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Published November 19, 2020 | Supplemental Material
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Temporal dynamics of human respiratory and gut microbiomes during the course of COVID-19 in adults

Abstract

SARS-CoV-2 infects multiple organs including the respiratory tract and gut. Whether regional microbiomes are disturbed significantly to affect the disease progression of COVID-19 is largely unknown. To address this question, we performed cross-sectional and longitudinal analyses of throat and anal swabs from 35 COVID-19 adults and 15 controls by 16S rRNA gene sequencing. The results allowed a partitioning of patients into 3-4 categories (I-IV) with distinct microbial community types in both sites. Lower-diversity community types often appeared in the early phase of COVID-19, and synchronous fast restoration of both the respiratory and gut microbiomes from early dysbiosis towards late near-normal was observed in 6/8 mild COVID-19 adult patients despite they had a relatively slow clinical recovery. The synchronous shift of the community types was associated with significantly positive bacterial interactions between the respiratory tract and gut, possibly along the airway-gut axis. These findings reveal previously unknown interactions between respiratory and gut microbiomes, and suggest that modulations of regional microbiota might help to improve the recovery from COVID-19 in adult patients.

Additional Information

The copyright holder for this preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. This version posted July 22, 2020. This work was supported by grants from the National Key Research and Development Program of China (2017ZX10103009-002, 2019YFC1200603 and 2018YFC2000500), Special fund for COVID-19 diagnosis and treatment of Nantong Science and Technology Bureau (SFCDT3-2), the Second Tibetan Plateau Scientific Expedition and Research (STEP) program (2019QZKK0503), the Key Research Program of the Chinese Academy of Sciences (FZDSW-219), and the Chinese National Natural Science Foundation (31970571). Data Availability: The raw data of 16S rRNA gene sequences are available at NCBI Sequence Read Archive (SRA) (https://www.ncbi.nlm.nih.gov/sra/) at BioProject ID PRJNA639286. https://www.ncbi.nlm.nih.gov/sra/ The authors have declared no competing interest. Author Declarations. I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes. The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The study was approved by Nantong Third Hospital Ethics Committee (EL2020006: 28 February 2020). Written informed consents were obtained from each of the involved individuals. All experiments were performed in accordance with relevant guidelines and regulations. All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived. Yes. I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes. I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes.

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Supplemental Material - 2020.07.21.20158758-2.xlsx

Supplemental Material - 2020.07.21.20158758-3.xlsx

Supplemental Material - 2020.07.21.20158758-4.xlsx

Supplemental Material - 2020.07.21.20158758v1.full.pdf

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Additional details

Created:
August 19, 2023
Modified:
October 20, 2023