Biology subjects

Adair, K. L.

Publications and source records attributed to Adair, K. L..

3 recordsLinked to original sources

bioRxiv2025

Assembly of skin microbiomes is more neutral than gut microbiomes in multiple animal species

The gut and external tissues of most animals are colonized by communities of microorganisms that can influence the health, development, and fitness of the host. The composition of these communities can vary greatly between individuals within a host species, and both selective factors (e.g. host immune response) and neutral processes (e.g. random loss of microbial cells) have been shown to contribute to this variation. While it is known that microbiome composition differs between tissues within an individual host, less is known about the ecological processes that underline these differences. To address this, we investigated whether the contribution of neutral ecological processes to microbiome assembly differs between external (skin and scale) and internal (gut) host tissues for a diverse panel of animal hosts. To do this, we fit a neutral ecological model to microbial communities from external and internal tissues across a variety of animal hosts. Strikingly, we discovered that the neutral model was equally or better fit to skin or scale microbial communities across all hosts, suggesting that neutral processes play a larger role in the assembly of skin or scale microbiomes compared to gut microbiomes. Furthermore, we observed that this trend is robust to different definitions of the metacommunity (i.e. the microbial taxa available to colonize a host). Finally, we leveraged a simulation framework to compare the model fits of empirical vs simulated microbial communities. We found that neutral model fits to empirical communities can differ from simulated communities, emphasizing the importance of temporal sampling in profiling animal microbiomes.

ecology↗

bioRxiv2025

Comparative analysis of novel Pseudobdellovibrionaceae genera and species yields insights into the genomics and evolution of bacterial predation mode

Bacteria of the family Pseudobdellovibrionaceae belong to a group of bacteria that kill and feed on other bacteria. The diversity of predation strategies, habitats, and genome characteristics of these bacteria are largely unexplored, despite their ecological and evolutionary importance in microbial communities. Therefore, we characterized new Pseudobdellovibrionaceae strains isolated from the direct environments of three animal hosts: the zebrafish (Danio rerio), the threespine stickleback fish (Gasterosteus aculeatus), and the nematode Caenorhabditis elegans. We used transmission electron microscopy (TEM) and genomic analyses to characterize the morphology and predation modes of our isolates. While most of our isolates exhibited periplasmic (i.e. endoparasitic) predation, one isolate clearly exhibited epibiotic (i.e. exoparasitic) predation and represents only the third confirmed epibiotic strain within its clade. Of our isolates, six are members of five new species in the genus Bdellovibrio and two strains likely represent new genera within the family Pseudobdellovibrionaceae. From metabarcoding data, we found indications that Pseudobdellovibrionaceae are widespread among our three animal hosts. Genomic analyses showed that epibiotic predators lack genes involved in host independence (i.e. prey-independent feeding) and peptidoglycan modification. However, genes unique to epibiotic predators may underlie this predation mode, particularly those involved in cell wall remodeling and recycling. With robust phylogenomic analyses, we show that our novel isolates cluster with previously described Pseudobdellovibrionaceae isolates according to predation mode. Further, by placing Pseudobdellovibrionaceae predators within a wider evolutionary history including other predatory and non-predatory bacteria, we postulate periplasmic predation as the ancestral mode, with more derived epibiotic predators exhibiting genome streamlining.

genomics↗

bioRxiv2023

Host and microbiome jointly contribute to adaptation to a complex environment

Most animals and plants have associated microorganisms, collectively referred to as their microbiomes, which can provide essential functions. Given their importance, host-associated microbiomes have the potential to contribute substantially to adaptation of the host-microbiome assemblage (the "metaorganism"). Microbiomes may be especially important for rapid adaptation to novel environments because microbiomes can change more rapidly than host genomes. However, it is not well understood how hosts and microbiomes jointly contribute to metaorganism adaptation. We developed a model system with which to disentangle the contributions of hosts and microbiomes to metaorganism adaptation. We established replicate mesocosms containing the nematode Caenorhabditis elegans co-cultured with microorganisms in a novel complex environment (laboratory compost). After approximately 30 nematode generations (100 days), we harvested worm populations and associated microbiomes, and subjected them to a common garden experiment designed to unravel the impacts of microbiome composition and host genetics on metaorganism adaptation. We observed that adaptation took different trajectories in different mesocosm replicates, with some increasing in fitness and others decreasing, and that interactions between host and microbiome played an important role in these contrasting evolutionary paths. We chose two exemplary mesocosms (one with a fitness increase and one with a decrease) for detailed study. For each example, we identified specific changes in both microbiome composition (for both bacteria and fungi) and nematode gene expression associated with each change in fitness. Our study provides experimental evidence that adaptation to a novel environment can be jointly influenced by host and microbiome.

evolutionary biology↗