Alterations in the human oral and gut microbiomes and lipidomics in COVID-19
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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
Ren Z, Wang H, Cui G, Lu H, Wang L, Luo H, Chen X, Ren H, Sun R, Liu W, Liu X, Liu C, Li A, Wang X, Rao B, Yuan C, Zhang H, Sun J, Chen X, Li B, Hu C, Wu Z, Yu Z, Kan Q, Li L
Journal
Gut
Year
2021
Keywords:
COVID-19, intestinal microbiology, lipid metabolism
OBJECTIVE: To characterise the oral microbiome, gut microbiome and serum lipid profiles in patients with active COVID-19 and recovered patients; evaluate the potential of the microbiome as a non-invasive biomarker for COVID-19; and explore correlations between the microbiome and lipid profile. DESIGN: We collected and sequenced 392 tongue-coating samples, 172 faecal samples and 155 serum samples from Central China and East China. We characterised microbiome and lipid molecules, constructed microbial classifiers in discovery cohort and verified their diagnostic potential in 74 confirmed patients (CPs) from East China and 37 suspected patients (SPs) with IgG positivity. RESULTS: Oral and faecal microbial diversity was significantly decreased in CPs versus healthy controls (HCs). Compared with HCs, butyric acid-producing bacteria were decreased and lipopolysaccharide-producing bacteria were increased in CPs in oral cavity. The classifiers based on 8 optimal oral microbial markers (7 faecal microbial markers) achieved good diagnostic efficiency in different cohorts. Importantly, diagnostic efficacy reached 87.24% in the cross-regional cohort. Moreover, the classifiers successfully diagnosed SPs with IgG antibody positivity as CPs, and diagnostic efficacy reached 92.11% (98.01% of faecal microbiome). Compared with CPs, 47 lipid molecules, including sphingomyelin (SM)(d40:4), SM(d38:5) and monoglyceride(33:5), were depleted, and 122 lipid molecules, including phosphatidylcholine(36:4p), phosphatidylethanolamine (PE)(16:0p/20:5) and diglyceride(20:1/18:2), were enriched in confirmed patients recovery. CONCLUSION: This study is the first to characterise the oral microbiome in COVID-19, and oral microbiomes and lipid alterations in recovered patients, to explore their correlations and to report the successful establishment and validation of a diagnostic model for COVID-19.
Experiment 1
Reviewed Marked as Reviewed by Fatima on 2022/06/1
Curated date: 2021/06/21
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
- Tongue Glossus,Tongue,tongue
- 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
- Confirmed COVID-19 patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Suspected COVID-19 cases with one of the following etiological or serological evidence: (1) Fluorescence RT-PCR detects the positive of the COVID-19 virus nucleic acid. (2) Viral gene sequencing finds highly homologous to COVID-19 virus
- Group 0 sample size Number of subjects in the control (unexposed) group
- 100
- Group 1 sample size Number of subjects in the case (exposed) group
- 48
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Receipt of antibiotics and/or probiotics within 8 weeks prior to enrollment
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V5
- 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)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/10
Source: Supplementary Figures 1E and 1G
Description: Differential microbial abundance in tongue-coating samples from healthy controls compared with confirmed COVID-19 patients
Abundance in Group 1: decreased abundance in Confirmed COVID-19 patients
Revision editor(s): Fatima, Claregrieve1
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/10
Source: Supplementary Figures 1E and 1G
Description: Differential microbial abundance in tongue-coating samples from healthy controls compared with confirmed COVID-19 patients
Abundance in Group 1: increased abundance in Confirmed COVID-19 patients
| NCBI | Quality Control | Links |
|---|---|---|
| Campylobacter | ||
| Cyanobacteriota | ||
| Granulicatella | ||
| Leptotrichia | ||
| Megasphaera | ||
| Ruminococcus sp. | ||
| Selenomonas | ||
| Spirochaeta | ||
| Tannerella |
Revision editor(s): Fatima, Claregrieve1
Experiment 2
Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/10
Curated date: 2021/06/22
Curator: Claregrieve1
Revision editor(s): Claregrieve1, WikiWorks, Victoria
Differences from previous experiment shown
Subjects
- 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
- Confirmed COVID-19 patients who recovered
- Group 0 sample size Number of subjects in the control (unexposed) group
- 150
- Group 1 sample size Number of subjects in the case (exposed) group
- 22
Lab analysis
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/10
Source: Figure 4c
Description: Differential microbial abundance in oral microbiome samples between recovered COVID-19 cases and healthy controls
Abundance in Group 1: decreased abundance in Recovered COVID-19 patients
| NCBI | Quality Control | Links |
|---|---|---|
| Candidatus Saccharimonas | ||
| Eubacteriales Family XIII. Incertae Sedis | ||
| Haemophilus | ||
| Parvimonas | ||
| Porphyromonas |
Revision editor(s): Claregrieve1
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/10
Source: Figure 4c
Description: Differential microbial abundance in oral microbiome samples between recovered COVID-19 cases and healthy controls
Abundance in Group 1: increased abundance in Recovered COVID-19 patients
| NCBI | Quality Control | Links |
|---|---|---|
| Centipeda | ||
| Leptotrichia | ||
| Megasphaera | ||
| Selenomonas |
Revision editor(s): Claregrieve1
Experiment 3
Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/10
Curated date: 2021/06/25
Curator: Claregrieve1
Revision editor(s): Claregrieve1, WikiWorks, Victoria
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
- Suspected COVID-19 cases with one of the following etiological or serological evidence: (1) Fluorescence RT-PCR detects the positive of the COVID-19 virus nucleic acid. (2) Viral gene sequencing finds highly homologous to COVID-19 virus
- Group 0 sample size Number of subjects in the control (unexposed) group
- 48
- Group 1 sample size Number of subjects in the case (exposed) group
- 24
Lab analysis
Statistical Analysis
- Statistical test
- LEfSe
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/10
Source: Figure 5c, S3E, S3G -Supp 05
Description: Differential microbial abundance between samples from healthy controls and samples from COVID-19 patients
Abundance in Group 1: decreased abundance in COVID-19 patients
Revision editor(s): Lwaldron, Claregrieve1
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/10
Source: Figure 5c
Description: Differential microbial abundance between samples from healthy controls and samples from COVID-19 patients
Abundance in Group 1: increased abundance in COVID-19 patients
Revision editor(s): Claregrieve1
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