Microbiome diversity (alpha / Shannon index)

Microbiome diversity describes the richness and evenness of microbial community composition within a single sample (alpha diversity) or across samples (beta diversity). The Shannon entropy index, which accounts for both species richness and relative abundance, is one of the most widely used alpha-diversity metrics; higher Shannon index values indicate a more complex community in which no single taxon dominates. Higher alpha diversity has been broadly associated with resilience, metabolic health and lower risk of conditions such as inflammatory bowel disease, though the relationship is not universal — some disease states feature increased diversity in anatomically inappropriate communities. Population studies consistently show that alpha diversity declines with age, particularly after the seventh decade, and that this decline correlates with frailty, hospitalisation and reduced survival. Diversity should be interpreted with caution as a standalone health proxy: functional redundancy means that a numerically diverse community can still lack critical pathways, and 16S rRNA sequencing depth and primers substantially affect measured diversity values.