Gut Microbiota May Not Be Fully Restored in Recovered COVID-19 Patients After 3-Month Recovery
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
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
Reviewed Marked as Reviewed by Fatima on 2022/05/21
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
Reviewed Marked as Reviewed by Fatima on 2022/05/21
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
Reviewed Marked as Reviewed by Fatima on 2022/05/21
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
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