Joint effects of pregnancy, sociocultural, and environmental factors on early life gut microbiome structure and diversity

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Curated date: 2022/06/13

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101, Lwaldron, WikiWorks

Subjects

Location of subjects: United States of America

Host species Species from which microbiome was sampled (if applicable): 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

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: ethnic group Ethnicity,race,ethnic group

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Caucasian + other races neonates by maternal profiles
Group 1 name Corresponds to the case (exposed) group for case-control studies: African American neonate by maternal profile
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Gut bacterial composition among neonates by maternal profiles. Microbiome Associated Maternal Profile (MMP3) as the most racially diverse was used for contrast.
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: 92
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): unspecified.

Lab analysis

Sequencing type: 16S

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

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

Statistical Analysis

Statistical test: PERMANOVA

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): .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, household income, breast feeding, delivery procedure, education level, marital status, smoking status

Alpha Diversity

Pielou Quantifies how equal the community is numerically: increased
Richness Number of species: increased

Signature 1

Needs review

Curated date: 2022/06/13

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101

Source: FIGURE 5

Description: Top genera are significantly associated with each factor retained in multi-factor neonatal gut microbiome composition models. For plotting purposes, “top” genera for each factor were defined using two characteristics: (1) the number of taxa significantly associated with it (to avoid spurious findings) and (2) how “discriminatory” the genera was, defined by consistency in the direction of taxa-specific associations. Each factor displays up to the top ten genera that best discriminated each factor, given the genera had at least 5 significant taxa. Abbreviations: ETS, environmental tobacco smoke; NSV, neonatal study visit at 1-month of age.

Abundance in Group 1: increased abundance in African American neonate by maternal profile

NCBI	Links
Akkermansia
Bifidobacterium
Lactobacillus
Megasphaera

Revision editor(s): Kaluifeanyi101

Signature 2

Needs review

Curated date: 2022/06/13

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101

Source: FIGURE 5

Description: Top genera are significantly associated with each factor retained in multi-factor neonatal gut microbiome composition models. For plotting purposes, “top” genera for each factor were defined using two characteristics: (1) the number of taxa significantly associated with it (to avoid spurious findings) and (2) how “discriminatory” the genera was, defined by consistency in the direction of taxa-specific associations. Each factor displays up to the top ten genera that best discriminated each factor, given the genera had at least 5 significant taxa. Abbreviations: ETS, environmental tobacco smoke; NSV, neonatal study visit at 1-month of age.

Abundance in Group 1: decreased abundance in African American neonate by maternal profile

NCBI	Links
Coprococcus
Oscillospira
Parabacteroides
Prevotella
Staphylococcus
Streptococcus

Revision editor(s): Kaluifeanyi101

Experiment 2

Your review change was submittedDuplicate this Experiment Add a new Signature

Needs review

Curated date: 2022/06/13

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101

Subjects

Location of subjects: United States of America

Host species Species from which microbiome was sampled (if applicable): 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

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: socioeconomic statussocioeconomic status

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Infants in household income =>$80,000.
Group 1 name Corresponds to the case (exposed) group for case-control studies: Infants in household income <$80,000.
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Gut bacterial composition among infants by maternal profiles. Microbiome Associated Maternal Profile (MMP3)

19.8% of the analytical sample(N =168)

Group 0 sample size Number of subjects in the control (unexposed) group: 52
Group 1 sample size Number of subjects in the case (exposed) group: 33
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): unspecified.

Lab analysis

Sequencing type: 16S

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

Statistical Analysis

Statistical test: PERMANOVA

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): .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, breast feeding, delivery procedure, education level, marital status, race, smoking status

Alpha Diversity

Pielou Quantifies how equal the community is numerically: decreased
Richness Number of species: decreased

Signature 1

Needs review

Curated date: 2022/06/13

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101

Source: FIGURE 6

Description: Top genera are significantly associated with each factor retained in multi-factor infant gut microbiome composition models. For plotting purposes, “top” genera for each factor were defined using two characteristics: (1) the number of taxa significantly associated with it (to avoid spurious findings) and (2) how “discriminatory” the genera was, defined by consistency in the direction of taxa-specific associations. Each factor displays up to the top ten genera that best discriminated each factor, given the genera had at least 5 significant taxa.

Abundance in Group 1: increased abundance in Infants in household income <$80,000.

NCBI	Links
Bacteroides
Ruminococcus
Streptococcus

Revision editor(s): Kaluifeanyi101

Signature 2