Meta-analysis of effects of exclusive breastfeeding on infant gut microbiota across populations

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Reviewed Marked as Reviewed by Peace Sandy on 2024-11-19

Curated date: 2024/10/02

Curator: Shulamite

Revision editor(s): Shulamite, Peace Sandy

Subjects

Location of subjects: Bangladesh

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: Breastfeeding duration Breastfeeding duration,breastfeeding duration

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Exclusive Breast Feeding (EBF)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Non_Exclusive Breast Feeding (Non-EBF)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Infants who was feed breast milk with either formula or solid.

Group 0 sample size Number of subjects in the control (unexposed) group: 138

Group 1 sample size Number of subjects in the case (exposed) group: 178

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).: relative abundances

Statistical test: Random Forest Analysis

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

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: age, sex

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: increased

Chao1 Abundance-based estimator of 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

Reviewed Marked as Reviewed by Peace Sandy on 2024-11-19

Curated date: 2024/10/02

Curator: Shulamite

Revision editor(s): Shulamite, Peace Sandy

Source: Table 11, Table 2, Table 3

Description: Gut bacterial taxa with differential relative abundances from 6 months to 2 years of age between infants with duration of exclusive breastfeeding >2 months vs. ≤2 months from birth.

Abundance in Group 1: increased abundance in Non_Exclusive Breast Feeding (Non-EBF)

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Bifidobacterium
Enterococcus

Revision editor(s): Shulamite, Peace Sandy

Signature 2

Reviewed Marked as Reviewed by Peace Sandy on 2024-11-19

Curated date: 2024/10/08

Curator: Shulamite

Revision editor(s): Shulamite, Rahila, Peace Sandy

Source: Table 11, Table 2, Table 3

Description: Gut bacterial taxa with differential relative abundances from 6 months to 2 years of age between infants with duration of exclusive breastfeeding >2 months vs. ≤2 months from birth.

Abundance in Group 1: decreased abundance in Non_Exclusive Breast Feeding (Non-EBF)

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Blautia
Catenibacterium
Collinsella
Lactobacillus
Prevotella
Ruminococcus
unclassified Clostridiaceae
unclassified Coriobacteriaceae
unclassified Lachnospiraceae

Revision editor(s): Shulamite, Rahila, Peace Sandy

Experiment 2

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Reviewed Marked as Reviewed by Peace Sandy on 2024-11-19

Curated date: 2024/10/02

Curator: Shulamite

Revision editor(s): Shulamite, Peace Sandy

Differences from previous experiment shown

Subjects

Location of subjects: Canada

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Increasing Exclusive Breast Feeding (EBF)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Reduced exclusivity of beast feeding to none breastfeeding

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Introducing other foods or liquids while still breastfeeding

Group 0 sample size Number of subjects in the control (unexposed) group: 86

Group 1 sample size Number of subjects in the case (exposed) group: 48

Lab analysis

Statistical Analysis

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.005

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: age

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: increased

Chao1 Abundance-based estimator of species richness: increased

Signature 1

Reviewed Marked as Reviewed by Peace Sandy on 2024-11-19

Curated date: 2024/10/03

Curator: Shulamite

Revision editor(s): Shulamite, Rahila, Peace Sandy

Source: Table 3, Table 2

Description: Meta-analysis of five studies that included a non-breastfeeding group for gut bacterial taxa with trend in relative abundance across exclusive breastfeeding, nonexclusive breastfeeding and non breastfeeding groups.

Abundance in Group 1: increased abundance in Reduced exclusivity of beast feeding to none breastfeeding

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Akkermansia
Bacillota
Bacteroidia
Blautia
Coprococcus
Eubacterium
Verrucomicrobiota
Bacteroides
Clostridium
Megasphaera
Veillonella
Eubacterium sp.

Revision editor(s): Shulamite, Rahila, Peace Sandy

Signature 2

Reviewed Marked as Reviewed by Peace Sandy on 2024-11-19

Curated date: 2024/10/03

Curator: Shulamite

Revision editor(s): Shulamite, Peace Sandy

Source: Table 3, Table 2

Description: Meta-analysis of five studies that included a non-breastfeeding group for gut bacterial taxa with trend in relative abundance across exclusive breastfeeding, nonexclusive breastfeeding and non breastfeeding groups.

Abundance in Group 1: decreased abundance in Reduced exclusivity of beast feeding to none breastfeeding

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Haemophilus
Staphylococcus

Revision editor(s): Shulamite, Peace Sandy

Experiment 3

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Reviewed Marked as Reviewed by Peace Sandy on 2024-11-19

Curated date: 2024/10/03

Curator: Shulamite

Revision editor(s): Shulamite, Peace Sandy

Differences from previous experiment shown

Subjects

Location of subjects: Haiti

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Exclusively Breastfeeding (EBF), Vaginally Born and C-section Born

Group 1 name Corresponds to the case (exposed) group for case-control studies: Non-Exclusive Breastfeeding (Non-EBF), Vaginally Born and C-section Born

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Infants fed with breast milk plus solid or formula

Group 0 sample size Number of subjects in the control (unexposed) group: 37

Group 1 sample size Number of subjects in the case (exposed) group: 11

Lab analysis

Statistical Analysis

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.05

Signature 1

Reviewed Marked as Reviewed by Peace Sandy on 2024-11-19

Curated date: 2024/10/03

Curator: Shulamite

Revision editor(s): Shulamite, Peace Sandy

Source: Table 2, Table 3.

Description: Meta-analysis of all seven included studies for gut bacterial taxa with differential relative abundances between non-exclusively breastfed vs. exclusively breastfed infants ≤6 months of age.

Meta-analysis of five studies that included a non-breastfeeding group for gut bacterial taxa with trend in relative abundance across exclusive breastfeeding, non-exclusive breastfeeding and non-breastfeeding groups.

Abundance in Group 1: increased abundance in Non-Exclusive Breastfeeding (Non-EBF), Vaginally Born and C-section Born

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Akkermansia
Bacillota
Blautia
Coprococcus
Eubacterium
Verrucomicrobiota

Revision editor(s): Shulamite, Peace Sandy

Experiment 4

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Peace Sandy on 2024-11-19

Curated date: 2024/10/03

Curator: Shulamite

Revision editor(s): Shulamite, Peace Sandy

Differences from previous experiment shown

Subjects

Location of subjects: South Africa

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Exclusive Breastfeeding (EBF)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Non-Exclusive Breastfeeding (Non-EBF)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Infants fed with breast milk plus solid or formula

Group 0 sample size Number of subjects in the control (unexposed) group: 86

Group 1 sample size Number of subjects in the case (exposed) group: 57

Lab analysis

Statistical Analysis

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: Not specified

Alpha Diversity

Chao1 Abundance-based estimator of species richness: increased

Signature 1

Reviewed Marked as Reviewed by Peace Sandy on 2024-11-19

Curated date: 2024/10/05

Curator: Shulamite

Revision editor(s): Shulamite, Rahila, Peace Sandy

Source: Table 2, Table 3.

Description: Meta-analysis of all seven included studies for gut bacterial taxa with differential relative abundances between non-exclusively breastfed vs. exclusively breastfed infants ≤6 months of age.

Meta-analysis of five studies that included a non-breastfeeding group for gut bacterial taxa with trend in relative abundance across exclusive breastfeeding, non-exclusive breastfeeding and non-breastfeeding groups.

Abundance in Group 1: increased abundance in Non-Exclusive Breastfeeding (Non-EBF)

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Bacteroides
Clostridium
Eubacterium
Megasphaera
Veillonella
Akkermansia
Bacillota
Blautia
Coprococcus
Verrucomicrobiota

Revision editor(s): Shulamite, Rahila, Peace Sandy

Signature 2

Reviewed Marked as Reviewed by Peace Sandy on 2024-11-20

Curated date: 2024/11/19

Curator: Peace Sandy

Revision editor(s): Peace Sandy

Source: Table 2, Table 3.

Description: Meta-analysis of all seven included studies for gut bacterial taxa with differential relative abundances between non-exclusively breastfed vs. exclusively breastfed infants ≤6 months of age.

Meta-analysis of five studies that included a non-breastfeeding group for gut bacterial taxa with trend in relative abundance across exclusive breastfeeding, non-exclusive breastfeeding and non-breastfeeding groups.

Abundance in Group 1: decreased abundance in Non-Exclusive Breastfeeding (Non-EBF)

NCBI	Quality Control	Links
Haemophilus
Staphylococcus

Revision editor(s): Peace Sandy

Experiment 5

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Peace Sandy on 2024-11-19

Curated date: 2024/10/04

Curator: Shulamite

Revision editor(s): Shulamite

Differences from previous experiment shown

Subjects

Location of subjects: United States of America

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Increasing Exclusive Breast Feeding (EBF)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Reduced exclusivity of beast feeding to none breastfeeding

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Exclusive breastfeeding to infants were reduced.

Group 0 sample size Number of subjects in the control (unexposed) group: 150

Group 1 sample size Number of subjects in the case (exposed) group: 68

Lab analysis

Statistical Analysis

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.005

Signature 1

Reviewed Marked as Reviewed by Peace Sandy on 2024-11-19

Curated date: 2024/10/04

Curator: Shulamite

Revision editor(s): Shulamite

Source: Table 7

Description: Meta-analysis stratified by mode of delivery for gut bacterial taxa with differential relative abundances between non-exclusively breastfed vs. exclusively breastfed infants ≤6 months of age.

Abundance in Group 1: increased abundance in Reduced exclusivity of beast feeding to none breastfeeding

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Acidaminococcus
Eubacterium
unclassified Lachnospiraceae
Bacteroides
Erysipelotrichaceae
unclassified Clostridiaceae
Aggregatibacter
Lactococcus
Blautia

Revision editor(s): Shulamite

Signature 3

Reviewed Marked as Reviewed by Peace Sandy on 2024-11-19

Curated date: 2024/10/08

Curator: Shulamite

Revision editor(s): Shulamite, Rahila

Source: Table 7

Description: Meta-analysis stratified by mode of delivery for gut bacterial taxa with differential relative abundances between non-exclusively breastfed vs. exclusively breastfed infants ≤6 months of age.

Abundance in Group 1: decreased abundance in Reduced exclusivity of beast feeding to none breastfeeding

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Anaerotruncus
Phascolarctobacterium
Proteus
Pseudomonadota
Staphylococcus
unclassified Enterobacteriaceae

Revision editor(s): Shulamite, Rahila

Experiment 6

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Peace Sandy on 2024-11-19

Curated date: 2024/10/04

Curator: Shulamite

Revision editor(s): Shulamite

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Exclusive BreastFeeding (EBF)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Non-Exclusive Breastfeeding (Non-EBF)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Infants fed with breast milk plus solid or formula.

Group 0 sample size Number of subjects in the control (unexposed) group: 38

Group 1 sample size Number of subjects in the case (exposed) group: 66

Lab analysis

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V3-V5

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Roche454

Statistical Analysis

Statistical test: Not specified

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: No

Signature 1

Reviewed Marked as Reviewed by Peace Sandy on 2024-11-19

Curated date: 2024/10/04

Curator: Shulamite

Revision editor(s): Shulamite

Source: Table 6

Description: Meta-analysis of six studies without data from VDAART trial study for gut bacterial taxa with differential relative abundances between non-exclusively breastfed vs. exclusively breastfed infants ≤6 months of age (sensitivity analysis).

Abundance in Group 1: increased abundance in Non-Exclusive Breastfeeding (Non-EBF)

NCBI	Quality Control	Links
Acidaminococcus
Bacteroides
Clostridium
Coprococcus
Eubacterium
Megasphaera
Veillonella

Revision editor(s): Shulamite

Experiment 7

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Peace Sandy on 2024-11-19

Curated date: 2024/10/05

Curator: Shulamite

Revision editor(s): Shulamite, Peace Sandy

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Increasing Exclusive Breast Feeding (EBF)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Reduced exclusivity of beast feeding to none breastfeeding

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Not specified

Group 0 sample size Number of subjects in the control (unexposed) group: 12

Group 1 sample size Number of subjects in the case (exposed) group: 8

Lab analysis

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V1-V2

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

Statistical test: Random Forest Analysis

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: Yes

Alpha Diversity

Richness Number of species: increased

Signature 1