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Temporal dynamics of human respiratory and gut microbiomes during the course of COVID-19 in adults

Xu, Rong and Lu, Renfei and Zhang, Tao and Wu, Qunfu and Cai, Weihua and Han, Xudong and Wan, Zhenzhou and Jin, Xia and Zhang, Zhigang and Zhang, Chiyu (2020) Temporal dynamics of human respiratory and gut microbiomes during the course of COVID-19 in adults. . (Unpublished) https://resolver.caltech.edu/CaltechAUTHORS:20201119-135010266

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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.


Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription
https://doi.org/10.1101/2020.07.21.20158758DOIDiscussion Paper
https://www.ncbi.nlm.nih.gov/sraRelated ItemNCBI Sequence Read Archive (SRA)
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.
Group:COVID-19
Funders:
Funding AgencyGrant Number
National Key Research and Development Program of China2017ZX10103009-002
National Key Research and Development Program of China2019YFC1200603
National Key Research and Development Program of China2018YFC2000500
Nantong Science and Technology BureauSFCDT3-2
Second Tibetan Plateau Scientific Expedition and Research Program2019QZKK0503
Chinese Academy of SciencesFZDSW-219
National Natural Science Foundation of China31970571
Record Number:CaltechAUTHORS:20201119-135010266
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20201119-135010266
Official Citation:Temporal dynamics of human respiratory and gut microbiomes during the course of COVID-19 in adults. Rong Xu, Renfei Lu, Tao Zhang, Qunfu Wu, Weihua Cai, Xudong Han, Xia Jin, Zhigang Zhang, Chiyu Zhang, Zhenzhou Wan. medRxiv 2020.07.21.20158758; doi: https://doi.org/10.1101/2020.07.21.20158758
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:106740
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:19 Nov 2020 22:22
Last Modified:02 Feb 2021 19:12

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