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-orga...

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Autores principales:	Niina Haiminen, Filippo Utro, Ed Seabolt, Laxmi Parida
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/f2bd8ec2d83d4acfa4362beb50ffe058
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spelling	oai:doaj.org-article:f2bd8ec2d83d4acfa4362beb50ffe0582021-12-02T13:17:41ZFunctional profiling of COVID-19 respiratory tract microbiomes10.1038/s41598-021-85750-02045-2322https://doaj.org/article/f2bd8ec2d83d4acfa4362beb50ffe0582021-03-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-85750-0https://doaj.org/toc/2045-2322Abstract 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.Niina HaiminenFilippo UtroEd SeaboltLaxmi ParidaNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-8 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Niina Haiminen Filippo Utro Ed Seabolt Laxmi Parida Functional profiling of COVID-19 respiratory tract microbiomes
description	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.
format	article
author	Niina Haiminen Filippo Utro Ed Seabolt Laxmi Parida
author_facet	Niina Haiminen Filippo Utro Ed Seabolt Laxmi Parida
author_sort	Niina Haiminen
title	Functional profiling of COVID-19 respiratory tract microbiomes
title_short	Functional profiling of COVID-19 respiratory tract microbiomes
title_full	Functional profiling of COVID-19 respiratory tract microbiomes
title_fullStr	Functional profiling of COVID-19 respiratory tract microbiomes
title_full_unstemmed	Functional profiling of COVID-19 respiratory tract microbiomes
title_sort	functional profiling of covid-19 respiratory tract microbiomes
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/f2bd8ec2d83d4acfa4362beb50ffe058
work_keys_str_mv	AT niinahaiminen functionalprofilingofcovid19respiratorytractmicrobiomes AT filippoutro functionalprofilingofcovid19respiratorytractmicrobiomes AT edseabolt functionalprofilingofcovid19respiratorytractmicrobiomes AT laxmiparida functionalprofilingofcovid19respiratorytractmicrobiomes
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Functional profiling of COVID-19 respiratory tract microbiomes

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