Temporal changes in fecal microbiota of patients infected with COVID-19: a longitudinal cohort/Experiment 2

From BugSigDB


Reviewed Marked as Reviewed by Peace Sandy on 2024-2-22

Curated date: 2023/10/14

Curator: Tolulopeo

Revision editor(s): Tolulopeo, Peace Sandy, Svetlana up

Subjects

Location of subjects
Switzerland
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
COVID-19 patients - Non-Ventilated
Group 1 name Corresponds to the case (exposed) group for case-control studies
COVID-19 patients - Ventilated
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
COVID-19 patients in Intensive Care Unit [ICU] - Ventilated
Group 0 sample size Number of subjects in the control (unexposed) group
43
Group 1 sample size Number of subjects in the case (exposed) group
14
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
3 Months

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
2.5

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged

Signature 1

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-22

Curated date: 2023/10/16

Curator: Tolulopeo

Revision editor(s): Tolulopeo, Davvve, Peace Sandy

Source: Fig 2 A

Description: Impact of COVID-19 severity on the taxa composition and longitudinal changes of the gut microbiota. A, B Differential abundance analysis and db-RDA analysis in ventilated and non-ventilated COVID-19 patients. A Genera differentially abundant among the two groups were identified by a complex model including ventilation, antibiotics and timepoint with longitudinal sampling correction using negative binomial and zero-inflated mixed model (NBZIMM). The taxa with p-value < 0.01 and effect size (log10) > 2.5 for each group are presented in the bar plot (**p < 0.01, ***p < 0.001).

Abundance in Group 1: increased abundance in COVID-19 patients - Ventilated

NCBI Quality ControlLinks
Campylobacter
Ruminococcus
Clostridium

Revision editor(s): Tolulopeo, Davvve, Peace Sandy

Signature 2

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-22

Curated date: 2023/10/16

Curator: Tolulopeo

Revision editor(s): Tolulopeo, Peace Sandy

Source: Fig 2 A

Description: Impact of COVID-19 severity on the taxa composition and longitudinal changes of the gut microbiota. A, B Differential abundance analysis and db-RDA analysis in ventilated and non-ventilated COVID-19 patients. A Genera differentially abundant among the two groups were identified by a complex model including ventilation, antibiotics and timepoint with longitudinal sampling correction using negative binomial and zero-inflated mixed model (NBZIMM). The taxa with p-value < 0.01 and effect size (log10) > 2.5 for each group are presented in the bar plot (**p < 0.01, ***p < 0.001).

Abundance in Group 1: decreased abundance in COVID-19 patients - Ventilated

NCBI Quality ControlLinks
Streptococcus
Faecalibacterium
Roseburia

Revision editor(s): Tolulopeo, Peace Sandy