Gut Microbiome Alterations following Postnatal Iron Supplementation Depend on Iron Form and Persist into Adulthood
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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
- United States of America
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Rattus norvegicus
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Cecum mucosa Caecum mucosa,Caecum mucosa of organ,Caecum mucous membrane,Caecum organ mucosa,Cecal mucosa,Cecum mucosa of organ,Cecum mucous membrane,Cecum organ mucosa,Intestinum crassum caecum mucosa,Intestinum crassum caecum mucosa of organ,Intestinum crassum caecum mucous membrane,Intestinum crassum caecum organ mucosa,Mucosa of caecum,Mucosa of cecum,Mucosa of intestinum crassum caecum,Mucosa of organ of caecum,Mucosa of organ of cecum,Mucosa of organ of intestinum crassum caecum,Mucous membrane of caecum,Mucous membrane of cecum,Mucous membrane of intestinum crassum caecum,Organ mucosa of caecum,Organ mucosa of cecum,Organ mucosa of intestinum crassum caecum,Cecum mucosa,cecum mucosa
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Iron biomarker measurement iron biomarker level,iron status biomarkers,Iron biomarker measurement,iron biomarker measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Vehicle control-supplemented (CON) pups
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Ferrous sulfate (FS) treated pups (PD 15)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Pre-weaning Sprague-Dawley rat pups given oral supplements of ferrous sulfate (FS) on postnatal day (PD) 2–14 and samples collected from 4–6 hours fasted animals on postnatal day (PD) 15.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 28
- Group 1 sample size Number of subjects in the case (exposed) group
- 27
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- None
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- 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).
- raw counts
- Statistical test
- DESeq2
- 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
- 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 2d + Figure 3 + Table S3 + Table S4
Description: Taxa Differing in Abundance Between Ferrous sulfate (FS) treated pups (PD 15) and Vehicle control-supplemented (CON) pups as determined by DESeq2
Abundance in Group 1: increased abundance in Ferrous sulfate (FS) treated pups (PD 15)
Revision editor(s): Keamy, Joan Chuks, MyleeeA
Signature 2
Source: Figure 2d + Figure 3 + Table S3 + Table S4
Description: Taxa Differing in Abundance Between Ferrous sulfate (FS) treated pups (PD 15) and Vehicle control-supplemented (CON) pups as determined by DESeq2
Abundance in Group 1: decreased abundance in Ferrous sulfate (FS) treated pups (PD 15)
Revision editor(s): Keamy, Joan Chuks
Experiment 2
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Ferrous bis-glycinate chelate (FC) treated pups (PD 15)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Pre-weaning Sprague-Dawley rat pups given oral supplements of ferrous bis-glycinate chelate (Ferrochel, FC) on postnatal day (PD) and samples collected from 4–6 hours fasted animals on postnatal day (PD) 15.
- Group 1 sample size Number of subjects in the case (exposed) group
- 29
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- 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 2d + Figure 3 + Table S3 + Table S4
Description: Taxa Differing in Abundance Between ferrous bis-glycinate chelate (FC) treated pups (PD 15) and Vehicle control-supplemented (CON) pups as determined by DESeq2
Abundance in Group 1: increased abundance in Ferrous bis-glycinate chelate (FC) treated pups (PD 15)
Signature 2
Source: Figure 2d + Figure 3 + Table S3 + Table S4
Description: Taxa Differing in Abundance Between ferrous bis-glycinate chelate (FC) treated pups (PD 15) and Vehicle control-supplemented (CON) pups as determined by DESeq2
Abundance in Group 1: decreased abundance in Ferrous bis-glycinate chelate (FC) treated pups (PD 15)
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Ferrous sulfate (FS) treated pups (PD 15)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Pre-weaning Sprague-Dawley rat pups given oral supplements of ferrous bis-glycinate chelate (Ferrochel, FC) on postnatal day (PD) 2-14 and samples collected from 4–6 hours-fasted animals on postnatal day (PD) 15
- Group 0 sample size Number of subjects in the control (unexposed) group
- 27
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- 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 S3 + Table S3 + Table S4
Description: Taxa Differing in Abundance Between Ferrous sulfate (FS) treated pups (PD 15) and Ferrous bis-glycinate chelate (FC) treated pups (PD 15) as determined by DESeq2
Abundance in Group 1: increased abundance in Ferrous bis-glycinate chelate (FC) treated pups (PD 15)
| NCBI | Quality Control | Links |
|---|---|---|
| Allobaculum | ||
| Candidatus Soleaferrea | ||
| Dubosiella | ||
| Streptococcus | ||
| Christensenellaceae R−7 groupChristensenellaceae R−7 group |
Revision editor(s): Keamy, Joan Chuks
Signature 2
Source: Figure S3 + Table S3 + Table S4
Description: Taxa Differing in Abundance Between Ferrous sulfate (FS) treated pups (PD 15) and Ferrous bis-glycinate chelate (FC) treated pups (PD 15) as determined by DESeq2
Abundance in Group 1: decreased abundance in Ferrous bis-glycinate chelate (FC) treated pups (PD 15)
Revision editor(s): Keamy, Joan Chuks, MyleeeA
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Vehicle control-supplemented (CON) young Adult (YA) rats
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Ferrous sulfate (FS) treated young Adult (YA) rats (PD 58 +/- 4)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Young Adult (YA) Sprague-Dawley rats given oral supplements of ferrous sulfate (FS) on postnatal day (PD) 2-20, weaned on postnatal day (PD) 21 and samples collected from 4–6 hours fasted animals on postnatal day (PD) 58 +/- 4.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 23
- Group 1 sample size Number of subjects in the case (exposed) group
- 23
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Richness Number of species
- increased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- increased
Signature 1
Source: Figure 5d and 6 +Figure S6 + Table S7 and S8
Description: Taxa Differing in Abundance Between Young Adult (YA) Sprague-Dawley rats given oral supplements of ferrous sulfate (FS) and Vehicle control-supplemented (CON) as determined by DESeq2
Abundance in Group 1: increased abundance in Ferrous sulfate (FS) treated young Adult (YA) rats (PD 58 +/- 4)
Signature 2
Source: Figure 5d,6 and S6 + Table S7and S8
Description: Taxa Differing in Abundance Between fYoung Adult (YA) Sprague-Dawley rats given oral supplements of ferrous sulfate (FS). and Vehicle control-supplemented (CON)
Abundance in Group 1: decreased abundance in Ferrous sulfate (FS) treated young Adult (YA) rats (PD 58 +/- 4)
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Vehicle control-supplemented (CON) young Adult rats
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Ferrous bis-glycinate chelate (FC) treated young Adult (YA) rats (PD 58 +/- 4)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Young Adult (YA) Sprague-Dawley rats given oral supplements of ferrous bis-glycinate chelate (FC) on postnatal day (PD) 2-20, weaned on postnatal day (PD) 21 and samples collected from 4–6 h-fasted animals on postnatal day (PD) 58 +/- 4.
- Group 1 sample size Number of subjects in the case (exposed) group
- 19
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- 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 5d + Figure 6 + Figure S6 + Table s7 +Table s8
Description: Taxa Differing in Abundance Between Ferrous bis-glycinate chelate (FC) treated young Adult (YA) rats (PD 58 +/- 4) and Vehicle control-supplemented (CON) young Adult rats as determined by DESeq2.
Abundance in Group 1: increased abundance in Ferrous bis-glycinate chelate (FC) treated young Adult (YA) rats (PD 58 +/- 4)
Revision editor(s): Keamy, Joan Chuks
Signature 2
Source: Figure 5d + Figure 6 + Figure S6 + Table s7 +Table s8
Description: Taxa Differing in Abundance Between Ferrous bis-glycinate chelate (FC) treated young Adult (YA) rats (PD 58 +/- 4) and Vehicle control-supplemented (CON) young Adult rats as determined by DESeq2.
Abundance in Group 1: decreased abundance in Ferrous bis-glycinate chelate (FC) treated young Adult (YA) rats (PD 58 +/- 4)
Revision editor(s): Keamy, Joan Chuks
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Ferrous sulfate (FS) treated young Adult (YA) rats (PD 58 +/- 4)
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- 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 5d + Figure 6 + Figure S6 + Table S7 and S8
Description: Taxa Differing in Abundance Between Ferrous bis-glycinate chelate (FC) treated young Adult (YA) rats (PD 58 +/- 4) and Ferrous Sulfate (FS) young Adult rats as determined by DESeq2.
Abundance in Group 1: increased abundance in Ferrous bis-glycinate chelate (FC) treated young Adult (YA) rats (PD 58 +/- 4)
Signature 2
Source: Figure 5d + Figure 6 + Figure S6 + Table S7 andS8
Description: Taxa Differing in Abundance Between Ferrous bis-glycinate chelate (FC) treated young Adult (YA) rats (PD 58 +/- 4) and Ferrous Sulfate (FS) young Adult rats as determined by DESeq2.
Abundance in Group 1: decreased abundance in Ferrous bis-glycinate chelate (FC) treated young Adult (YA) rats (PD 58 +/- 4)
