19. Nasopharyngeal Paracoccus was depleted while nasopharyngeal Proteus, Cupravidus, and Lactobacillus were increased in patients with severe COVID-19.Further analysis revealed that the abundance of oral Bifidobacterium was negatively associated with plasma concentrations of known COVID-19 biomarkers interleukin 17F and monocyte chemoattractant protein-1. Our results suggest COVID-19 disease severity is associated with the relative abundance of certain bacterial taxa.

Hospital antimicrobial stewardship: profiling the oral microbiome after exposure to COVID-19 and antibiotics

“…Fusobacterium periodonticum (Fp) was among the most significantly reduced species in the COVID-19 patients as compared to the false positives, in line with a nasopharyngeal microbiome case/control study ( Nardelli et al, 2021 ), with similar trends observed between the salivary and nasopharyngeal microbiome ( Kim et al, 2023 ). Nardelli et al (2021) reported that Fp can perform surface sialylation and that some sialic acid residues on the cell surface could work as additional S protein of SARS-CoV-2 receptors.…”

Lactobacilli in COVID-19: A Systematic Review Based on Next-Generation Sequencing Studies

“…Nevertheless, we chose to include only works published in the English language. Four studies assessed the upper respiratory tract [ 21 , 22 , 23 , 24 ], including samples such as saliva, throat, tongue, oral, and nasopharyngeal. Four studies examined stool samples [ 25 , 26 , 27 , 28 ], and only one study evaluated the microbiome in both the gut and URT [ 29 ].…”

“…Whole genome sequencing methodology was applied in two studies [ 20 , 24 ]. There was a notable variation in the selection of databases used for taxonomy classification among studies, with four studies using the Greengenes database [ 21 , 22 , 23 , 25 ]; the RDP [ 22 ], SILVA v132 [ 23 ], SILVA v138 [ 21 ], and MetaPhlAn2 (V.20) [ 28 ] databases were used in only one study each ( Figure 2 ). One study did not specify the database [ 24 ].…”

Microbiome and intestinal pathophysiology in post-acute sequelae of COVID-19

“…Meanwhile, as one of the viruses infecting our respiratory tract, SARS-CoV-2 infects and contacts the nasopharyngeal cells first. It is not surprising that the salivary and nasopharyngeal microbiota was altered during SARS-CoV-2 infection, 47 , 48 such as depletion of oral Bifidobacterium , Lactobacillus , and Solobacterium , and nasopharyngeal Paracoccus , and enrichment of nasopharyngeal Proteus , Cupravidus , and Lactobacillus in severe COVID-19 patients. 47 Similar phenomena were also found in the lower respiratory tract bacterial microbiome of COVID-19 critically ill patients who were characterized with Pseudomonas alcaligenes , Clostridium hiranonis , Acinetobacter schindleri , Sphingobacterium spp., Acinetobacter spp.…”

“…It is not surprising that the salivary and nasopharyngeal microbiota was altered during SARS-CoV-2 infection, 47 , 48 such as depletion of oral Bifidobacterium , Lactobacillus , and Solobacterium , and nasopharyngeal Paracoccus , and enrichment of nasopharyngeal Proteus , Cupravidus , and Lactobacillus in severe COVID-19 patients. 47 Similar phenomena were also found in the lower respiratory tract bacterial microbiome of COVID-19 critically ill patients who were characterized with Pseudomonas alcaligenes , Clostridium hiranonis , Acinetobacter schindleri , Sphingobacterium spp., Acinetobacter spp. and Enterobacteriaceae , while control patients characterized with lung commensal bacteria Haemophilus influenzae , Veillonella dispar , Granulicatella spp., Porphyromonas spp., and Streptococcus spp.…”