Family SES Is Associated with the Gut Microbiome in Infants and Children

Study information

Reviewed Marked as Reviewed by Fatima on 2022/06/22

study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

34442687

DOI Digital object identifier for electronic documents.

10.3390/microorganisms9081608

URI

https://pubmed.ncbi.nlm.nih.gov/34442687/

Authors

Lewis CR, Bonham KS, McCann SH, Volpe AR, D'Sa V, Naymik M, De Both MD, Huentelman MJ, Lemery-Chalfant K, Highlander SK, Deoni SCL, Klepac-Ceraj V

Journal

Microorganisms

Year

2021

Keywords:

childhood, infant, microbiome, socioeconomic status, stress

BACKGROUND: While early life exposures such as mode of birth, breastfeeding, and antibiotic use are established regulators of microbiome composition in early childhood, recent research suggests that the social environment may also exert influence. Two recent studies in adults demonstrated associations between socioeconomic factors and microbiome composition. This study expands on this prior work by examining the association between family socioeconomic status (SES) and host genetics with microbiome composition in infants and children. METHODS: Family SES was used to predict a latent variable representing six genera abundances generated from whole-genome shotgun sequencing. A polygenic score derived from a microbiome genome-wide association study was included to control for potential genetic associations. Associations between family SES and microbiome diversity were assessed. RESULTS: Anaerostipes, Bacteroides, Eubacterium, Faecalibacterium, and Lachnospiraceae spp. significantly loaded onto a latent factor, which was significantly predicted by SES (p < 0.05) but not the polygenic score (p > 0.05). Our results indicate that SES did not predict alpha diversity but did predict beta diversity (p < 0.001). CONCLUSIONS: Our results demonstrate that modifiable environmental factors influence gut microbiome composition at an early age. These results are important as our understanding of gut microbiome influences on health continue to expand.

Experiment 1

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Reviewed Marked as Reviewed by Chloe on 2024-2-15

Curated date: 2022/06/06

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101, Chloe

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: Socioeconomic status class,Socioeconomic status,socioeconomic status,socioeconomic factors

Group 0 name Corresponds to the control (unexposed) group for case-control studies: lower socioeconomic status

Group 1 name Corresponds to the case (exposed) group for case-control studies: Increasing socioeconomic status

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: 588 Metagenomics from infants and children of high and low socioeconomic families as continuous variables.

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 2 weeks

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: Structural Equation Modelling Statistical test: "Structural Equation Modelling" is not in the list (ANCOM, ANOSIM, ANOVA, Beta Binomial Regression, Chi-Square, Cox Proportional-Hazards Regression, Dunn's test, DESeq2, edgeR, Fisher's Exact Test, ...) of allowed values.

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): .05

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: age, delivery procedure, race, sex, Confounders controlled for: "polygenic gene score" 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.polygenic gene score

Alpha Diversity

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

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Reviewed Marked as Reviewed by Chloe on 2024-2-15

Curated date: 2022/06/06

Curator: Kaluifeanyi101

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Source: FIGURE 2; FIGURE 3

Description: Figure 2. Model Taxonomic Summaries. Stacked bar plots showing the average relative abundance of the genera assessed with socioeconomic status (SES).

Variables are continuous measures. Each of the gut microbiomes increases for a 1 unit increase in SES.

Figure 3. Parents with higher SES(higher years of education) had children who scored higher in the latent microbiome factor. That is, they were higher on Faecalibacterium, Eubacterium, Anaerostipes, and Lachnospiraceae compared with the scores of infants and children from low SES families.

Abundance in Group 1: increased abundance in Increasing socioeconomic status

NCBI	Quality Control	Links
Anaerostipes
Eubacterium
Faecalibacterium
Lachnospiraceae

Revision editor(s): Kaluifeanyi101

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Reviewed Marked as Reviewed by Chloe on 2024-2-15

Curated date: 2022/06/06

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101

Source: FIGURE 3

Description: Parents with higher SES (higher years of education) had children who scored lower in Bacteroides relative abundance compared with infants and children from families of low SES.

Variables are continuous measures. The gut microbiome decreases for a 1 unit increase in SES.

Abundance in Group 1: decreased abundance in Increasing socioeconomic status

NCBI	Quality Control	Links
Bacteroides

Revision editor(s): Kaluifeanyi101