A comparison of the infant gut microbiome before versus after the start of the covid-19 pandemic
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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
Querdasi FR, Vogel SC, Thomason ME, Callaghan BL, Brito NH
Journal
Scientific reports
Year
2023
The COVID-19 pandemic and resulting public health directives led to many changes in families' social and material environments. Prior research suggests that these changes are likely to impact composition of the gut microbiome, particularly during early childhood when the gut microbiome is developing most rapidly. Importantly, disruption to the gut microbiome during this sensitive period can have potentially long-lasting impacts on health and development. In the current study, we compare gut microbiome composition among a socioeconomically and racially diverse group of 12-month old infants living in New York City who provided stool samples before the pandemic (N = 34) to a group who provided samples during the first 9-months of the pandemic (March-December 2020; N = 20). We found that infants sampled during the pandemic had lower alpha diversity of the microbiome, lower abundance of Pasteurellaceae and Haemophilus, and significantly different beta diversity based on unweighted Unifrac distance than infants sampled before the pandemic. Exploratory analyses suggest that gut microbiome changes due to the pandemic occurred relatively quickly after the start of the pandemic and were sustained. Our results provide evidence that pandemic-related environmental disruptions had an impact on community-level taxonomic diversity of the developing gut microbiome, as well as abundance of specific members of the gut bacterial community.
Experiment 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-5
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 with covariates controlled for
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- pandemic group with 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 with covariates ( diet(average fat intake), child sex, still breastfeeding at sample collection, and birth mode) controlled for.
- 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
- diet, breast feeding, delivery procedure, sex
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
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-5
Source: figure 6, figure 7
Description: differential analysis of gut microbiome by pandemic group with covariates controlled for.
Abundance in Group 1: decreased abundance in pandemic group with covariates controlled for
| NCBI | Quality Control | Links |
|---|---|---|
| Haemophilus | ||
| Pasteurellaceae |
Revision editor(s): Folakunmi
Experiment 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-5
Differences from previous experiment shown
Subjects
- 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.
Lab analysis
Statistical Analysis
- 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
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-5
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
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-5
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
Experiment 3
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-5
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- pandemic group (without covariates)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- pandemic group according to the number of days
- 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 according to the number of days since the pandemic began. Due to the small sample size of the during pandemic group (N = 20), analyses restricted to this group did not include any covariates.
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- diet, breast feeding, delivery procedure, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-5
Source: Results within text: Page 4, under sub-heading "Differential abundance of gut microbiota by days since the start of the pandemic among the pandemic group".
Description: Differential abundance of gut microbiota by days since the start of the pandemic among the pandemic group.
Abundance in Group 1: decreased abundance in pandemic group according to the number of days
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacteriaceae |
Revision editor(s): Folakunmi, ChiomaBlessing
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