Traditional nutrition studies examining the human gut microbiome have relied heavily on metagenomic data, which provides both taxonomic and inferred functional information about the microbial community in a sample. However, this approach has sometimes led to conflicting results between studies due to various factors, including individual variability, which makes it difficult to predict responders.
In this study, we employed a longitudinal, multi-omic approach—including shotgun metagenomics, metatranscriptomics, and metabolomics—to investigate the impact of intermittent fasting (IF) on the gut microbiome of healthy individuals and to assess whether this multi-omic approach offers additional utility for gut microbiome research.
In general, metatranscriptomics (MTS) sequencing profiles were significantly more variable and dynamic than metagenomic (MGS) sequencing profiles, with some individuals showing a strong correlation between diet and MTS functional profiles. Additional metabolic results and analyses indicated pathway enrichment related to fasting, adding another layer of functional information.
In conclusion, our results suggest that metatranscriptomics can reveal discrete changes in microbial community functional profiles that are not detected by DNA-based methods. This approach may be better suited for understanding biological responses to dietary modifications, such as intermittent fasting, and could help identify individuals who respond to these interventions.