Gut microbiota dynamics in a prospective cohort of patients with post-acute COVID-19 syndrome (original) (raw)

Gut microbiota dynamics in a prospective cohort of patients with post-acute COVID-19 syndrome

Qin Liu1,2,3,4,
http://orcid.org/0000-0001-5221-7349Joyce Wing Yan Mak1,2,3,
Qi Su1,2,3,4,
http://orcid.org/0000-0003-0241-6117Yun Kit Yeoh1,4,5,
Grace Chung-Yan Lui2,6,
Susanna So Shan Ng2,
http://orcid.org/0000-0003-0887-1073Fen Zhang1,2,3,4,
Amy Y L Li1,2,3,
Wenqi Lu1,2,3,4,
David Shu-Cheong Hui6,
Paul KS Chan1,5,
http://orcid.org/0000-0001-7388-2436Francis K L Chan1,2,3,4,
http://orcid.org/0000-0002-6850-4454Siew C Ng1,2,3,4
1Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
2Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
3State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Science, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
4Microbiota I-Center (MagIC), Hong Kong, Hong Kong SAR, China
5Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
6Stanley Ho Centre for Emerging Infectious Diseases, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
Correspondence to Professor Siew C Ng, Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, Hong Kong; siewchienng{at}cuhk.edu.hk

Abstract

Background Long-term complications after COVID-19 are common, but the potential cause for persistent symptoms after viral clearance remains unclear.

Objective To investigate whether gut microbiome composition is linked to post-acute COVID-19 syndrome (PACS), defined as at least one persistent symptom 4 weeks after clearance of the SARS-CoV-2 virus.

Methods We conducted a prospective study of 106 patients with a spectrum of COVID-19 severity followed up from admission to 6 months and 68 non-COVID-19 controls. We analysed serial faecal microbiome of 258 samples using shotgun metagenomic sequencing, and correlated the results with persistent symptoms at 6 months.

Results At 6 months, 76% of patients had PACS and the most common symptoms were fatigue, poor memory and hair loss. Gut microbiota composition at admission was associated with occurrence of PACS. Patients without PACS showed recovered gut microbiome profile at 6 months comparable to that of non-COVID-19 controls. Gut microbiome of patients with PACS were characterised by higher levels of Ruminococcus gnavus, Bacteroides vulgatus and lower levels of Faecalibacterium prausnitzii. Persistent respiratory symptoms were correlated with opportunistic gut pathogens, and neuropsychiatric symptoms and fatigue were correlated with nosocomial gut pathogens, including Clostridium innocuum and Actinomyces naeslundii (all p<0.05). Butyrate-producing bacteria, including Bifidobacterium pseudocatenulatum and Faecalibacterium prausnitzii showed the largest inverse correlations with PACS at 6 months.

Conclusion These findings provided observational evidence of compositional alterations of gut microbiome in patients with long-term complications of COVID-19. Further studies should investigate whether microbiota modulation can facilitate timely recovery from post-acute COVID-19 syndrome.

COVID-19
intestinal microbiology

Data availability statement

Data are available in a public, open access repository. Raw data are deposited in a BioProject in the NCBI Sequence Read Archive: PRJNA714459.

This article is made freely available for personal use in accordance with BMJ’s website terms and conditions for the duration of the covid-19 pandemic or until otherwise determined by BMJ. You may use, download and print the article for any lawful, non-commercial purpose (including text and data mining) provided that all copyright notices and trade marks are retained.

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