Variability of Bacteria in Human Populations: Axes, Drivers, Methods, and Implications

Abstract

Bacteria in a human population differ in three interrelated aspects. The first is community composition, or which taxa are there in which proportion. The second is strain genetics, or the lineages and mobile elements like plasmids, integrons, and phages. The third is the function of which metabolic pathways, virulence factors, and antimicrobial-resistance genes are present. A variety of factors influence the patterns seen in the development of infections. These factors include the food systems that we are subjected to in addition to our diets, exposure to antibiotics from humans and animals, the sanitation and water supplies, air quality and the built system, early life factors such as the delivery mode, breastfeeding, and host genetics such as FUT2 secretor status, vaccination and serotype replacement, health systems and infection control, urbanization and mobility, and animal-human interfaces. Comparative cross-continental studies reveal strong lifestyle gradients, such as those between rural/traditional versus urbanized cohorts. The genomic epidemiology shows vaccine-forced serotype turnover (pneumococci), hospital-adapted clonal cycles (MRSA), and pandemic lineages of enteric pathogens. Through shotgun metagenomics, isolate WGS, multi-omics, and wastewater metagenomics, we can resolve population-level surveillance. The consequences range from local resistomes, vaccine strategy, sanitation priority, and One Health to clinical empiric therapy.