Skin, gut, and sand metagenomic data tables on placebo-controlled sandbox biodiversity intervention study
Description
The metagenomic data are related to the published research of “A Placebo-controlled double-blinded test of the biodiversity hypothesis of immune-mediated diseases: Environmental microbial diversity elicits changes in cytokines and increase in T regulatory cells in young children” and Data in Brief article "Skin, gut, and sand metagenomic data on placebo-controlled sandbox biodiversity intervention study". This database contains 16S ribosomal RNA (rRNA) metagenomics of sandbox sand and skin and gut microbiota of children in the intervention and placebo daycares. In intervention daycares, children aged 3–5 years were exposed to playground sand enriched with microbially diverse soil. In placebo daycares, children were exposed to visually similar as in intervention daycares, but microbially poor sand colored with peat. Sand, skin and gut metagenomics were analyzed at baseline and after 14 and 28 days of intervention by high throughput sequencing of bacterial 16S rRNA gene on the Illumina MiSeq platform. We herein report the richness, diversity, relative abundance (Table 1) and community composition (Table 2) of sand bacteria between enriched intervention and placebo sandbox sand, and bacterial relative abundance shifts on the skin (Table 3) and in the gut between intervention and placebo groups (Table 4 and 5).
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Sand bacterial metagenomes were obtained from sandboxes in the yards of intervention and placebo daycares. In intervention daycares, the sandboxes were filled with regular sand that was enriched composted materials. In the placebo daycares, the sandbox was filled with regular sandbox sand accompanied with placebo material, blond peat. The skin and gut bacterial metagenome was obtained from twenty-six children, aged between 3 and 5 at baseline, after 14 days of organized activities (supervised period) in the sandbox and after 28 days (follow-up period). The amplicon sequencing of V4 region of 16S rRNA was performed on an Illumina Miseq instrument using a v3 reagent kit. Raw paired-end sequence files were processed using Mothur version v1.35.1. Samples were subsampled to the smallest sample sequence depth for community composition analyses. Skin samples were subsampled to 1968, stool samples to 1460 and soil samples to 4274 sequences. All the statistical tests were done with R v3.6.1 and with vegan and lme4 packages. The differences in the bacterial variables between daycare treatments were also determined using t-test or, in cases of non-normally distributed data, with Wilcoxon signed-rank test. Betadiversity of bacteria was analyzed between children in intervention and placebo daycare centers with Permutational Multivariate Analysis of Covariance (PERMANOVA, function adonis in vegan package) using Bray-Curtis distances. Linear mixed-effect models (LMM) (function lmer in lme4 package) were constructed to analyze temporal shifts in bacterial variables, taking into account clustering of participants into the daycare centers. To test differences in bacterial measurements between daycare treatments: bacterial richness, diversity or relative abundance was used as the dependent variable; daycare treatment and time-point as a repeated measures factor (fixed factor); and individual participants nested within the cluster (daycare center) as a grouping variable (random factor) in LMM models. Detailed methods are in related research article.