Altered oral and gut microbiota and its association with SARS-CoV-2 viral load in COVID-19 patients during hospitalization

Abstract

The human oral and gut commensal microbes play vital roles in the development and maintenance of immune homeostasis, while its association with susceptibility and severity of SARS-CoV-2 infection is barely understood. In this study, we investigated the dynamics of the oral and intestinal flora before and after the clearance of SARS-CoV-2 in 53 COVID-19 patients, and then examined their microbiome alterations in comparison to 76 healthy individuals. A total of 140 throat swab samples and 81 fecal samples from these COVID-19 patients during hospitalization, and 44 throat swab samples and 32 fecal samples from sex and age-matched healthy individuals were collected and then subjected to 16S rRNA sequencing and viral load inspection. We found that SARS-CoV-2 infection was associated with alterations of the microbiome community in patients as indicated by both alpha and beta diversity indexes. Several bacterial taxa were identified related to SARS-CoV-2 infection, wherein elevated Granulicatella and Rothia mucilaginosa were found in both oral and gut microbiome. The SARS-CoV-2 viral load in those samples was also calculated to identify potential dynamics between COVID-19 and the microbiome. These findings provide a meaningful baseline for microbes in the digestive tract of COVID-19 patients and will shed light on new dimensions for disease pathophysiology, potential microbial biomarkers, and treatment strategies for COVID-19.

Beware of pharyngeal Fusobacterium nucleatum in COVID-19

“…The pharynx is one of the main entrance into the gastrointestinal tract for microorganisms. Both the pharynx and gastrointestinal tract are recognised as crucial sites for the pathogenesis of SARS-CoV-2 infection [ 7 , 8 ]. SARS-CoV-2 infection and invasion in these sites may cause local microbiome dysbiosis and thus lead to secondary bacterial infection [ 9 – 11 ].…”

“…SARS-CoV-2 infection and invasion in these sites may cause local microbiome dysbiosis and thus lead to secondary bacterial infection [ 9 – 11 ]. The host-microbe interactions in the two sites are complex and key for the understanding of the physiology and mechanism of the immune response and microbiome during SARS-CoV-2 infection [ 8 , 12 , 13 ]. Each disease has its own specific microbial characteristics.…”

“…Each disease has its own specific microbial characteristics. Metagenomic next-generation sequencing (mNGS) analysis has revealed the pharyngeal microbiota alterations of SARS-COV-2 infected patients [ 8 , 12 , 14 , 15 ], and oropharyngeal microbiota alterations were associated with COVID-19 severity [ 12 ]. A recent study [ 7 ] found that several oral microbial markers (like TM7, Haemophilus , Actinomyces , Prevotella , Oribacterium and Fusobacterium ) could specifically identify patients with COVID-19 from the health controls in the random forest model.…”

Prospects of using adaptive phage therapy in the rehabilitation of post-COVID-19 patients

“…Данные свидетельствуют о том, что инфекция, вызванная вирусом SARS-CoV-2, повышает восприимчивость пациентов к развитию суперинфекции, приводя к увеличению тяжести заболевания и смертности [22]. Ряд работ демонстрирует радикальное изменение микробиоты кишечника пациентов, перенесших COVID-19, характеризующееся пролиферацией условно-патогенных микроорганизмов и истощением благоприятных комменсалов по сравнению со здоровыми людьми [23,24]. Кроме того, на примере пациентов, инфицированных вирусом гриппа, показано, что восстановление гомеостаза нарушенной микробиоты кишечника совпадает с выздоровлением и элиминацией вируса [25].…”

A State-of-the-Art Scoping Review on SARS-CoV-2 in Sewage Focusing on the Potential of Wastewater Surveillance for the Monitoring of the COVID-19 Pandemic

“…Significant concentrations of SARS-CoV-2 RNA have been detected in the feces of infected individuals, both asymptomatic and symptomatic, even after recovery from respiratory symptoms (Alberca et al, 2021 , Dergram et al, 2021 ; Joukar et al, 2021 ; Nishiura et al, 2020 , Pedersen et al, 2021 ; Petrillo et al, 2021 ; Treibel et al, 2020 , Wölfel et al, 2020 ; Wu et al, 2021 ; Zhang et al, 2021 ), with concentrations up to 10 7 copies per gram of feces, depending on the course of infection (Guo et al, 2021 ; Saawarn & Hait, 2021 ). This has raised concerns about the possibility of fecal–oral transmission of the virus, although the main infection routes are currently believed to be by respiratory droplets, airborne transmission, and direct or indirect contact (Greenhalgh et al, 2021 ; Lodder & de Roda Husman, 2020 ; van Doorn et al, 2020 ).…”