Alterations of the Gut Microbiota in Patients With Coronavirus Disease 2019 or H1N1 Influenza
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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
Gu S, Chen Y, Wu Z, Chen Y, Gao H, Lv L, Guo F, Zhang X, Luo R, Huang C, Lu H, Zheng B, Zhang J, Yan R, Zhang H, Jiang H, Xu Q, Guo J, Gong Y, Tang L, Li L
Journal
Clinical infectious diseases : an official publication of the Infectious Diseases Society of America
Year
2020
Keywords:
COVID-19, H1N1, biomarker, dysbiosis, intestinal microbiota
BACKGROUND: Coronavirus disease 2019 (COVID-19) is an emerging serious global health problem. Gastrointestinal symptoms are common in COVID-19 patients, and severe acute respiratory syndrome coronavirus 2 RNA has been detected in stool specimens. However, the relationship between the gut microbiome and disease remains to be established. METHODS: We conducted a cross-sectional study of 30 patients with COVID-19, 24 patients with influenza A(H1N1), and 30 matched healthy controls (HCs) to identify differences in the gut microbiota by 16S ribosomal RNA gene V3-V4 region sequencing. RESULTS: Compared with HCs, COVID-19 patients had significantly reduced bacterial diversity; a significantly higher relative abundance of opportunistic pathogens, such as Streptococcus, Rothia, Veillonella, and Actinomyces; and a lower relative abundance of beneficial symbionts. Five biomarkers showed high accuracy for distinguishing COVID-19 patients from HCs with an area under the curve (AUC) up to 0.89. Patients with H1N1 displayed lower diversity and different overall microbial composition compared with COVID-19 patients. Seven biomarkers were selected to distinguish the 2 cohorts (AUC = 0.94). CONCLUSIONS: The gut microbial signature of patients with COVID-19 was different from that of H1N1 patients and HCs. Our study suggests the potential value of the gut microbiota as a diagnostic biomarker and therapeutic target for COVID-19, but further validation is needed.
Experiment 1
Reviewed Marked as Reviewed by Fatima on 2021/06/30
Curated date: 2021/06/03
Curator: Claregrieve1
Revision editor(s): Fatima, Claregrieve1, WikiWorks, Peace Sandy
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- 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,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,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
- COVID-19 cases
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- viral COVID-19 infections confirmed by real-time reverse-transcription polymerase chain reaction
- Group 0 sample size Number of subjects in the control (unexposed) group
- 30
- Group 1 sample size Number of subjects in the case (exposed) group
- 30
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 4 weeks
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
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- 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)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3.5
- Matched on Factors on which subjects have been matched on in a case-control study
- age, body mass index, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Reviewed Marked as Reviewed by Fatima on 2021/06/30
Source: Figure 3a
Description: Differences in microbial composition between patients with coronavirus disease 2019 and healthy controls
Abundance in Group 1: increased abundance in COVID-19 cases
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus | ||
| Rothia | ||
| Veillonella | ||
| Thomasclavelia | ||
| Actinomyces |
Revision editor(s): Claregrieve1
Signature 2
Reviewed Marked as Reviewed by Fatima on 2021/06/30
Source: Figure 3a
Description: Differences in microbial composition between patients with coronavirus disease 2019 and healthy controls
Abundance in Group 1: decreased abundance in COVID-19 cases
| NCBI | Quality Control | Links |
|---|---|---|
| Agathobacter | ||
| Anaerobutyricum hallii | ||
| Anaerostipes | ||
| Dorea | ||
| Faecalibacterium | ||
| Fusicatenibacter | ||
| Intestinibacter | ||
| Klebsiella | ||
| Romboutsia | ||
| Turicibacter | ||
| [Ruminococcus] torques | ||
| Clostridium |
Revision editor(s): Fatima, Claregrieve1
Experiment 2
Reviewed Marked as Reviewed by Fatima on 2021/07/16
Curated date: 2021/06/03
Curator: Claregrieve1
Revision editor(s): LGeistlinger, Claregrieve1, WikiWorks
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Influenza A (H1N1) Influenza A (H1N1),influenza A (H1N1)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- H1N1 cases
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- H1N1 patients with viral infection confirmed by real-time reverse-transcription polymerase chain reaction hospitalized between January 2018 and March 2019 with severe disease at time of admission
- Group 1 sample size Number of subjects in the case (exposed) group
- 24
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Needs review
Source: Supplementary Figure 2
Description: Comparison of estimated fecal microbiome phylotypes in H1N1 patients and healthy controls
Abundance in Group 1: decreased abundance in H1N1 cases
| NCBI | Quality Control | Links |
|---|---|---|
| Blautia | ||
| Romboutsia | ||
| Collinsella | ||
| Anaerobutyricum hallii | ||
| Bifidobacterium | ||
| Agathobacter | ||
| Fusicatenibacter | ||
| [Ruminococcus] torques | ||
| Anaerostipes | ||
| Dorea | ||
| Ruminococcus sp. |
Revision editor(s): Claregrieve1
Signature 2
Needs review
Source: Supplementary Figure 2
Description: Comparison of estimated fecal microbiome phylotypes in H1N1 patients and healthy controls
Abundance in Group 1: increased abundance in H1N1 cases
| NCBI | Quality Control | Links |
|---|---|---|
| Enterococcus | ||
| Prevotella | ||
| Finegoldia | ||
| Peptoniphilus |
Revision editor(s): Claregrieve1
Experiment 3
Reviewed Marked as Reviewed by Fatima on 2021/06/30
Differences from previous experiment shown
Subjects
- 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,cOVID-19
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- H1N1 patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- COVID-19 patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- viral COVID-19 infections confirmed by real-time reverse-transcription polymerase chain reaction
- Group 0 sample size Number of subjects in the control (unexposed) group
- 24
- Group 1 sample size Number of subjects in the case (exposed) group
- 30
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- subjects who received antibiotics and/or probiotics within 4 weeks of enrollment were excluded
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Reviewed Marked as Reviewed by Fatima on 2021/06/30
Source: Figure 4a
Description: Differences in microbiota composition between COVID-19 patients and H1N1 patients
Abundance in Group 1: increased abundance in COVID-19 patients
Revision editor(s): Fatima, Claregrieve1
Signature 2
Reviewed Marked as Reviewed by Fatima on 2021/06/30
Source: Figure 4a
Description: Differences in microbiota composition between COVID-19 patients and H1N1 patients
Abundance in Group 1: decreased abundance in COVID-19 patients
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella | ||
| Ezakiella | ||
| Akkermansia | ||
| Murdochiella | ||
| Porphyromonas |
Revision editor(s): Claregrieve1
Experiment 4
Differences from previous experiment shown
Subjects
- 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
- COVID-19 cases
- Group 0 sample size Number of subjects in the control (unexposed) group
- 30
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 4 weeks
Lab analysis
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
- Matched on Factors on which subjects have been matched on in a case-control study
- age, body mass index, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Source: Figure 2A, 2B, 2C, 2D
Description: Taxonomic differences in fecal microbiota between patients with covid-19 and healthy controls
Abundance in Group 1: increased abundance in COVID-19 cases
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcaceae | ||
| Streptococcus | ||
| Bacilli |
Revision editor(s): Fatima
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