Analysis of bronchoalveolar lavage fluid metatranscriptomes among patients with COVID-19 disease
Abstract
To better understand the potential relationship between COVID-19 disease and hologenome microbial community dynamics and functional profiles, we conducted a multivariate taxonomic and functional microbiome comparison of publicly available human bronchoalveolar lavage fluid (BALF) metatranscriptome samples amongst COVID-19 (n = 32), community acquired pneumonia (CAP) (n = 25), and uninfected samples (n = 29). We then performed a stratified analysis based on mortality amongst the COVID-19 cohort with known outcomes of deceased (n = 10) versus survived (n = 15). Our overarching hypothesis was that there are detectable and functionally significant relationships between BALF microbial metatranscriptomes and the severity of COVID-19 disease onset and progression. We observed 34 functionally discriminant gene ontology (GO) terms in COVID-19 disease compared to the CAP and uninfected cohorts, and 21 GO terms functionally discriminant to COVID-19 mortality (q Sphingomonas,belonging to the Sphingomonadacae family,Variovorax,belonging to the Comamonadaceae family, and in the class Bacteroidia,belonging to the order Bacteroidales. To our knowledge, this is the first study to evaluate significant differences in taxonomic and functional signatures between BALF metatranscriptomes from COVID-19, CAP, and uninfected cohorts, as well as associating these taxa and microbial gene functions with COVID-19 mortality. Collectively, while this data does not speak to causality nor directionality of the association, it does demonstrate a significant relationship between the human microbiome and COVID-19. The results from this study have rendered testable hypotheses that warrant further investigation to better understand the causality and directionality of host–microbiome–pathogen interactions.
Document Details
- Document Type
- Pub Defense Publication
- Publication Date
- Dec 07, 2022
- Source ID
- 10.1038/s41598-022-25463-0
Entities
People
- Elizabeth Vitalis
- Kjersti M Aagaard
- Krista L Ternus
- Kristen Curry
- Michael D Lee
- Michael Jochum
- Todd J Treangen
- Victoria Zaksas
Organizations
- Intelligence Advanced Research Projects Activity
- National Institute of Allergy and Infectious Diseases
- National Institutes of Health