Meta-Analysis Reveals Reproducible Gut Microbiome Alterations in Response to a High-Fat Diet

Multiple research groups have shown that diet impacts the gut microbiome; however, variability in experimental design and quantitative assessment have made it challenging to assess the degree to which similar diets have reproducible effects across studies. Through an unbiased subject-level meta-analysis framework, we re-analyzed 27 dietary studies including 1,101 samples from rodents and humans. We demonstrate that a high-fat diet (HFD) reproducibly changes gut microbial community structure. Finer taxonomic analysis revealed that the most reproducible signals of a HFD are Lactococcus species, which we experimentally demonstrate to be common dietary contaminants. Additionally, a machine-learning approach defined a signature that predicts the dietary intake of mice and demonstrated that phylogenetic and gene-centric transformations of this model can be translated to humans. Together, these results demonstrate the utility of microbiome meta-analyses in identifying robust and reproducible features for mechanistic studies in preclinical models. [Display omitted] •A generalizable approach is presented for meta-analysis of microbiome datasets•High-fat diets induce reproducible shifts in the mouse gut microbiome•Nonviable Lactococcus contamination is widespread in experimental diets•Phylogenetic and gene signatures translate to human microbiomes Bisanz and Upadhyay et al. execute a meta-analysis of previous studies evaluating the effect of a high-fat diet on the gut microbiome. They define reproducible features across studies for mechanistic experimentation and uncover that residual DNA contamination in experimental diets should be measured and accounted for in study design.