Our gut microbes have evolved with us over millennia, adapting to changes in our diet, lifestyle, and geographical locations. Their adaptability allows them to respond effectively to both short-term fluctuations and long-term shifts in host associated conditions. Consequently, they continuously generate new lineages, some of which exhibit greater fitness in specific environments and dominate under favorable conditions. Recent studies show even within the same species, certain strains demonstrate varying levels of fitness in relation to health, disease, and geographical location. However, the mechanisms underlying their differential fitness, and functional changes remain poorly characterized, posing significant challenges to the success of microbiota-aided interventions. Approximately 70% of our gut microbes remain uncharacterized, and their unique or overlapping functionalities remain largely unknown. My objective is to study the factors contributing to microbial adaptation and fitness across diverse host conditions. We will investigate the mechanisms underlying adaptation in two scenarios characterized by gradual selection pressures: a) the transition of children's microbiota upon introduction to solid foods, and b) changes in the gut microbiota of healthy adults over time compared to those at risk of cardiometabolic conditions. The second project aims to establish connections between genes or gene clusters and microbial genomes to bridge taxonomic and functional disparities. Finally, the third project seeks to identify variations in gut microbial strains among the Swedish population compared to global populations.