Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth
-
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 Kingdom
- 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
- Delivery measurement Delivery measurement,delivery measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Vaginal mode of delivery during early transmission - Transmission vs Vaginal mode of delivery during early transmission - No Transmission
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Caesarean section (CS) mode of delivery during early transmission - Transmission vs CS mode of delivery during early transmission - No Transmission
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Babies delivered by caesarean section exhibit markedly reduced rates of maternal microbial strain transmission in comparison to those delivered vaginally, as well as a persistent depletion of Bacteroides species and other commensals.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 35
- Group 1 sample size Number of subjects in the case (exposed) group
- 24
Lab analysis
- Sequencing type
- WMS
- 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
- Fisher's Exact Test
- 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
Signature 1
Source: Fig. 3a, Table S7
Description: Maternal microbial strain transmission frequencies between vaginally and caesarean-delivered babies, longitudinally sampled during the neonatal (early) period.
Abundance in Group 1: decreased abundance in Caesarean section (CS) mode of delivery during early transmission - Transmission vs CS mode of delivery during early transmission - No Transmission
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium longum | ||
| Phocaeicola vulgatus | ||
| Streptococcus salivarius | ||
| Streptococcus thermophilus | ||
| [Ruminococcus] torques |
Revision editor(s): Ameenatoloko
Signature 2
Source: Fig. 3a, Table S7
Description: Maternal microbial strain transmission frequencies between vaginally and caesarean delivered babies, longitudinally sampled during the neonatal (early) period.
Abundance in Group 1: increased abundance in Caesarean section (CS) mode of delivery during early transmission - Transmission vs CS mode of delivery during early transmission - No Transmission
| NCBI | Quality Control | Links |
|---|---|---|
| Escherichia coli | ||
| Bifidobacterium bifidum | ||
| [Ruminococcus] torques | ||
| Bacteroides fragilis | ||
| Bifidobacterium pseudocatenulatum |
Revision editor(s): Ameenatoloko
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Vaginal mode of delivery during late transmission - Transmission vs Vaginal mode of delivery during late transmission - No Transmission
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Caesarean section (CS) mode of delivery during late transmission - Transmission vs CS mode of delivery during late transmission - No Transmission
Lab analysis
Statistical Analysis
Signature 1
Source: Fig. 3a, Table S7
Description: Maternal microbial strain transmission frequencies between vaginally and caesarean-delivered babies, longitudinally sampled during the infancy (late) period.
Abundance in Group 1: increased abundance in Caesarean section (CS) mode of delivery during late transmission - Transmission vs CS mode of delivery during late transmission - No Transmission
Revision editor(s): Ameenatoloko
Signature 2
Source: Fig. 3a, Table S7
Description: Maternal microbial strain transmission frequencies between vaginally and caesarean-delivered babies, longitudinally sampled during the infancy (late) period.
Abundance in Group 1: decreased abundance in Caesarean section (CS) mode of delivery during late transmission - Transmission vs CS mode of delivery during late transmission - No Transmission
| NCBI | Quality Control | Links |
|---|---|---|
| [Ruminococcus] torques | ||
| Streptococcus salivarius | ||
| Streptococcus thermophilus | ||
| Phocaeicola vulgatus | ||
| Collinsella aerofaciens | ||
| Faecalibacterium prausnitzii |
Revision editor(s): Ameenatoloko
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Babies delivered vaginally in the early neonatal period - Transmission vs Babies delivered vaginally in the early neonatal period - No Transmission
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Babies delivered by caesarean section (CS) in the early neonatal period - Transmission vs Babies delivered by CS in the early neonatal period - No Transmission
- Group 0 sample size Number of subjects in the control (unexposed) group
- 112
- Group 1 sample size Number of subjects in the case (exposed) group
- 66
Lab analysis
Statistical Analysis
Signature 1
Source: Extended Data Fig. 4, Fig. S6
Description: Transmission of maternal microbial strains during the early neonatal period.
Abundance in Group 1: increased abundance in Babies delivered by caesarean section (CS) in the early neonatal period - Transmission vs Babies delivered by CS in the early neonatal period - No Transmission
Revision editor(s): Ameenatoloko
Signature 2
Source: Extended Data Fig. 4, Fig. S6
Description: Transmission of maternal microbial strains during the early neonatal period.
Abundance in Group 1: decreased abundance in Babies delivered by caesarean section (CS) in the early neonatal period - Transmission vs Babies delivered by CS in the early neonatal period - No Transmission
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus salivarius | ||
| Bacteroides uniformis | ||
| Streptococcus vestibularis | ||
| Streptococcus thermophilus | ||
| Streptococcus parasanguinis |
Revision editor(s): Ameenatoloko
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Babies delivered vaginally
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Babies delivered by caesarean section
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Babies delivered by caesarean section were deprived of maternally transmitted commensal bacteria but had a substantially higher relative abundance of opportunistic pathogens commonly associated with the hospital environment.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 606
- Group 1 sample size Number of subjects in the case (exposed) group
- 596
Signature 1
Source: Fig. 4a
Description: Extensive and frequent colonization of babies delivered by caesarean section with diverse opportunistic pathogens.
Abundance in Group 1: increased abundance in Babies delivered by caesarean section
| NCBI | Quality Control | Links |
|---|---|---|
| Enterococcus faecalis | ||
| Enterococcus faecium | ||
| Enterobacter cloacae | ||
| Klebsiella pneumoniae | ||
| Klebsiella oxytoca | ||
| Clostridium perfringens |
Revision editor(s): Ameenatoloko
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Babies delivered vaginally sampled during the neonatal period on day 4 (n = 310)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Babies delivered by caesarean section sampled during the neonatal period on day 4 (n = 310)
- 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
- 282
Lab analysis
Statistical Analysis
Signature 1
Source: Extended Data Fig. 5a
Description: Frequency and abundance of opportunistic pathogens in the neonatal gut microbiota.
Abundance in Group 1: increased abundance in Babies delivered by caesarean section sampled during the neonatal period on day 4 (n = 310)
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridium perfringens | ||
| Enterobacter cloacae | ||
| Enterococcus faecalis | ||
| Enterococcus faecium | ||
| Klebsiella oxytoca | ||
| Klebsiella pneumoniae |
Revision editor(s): Ameenatoloko
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Babies delivered vaginally sampled during the neonatal period on day 7 (n = 532)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Babies delivered by caesarean section sampled during the neonatal period on day 7 (n = 532)
Lab analysis
Statistical Analysis
Signature 1
Source: Extended Data Fig. 5a
Description: Frequency and abundance of opportunistic pathogens in the neonatal gut microbiota.
Abundance in Group 1: increased abundance in Babies delivered by caesarean section sampled during the neonatal period on day 7 (n = 532)
| NCBI | Quality Control | Links |
|---|---|---|
| Klebsiella pneumoniae | ||
| Klebsiella oxytoca | ||
| Enterobacter cloacae | ||
| Clostridium perfringens | ||
| Enterococcus faecium | ||
| Enterococcus faecalis |
Revision editor(s): Ameenatoloko
Experiment 7
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Babies delivered vaginally sampled during the neonatal period on day 21 (n = 325)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Babies delivered by caesarean section sampled during the neonatal period on day 21 (n = 325)
Lab analysis
Statistical Analysis
Signature 1
Source: Extended Data Fig. 5a
Description: Frequency and abundance of opportunistic pathogens in the neonatal gut microbiota.
Abundance in Group 1: increased abundance in Babies delivered by caesarean section sampled during the neonatal period on day 21 (n = 325)
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridium perfringens | ||
| Enterococcus faecalis | ||
| Enterobacter cloacae | ||
| Enterococcus faecium | ||
| Klebsiella oxytoca | ||
| Klebsiella pneumoniae |
Revision editor(s): Ameenatoloko
Experiment 8
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Response to antibiotic Response to antibiotic,response to antibiotic
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Abx_mother_labour_IAP on day 4 (n=310) for vaginal delivery[where Abx is antibiotics, and IAP is Intrapartum antibiotic prophylaxis]
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- No Abx_mother_labour_IAP on day 4 (n=310) for vaginal delivery[where Abx is antibiotics, and IAP is Intrapartum antibiotic prophylaxis]
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mothers who did not receive antibiotics during labour.
- 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
- Not specified
Lab analysis
Statistical Analysis
- Statistical test
- Linear Regression
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- maternal age, Confounders controlled for: "mode of delivery" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.mode of delivery, Confounders controlled for: "maternal intrapartum antibiotics" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.maternal intrapartum antibiotics, Confounders controlled for: "postnatal stay in hospital" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.postnatal stay in hospital, Confounders controlled for: "partial breastfeeding" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.partial breastfeeding, Confounders controlled for: "exclusive breastfeeding" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.exclusive breastfeeding, Confounders controlled for: "hospital site" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.hospital site, Confounders controlled for: "immediate breastfeeding after birth" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.immediate breastfeeding after birth, Confounders controlled for: "postnatal antibiotics" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.postnatal antibiotics, Confounders controlled for: "gender" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.gender
Signature 1
Source: Table S5
Description: Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.
Abundance in Group 1: increased abundance in No Abx_mother_labour_IAP on day 4 (n=310) for vaginal delivery[where Abx is antibiotics, and IAP is Intrapartum antibiotic prophylaxis]
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium breve |
Revision editor(s): Ameenatoloko
Signature 2
Source: Table S5
Description: Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.
Abundance in Group 1: decreased abundance in No Abx_mother_labour_IAP on day 4 (n=310) for vaginal delivery[where Abx is antibiotics, and IAP is Intrapartum antibiotic prophylaxis]
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium bifidum |
Revision editor(s): Ameenatoloko
Experiment 9
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- No Abx_mother_prior_birth on day 4 (n=310) [where Abx is antibiotics]
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Abx_mother_prior_birth on day 4 (n=310) [where Abx is antibiotics]
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Antibiotics were administered to mothers before their baby/babies were born.
- Group 0 sample size Number of subjects in the control (unexposed) group
- Not specified
Lab analysis
Statistical Analysis
Signature 1
Source: Table S5
Description: Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.
Abundance in Group 1: increased abundance in Abx_mother_prior_birth on day 4 (n=310) [where Abx is antibiotics]
| NCBI | Quality Control | Links |
|---|---|---|
| Escherichia coli |
Revision editor(s): Ameenatoloko
Experiment 10
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Breastfeeding duration Breastfeeding duration,breastfeeding duration
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- No Breastfeeding_status on day 4 (n=310)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Breastfeeding_status on day 4 (n=310)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Babies that were breastfed during the neonatal period (≤1 month).
Lab analysis
Statistical Analysis
Signature 1
Source: Table S5
Description: Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.
Abundance in Group 1: increased abundance in Breastfeeding_status on day 4 (n=310)
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus lugdunensis | ||
| Haemophilus parainfluenzae | ||
| Staphylococcus epidermidis |
Revision editor(s): Ameenatoloko
Signature 2
Source: Table S5
Description: Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.
Abundance in Group 1: decreased abundance in Breastfeeding_status on day 4 (n=310)
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium bifidum | ||
| Clostridium perfringens | ||
| Streptococcus thermophilus |
Revision editor(s): Ameenatoloko
Experiment 11
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Delivery measurement Delivery measurement,delivery measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Deliveries by caesarean section on day 4 (n=310)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Vaginal deliveries on day 4 (n=310)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Babies that were born vaginally.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 282
Lab analysis
Statistical Analysis
Signature 1
Source: Table S5
Description: Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.
Abundance in Group 1: increased abundance in Vaginal deliveries on day 4 (n=310)
Revision editor(s): Ameenatoloko
Signature 2
Source: Table S5
Description: Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.
Abundance in Group 1: decreased abundance in Vaginal deliveries on day 4 (n=310)
Revision editor(s): Ameenatoloko
Experiment 12
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Place of residence measurement Place of residence measurement,place of residence measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- The Barking, Havering and Redbridge University Hospitals NHS Trust and the University College London Hospitals NHS Foundation Trust (BHR + UCLH) on day 4 (n=310)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- The University Hospitals Leicester NHS Trust (LEI) on day 4 (n=310)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Babies born in the University Hospitals Leicester NHS Trust (LEI) from May 2014 to December 2017.
- Group 0 sample size Number of subjects in the control (unexposed) group
- Not specified
Lab analysis
Statistical Analysis
Signature 1
Source: Table S5
Description: Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.
Abundance in Group 1: decreased abundance in The University Hospitals Leicester NHS Trust (LEI) on day 4 (n=310)
| NCBI | Quality Control | Links |
|---|---|---|
| Enterococcus faecalis | ||
| Gemella haemolysans |
Revision editor(s): Ameenatoloko
Experiment 13
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Response to antibiotic Response to antibiotic,response to antibiotic
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- No Abx_mother_labour_IAP on day 7 (n=532) for vaginal delivery[where Abx is antibiotics, and IAP is Intrapartum antibiotic prophylaxis]
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Abx_mother_labour_IAP on day 7 (n=532) for vaginal delivery[where Abx is antibiotics, and IAP is Intrapartum antibiotic prophylaxis]
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Antibiotics were administered to mothers during labour.
- Group 1 sample size Number of subjects in the case (exposed) group
- 23
Lab analysis
Statistical Analysis
Signature 1
Source: Table S5
Description: Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.
Abundance in Group 1: decreased abundance in Abx_mother_labour_IAP on day 7 (n=532) for vaginal delivery[where Abx is antibiotics, and IAP is Intrapartum antibiotic prophylaxis]
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium longum |
Revision editor(s): Ameenatoloko
Experiment 14
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Breastfeeding duration Breastfeeding duration,breastfeeding duration
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- No Breastfeeding_status on day 7 (n=532)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Breastfeeding_status on day 7 (n=532)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Babies that were breastfed during the neonatal period (≤1 month).
- Group 1 sample size Number of subjects in the case (exposed) group
- Not specified
Lab analysis
Statistical Analysis
Signature 1
Source: Table S5
Description: Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.
Abundance in Group 1: increased abundance in Breastfeeding_status on day 7 (n=532)
| NCBI | Quality Control | Links |
|---|---|---|
| Gemella haemolysans | ||
| Haemophilus parainfluenzae | ||
| Streptococcus oralis | ||
| Staphylococcus epidermidis |
Revision editor(s): Ameenatoloko
Signature 2
Source: Table S5
Description: Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.
Abundance in Group 1: decreased abundance in Breastfeeding_status on day 7 (n=532)
| NCBI | Quality Control | Links |
|---|---|---|
| Klebsiella oxytoca | ||
| Streptococcus parasanguinis | ||
| Streptococcus vestibularis | ||
| Streptococcus thermophilus |
Revision editor(s): Ameenatoloko
Experiment 15
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Delivery measurement Delivery measurement,delivery measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Deliveries by caesarean section on day 7 (n=532)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Vaginal deliveries on day 7 (n=532)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Babies that were born vaginally.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 282
Lab analysis
Statistical Analysis
Signature 1
Source: Table S5
Description: Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.
Abundance in Group 1: increased abundance in Vaginal deliveries on day 7 (n=532)
Revision editor(s): Ameenatoloko
Signature 2
Source: Table S5
Description: Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.
Abundance in Group 1: decreased abundance in Vaginal deliveries on day 7 (n=532)
Revision editor(s): Ameenatoloko
Experiment 16
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Place of residence measurement Place of residence measurement,place of residence measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- The Barking, Havering and Redbridge University Hospitals NHS Trust and the University College London Hospitals NHS Foundation Trust (BHR + UCLH) on day 7 (n=532)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- The University Hospitals Leicester NHS Trust (LEI) on day 7 (n=532)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Babies born in the University Hospitals Leicester NHS Trust (LEI) from May 2014 to December 2017.
- Group 0 sample size Number of subjects in the control (unexposed) group
- Not specified
Lab analysis
Statistical Analysis
Signature 1
Source: Table S5
Description: Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.
Abundance in Group 1: decreased abundance in The University Hospitals Leicester NHS Trust (LEI) on day 7 (n=532)
| NCBI | Quality Control | Links |
|---|---|---|
| Gemella haemolysans |
Revision editor(s): Ameenatoloko
Experiment 17
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Response to antibiotic Response to antibiotic,response to antibiotic
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- No Abx_Baby_after_discharge on day 21 (n=325) [where Abx is antibiotics]
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Abx_Baby_after_discharge on day 21 (n=325) [where Abx is antibiotics]
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Antibiotics were given to babies in the neonatal period after discharge.
Lab analysis
Statistical Analysis
Signature 1
Source: Table S5
Description: Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.
Abundance in Group 1: decreased abundance in Abx_Baby_after_discharge on day 21 (n=325) [where Abx is antibiotics]
| NCBI | Quality Control | Links |
|---|---|---|
| Rothia mucilaginosa |
Revision editor(s): Ameenatoloko
Experiment 18
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Abx_mother_labour_IAP on day 21 (n=325) for vaginal delivery[where Abx is antibiotics, and IAP is Intrapartum antibiotic prophylaxis]
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- No Abx_mother_labour_IAP on day 21 (n=325) for vaginal delivery[where Abx is antibiotics, and IAP is Intrapartum antibiotic prophylaxis]
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mothers who did not receive antibiotics during labour.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 23
Lab analysis
Statistical Analysis
Signature 1
Source: Table S5
Description: Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.
Abundance in Group 1: decreased abundance in No Abx_mother_labour_IAP on day 21 (n=325) for vaginal delivery[where Abx is antibiotics, and IAP is Intrapartum antibiotic prophylaxis]
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium bifidum |
Revision editor(s): Ameenatoloko
Experiment 19
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- No Abx_mother_labour_IAP on day 21 (n=325) for vaginal delivery[where Abx is antibiotics, and IAP is Intrapartum antibiotic prophylaxis]
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Abx_mother_labour_IAP on day 21 (n=325) for vaginal delivery[where Abx is antibiotics, and IAP is Intrapartum antibiotic prophylaxis]
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Antibiotics were administered to mothers during labour.
- 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
- 23
Lab analysis
Statistical Analysis
Signature 1
Source: Table S5
Description: Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.
Abundance in Group 1: decreased abundance in Abx_mother_labour_IAP on day 21 (n=325) for vaginal delivery[where Abx is antibiotics, and IAP is Intrapartum antibiotic prophylaxis]
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium bifidum |
Revision editor(s): Ameenatoloko
Experiment 20
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- No Abx_mother_prior_birth on day 21 (n=325) [where Abx is antibiotics]
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Abx_mother_prior_birth on day 21 (n=325) [where Abx is antibiotics]
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Antibiotics were administered to mothers before their baby/babies were born.
- Group 1 sample size Number of subjects in the case (exposed) group
- Not specified
Lab analysis
Statistical Analysis
Signature 1
Source: Table S5
Description: Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.
Abundance in Group 1: increased abundance in Abx_mother_prior_birth on day 21 (n=325) [where Abx is antibiotics]
| NCBI | Quality Control | Links |
|---|---|---|
| Escherichia coli |
Revision editor(s): Ameenatoloko
Experiment 21
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Breastfeeding duration Breastfeeding duration,breastfeeding duration
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- No Breastfeeding_status on day 21 (n=325)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Breastfeeding_status on day 21 (n=325)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Babies that were breastfed during the neonatal period (≤1 month).
Lab analysis
Statistical Analysis
Signature 1
Source: Table S5
Description: Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.
Abundance in Group 1: increased abundance in Breastfeeding_status on day 21 (n=325)
| NCBI | Quality Control | Links |
|---|---|---|
| Haemophilus parainfluenzae | ||
| Staphylococcus epidermidis | ||
| Streptococcus oralis | ||
| Cutibacterium avidum |
Revision editor(s): Ameenatoloko
Signature 2
Source: Table S5
Description: Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.
Abundance in Group 1: decreased abundance in Breastfeeding_status on day 21 (n=325)
| NCBI | Quality Control | Links |
|---|---|---|
| Enterococcus faecalis | ||
| Intestinibacter bartlettii | ||
| Klebsiella oxytoca | ||
| Streptococcus vestibularis | ||
| Veillonella parvula | ||
| Streptococcus thermophilus | ||
| Finegoldia magna |
Revision editor(s): Ameenatoloko
Experiment 22
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Delivery measurement Delivery measurement,delivery measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Deliveries by caesarean section on day 21 (n=325)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Vaginal deliveries on day 21 (n=325)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Babies that were born vaginally.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 282
Lab analysis
Statistical Analysis
Signature 1
Source: Table S5
Description: Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.
Abundance in Group 1: increased abundance in Vaginal deliveries on day 21 (n=325)
Revision editor(s): Ameenatoloko
Signature 2
Source: Table S5
Description: Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.
Abundance in Group 1: decreased abundance in Vaginal deliveries on day 21 (n=325)
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium dentium | ||
| Enterococcus faecalis | ||
| Clostridium perfringens | ||
| Enterococcus faecium | ||
| Streptococcus parasanguinis | ||
| Klebsiella oxytoca |
Revision editor(s): Ameenatoloko
Experiment 23
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Sex design sex_design,Sex design,sex design
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Female gender on day 21 (n=325)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Male gender on day 21 (n=325)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Male newborn baby/babies.
- Group 0 sample size Number of subjects in the control (unexposed) group
- Not specified
Lab analysis
Statistical Analysis
Signature 1
Source: Table S5
Description: Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.
Abundance in Group 1: increased abundance in Male gender on day 21 (n=325)
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus hominis |
Revision editor(s): Ameenatoloko
Experiment 24
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Place of residence measurement Place of residence measurement,place of residence measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- The Barking, Havering and Redbridge University Hospitals NHS Trust and the University College London Hospitals NHS Foundation Trust (BHR + UCLH) on day 21 (n=325)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- The University Hospitals Leicester NHS Trust (LEI) on day 21 (n=325)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Babies born in the University Hospitals Leicester NHS Trust (LEI) from May 2014 to December 2017.
Lab analysis
Statistical Analysis
Signature 1
Source: Table S5
Description: Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.
Abundance in Group 1: decreased abundance in The University Hospitals Leicester NHS Trust (LEI) on day 21 (n=325)
| NCBI | Quality Control | Links |
|---|---|---|
| Klebsiella pneumoniae | ||
| Veillonella parvula |
Revision editor(s): Ameenatoloko
Experiment 25
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Breastfeeding duration Breastfeeding duration,breastfeeding duration
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- No Breastfeeding_status at infancy (n=302)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Breastfeeding_status at infancy (n=302)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Babies who were breastfed during infancy (at 4 to 12 months of age).
Lab analysis
Statistical Analysis
Signature 1
Source: Table S5
Description: Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.
Abundance in Group 1: increased abundance in Breastfeeding_status at infancy (n=302)
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus peroris | ||
| Megasphaera nov.Megasphaera nov. |
Revision editor(s): Ameenatoloko
Signature 2
Source: Table S5
Description: Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.
Abundance in Group 1: decreased abundance in Breastfeeding_status at infancy (n=302)
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerostipes caccae | ||
| Bacteroides caccae | ||
| Bacteroides ovatus | ||
| Bilophila wadsworthia | ||
| Hungatella hathewayi | ||
| Parabacteroides merdae | ||
| [Clostridium] symbiosum |
Revision editor(s): Ameenatoloko
Experiment 26
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Delivery measurement Delivery measurement,delivery measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Deliveries by caesarean section at infancy (n=302)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Vaginal deliveries at infancy (n=302)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Babies that were born vaginally and later sampled at infancy between 4 to 12 months of their lives.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 282
Lab analysis
Statistical Analysis
Signature 1
Source: Table S5
Description: Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.
Abundance in Group 1: increased abundance in Vaginal deliveries at infancy (n=302)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides thetaiotaomicron | ||
| Phocaeicola dorei | ||
| Phocaeicola vulgatus | ||
| Parabacteroides merdae | ||
| Parabacteroides distasonis | ||
| Bacteroides uniformis | ||
| Bacteroides caccae |
Revision editor(s): Ameenatoloko
Experiment 27
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Response to antibiotic Response to antibiotic,response to antibiotic
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- No Abx_mother_prior_birth for the mother (n=175) [where Abx is antibiotics]
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Abx_mother_prior_birth for the mother (n=175) [where Abx is antibiotics]
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Antibiotics were administered to mothers before their baby/babies were born.
- Group 0 sample size Number of subjects in the control (unexposed) group
- Not specified
Lab analysis
Statistical Analysis
Signature 1
Source: Table S5
Description: Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.
Abundance in Group 1: increased abundance in Abx_mother_prior_birth for the mother (n=175) [where Abx is antibiotics]
| NCBI | Quality Control | Links |
|---|---|---|
| Veillonella parvula |
Revision editor(s): Ameenatoloko
Experiment 28
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Place of residence measurement Place of residence measurement,place of residence measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- The Barking, Havering and Redbridge University Hospitals NHS Trust and the University College London Hospitals NHS Foundation Trust (BHR + UCLH) for the mother (n=175)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- The University Hospitals Leicester NHS Trust (LEI) for the mother (n=175)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mothers who gave birth in the University Hospitals Leicester NHS Trust (LEI) from May 2014 to December 2017.
Lab analysis
Statistical Analysis
Signature 1
Source: Table S5
Description: Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.
Abundance in Group 1: decreased abundance in The University Hospitals Leicester NHS Trust (LEI) for the mother (n=175)
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium animalis |
Revision editor(s): Ameenatoloko
Experiment 29
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Response to antibiotic Response to antibiotic,response to antibiotic
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- No Abx_mother_after_hospital on day 21 (n=325) [where Abx is antibiotics]
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Abx_mother_after_hospital on day 21 (n=325) [where Abx is antibiotics]
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Antibiotics were given to mothers after they left the hospital where they gave birth.
Lab analysis
Statistical Analysis
Signature 1
Source: Table S5
Description: Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.
Abundance in Group 1: increased abundance in Abx_mother_after_hospital on day 21 (n=325) [where Abx is antibiotics]
| NCBI | Quality Control | Links |
|---|---|---|
| Klebsiella pneumoniae |
Revision editor(s): Ameenatoloko
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
- 26 Experiment 26
- 27 Experiment 27
- 28 Experiment 28
- 29 Experiment 29
