Dispersal strategies shape persistence and evolution of human gut bacteria

Human gut bacterial strains can co-exist with their hosts for decades, but little is known about how these microbes persist and disperse, and evolve thereby. Here, we examined these processes in 5,278 adult and infant fecal metagenomes, longitudinally sampled in individuals and families. Our analyses revealed that a subset of gut species is extremely persistent in individuals, families, and geographic regions, represented often by locally successful strains of the phylum Bacteroidota. These “tenacious” bacteria show high levels of genetic adaptation to the human host but a high probability of loss upon antibiotic interventions. By contrast, heredipersistent bacteria, notably Firmicutes, often rely on dispersal strategies with weak phylogeographic patterns but strong family transmissions, likely related to sporulation. These analyses describe how different dispersal strategies can lead to the long-term persistence of human gut microbes with implications for gut flora modulations. [Display omitted] •Bacterial strains may persist within family members through transfer•Bacteria adapt dispersal strategies: heredipersistent, spatiopersistent, and tenacious•Dispersal strategies correlate with genetic bottlenecks and effective population size Hildebrand et al., investigated strategies of bacterial persistence using publicly available time series metagenomes from stool samples. They found that three major dispersal strategies underlie human gut bacterial persistence. These have distinct evolutionary patterns such as the accumulation of rare variation and differences in their strength of selection.