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Diet standardization reduces intra-individual microbiome variation.

ABSTRACT: The human gut microbiota is highly heterogenous between individuals and also exhibits considerable day-to-day variation within individuals. We hypothesized that diet contributed to such inter- and/or intra-individual variance. Hence, we investigated the extent to which diet normalization impacted microbiota heterogeneity. We leveraged the control arm of our recently reported controlled-feeding study in which nine healthy individuals consumed a standardized additive-free diet for 10 days. Diet normalization did not impact inter-individual differences but reduced the extent of intra-individual day-to-day variation in fecal microbiota composition. Such decreased heterogeneity reflected individual-specific enrichment and depletion of an array of taxa microbiota members and was paralleled by a trend toward reduced intra-individual variance in fecal LPS and flagellin, which, collectively, reflect microbiota's pro-inflammatory potential. Yet, the microbiota of some subjects did not change significantly over the course of the study, suggesting heterogeneity in microbiota resilience to dietary stress or that baseline diets of some subjects were perhaps similar to our study's standardized diet. Collectively, our results indicate that short-term diet heterogeneity contributes to day-to-day intra-individual microbiota composition variance.

SUBMITTER: Delaroque C

PROVIDER: S-EPMC9704386 | biostudies-literature | 2022 Jan-Dec

REPOSITORIES: biostudies-literature

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Diet standardization reduces intra-individual microbiome variation.

Delaroque Clara C Wu Gary D GD Compher Charlene C Ni Josephine J Albenberg Lindsey L Liu Qing Q Tian Yuan Y Patterson Andrew D AD Lewis James D JD Gewirtz Andrew T AT Chassaing Benoit B

Gut microbes 20220101 1

The human gut microbiota is highly heterogenous between individuals and also exhibits considerable day-to-day variation within individuals. We hypothesized that diet contributed to such inter- and/or intra-individual variance. Hence, we investigated the extent to which diet normalization impacted microbiota heterogeneity. We leveraged the control arm of our recently reported controlled-feeding study in which nine healthy individuals consumed a standardized additive-free diet for 10 days. Diet no ...[more]

PMID: 36426908

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Project description:Background: Gene expression variation is a phenotypic trait of particular interest as it represents the initial link between genotype and other phenotypes. Analyzing how such variation apportions among and within groups allows for the evaluation of how genetic and environmental factors influence such traits. It also provides opportunities to identify genes and pathways that may have been influenced by non-neutral processes. Here we use a population genetics framework and next generation sequencing to evaluate how gene expression variation is apportioned among four human groups in a natural biological tissue, the placenta. Results: We estimate that on average, 33.2%, 58.9% and 7.8% of the placental transcriptome is explained by variation within individuals, among individuals and among human groups, respectively. Additionally, when technical and biological traits are included in models of gene expression they account for roughly 2% of total gene expression variation. Notably, the variation that is significantly different among groups is enriched in biological pathways associated with immune response, cell signaling and metabolism. Many biological traits demonstrated correlated changes in expression in numerous pathways of potential interest to clinicians and evolutionary biologists. Finally, we estimate that the majority of the human placental transcriptome (65% of expressed genes) exhibits expression profiles consistent with neutrality; the remainder are consistent with stabilizing selection (26%), directional selection (4.9%), or diversifying selection (4.8%). Conclusion: We apportion placental gene expression variation into individual, population and biological trait factors and identify how each influence the transcriptome. Additionally, we advance methods to associate expression profiles with different forms of selection. Placental mRNA was sequenced on an Illumina GAIIx. Samples were derived from 4 human groups, 10 individuals per group, 2 samples per individual

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Diet standardization reduces intra-individual microbiome variation.

Publications

Diet standardization reduces intra-individual microbiome variation.

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