Nasopharyngeal Microbial Communities of Patients Infected With SARS-CoV-2 That Developed COVID-19

Ventero, María Paz; Cuadrat, Rafael R C; Vidal, Inmaculada; Andrade, Bruno de Bezerril; Molina-Pardines, Carmen; Haro-Moreno, José M.; Coutinho, Felipe H.; Merino, Esperanza; Regitano, L. C. A.; Silveira, Cynthia B.; Afli, Haithem; López‐Pérez, Mario; Rodrı́guez, Juan Carlos

doi:10.3389/fmicb.2021.637430

Cited by 56 publications

(84 citation statements)

References 42 publications

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“…However, it should be noted that in that work, only patients with mild COVID-19 that did not develop pneumonia were included to evaluate the differences in bacterial richness and diversity, in comparison to uninfected patients. In contrast, Ventero et al [ 10 ] studied the microbiota of the nasopharyngeal tract in COVID-19 patients with different degrees of severity by using advanced techniques of molecular microbiology, and revealed a differential abundance in several bacterial taxa among the COVID-19 cases. The metagenomic study found that more than sixty operational taxonomic units (OTUs) were exclusive to SARS-CoV-2-positive patients, most of these microorganisms being members of the phylum Bacteroidota and Firmicutes .…”

Section: Discussionmentioning

confidence: 99%

“…[ 25 ]. Interestingly, Ventero et al [ 10 ] found that Corynebacterium was positively associated with Dolosigranulum in the co-abundance network analysis, indicating that in mild symptomatic SARS-CoV-2-infected patients, those two taxa form a consortium that might protect against COVID-19 development. This co-abundance connection was lost in severe cases of COVID-19.…”

Section: Discussionmentioning

confidence: 99%

“…To date, studies of the respiratory microbiota and SARS-CoV-2 infection have been conducted among small cohorts of patients with different degrees of COVID-19 severity [ 9 , 10 , 11 ]. In addition, the samples for the evaluation of the respiratory microbiota were collected at a single time point after SARS-CoV-2 infection, and studies did not evaluate samples prior to the viral challenge.…”

Section: Discussionmentioning

confidence: 99%

“…However, recent studies indicate that a third actor could be important in the progression and severity of COVID-19: the respiratory microbiota. In this regard, some works have studied the potential impact of the respiratory microbiota on the severity and outcome of SARS-CoV-2 infection [ 9 , 10 , 11 ]. A study investigated the nasopharynx microbial community of patients that developed different severity levels of COVID-19, including mild, moderate and critical cases [ 10 ].…”

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Dolosigranulum pigrum Modulates Immunity against SARS-CoV-2 in Respiratory Epithelial Cells

et al. 2021

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In a previous work, we demonstrated that nasally administered Dolosigranulum pigrum 040417 beneficially modulated the respiratory innate immune response triggered by the activation of Toll-like receptor 3 (TLR3) and improved protection against Respiratory Syncytial Virus (RSV) in mice. In this work, we aimed to evaluate the immunomodulatory effects of D. pigrum 040417 in human respiratory epithelial cells and the potential ability of this immunobiotic bacterium to increase the protection against Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). The respiratory commensal bacterium D. pigrum 040417 differentially modulated the production of IFN-β, IL-6, CXCL8, CCL5 and CXCL10 in the culture supernatants of Calu-3 cells stimulated with poly(I:C) or challenged with SARS-CoV-2. The differential cytokine profile induced by the 040417 strain was associated with a significant reduction in viral replication and cellular damage after coronavirus infection. Of note, D. pigrum 030918 was not able to modify the resistance of Calu-3 cells to SARS-CoV-2 infection, indicating a strain-specific immunomodulatory effect for respiratory commensal bacteria. The findings of this work improve our understanding of the immunological mechanisms involved in the modulation of respiratory immunity induced by respiratory commensal bacteria, by demonstrating their specific effect on respiratory epithelial cells. In addition, the results suggest that particular strains such as D. pigrum 040417 could be used as a promising alternative for combating SARS-CoV-2 and reducing the severity of COVID-19.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Dolosigranulum pigrum Modulates Immunity against SARS-CoV-2 in Respiratory Epithelial Cells

et al. 2021

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

Kim

Rauseo

et al. 2023

Journal of Medical Virology

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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.

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The Upper Respiratory Tract Microbiome Network Impacted by SARS-CoV-2

2022

Microb Ecol

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The microbiome of upper respiratory tract (URT) acts as a gatekeeper to respiratory health of the host. However, little is still known about the impacts of SARS-CoV-2 infection on the microbial species composition and co-occurrence correlations of the URT microbiome, especially the relationships between SARS-CoV-2 and other microbes. Here, we characterized the URT microbiome based on RNA metagenomic-sequencing datasets from 1737 nasopharyngeal samples collected from COVID-19 patients. The URT-microbiome network consisting of bacteria, archaea, and RNA viruses was built and analyzed from aspects of core/periphery species, cluster composition, and balance between positive and negative interactions. It is discovered that the URT microbiome in the COVID-19 patients is enriched with Enterobacteriaceae , a gut associated family containing many pathogens. These pathogens formed a dense cooperative guild that seemed to suppress beneficial microbes collectively. Besides bacteria and archaea, 72 eukaryotic RNA viruses were identified in the URT microbiome of COVID-19 patients. Only five of these viruses were present in more than 10% of all samples, including SARS-CoV-2 and a bat coronavirus (i.e., BatCoV BM48-31) not detected in humans by routine means. SARS-CoV-2 was inhibited by a cooperative alliance of 89 species, but seems to cooperate with BatCoV BM48-31 given their statistically significant, positive correlations. The presence of cooperative bat-coronavirus partner of SARS-CoV-2 (BatCoV BM48-31), which was previously discovered in bat but not in humans to the best of our knowledge, is puzzling and deserves further investigation given their obvious implications. Possible microbial translocation mechanism from gut to URT also deserves future studies. Supplementary Information The online version contains supplementary material available at 10.1007/s00248-022-02148-9.

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Nasopharyngeal Microbial Communities of Patients Infected With SARS-CoV-2 That Developed COVID-19

Cited by 56 publications

References 42 publications

Dolosigranulum pigrum Modulates Immunity against SARS-CoV-2 in Respiratory Epithelial Cells

Dolosigranulum pigrum Modulates Immunity against SARS-CoV-2 in Respiratory Epithelial Cells

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

The Upper Respiratory Tract Microbiome Network Impacted by SARS-CoV-2

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