Microbial composition of the human nasopharynx varies according to influenza virus type and vaccination status

Abstract

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Nasopharyngeal Microbiota Profiling of SARS-CoV-2 Infected Patients

“…Genomic DNA was extracted using the QIAGEN EZ1 Advanced XL system and the V5-V6 hypervariable region of the bacterial 16S rRNA gene was sequenced using an Illumina MiSeq V2 chemistry (2x250 bp) as described [11]. Sequencing data were processed for alignment and quality ltering in QIIME2 v2019.1 [15,16], and representative amplicon sequence variants were obtained by the DADA2 algorithm [17] available at https://doi.org/10.1038/s41587-019-0209-9.…”

“…Unlike in uenza virus [9][10][11][12], no studies have explored the relationship between SARS-CoV-2 infection and the bacterial community (also referred to as microbiota) within the nasopharynx. Therefore, we investigated whether the presence of the virus in the nasopharynx might re ect alterations of the resident microbiota by comparing the bacterial communities of SARS-CoV-2 infected and uninfected patients.…”

Nasopharyngeal Microbiota Profiling of SARS-CoV-2 Infected Patients

“…Unlike influenza virus [9][10][11][12], no studies have explored the relationship between SARS-CoV-2 infection and the bacterial community (also referred to as microbiota) within the nasopharynx. Therefore, we investigated whether the presence of the virus in the nasopharynx might reflect alterations of the resident microbiota by comparing the bacterial communities of SARS-CoV-2 infected and uninfected patients.…”

Microbial Community Structure and Composition is Associated With Host Species and Sex in Sigmodon Cotton Rats

“…Further, it has also been shown that transplantation of the gut microbiome of wild-caught mice to laboratory mice can promote host tness and improve disease resistance and pathogenesis (46). In light of the above literature suggesting that the microbiome may play a key role in respiratory viral disease exacerbation or remediation and vaccine response (42)(43)(44)(45)47), our ndings exemplify the usefulness of this small animal model for understanding viral pathogenesis in the context of different microbial communities. Furthermore, the cotton rat model could be an optimal subject to uncovering and examining the full therapeutic potential of the microbiome by understanding how the host regulates and modulates bacterial communities.…”

“…Recent studies have shown that gut microbiome composition and disruptions by antibiotics may affect some immune responses to u vaccination (42,43). Similarly, there are important correlations between vaccination status and the microbiome of the gut and lung (44,45). Further, it has also been shown that transplantation of the gut microbiome of wild-caught mice to laboratory mice can promote host tness and improve disease resistance and pathogenesis (46).…”