Gut Microbiota May Not Be Fully Restored in Recovered COVID-19 Patients After 3-Month Recovery

Study information

Reviewed Marked as Reviewed by Fatima on 2022/05/21

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

34055851

DOI Digital object identifier for electronic documents.

10.3389/fnut.2021.638825

URI

Authors

Tian Y, Sun KY, Meng TQ, Ye Z, Guo SM, Li ZM, Xiong CL, Yin Y, Li HG, Zhou LQ

Journal

Frontiers in nutrition

Year

2021

Keywords:

16S sequence, SARS-CoV-2, gut microbiota, recovered COVID-19 patient, short chain fatty acids

Coronavirus disease 2019 (COVID-19) has infected over 124 million people worldwide. In addition to the development of therapeutics and vaccines, the evaluation of the sequelae in recovered patients is also important. Recent studies have indicated that COVID-19 has the ability to infect intestinal tissues and to trigger alterations of the gut microbiota. However, whether these changes in gut microbiota persist into the recovery stage remains largely unknown. Here, we recruited seven healthy Chinese men and seven recovered COVID-19 male patients with an average of 3-months after discharge and analyzed their fecal samples by 16S rRNA sequencing analysis to identify the differences in gut microbiota. Our results suggested that the gut microbiota differed in male recovered patients compared with healthy controls, in which a significant difference in Chao index, Simpson index, and β-diversity was observed. And the relative abundance of several bacterial species differed clearly between two groups, characterized by enrichment of opportunistic pathogens and insufficiency of some anti-inflammatory bacteria in producing short chain fatty acids. The above findings provide preliminary clues supporting that the imbalanced gut microbiota may not be fully restored in recovered patients, highlighting the importance of continuous monitoring of gut health in people who have recovered from COVID-19.

Experiment 1

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Reviewed Marked as Reviewed by Fatima on 2022/05/21

Curated date: 2021/06/29

Curator: Claregrieve1

Revision editor(s): Claregrieve1, WikiWorks

Subjects

Location of subjects: China

Host species Species from which microbiome was sampled (if applicable): Homo sapiens

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: COVID-19 2019 novel coronavirus,2019 novel coronavirus infection,2019-nCoV,2019-nCoV infection,beta-CoV,beta-CoVs,betacoronavirus,coronavirus disease 2019,SARS-coronavirus 2,SARS-CoV-2,severe acute respiratory syndrome coronavirus 2,severe acute respiratory syndrome coronavirus 2 infectious disease,β-coronavirus,β-CoV,β-CoVs,COVID-19

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Healthy controls
Group 1 name Corresponds to the case (exposed) group for case-control studies: Recovered COVID-19 patients
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Patients between 25-45 years of age with documented recovery from COVID-19, detailed medical records during hospitalization and discharge certificate
Group 0 sample size Number of subjects in the control (unexposed) group: 7
Group 1 sample size Number of subjects in the case (exposed) group: 7
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): Participants instructed to avoid any drugs affecting gastrointestinal function before sampling

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V3-V4

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

Statistical test: LEfSe

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.05
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: No
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 3.5

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged
Chao1 Abundance-based estimator of species richness: decreased
Simpson Estimator of species richness and species evenness: more weight on species evenness: decreased

Signature 1

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Reviewed Marked as Reviewed by Fatima on 2022/05/21

Curated date: 2021/06/29

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Figure 4b

Description: Differential abundance of microbial taxa between controls and recovered COVID-19 patients

Abundance in Group 1: increased abundance in Recovered COVID-19 patients

NCBI	Quality Control	Links
Acidimicrobiia
Microtrichalus
Candidatus Microthrix
Microthrixaceae
Rothia
Micrococcales
Thomasclavelia
Micrococcaceae

Revision editor(s): Claregrieve1

Signature 2

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Reviewed Marked as Reviewed by Fatima on 2022/05/21

Curated date: 2021/06/29

Curator: Claregrieve1

Revision editor(s): Claregrieve1, Merit

Source: Figure 4b

Description: Differential abundance of microbial taxa between controls and recovered COVID-19 patients

Abundance in Group 1: decreased abundance in Recovered COVID-19 patients

NCBI	Quality Control	Links
Anaerobutyricum hallii
Collinsella
Coriobacteriaceae
Faecalibacterium
Oscillospira
Ruminococcus sp.
Oscillospiraceae bacterium
unclassified Oscillospiraceae
Ruminococcus

Revision editor(s): Claregrieve1, Merit