Gut Microbiota May Not Be Fully Restored in Recovered COVID-19 Patients After 3-Month Recovery/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Fatima on 2022/05/21
Curated date: 2021/06/29
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
- 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
- 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
- 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
- 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
