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

From BugSigDB
Needs review
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
Authors
Levin AM, Sitarik AR, Havstad SL, Fujimura KE, Wegienka G, Cassidy-Bushrow AE, Kim H, Zoratti EM, Lukacs NW, Boushey HA, Ownby DR, Lynch SV, Johnson CC
Journal
Scientific reports
Year
2016
The joint impact of pregnancy, environmental, and sociocultural exposures on early life gut microbiome is not yet well-characterized, especially in racially and socioeconomically diverse populations. Gut microbiota of 298 children from a Detroit-based birth cohort were profiled using 16S rRNA sequencing: 130 neonates (median age = 1.2 months) and 168 infants (median age = 6.6 months). Multiple factors were associated with neonatal gut microbiome composition in both single- and multi-factor models, with independent contributions of maternal race-ethnicity, breastfeeding, mode of delivery, marital status, exposure to environmental tobacco smoke, and indoor pets. These findings were consistent in the infants, and networks demonstrating the shared impact of factors on gut microbial composition also showed notable topological similarity between neonates and infants. Further, latent groups defined by these factors explained additional variation, highlighting the importance of combinatorial effects. Our findings also have implications for studies investigating the impact of the early life gut microbiota on disease.

Experiment 1


Needs review

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 Quality ControlLinks
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 Quality ControlLinks
Coprococcus
Oscillospira
Parabacteroides
Prevotella
Staphylococcus
Streptococcus

Revision editor(s): Kaluifeanyi101

Experiment 2


Needs review

Curated date: 2022/06/13

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101

Differences from previous experiment shown

Subjects

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

Lab analysis

Statistical Analysis

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 Quality ControlLinks
Bacteroides
Ruminococcus
Streptococcus

Revision editor(s): Kaluifeanyi101

Signature 2

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: decreased abundance in Infants in household income <$80,000.

NCBI Quality ControlLinks
Akkermansia
Bifidobacterium
Coprococcus
Faecalibacterium
Prevotella
Staphylococcus
Veillonella

Revision editor(s): Kaluifeanyi101