Biology subjects

Dillard, B. A.

Publications and source records attributed to Dillard, B. A..

3 recordsLinked to original sources

bioRxiv2025

Isolation by distance promotes strain diversification in the wild mouse gut microbiota

Bacterial species within the mammalian gut microbiota exhibit considerable strain diversity associated with both geography and host genetic ancestry. However, because geography and host ancestry are typically confounded, disentangling their contributions to the diversification of gut bacterial strains has remained challenging. Here, we show through joint profiling of gut bacterial and mitochondrial genomes from wild-living populations of deer mice (Peromyscus maniculatus) sampled across the United States that isolation by distance (IBD) drives gut bacterial strain diversification independently of the effects of host ancestry. Analyses revealed significant IBD in 27 predominant gut bacterial species, including members of the Muribaculaceae and Lachnospiraceae, but limited evidence for co-inheritance of gut bacterial genomes with mitochondria during the diversification of extant mouse populations. Gut bacterial species capable of forming spores exhibited reduced IBD independently of phylogenetic history, indicating that adaptations facilitating bacterial dispersal can mitigate the geographic structuring of strain diversity. These results show that the diversification of gut bacterial strains within rodent species has been mediated by geographic separation of host populations rather than host genealogical divergence.

microbiology↗

bioRxiv2024

Recent genetic drift in the co-diversified gut bacterial symbionts of laboratory mice

Laboratory mice (Mus musculus domesticus) harbor gut bacterial strains that are distinct from those of wild mice1 but whose evolutionary histories are poorly understood. Understanding the divergence of laboratory-mouse gut microbiota (LGM) from wild-mouse gut microbiota (WGM) is critical, because LGM and WGM have been previously shown to differentially affect mouse immune-cell proliferation2,3, infection resistance4, cancer progression2, and ability to model drug outcomes for humans5. Here, we show that laboratory mice have retained gut bacterial symbiont lineages that diversified in parallel (co-diversified) with rodent species for > 25 million years, but that LGM strains of these ancestral symbionts have experienced accelerated accumulation of genetic load during the past [~] 120 years of captivity. Compared to closely related WGM strains, co-diversified LGM strains displayed significantly faster genome-wide rates of fixation of nonsynonymous mutations, indicating elevated genetic drift, a difference that was absent in non-co-diversified symbiont clades. Competition experiments in germ-free mice further indicated that LGM strains within co-diversified clades displayed significantly reduced fitness in vivo compared to WGM relatives to an extent not observed within non-co-diversified clades. Thus, stochastic processes (e.g., bottlenecks), not natural selection in the laboratory, have been the predominant evolutionary forces underlying divergence of co-diversified symbiont strains between laboratory and wild house mice. Our results show that gut bacterial lineages conserved in diverse rodent species have acquired novel mutational burdens in laboratory mice, providing an evolutionary rationale for restoring laboratory mice with wild gut bacterial strain diversity.

evolutionary biology↗

bioRxiv2022

Humanization of wildlife gut microbiota in urban environments

Urbanization is rapidly altering Earths environments, demanding investigations of the impacts on resident wildlife. Here, we show that urban populations of coyotes (Canis latrans) and crested anole lizards (Anolis cristatellus) acquire gut microbiota constituents found in humans, including the gut bacterial lineages most significantly associated with urbanization in humans (e.g., Bacteroides). Comparisons of urban and rural wildlife and human populations revealed significant convergence of the gut microbiota among urban host populations. Remarkably, all microbial lineages found in humans that were overrepresented in urban wildlife relative to rural wildlife were also overrepresented in urban humans relative to rural humans. These results indicate parallel effects of urbanization on human and wildlife gut microbiota and suggest spillover of bacteria from humans into wildlife in cities.

ecology↗