Using low pass whole metagenome sequencing for gut microbiome profiling in an Argentine urban population

Modern urban diets are linked to gut microbiome dysbiosis and increased risk of chronic disease. While 16S rRNA sequencing is widely used, low-pass whole metagenome sequencing (WMS) offers superior insight into microbial functional capacity and community structures. In this study, we utilized low-pass WMS to characterize the gut microbiome of an Argentine urban population. We compared a health-screened ‘Reference’ cohort (n=94) with an unscreened ‘Average’ urban cohort (n=527), for which we analyzed taxonomic structure, microbial diversity, and predicted metabolic potential.

The ‘Average’ cohort displayed significantly lower alpha-diversity, primarily driven by reduced community evenness rather than richness. Functionally, this cohort showed a significantly diminished predicted capacity for synthesizing beneficial short-chain fatty acids (SCFAs) and essential vitamins B9 and B12. A longitudinal analysis of a subgroup (n=9) undertaking lifestyle modifications demonstrated that while microbial richness and SCFA production could be significantly improved, responses were highly individualized.

These results reveal key functional deficits in the gut microbiome of a typical urban population, reflecting a mismatch with ancestral dietary patterns. The high inter-individual variability in response to changes in dietary patterns challenges one-size-fits-all dietary recommendations and highlights the need for personalized nutritional strategies informed by functional microbiome data.