Altered oral and gut microbiota and its association with SARS-CoV-2 viral load in COVID-19 patients during hospitalization
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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
Wu Y, Cheng X, Jiang G, Tang H, Ming S, Tang L, Lu J, Guo C, Shan H, Huang X
Journal
NPJ biofilms and microbiomes
Year
2021
The human oral and gut commensal microbes play vital roles in the development and maintenance of immune homeostasis, while its association with susceptibility and severity of SARS-CoV-2 infection is barely understood. In this study, we investigated the dynamics of the oral and intestinal flora before and after the clearance of SARS-CoV-2 in 53 COVID-19 patients, and then examined their microbiome alterations in comparison to 76 healthy individuals. A total of 140 throat swab samples and 81 fecal samples from these COVID-19 patients during hospitalization, and 44 throat swab samples and 32 fecal samples from sex and age-matched healthy individuals were collected and then subjected to 16S rRNA sequencing and viral load inspection. We found that SARS-CoV-2 infection was associated with alterations of the microbiome community in patients as indicated by both alpha and beta diversity indexes. Several bacterial taxa were identified related to SARS-CoV-2 infection, wherein elevated Granulicatella and Rothia mucilaginosa were found in both oral and gut microbiome. The SARS-CoV-2 viral load in those samples was also calculated to identify potential dynamics between COVID-19 and the microbiome. These findings provide a meaningful baseline for microbes in the digestive tract of COVID-19 patients and will shed light on new dimensions for disease pathophysiology, potential microbial biomarkers, and treatment strategies for COVID-19.
Experiment 1
Reviewed Marked as Reviewed by Fatima on 2022/05/4
Curated date: 2021/08/02
Curator: Claregrieve1
Revision editor(s): 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
- Oropharynx Mesopharynx,Oral part of pharynx,Pars oralis pharyngis,Oropharynx,oropharynx
- 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 patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with confirmed COVID-19 infection per 2 sequential positive RT-PCR tests
- Group 0 sample size Number of subjects in the control (unexposed) group
- 44
- Group 1 sample size Number of subjects in the case (exposed) group
- 140
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- No antibiotics or probiotics within 8 weeks prior to COVID-19 infection (also true for controls)
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
- Linear Regression
- 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
- 2
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
Alpha Diversity
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Fatima on 2022/05/4
Source: Figure 2D
Description: Differential microbial abundance between healthy controls and COVID-19 patients
Abundance in Group 1: increased abundance in COVID-19 patients
| NCBI | Quality Control | Links |
|---|---|---|
| Haemophilus parainfluenzae | ||
| Veillonella | ||
| Campylobacter | ||
| Rothia mucilaginosa | ||
| Granulicatella | ||
| Neisseria subflava | ||
| Kingella | ||
| Filifactor |
Revision editor(s): Claregrieve1
Signature 2
Reviewed Marked as Reviewed by Fatima on 2022/05/4
Source: Figure 2D
Description: Differential microbial abundance between healthy controls and COVID-19 patients
Abundance in Group 1: decreased abundance in COVID-19 patients
| NCBI | Quality Control | Links |
|---|---|---|
| Neisseria | ||
| Corynebacterium | ||
| Actinobacillus | ||
| Moryella | ||
| Aggregatibacter | ||
| Prevotella intermedia | ||
| Treponema | ||
| Pseudomonas | ||
| Treponema amylovorum |
Revision editor(s): Claregrieve1
Experiment 2
Reviewed Marked as Reviewed by Fatima on 2022/05/4
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- COVID-19 patients (mild/moderate)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- COVID-19 patients (severe/critical)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with confirmed COVID-19 infection per 2 sequential positive RT-PCR tests deemed to have severe/critical disease
- 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
- 22
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- Not specified
Alpha Diversity
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Fatima on 2022/05/4
Source: Supplementary Table 3
Description: Differential microbial abundance between mild/moderate and severe/critical COVID-19 patients
Abundance in Group 1: decreased abundance in COVID-19 patients (severe/critical)
| NCBI | Quality Control | Links |
|---|---|---|
| Treponema | ||
| Aggregatibacter | ||
| Aggregatibacter segnis | ||
| Prevotella intermedia | ||
| Streptococcus anginosus | ||
| Selenomonas | ||
| Filifactor | ||
| Treponema amylovorum | ||
| Peptococcus |
Revision editor(s): Claregrieve1
Experiment 3
Reviewed Marked as Reviewed by Fatima on 2022/05/4
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 patients not treated with antibiotics
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with confirmed COVID-19 infection per 2 sequential positive RT-PCR tests who were not treated with antibiotics
- Group 0 sample size Number of subjects in the control (unexposed) group
- 44
- Group 1 sample size Number of subjects in the case (exposed) group
- 17
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- No antibiotics or probiotics within 8 weeks prior to or during COVID-19 infection (also true for controls)
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by Fatima on 2022/05/4
Source: Supplementary Table 3
Description: Differential microbial abundance between COVID-19 patients who were not treated with antibiotics and healthy controls
Abundance in Group 1: increased abundance in COVID-19 patients not treated with antibiotics
| NCBI | Quality Control | Links |
|---|---|---|
| Neisseria subflava | ||
| Granulicatella | ||
| Veillonella | ||
| Campylobacter | ||
| Rothia mucilaginosa | ||
| Veillonella dispar | ||
| Peptoniphilus |
Revision editor(s): Claregrieve1
Signature 2
Reviewed Marked as Reviewed by Fatima on 2022/05/4
Source: Supplementary Table 3
Description: Differential microbial abundance between COVID-19 patients who were not treated with antibiotics and healthy controls
Abundance in Group 1: decreased abundance in COVID-19 patients not treated with antibiotics
| NCBI | Quality Control | Links |
|---|---|---|
| Moryella | ||
| Treponema | ||
| Prevotella intermedia |
Revision editor(s): Claregrieve1
Experiment 4
Reviewed Marked as Reviewed by Fatima on 2022/05/4
Differences from previous experiment shown
Subjects
- 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
- 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
- Patients with confirmed COVID-19 infection per 2 sequential positive RT-PCR tests
- Group 0 sample size Number of subjects in the control (unexposed) group
- 32
- Group 1 sample size Number of subjects in the case (exposed) group
- 81
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- No antibiotics or probiotics within 8 weeks prior to COVID-19 infection (also true for controls)
Lab analysis
Statistical Analysis
Alpha Diversity
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Fatima on 2022/05/4
Source: Supplementary Table 4
Description: Differential microbial abundance between healthy controls and COVID-19 patients
Abundance in Group 1: increased abundance in COVID-19 patients
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus | ||
| Weissella | ||
| Enterococcus | ||
| Enterocloster citroniae | ||
| Bifidobacterium longum | ||
| Rothia mucilaginosa | ||
| Rothia | ||
| Lactobacillus | ||
| Actinomyces | ||
| Granulicatella |
Revision editor(s): Claregrieve1
Signature 2
Reviewed Marked as Reviewed by Fatima on 2022/05/4
Source: Supplementary Table 4
Description: Differential microbial abundance between healthy controls and COVID-19 patients
Abundance in Group 1: decreased abundance in COVID-19 patients
| NCBI | Quality Control | Links |
|---|---|---|
| Blautia | ||
| Coprococcus | ||
| Bacteroides caccae | ||
| Blautia obeum | ||
| [Clostridium] colinum | ||
| Collinsella | ||
| Phocaeicola coprophilus |
Revision editor(s): Claregrieve1
Experiment 5
Reviewed Marked as Reviewed by Fatima on 2022/05/4
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- COVID-19 patients not treated with antibiotics
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with confirmed COVID-19 infection per 2 sequential positive RT-PCR tests who were not treated with antibiotics
- Group 1 sample size Number of subjects in the case (exposed) group
- 13
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- No antibiotics or probiotics within 8 weeks prior to or during COVID-19 infection (also true for controls)
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by Fatima on 2022/05/4
Source: Supplementary Table 5
Description: Differential microbial abundance between COVID-19 patients who were not treated with antibiotics and healthy controls
Abundance in Group 1: increased abundance in COVID-19 patients not treated with antibiotics
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus | ||
| Enterocloster citroniae | ||
| Anaerococcus | ||
| Streptococcus anginosus | ||
| Peptoniphilus | ||
| Campylobacter | ||
| Atopobium |
Revision editor(s): Claregrieve1
Signature 2
Reviewed Marked as Reviewed by Fatima on 2022/05/4
Source: Supplementary Table 5
Description: Differential microbial abundance between COVID-19 patients who were not treated with antibiotics and healthy controls
Abundance in Group 1: decreased abundance in COVID-19 patients not treated with antibiotics
| NCBI | Quality Control | Links |
|---|---|---|
| Blautia | ||
| Coprococcus | ||
| Bacteroides eggerthii | ||
| Phocaeicola coprophilus | ||
| Blautia obeum | ||
| Blautia producta | ||
| Anaerostipes | ||
| [Clostridium] colinum | ||
| Neisseria |
Revision editor(s): Claregrieve1
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