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

From BugSigDB
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-28
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


Reviewed Marked as Reviewed by Peace Sandy on 2024-2-28

Curated date: 2022/06/13

Curator: Kaluifeanyi101

Revision editor(s): WikiWorks, Lwaldron, Kaluifeanyi101, Peace Sandy

Subjects

Location of subjects
United States of America
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
Gut microbiome measurement Gut microbiome measurement,gut microbiome measurement
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Neonates (median age = 1.2 months)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Infants (median age = 6.6 months)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Infants (median age: 6.6 months) children from a Detroit-based birth cohort
Group 0 sample size Number of subjects in the control (unexposed) group
130
Group 1 sample size Number of subjects in the case (exposed) group
168
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
NIL

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).
raw counts
Statistical test
Zero-Inflated Negative Binomial Regression
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, 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

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-28

Curated date: 2022/06/13

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101, Peace Sandy

Source: FIGURE 5 , FIGURE 6

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.

Top genera significantly associated with each factor retained in multi-factor models of infant gut microbiome composition. 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: BMI, body mass index; ISV, infant study visit at 6-months of age.

Abundance in Group 1: increased abundance in Infants (median age = 6.6 months)

NCBI Quality ControlLinks
Akkermansia
Bifidobacterium
Blautia
Clostridium
Coprococcus
Eubacterium
Lactobacillus
Lactococcus
Prevotella
Roseburia
Ruminococcus
Staphylococcus
Parabacteroides
Faecalibacterium
Dorea
Megamonas
Paraprevotella
Peptoniphilus
Enterococcus
Candidatus Epulonipiscium
Bacteroides
Dysgonomonas
Veillonella

Revision editor(s): Kaluifeanyi101, Peace Sandy

Signature 2

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-28

Curated date: 2022/06/13

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101, Peace Sandy

Source: FIGURE 5 , FIGURE 6

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.

Top genera significantly associated with each factor retained in multi-factor models of infant gut microbiome composition. 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: BMI, body mass index; ISV, infant study visit at 6-months of age.

Abundance in Group 1: decreased abundance in Infants (median age = 6.6 months)

NCBI Quality ControlLinks
Akkermansia
Bifidobacterium
Blautia
Clostridium
Coprococcus
Eubacterium
Lactobacillus
Lactococcus
Prevotella
Roseburia
Ruminococcus
Staphylococcus
Megasphaera
Varibaculum
Oscillospira
Streptococcus

Revision editor(s): Kaluifeanyi101, Peace Sandy