Industrialization is associated with elevated rates of horizontal gene transfer in the human microbiome

Abstract

Horizontal Gene Transfer, the process by which bacteria acquire new genes and functions from non-parental sources, is common in the human microbiome 1,2 . If the timescale of HGT is rapid compared to the timescale of human colonization, then it could have the effect of 'personalizing' bacterial genomes by providing incoming strains with the genes necessary to adapt to the diet or lifestyle of a new host. The extent to which HGT occurs on the timescale of human colonization, however, remains unclear. Here, we analyzed 6,188 newly isolated and sequenced gut bacteria from 34 individuals in 9 human populations, and show that HGT is more common among bacteria isolated from the same human host, indicating that the timescale of transfer is short compared to the timescale of human colonization. Comparing across 9 human populations reveals that high rates of transfer may be a recent development in human history linked to industrialization and urbanization. In addition, we find that the genes involved in transfer reflect the lifestyle of the human hosts, with elevated transfer of carbohydrate metabolism genes in hunter gatherer populations, and transfer of antibiotic resistance genes among pastoralists who live in close contact with livestock. These results suggest that host-associated bacterial genomes are not static within individuals, but continuously acquire new functionality based on host diet and lifestyle.

Plasmids shape the diverse accessory resistomes of Escherichia coli ST131

“… E. coli is the most common initial coloniser of infant intestines [ 23 ], where most are commensal [ 24 ] and some protect against pathogen invasion [ 25 ]. Nonetheless, AMR is prevalent in neonatal units [ 26 ] and within-host gene exchange between commensal and pathogenic bacteria may occur [ 27 ]. ST131 spreads between mother-infant pairs [ 28 ] likely via an oro-faecal transmission route [ 29 ], and such colonisation of infants can last for long periods [ 30 ].…”

Translating the human microbiome: a path to improving health

“…Isolate collections comprising strains from industrialized and non-industrialized populations are valuable not only to determine the impact of lifestyle on microbiome composition and diversity but also to investigate adaptation within bacterial genomes. Higher rates of horizontal gene transfer were found in the microbiomes of industrialized populations, indicating that microbes acquire new functionalities suited to the host lifestyle [ 19 ].…”

Microbe-seq: high-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome

“…One method to establish HGT between two different microbial species identifies common sequences that occur in the genomes of both, and often utilizes cultured isolates (Groussin et al, 2020;Smillie et al, 2011). Reads from each cultured isolate descend ultimately from a single microbe; consequently, these reads are usually connected to the genome of a single strain.…”