The long-term gut bacterial signature of a wild primate is associated with a timing effect of pre- and postnatal maternal glucocorticoid levels
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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
Subjects
- Location of subjects
- Thailand
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Macaca assamensis
- 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
- Response to glucocorticoid response to glucocorticoid stimulus,Response to glucocorticoid,response to glucocorticoid
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Early pregnancy glucocorticoid(Early-preGC) exposure in 4.7years (mean age)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Early pregnancy glucocorticoid (Early-preGC) exposure in 2.3years (mean age -1SD)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Assamese macaques aged 2.3 years (roughly equivalent to infants age class), who were exposed to prenatal, maternal glucocorticoid in early pregnancy/gestation (Early-preGC) during the Rich season(periods of abundant food availability)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 16
- Group 1 sample size Number of subjects in the case (exposed) group
- 16
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
- ANCOM
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
- Richness Number of species
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Source: Figure 4A
Description: Bacteria Taxa determined by ANCOM-BC to be differentially abundant in 2.3years old Assamese macaques (mean age -1SD, equivalent to infant age class) Versus 4.7years old Assamese macaques (mean age, equivalent to Juvenile age class), exposed to prenatal, maternal glucocorticoid during early pregnancy/gestation (Early-preGC), as assessed within the rich season.
Abundance in Group 1: increased abundance in Early pregnancy glucocorticoid (Early-preGC) exposure in 2.3years (mean age -1SD)
Revision editor(s): Ikehdarlington, Joan Chuks
Signature 2
Source: Figure 4A
Description: Bacteria Taxa determined by ANCOM-BC to be differentially abundant in 2.3years old Assamese macaques (mean age -1SD, equivalent to infant age class) Versus 4.7years old Assamese macaques (mean age, equivalent to Juvenile age class), exposed to prenatal, maternal glucocorticoid during early pregnancy/gestation (Early-preGC), as assessed within the rich season.
Abundance in Group 1: decreased abundance in Early pregnancy glucocorticoid (Early-preGC) exposure in 2.3years (mean age -1SD)
Revision editor(s): Ikehdarlington, Joan Chuks
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Early pregnancy glucocorticoid(Early-preGC) exposure in 4.7years old(mean age)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Early pregnancy glucocorticoid (Early-preGC) exposure in 7.1years old(mean age +1SD)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Assamese macaques aged 7.1years (equivalent to Adult age class), who were exposed to prenatal, maternal glucocorticoid in early pregnancy/gestation (Early-preGC) during the Rich season (periods of abundant food availability).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
- Richness Number of species
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Source: Figure 4A
Description: Bacteria Taxa determined by ANCOM-BC to be differentially abundant in 7.1 years old Assamese macaques (mean age +1SD-equivalent to Adult age class) Versus 4.7 years old Assamese macaques (mean age: equivalent to Juvenile age class), exposed to prenatal, maternal glucocorticoid during early pregnancy/gestation (Early-preGC), as assessed within the rich season.
Abundance in Group 1: increased abundance in Early pregnancy glucocorticoid (Early-preGC) exposure in 7.1years old(mean age +1SD)
Revision editor(s): Joan Chuks, Ikehdarlington
Signature 2
Source: Figure 4A
Description: Bacteria Taxa determined by ANCOM-BC to be differentially abundant in 7.1 years old Assamese macaques (mean age +1SD-equivalent to Adult age class) Versus 4.7 years old Assamese macaques (mean age: equivalent to Juvenile age class), exposed to prenatal, maternal glucocorticoid during early pregnancy/gestation (Early-preGC), as assessed within the rich season.
Abundance in Group 1: decreased abundance in Early pregnancy glucocorticoid (Early-preGC) exposure in 7.1years old(mean age +1SD)
Revision editor(s): Joan Chuks, Ikehdarlington
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Late pregnancy glucocorticoid (Late-preGC) exposure in 4.7years old (mean age)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Late pregnancy glucocorticoid (Late-preGC) exposure in 2.3years old (mean age -1SD)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Assamese macaques aged 2.3 years (equivalent to infant age class), who were exposed to prenatal, maternal glucocorticoid in late pregnancy/gestation (Late-preGC) during the Rich season (periods of abundant food availability).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Source: Figure 4B
Description: Bacteria Taxa determined by ANCOM-BC to be differentially abundant in 2.3 years old Assamese macaques (mean age -1SD = equivalent to infant age class) Versus 4.7 years old Assamese macaques (mean age =equivalent to Juvenile age class), exposed to prenatal, maternal glucocorticoid during Late pregnancy/gestation (Late-preGC), as assessed within the rich season.
Abundance in Group 1: increased abundance in Late pregnancy glucocorticoid (Late-preGC) exposure in 2.3years old (mean age -1SD)
Revision editor(s): Joan Chuks, Ikehdarlington
Signature 2
Source: Figure 4B
Description: Bacteria Taxa determined by ANCOM-BC to be differentially abundant in 2.3 years old Assamese macaques (mean age -1SD = equivalent to infant age class) Versus 4.7 years old Assamese macaques (mean age = equivalent to Juvenile age class), exposed to prenatal, maternal glucocorticoid during Late pregnancy/gestation (Late-preGC), as assessed within the rich season.
Abundance in Group 1: decreased abundance in Late pregnancy glucocorticoid (Late-preGC) exposure in 2.3years old (mean age -1SD)
Revision editor(s): Joan Chuks, Ikehdarlington
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Late pregnancy glucocorticoid(Late-preGC) exposure in 4.7years old(mean age)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Late pregnancy glucocorticoid (Late-preGC) exposure in 7.1years old(mean age +1SD)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Assamese macaques aged 7.1 years (equivalent to Adult age class), who were exposed to prenatal, maternal glucocorticoid in late pregnancy/gestation (Late-preGC) during the Rich season (periods of abundant food availability).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Source: Figure 4B
Description: Bacteria Taxa determined by ANCOM-BC to be differentially abundant in 7.1 years old Assamese macaques (mean age +1SD-equivalent to Adult age class) Versus 4.7 years old Assamese macaques (mean age: equivalent to Juvenile age class), exposed to prenatal, maternal glucocorticoid during Late pregnancy/gestation (Late-preGC), as assessed within the rich season.
Abundance in Group 1: increased abundance in Late pregnancy glucocorticoid (Late-preGC) exposure in 7.1years old(mean age +1SD)
Revision editor(s): Joan Chuks, Ikehdarlington
Signature 2
Source: Figure 4B
Description: Bacteria Taxa determined by ANCOM-BC to be differentially abundant in 7.1 years old Assamese macaques (mean age +1SD, equivalent to Adult age class) Versus 4.7 years old Assamese macaques (mean age, equivalent to Juvenile age class), exposed to prenatal, maternal glucocorticoid during Late pregnancy/gestation (Late-preGC), as assessed within the rich season.
Abundance in Group 1: decreased abundance in Late pregnancy glucocorticoid (Late-preGC) exposure in 7.1years old(mean age +1SD)
Revision editor(s): Joan Chuks, Ikehdarlington
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Post-pregnancy glucocorticoid(PostGC) exposure in 4.7years old(mean age)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Post-pregnancy glucocorticoid (PostGC) exposure in 2.3years old(mean age -1SD)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Assamese macaques aged 2.3 years (equivalent to infant age class), who were exposed to postnatal, maternal glucocorticoid in post pregnancy/lactation (PostGC) for the first 6 months of life during the Rich season (periods of abundant food availability)
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Source: Figure 4C
Description: Bacteria Taxa determined by ANCOM-BC to be differentially abundant in 2.3 years old Assamese macaques (mean age -1SD, equivalent to infant age class) Versus 4.7 years old Assamese macaques (mean age, equivalent to Juvenile age class), exposed to prenatal, maternal glucocorticoid during Lactation/Post pregnancy (PostGC), as assessed within the rich season.
Abundance in Group 1: increased abundance in Post-pregnancy glucocorticoid (PostGC) exposure in 2.3years old(mean age -1SD)
Revision editor(s): Joan Chuks, Ikehdarlington
Signature 2
Source: Figure 4C
Description: Bacteria Taxa determined by ANCOM-BC to be differentially abundant in 2.3 years old Assamese macaques (mean age -1SD, equivalent to infant age class) Versus 4.7 years old Assamese macaques (mean age, equivalent to Juvenile age class), exposed to prenatal, maternal glucocorticoid during Lactation/Post pregnancy (PostGC), as assessed within the rich season.
Abundance in Group 1: decreased abundance in Post-pregnancy glucocorticoid (PostGC) exposure in 2.3years old(mean age -1SD)
Revision editor(s): Joan Chuks, Ikehdarlington
Experiment 6
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Post-pregnancy glucocorticoid (PostGC) exposure in 7.1years old(mean age +1SD)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Assamese macaques aged 7.1 years (equivalent toAdult age class), who were exposed to postnatal, maternal glucocorticoid in post pregnancy/lactation (PostGC) for the first 6 months of life during the Rich season (periods of abundant food availability)
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Source: Figure 4C
Description: Bacteria Taxa determined by ANCOM-BC to be differentially abundant in 7.1 years old Assamese macaques (mean age +1SD, equivalent to Adult age class) Versus 4.7 years old Assamese macaques (mean age, equivalent to Juvenile age class), exposed to prenatal, maternal glucocorticoid during Lactation/Post pregnancy (PostGC), as assessed within the rich season.
Abundance in Group 1: increased abundance in Post-pregnancy glucocorticoid (PostGC) exposure in 7.1years old(mean age +1SD)
Revision editor(s): Joan Chuks, Ikehdarlington
Signature 2
Source: Figure 4C
Description: Bacteria Taxa determined by ANCOM-BC to be differentially abundant in 7.1 years old Assamese macaques (mean age +1SD, equivalent to Adult age class) Versus 4.7 years old Assamese macaques (mean age, equivalent to Juvenile age class), exposed to prenatal, maternal glucocorticoid during Lactation/Post pregnancy (PostGC), as assessed within the rich season.
Abundance in Group 1: decreased abundance in Post-pregnancy glucocorticoid (PostGC) exposure in 7.1years old(mean age +1SD)
Revision editor(s): Joan Chuks, Ikehdarlington
Experiment 7
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Offspring glucocorticoid (OffspringGC) in 4.7 years old (mean age)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Offspring glucocorticoid (OffspringGC) in 2.3 years old (mean age -1SD)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Assamese macaques aged 2.3 years (equivalent to infant age class), who were affected by increased Offspring Glucocorticoid level (OffspringGC) during the Rich season (periods of abundant food availability)
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Source: Figure 5
Description: Bacteria Taxa affected by Offspring glucocorticoid (OffspringGC) and determined by ANCOM-BC to be differentially abundant in 2.3 years old Assamese macaques (mean age -1SD, equivalent to infant age class) Versus 4.7 years old Assamese macaques (mean age, equivalent to Juvenile age class) as assessed during the rich season.
Abundance in Group 1: increased abundance in Offspring glucocorticoid (OffspringGC) in 2.3 years old (mean age -1SD)
Revision editor(s): Ikehdarlington, Joan Chuks
Signature 2
Source: Figure 5
Description: Bacteria Taxa affected by Offspring glucocorticoid (OffspringGC) and determined by ANCOM-BC to be differentially abundant in 2.3 years old Assamese macaques (mean age -1SD, equivalent to infant age class) Versus 4.7 years old Assamese macaques (mean age, equivalent to Juvenile age class) as assessed during the rich season.
Abundance in Group 1: decreased abundance in Offspring glucocorticoid (OffspringGC) in 2.3 years old (mean age -1SD)
Revision editor(s): Ikehdarlington, Joan Chuks
Experiment 8
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Offspring glucocorticoid (OffspringGC) in 7.1 years old (mean age +1SD)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Assamese macaques aged 7.1 years (equivalent to Adult age class), who were affected by increased Offspring Glucocorticoid level (OffspringGC) during the Rich season (periods of abundant food availability).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Source: Figure 5
Description: Bacteria Taxa affected by Offspring glucocorticoid (OffspringGC) and determined by ANCOM-BC to be differentially abundant in 7.1 years old Assamese macaques (mean age +1SD, equivalent to Adult age class) Versus 4.7 years old Assamese macaques (mean age, equivalent to Juvenile age class) as assessed within the rich season.
Abundance in Group 1: increased abundance in Offspring glucocorticoid (OffspringGC) in 7.1 years old (mean age +1SD)
Revision editor(s): Joan Chuks, Ikehdarlington
Signature 2
Source: Figure 5
Description: Bacteria Taxa affected by Offspring glucocorticoid (OffspringGC) and determined by ANCOM-BC to be differentially abundant in 7.1 years old Assamese macaques (mean age +1SD, equivalent to Adult age class) Versus 4.7 years old Assamese macaques (mean age, equivalent to Juvenile age class) as assessed within the rich season.
Abundance in Group 1: decreased abundance in Offspring glucocorticoid (OffspringGC) in 7.1 years old (mean age +1SD)
Revision editor(s): Joan Chuks, Ikehdarlington
Experiment 9
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Gut microbiome measurement Gut microbiome measurement,gut microbiome measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Infant macaques
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Adult macaques
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Assamese macaques aged 6–10 years
- Group 1 sample size Number of subjects in the case (exposed) group
- 7
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
- Richness Number of species
- increased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- increased
Experiment 10
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Juvenile macaques
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Assamese macaques aged 4–5 years
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
- Richness Number of species
- increased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- increased
Experiment 11
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Lean season
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Rich season
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The hot and rainy season in the Assamese macaques' habitat, usually occurring between March to October and marked by abundant food availability
- Group 0 sample size Number of subjects in the control (unexposed) group
- 30
- Group 1 sample size Number of subjects in the case (exposed) group
- 16
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
- Richness Number of species
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Experiment 12
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- MOT
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- MST
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Second grouping of Assamese macaques by research team.
- Group 0 sample size Number of subjects in the control (unexposed) group
- Not specified
- Group 1 sample size Number of subjects in the case (exposed) group
- Not specified
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- decreased
- Richness Number of species
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Experiment 13
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- SST
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Third grouping of Assamese macaques by the research team
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- decreased
- Richness Number of species
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
