Functional profiling of COVID-19 respiratory tract microbiomes

Abstract

In response to the ongoing global pandemic, characterizing the molecular-level host interactions of the new coronavirus SARS-CoV-2 responsible for COVID-19 has been at the center of unprecedented scientific focus. However, when the virus enters the body it also interacts with the micro-organisms already inhabiting the host. Understanding the virus-host-microbiome interactions can yield additional insights into the biological processes perturbed by viral invasion. Alterations in the gut microbiome species and metabolites have been noted during respiratory viral infections, possibly impacting the lungs via gut-lung microbiome crosstalk. To better characterize microbial functions in the lower respiratory tract during COVID-19 infection, we carry out a functional analysis of previously published metatranscriptome sequencing data of bronchoalveolar lavage fluid from eight COVID-19 cases, twenty-five community-acquired pneumonia patients, and twenty healthy controls. The functional profiles resulting from comparing the sequences against annotated microbial protein domains clearly separate the cohorts. By examining the associated metabolic pathways, distinguishing functional signatures in COVID-19 respiratory tract microbiomes are identified, including decreased potential for lipid metabolism and glycan biosynthesis and metabolism pathways, and increased potential for carbohydrate metabolism pathways. The results include overlap between previous studies on COVID-19 microbiomes, including decrease in the glycosaminoglycan degradation pathway and increase in carbohydrate metabolism. The results also suggest novel connections to consider, possibly specific to the lower respiratory tract microbiome, calling for further research on microbial functions and host-microbiome interactions during SARS-CoV-2 infection.

Pathophysiology of SARS-CoV-2 Infection in the Upper Respiratory Tract and Its Relation to Breath Volatile Organic Compounds

“…We suggest conducting a longitudinal study in which nasal samples are collected from healthy individuals and COVID-19 patients (both symptomatic and asymptomatic) and used for microbiome profiling via sequencing and metatranscriptomics. Functional analyses could distinguish the pathways associated with different disease states, including metabolites that serve as biomarkers ( 19 ). From these data, a target VOC signature could be identified and used in breath-based diagnostic tools with great impact.…”

“…The effect SARS-CoV-2 infection has on the upper respiratory microbiome is less known. Haiminen et al ( 19 ) compared COVID-19 patients to healthy peers and to non-COVID-19-related pneumonia patients. After successfully differentiating patient groups by microbiome composition, they detected significant changes in bacterial metabolism pathways ( 19 ).…”

“…Haiminen et al ( 19 ) compared COVID-19 patients to healthy peers and to non-COVID-19-related pneumonia patients. After successfully differentiating patient groups by microbiome composition, they detected significant changes in bacterial metabolism pathways ( 19 ). This study suggests that, as in other health conditions, metabolically detectable changes in the microbiome occur in SARS-CoV-2 infection.…”

A comprehensive review of the analysis and integration of omics data for SARS-CoV-2 and COVID-19

“…The interactions of the host with the microbiota are complex, numerous and bidirectional [ 59 ]. Therefore, the virus–host–microbiome interactions can yield further insights into the perturbed biological processes and their connections with disease risk factors [ 60 ]. Shen et al .…”

Is the Gut Microbiome a Target for Adjuvant Treatment of COVID-19?

“…It has been shown that SARS-CoV-2 infection alters the microbiome of the lung and leads to reduced diversity and in some cases to community collapse [61], shows different bacterial diversity and fewer commensals compared to non-COVID-19 pneumonia [62], and on a functional analysis "decreased potential for lipid metabolism and glycan biosynthesis and metabolism pathways, and increased potential for carbohydrate metabolism pathways" [63]. There is crosstalk between the gut and the lung, often referred to as the "gut-lung axis".…”