Industrialization restructures the domestic dog gut microbiome while preserving host specificity

Industrialization has reshaped human gut microbiomes, but its effects on other human-associated mammals remain poorly understood. Domestic dogs provide an informative comparative system because they have shared human environments and food systems for millennia yet retain distinct host biology. However, most canine microbiome studies have focused on industrialized companion, colony, or controlled-feeding dogs, limiting our understanding of the ecological range of the domestic dog gut microbiome. We analyzed fecal 16S rRNA gene profiles from 261 dogs sampled across Nepal, Thailand, the United Arab Emirates, and the United States, spanning forager, agrarian, pastoralist, urban, and industrialized lifestyles; 257 dogs remained after excluding those with reported recent antibiotic exposure. Lifestyle was the strongest measured correlate of canine gut bacterial composition, and this association persisted in restricted analyses of mature, non-shelter dogs sampled from temperate regions. Industrialized dogs differed from non-industrialized dogs through directional genus-level shifts, prevalence-defined VANISH-like and BloSSUM-like bacterial guilds, coabundance structure, and shifts in predicted functional potential. Non-industrialized dogs were not microbiologically uniform: pastoralist dogs showed non-industrialized gut bacterial community profiles but diverged from a simple forager-to-industrialized continuum. Cross-species comparisons with humans sampled across matched lifestyle categories showed parallel lifestyle-associated restructuring in both hosts, but host species remained the dominant axis of variation, and genus-level responses were largely host specific. These findings expand the ecological baseline for canine gut bacterial communities and identify industrialization-associated lifestyle change as a major axis of gut bacterial community restructuring in a long-term human-associated mammal. More broadly, they show that shared lifestyle transitions can impose parallel ecological pressures across host species without overriding host-specific community assembly.

Domestic dogs are one of the closest animal companions of humans, yet we know surprisingly little about how their gut microbiomes vary outside industrialized pet populations. This study shows that industrialization-associated lifestyle change is not only relevant to human microbiomes but also a broader ecological force that reshapes gut microbial communities in animals living alongside us. By comparing dogs across diverse human lifestyles, we show that shared environments can impose parallel pressures on the gut bacterial communities of humans and dogs, while each host maintains a distinct microbial identity. These findings suggest that gut microbial communities are shaped by the interaction between host biology and changing ecological conditions. Expanding microbiome research beyond industrialized settings is therefore essential for understanding what microbial diversity has been retained, altered, or lost during recent lifestyle transitions.