Defining reference values for the gut microbiota in a Southern European population

The clinical implementation of gut microbiota analysis requires the definition of reliable reference values derived from standardized and certified methodologies applied to a population representative of the intended clinical setting.

In this study, 250 fecal samples were analyzed using a CE-certified 16S rRNA bacterial profiling assay for taxonomic characterization across multiple bacterial levels. Sequencing reads were quality-filtered and aligned against the RDP database (release 11, update 5); only sequences with ≥80% alignment coverage and ≥97% similarity were retained.

The resulting taxonomic distributions were first compared with data previously obtained from a similar population, revealing only minor differences. As an additional validation, comparative analyses were performed with data from a clinical study on fecal microbiota transplantation (FMT). Donor profiles were highly consistent with those obtained in the present study, whereas pre-transplant samples showed marked deviations from the reference ranges; post-transplant profiles progressively converged toward them.

Although the limited sample size precludes accurate assessment of rare taxa (<0.1% relative abundance), the use of a single Next-Generation Sequencing (NGS) platform and the focus on a Southern European population characterized by the Mediterranean diet allowed the establishment of the first set of gut microbiota reference values derived from a certified in-vitro diagnostic workflow. These data represent an essential step toward the integration of gut microbiota testing into clinical laboratory practice, enabling standardized interpretation of microbiota imbalance and supporting targeted medical interventions aimed at restoring microbial equilibrium.