Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial
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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.
Authors
Chong CYL, Vatanen T, Alexander T, Bloomfield FH, O'Sullivan JM
Journal
Frontiers in cellular and infection microbiology
Year
2021
Keywords:
early life nutrition, ethnicity, gut microbiome, moderate–late preterm infant, socioeconomic status
The gut microbiota of preterm infants is affected by perinatal factors and, in turn, may impact upon infant health. In this study, we collected fecal samples at Day-10 (D10) and 4-months corrected-age (4M) from 227 moderate-late preterm (MLPT) babies enrolled in a randomized controlled trial of nutritional management. A total of 320 samples underwent 16S amplicon sequencing, and shotgun metagenomic sequencing was performed on 94 samples from the 4M time point. The microbiome of babies whose families lived in lower socioeconomic status (SES) areas exhibited a significantly higher microbial alpha diversity at D10 (Wilcoxon test, p = 0.021), greater abundance of Bifidobacterium (linear model, q = 0.020) at D10 and Megasphaera (q = 0.031) at 4M. Hospital of birth explained 5.2% of the observed variance in 4M samples (PERMANOVA, p = 0.038), with Staphylococcus aureus more abundant in fecal samples from babies born in Middlemore hospital (linear model, q = 0.016). Maternal antibiotic (Wilcoxon test, p = 0.013) and probiotic (p = 0.04) usage within the four-week period before sample collection was associated with a reduction in the alpha diversity of D10 samples. Infant probiotic intake explained 2.1% (PERMANOVA, p = 0.021) of the variance in the D10 microbial profile with increased Lactobacillus (linear model, q = 1.1 × 10-10) levels. At 4M, the microbiome of infants who were breastmilk fed had reduced alpha diversity when compared to non-breastmilk fed infants (Wilcoxon test, p < 0.05). Although causality cannot be inferred within our study, we conclude that in MLPT babies, maternal socioeconomic factors, as well as the perinatal medical environment and nutrition impact on the development of the newborn microbiome.
Experiment 1
Needs review
Curated date: 2022/07/20
Curator: Uyokeeswaran
Revision editor(s): WikiWorks, Lwaldron, Uyokeeswaran, Tolulopeo, Hodan Issah, Scholastica
Subjects
- Location of subjects
- New Zealand
- 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
- Spontaneous preterm birth Spontaneous preterm birth,spontaneous preterm birth
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Day-10 (D10) (chronological age)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- 4-months corrected age (4M)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Faecal samples collected from moderate–late preterm (MLPT) babies enrolled in a randomized controlled trial of nutritional management at 4-months corrected age (4M).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 207
- Group 1 sample size Number of subjects in the case (exposed) group
- 118
- 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
- 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
- MaAsLin2
- 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
- increased
Signature 1
Needs review
Source: Text (page 5)
Description: Significantly abundant taxa between the two time points; day-10 (D10) (chronological age) and at 4-months corrected age (4M).
Abundance in Group 1: increased abundance in 4-months corrected age (4M)
Revision editor(s): Scholastica
Signature 2
Needs review
Source: Text (page 5)
Description: Significantly abundant taxa between the two time points; day-10 (D10) (chronological age) and at 4-months corrected age (4M).
Abundance in Group 1: decreased abundance in 4-months corrected age (4M)
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcaceae | ||
| Corynebacteriaceae | ||
| Pasteurellaceae |
Revision editor(s): Scholastica
Experiment 2
Needs review
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Higher SES (D10)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Lower SES (D10)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Moderate–late preterm (MLPT) babies at Day-10 (D10) whose families lived in the lower SES (socioeconomic status) areas
- Group 0 sample size Number of subjects in the control (unexposed) group
- 59
- Group 1 sample size Number of subjects in the case (exposed) group
- 80
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Needs review
Source: Text (page 5)
Description: Significantly abundant taxa in MLPT babies from lower socioeconomic status (SES) group compared to the higher SES group at D10
Abundance in Group 1: increased abundance in Lower SES (D10)
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium |
Revision editor(s): Scholastica
Experiment 3
Needs review
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Higher SES (4M)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Lower SES (4M)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Moderate–Late Preterm (MLPT) babies at 4-months corrected-age (4M) whose families lived in the lower SES (socioeconomic status) areas
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Needs review
Source: Text (page 5)
Description: Significantly abundant taxa in MLPT babies from lower socioeconomic status (SES) group compared to the higher SES group at 4M
Abundance in Group 1: increased abundance in Lower SES (4M)
| NCBI | Quality Control | Links |
|---|---|---|
| Megasphaera |
Revision editor(s): Scholastica
Experiment 4
Needs review
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- European (D10)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Maori (D10)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Moderate–Late Preterm (MLPT) Babies at D10 born to mothers self-reporting as Maori
- Group 0 sample size Number of subjects in the control (unexposed) group
- 77
- Group 1 sample size Number of subjects in the case (exposed) group
- 24
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Experiment 5
Needs review
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Asian (4M)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Maori (4M)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Moderate–Late Preterm (MLPT) babies at 4M born to mothers self-reporting as Maori
- Group 0 sample size Number of subjects in the control (unexposed) group
- 72
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Needs review
Source: Text (page 5)
Description: Significantly abundant taxa in MLPT Babies at 4M born to mothers self-reporting as Maori compared to Asian
Abundance in Group 1: decreased abundance in Maori (4M)
| NCBI | Quality Control | Links |
|---|---|---|
| Rothia | ||
| Staphylococcus |
Revision editor(s): Scholastica, MyleeeA
Experiment 6
Needs review
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Pacifica (4M)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Moderate–Late Preterm (MLPT) babies at 4-months born to mothers self-reporting as Pacifica
- Group 1 sample size Number of subjects in the case (exposed) group
- 36
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Needs review
Source: Text (page 5)
Description: Significantly abundant taxa in MLPT Babies at 4-months born to mothers self-reporting as Pacifica compared to Asian
Abundance in Group 1: decreased abundance in Pacifica (4M)
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus |
Revision editor(s): Scholastica, MyleeeA
Experiment 7
Needs review
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- No University (4M)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- University (4M)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Moderate–late preterm (MLPT) babies at 4-months whose mothers have a university degree
- Group 0 sample size Number of subjects in the control (unexposed) group
- 108
- Group 1 sample size Number of subjects in the case (exposed) group
- 105
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Source: Supplementary Table S4
Description: Linear modelling results showing taxa associated with factors at 4-month corrected age, measured by 16S amplicon data. Only results with Q-value<0.25 are shown.
Abundance in Group 1: decreased abundance in University (4M)
| NCBI | Quality Control | Links |
|---|---|---|
| Eggerthella |
Revision editor(s): MyleeeA
Experiment 8
Needs review
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Mix feeding (4M)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Breastmilk feeding (4M)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Moderate–late preterm (MLPT) babies at 4-months corrected age who were breastmilk fed
- Group 0 sample size Number of subjects in the control (unexposed) group
- 95
- Group 1 sample size Number of subjects in the case (exposed) group
- 36
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Experiment 9
Needs review
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Only formula (4M)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 42
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Needs review
Source: Text (page 6)
Description: Significantly abundant taxa in MLPT Babies at 4-months corrected age who were breastmilk fed compared to babies that were fed only formula
Abundance in Group 1: increased abundance in Breastmilk feeding (4M)
| NCBI | Quality Control | Links |
|---|---|---|
| Megasphaera |
Revision editor(s): Scholastica
Experiment 10
Needs review
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mixed feeding (4M)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Moderate–late preterm (MLPT) babies at 4-months corrected age who were mix fed
- Group 1 sample size Number of subjects in the case (exposed) group
- 95
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Experiment 11
Needs review
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- No maternal antibiotics
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Yes maternal antibiotics
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Maternal use of antibiotics within the four-week period before the D10 fecal sample collection
- Group 0 sample size Number of subjects in the control (unexposed) group
- 69
- Group 1 sample size Number of subjects in the case (exposed) group
- 130
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Experiment 12
Needs review
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- No maternal probiotics
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Yes maternal probiotics
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Maternal use of probiotics within the four-week period before the D10 fecal sample collection
- Group 0 sample size Number of subjects in the control (unexposed) group
- 147
- 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
Signature 1
Source: Supplementary Table S4
Description: Linear modelling results showing taxa associated with different factors at day10, measured by 16S amplicon data. Only results with Q-value < 0.25 are shown.
Abundance in Group 1: increased abundance in Yes maternal probiotics
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium | ||
| Lactobacillus |
Revision editor(s): MyleeeA
Experiment 13
Needs review
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- No infant probiotics
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Yes infant probiotics
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- D10 fecal samples of infants who themselves received probiotics during their admission
- Group 0 sample size Number of subjects in the control (unexposed) group
- 159
- Group 1 sample size Number of subjects in the case (exposed) group
- 40
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Needs review
Source: Text (page 6)
Description: Significantly abundant taxa in samples of MLPT infants at D10 who themselves received probiotics during their admission
Abundance in Group 1: increased abundance in Yes infant probiotics
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus |
Revision editor(s): Scholastica
Experiment 14
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- No Antibiotics
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Yes Antibiotics
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Infant who received antibiotic within the month immediately preceding the 4-month follow-up appointment
- Group 0 sample size Number of subjects in the control (unexposed) group
- 5
- Group 1 sample size Number of subjects in the case (exposed) group
- 108
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- N/A
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Table S4 and Text (Page 7)
Description: Linear modelling results showing taxa associated with factors at 4-month corrected age, measured by 16S amplicon data.
Abundance in Group 1: increased abundance in Yes Antibiotics
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridium |
Revision editor(s): MyleeeA
Experiment 15
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Only Formula (4M)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Breast Milk (4M)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Moderate–late preterm (MLPT) babies at 4-months corrected age who were breastmilk fed
- Group 0 sample size Number of subjects in the control (unexposed) group
- 42
- Group 1 sample size Number of subjects in the case (exposed) group
- 36
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Experiment 16
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Only Formula (D10)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Breast Milk (D10)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Moderate–late preterm (MLPT) babies at Day 10 who were breastmilk fed
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Source: Supplementary Table S4
Description: Linear modelling results showing taxa associated with factors at 4-month corrected age, measured by 16S amplicon data.
Abundance in Group 1: increased abundance in Breast Milk (D10)
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium |
Revision editor(s): MyleeeA
Experiment 17
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Mixed Feeding (4M)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Breast Milk (4M)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Moderate–late preterm (MLPT) babies at 4-months corrected age who were breastmilk fed
- Group 0 sample size Number of subjects in the control (unexposed) group
- 95
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Supplementary Table S4
Description: Linear modelling results showing taxa associated with factors at 4-month corrected age, measured by shotgun metagenomics data.
Abundance in Group 1: increased abundance in Breast Milk (4M)
| NCBI | Quality Control | Links |
|---|---|---|
| unclassified Bilophila |
Revision editor(s): MyleeeA
Experiment 18
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Mixed Feeding (D10)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Only Formula (D10)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Moderate–late preterm (MLPT) babies at Day 10 who were fed with only formula
- Group 1 sample size Number of subjects in the case (exposed) group
- 42
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Source: Supplementary Table S4
Description: Linear modelling results showing taxa associated with different factors at day10, measured by 16S amplicon data.
Abundance in Group 1: increased abundance in Only Formula (D10)
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium |
Revision editor(s): MyleeeA
Experiment 19
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- No Antibiotics (4M)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Yes Antibiotics (4M)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Maternal use of antibiotics within the one month preceding the four-month follow-up period
- Group 0 sample size Number of subjects in the control (unexposed) group
- 69
- Group 1 sample size Number of subjects in the case (exposed) group
- 130
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Supplementary Table S4
Description: Linear modelling results showing taxa associated with factors at 4-month corrected age, measured by 16S amplicon data.
Abundance in Group 1: increased abundance in Yes Antibiotics (4M)
| NCBI | Quality Control | Links |
|---|---|---|
| Lachnoclostridium | ||
| Intestinibacter |
Revision editor(s): MyleeeA
Experiment 20
Needs review
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- No Infant Antibiotics (4M)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Yes Infant Antibiotics (4M)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Infant use of antibiotics within the one month preceding the 4-month follow-up appointment
- Group 0 sample size Number of subjects in the control (unexposed) group
- 89
- Group 1 sample size Number of subjects in the case (exposed) group
- 4
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Experiment 21
Needs review
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- No Infant Antibiotics (D10)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Yes Infant Antibiotics (D10)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Infants who themselves use antibiotic during neonatal admission at D10
- Group 0 sample size Number of subjects in the control (unexposed) group
- 97
- Group 1 sample size Number of subjects in the case (exposed) group
- 102
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Needs review
Source: Supplementary Table S4
Description: Linear modelling results showing taxa associated with different factors at day10, measured by 16S amplicon data. Only results with Q-value < 0.25 are shown.
Abundance in Group 1: increased abundance in Yes Infant Antibiotics (D10)
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium |
Revision editor(s): Scholastica
Experiment 22
Needs review
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Caesarean section (D10)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Vaginal delivery (D10)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- D10 fecal samples of MLPT babies born vaginally
- Group 0 sample size Number of subjects in the control (unexposed) group
- 136
- Group 1 sample size Number of subjects in the case (exposed) group
- 77
Lab analysis
Statistical Analysis
Signature 1
Needs review
Source: Text (page 8), Supplementary Table S4
Description: Linear modelling results showing taxa associated with different factors at day10, measured by 16S amplicon data. Only results with Q-value < 0.25 are shown.
Abundance in Group 1: increased abundance in Vaginal delivery (D10)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides |
Revision editor(s): Scholastica
Experiment 23
Needs review
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Singletons (4M)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Twins (4M)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Fecal samples of MLPT babies born as twins at 4-month corrected age
- Group 0 sample size Number of subjects in the control (unexposed) group
- 63
- Group 1 sample size Number of subjects in the case (exposed) group
- 31
Lab analysis
Statistical Analysis
Signature 1
Needs review
Source: Supplementary Table S4
Description: Linear modelling results showing taxa associated with factors at 4-month corrected age, measured by 16S amplicon data. Only results with Q-value<0.25 are shown.
Abundance in Group 1: increased abundance in Twins (4M)
| NCBI | Quality Control | Links |
|---|---|---|
| Ruminiclostridium |
Revision editor(s): Scholastica
Experiment 24
Needs review
Differences from previous experiment shown
Subjects
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
Statistical Analysis
Signature 1
Needs review
Source: Text (page 8), Supplementary Table S4
Description: Linear modelling results showing taxa associated with factors at 4-month corrected age, measured by 16S amplicon data. Only results with Q-value<0.25 are shown.
Abundance in Group 1: increased abundance in Twins (4M)
| NCBI | Quality Control | Links |
|---|---|---|
| Eggerthella lenta |
Revision editor(s): Scholastica
Experiment 25
Needs review
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Auckland city hospital (4M)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Middlemore Hospital (4M)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- MLPT babies born at Middlemore Hospital at 4-month corrected age
- 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
- 80
Lab analysis
Statistical Analysis
Signature 1
Needs review
Source: Text (page 8), Supplementary Table S4
Description: Linear modelling results showing taxa associated with factors at 4-month corrected age, measured by shotgun metagenomics data, (Q-value<0.25).
Abundance in Group 1: increased abundance in Middlemore Hospital (4M)
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus aureus |
Revision editor(s): Scholastica
Contents
- 1 Experiment 1
- 2 Experiment 2
- 3 Experiment 3
- 4 Experiment 4
- 5 Experiment 5
- 6 Experiment 6
- 7 Experiment 7
- 8 Experiment 8
- 9 Experiment 9
- 10 Experiment 10
- 11 Experiment 11
- 12 Experiment 12
- 13 Experiment 13
- 14 Experiment 14
- 15 Experiment 15
- 16 Experiment 16
- 17 Experiment 17
- 18 Experiment 18
- 19 Experiment 19
- 20 Experiment 20
- 21 Experiment 21
- 22 Experiment 22
- 23 Experiment 23
- 24 Experiment 24
- 25 Experiment 25
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