A comparison of the infant gut microbiome before versus after the start of the covid-19 pandemic/Experiment 2
Subjects
- Location of subjects
- United States of America
- 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
- Health study participation health questionnaire participation,health survey participation,Health study participation,health study participation
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- pre-pandemic group without covariates controlled for
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- pandemic group without covariates controlled for
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- healthy 12-month old infants who provided stool samples during the first 9 months of the pandemic without controlling for covariates.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 34
- Group 1 sample size Number of subjects in the case (exposed) group
- 20
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- no antibiotic within a month preceding stool collection.
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- 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
- MaAsLin2
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.25
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, diet, breast feeding, delivery procedure
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Source: Supplementary information: Page 5, under sub-heading- “Differential abundance of gut microbiome by pandemic group without controlling for covariates”
Description: Differential abundance of gut microbiome by pandemic group without controlling for covariates.
Abundance in Group 1: increased abundance in pandemic group without covariates controlled for
| NCBI | Quality Control | Links |
|---|---|---|
| Pasteurellaceae |
Revision editor(s): Folakunmi, ChiomaBlessing
Signature 2
Source: Supplementary information: Page 5, under sub-heading- “Differential abundance of gut microbiome by pandemic group without controlling for covariates”
Description: Differential abundance of gut microbiome by pandemic group without controlling for covariates.
Abundance in Group 1: decreased abundance in pandemic group without covariates controlled for
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillaceae |
Revision editor(s): Folakunmi, ChiomaBlessing
