Joint effects of pregnancy, sociocultural, and environmental factors on early life gut microbiome structure and diversity
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
Curated date: 2022/06/13
Curator: Kaluifeanyi101
Revision editor(s): Kaluifeanyi101, Lwaldron, WikiWorks
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled (if applicable)
- 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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- ethnic group Ethnicity,race,ethnic group
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Caucasian + other races neonates by maternal profiles
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- African American neonate by maternal profile
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Gut bacterial composition among neonates by maternal profiles. Microbiome Associated Maternal Profile (MMP3) as the most racially diverse was used for contrast.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 83
- Group 1 sample size Number of subjects in the case (exposed) group
- 92
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- unspecified.
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- PERMANOVA
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- .05
- 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, household income, breast feeding, delivery procedure, education level, marital status, smoking status
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- increased
- Richness Number of species
- increased
Signature 1
Source: FIGURE 5
Description: Top genera are significantly associated with each factor retained in multi-factor neonatal gut microbiome composition models. For plotting purposes, “top” genera for each factor were defined using two characteristics: (1) the number of taxa significantly associated with it (to avoid spurious findings) and (2) how “discriminatory” the genera was, defined by consistency in the direction of taxa-specific associations. Each factor displays up to the top ten genera that best discriminated each factor, given the genera had at least 5 significant taxa. Abbreviations: ETS, environmental tobacco smoke; NSV, neonatal study visit at 1-month of age.
Abundance in Group 1: increased abundance in African American neonate by maternal profile
NCBI | Quality Control | Links |
---|---|---|
Akkermansia | ||
Bifidobacterium | ||
Lactobacillus | ||
Megasphaera |
Revision editor(s): Kaluifeanyi101
Signature 2
Source: FIGURE 5
Description: Top genera are significantly associated with each factor retained in multi-factor neonatal gut microbiome composition models. For plotting purposes, “top” genera for each factor were defined using two characteristics: (1) the number of taxa significantly associated with it (to avoid spurious findings) and (2) how “discriminatory” the genera was, defined by consistency in the direction of taxa-specific associations. Each factor displays up to the top ten genera that best discriminated each factor, given the genera had at least 5 significant taxa. Abbreviations: ETS, environmental tobacco smoke; NSV, neonatal study visit at 1-month of age.
Abundance in Group 1: decreased abundance in African American neonate by maternal profile
NCBI | Quality Control | Links |
---|---|---|
Coprococcus | ||
Oscillospira | ||
Parabacteroides | ||
Prevotella | ||
Staphylococcus | ||
Streptococcus |
Revision editor(s): Kaluifeanyi101
Experiment 2
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- socioeconomic statussocioeconomic status
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Infants in household income =>$80,000.
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Infants in household income <$80,000.
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Gut bacterial composition among infants by maternal profiles. Microbiome Associated Maternal Profile (MMP3)
19.8% of the analytical sample(N =168)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 52
- Group 1 sample size Number of subjects in the case (exposed) group
- 33
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, breast feeding, delivery procedure, education level, marital status, race, smoking status
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- decreased
- Richness Number of species
- decreased
Signature 1
Source: FIGURE 6
Description: Top genera are significantly associated with each factor retained in multi-factor infant gut microbiome composition models. For plotting purposes, “top” genera for each factor were defined using two characteristics: (1) the number of taxa significantly associated with it (to avoid spurious findings) and (2) how “discriminatory” the genera was, defined by consistency in the direction of taxa-specific associations. Each factor displays up to the top ten genera that best discriminated each factor, given the genera had at least 5 significant taxa.
Abundance in Group 1: increased abundance in Infants in household income <$80,000.
NCBI | Quality Control | Links |
---|---|---|
Bacteroides | ||
Ruminococcus | ||
Streptococcus |
Revision editor(s): Kaluifeanyi101
Signature 2
Source: FIGURE 6
Description: Top genera are significantly associated with each factor retained in multi-factor infant gut microbiome composition models. For plotting purposes, “top” genera for each factor were defined using two characteristics: (1) the number of taxa significantly associated with it (to avoid spurious findings) and (2) how “discriminatory” the genera was, defined by consistency in the direction of taxa-specific associations. Each factor displays up to the top ten genera that best discriminated each factor, given the genera had at least 5 significant taxa.
Abundance in Group 1: decreased abundance in Infants in household income <$80,000.
NCBI | Quality Control | Links |
---|---|---|
Akkermansia | ||
Bifidobacterium | ||
Coprococcus | ||
Faecalibacterium | ||
Prevotella | ||
Staphylococcus | ||
Veillonella |
Revision editor(s): Kaluifeanyi101