Temporal association between human upper respiratory and gut bacterial microbiomes during the course of COVID-19 in adults
Open Access
- 18 February 2021
- journal article
- research article
- Published by Springer Science and Business Media LLC in Communications Biology
- Vol. 4 (1), 1-11
- https://doi.org/10.1038/s42003-021-01796-w
Abstract
SARS-CoV-2 is the cause of COVID-19. It infects multiple organs including the respiratory tract and gut. Dynamic changes of regional microbiomes in infected adults are largely unknown. Here, we performed longitudinal analyses of throat and anal swabs from 35 COVID-19 and 19 healthy adult controls, as well as 10 non-COVID-19 patients with other diseases, by 16 S rRNA gene sequencing. The results showed a partitioning of the patients into 3-4 categories based on microbial community types (I-IV) in both sites. The bacterial diversity was lower in COVID-19 patients than healthy controls and decreased gradually from community type I to III/IV. Although the dynamic change of microbiome was complex during COVID-19, a synchronous restoration of both the upper respiratory and gut microbiomes from early dysbiosis towards late more diverse status was observed in 6/8 mild COVID-19 adult patients. These findings reveal previously unknown interactions between upper respiratory and gut microbiomes during COVID-19.Funding Information
- Chinese Academy of Sciences Key Project (2017ZX10103009-002, 2018YFC2000500)
This publication has 61 references indexed in Scilit:
- Dynamics and associations of microbial community types across the human bodyNature, 2014
- Ribosomal Database Project: data and tools for high throughput rRNA analysisNucleic Acids Research, 2013
- UPARSE: highly accurate OTU sequences from microbial amplicon readsNature Methods, 2013
- ACE2 – From the renin–angiotensin system to gut microbiota and malnutritionMicrobes and Infection, 2013
- Dirichlet Multinomial Mixtures: Generative Models for Microbial MetagenomicsPLOS ONE, 2012
- Improving indicator species analysis by combining groups of sitesOikos, 2010
- QIIME allows analysis of high-throughput community sequencing dataNature Methods, 2010
- Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial CommunitiesApplied and Environmental Microbiology, 2009
- Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial TaxonomyApplied and Environmental Microbiology, 2007
- Non‐parametric multivariate analyses of changes in community structureAustralian Journal of Ecology, 1993