Wilber, M. | Search bioRxiv

bioRxiv2025

A continuous-time microparasite model incorporating infection intensity and parasite aggregation

Disease outcomes depend heavily on infection intensity which is often heterogeneous across and within host populations. Most individuals carry low pathogen loads and a few carry high loads, a pattern known as aggregation. While well-characterized in macroparasite systems, aggregation and infection intensity are rarely incorporated into microparasite models. This raises key questions: Do similar mechanisms underlie aggregation in macro- and microparasite systems? And how do aggregation and load-dependent effects shape outcomes such as host suppression and virulence-transmission trade-offs? To address these questions, we developed a novel continuous time microparasite model that allows the pathogen load distribution across hosts to evolve dynamically, shaped by within- and between-host processes. We applied this framework to the amphibian chytrid fungus system involving Batrachochytrium den-drobatidis (Bd), a fungal pathogen threatening amphibian populations worldwide. Our results show that load-dependent mortality reduces aggregation, while faster within-host replication increases it. Aggregation, in turn, weakens host suppression and flat-tens virulence-transmission trade-off, shifting peak transmission to higher replication rates. Overall, our continuous-time microparasite model provides new insights into how infection intensity and aggregation influence host-pathogen dynamics and offers a valuable framework for advancing theoretical and data-driven understanding of how within-host processes scale to population-level disease dynamics for microparasites.

ecology↗

bioRxiv2017

xenoGI: reconstructing the history of genomic island insertions in clades of closely related bacteria

BackgroundGenomic islands play an important role in microbial genome evolution, providing a mechanism for strains to adapt to new ecological conditions. A variety of computational methods, both genome-composition based and comparative have been developed to identify them. Some of these methods are explicitly designed to work in single strains, while others make use of multiple strains. In general, existing methods do not identify islands in the context of the phylogeny in which they evolved. Even multiple strain approaches are best suited to identifying genomic islands that are present in one strain but absent in others. They do not automatically recognize islands which are shared between some strains in the clade or determine the branch on which these islands inserted within the phylogenetic tree.\n\nResultsWe have developed a software package, xenoGI, that identifies genomic islands and maps their origin within a clade of closely related bacteria, determining which branch they inserted on. It takes as input a set of sequenced genomes and a tree specifying their phylogenetic relationships. Making heavy use of synteny information, the package builds gene families in a species-tree-aware way, and then attempts to combine into islands those families whose members are adjacent and whose most recent common ancestor is shared. The package provides a variety of text-based analysis functions, as well as the ability to export genomic islands into formats suitable for viewing in a genome browser. We demonstrate the capabilities of the package with several examples from enteric bacteria, including an examination of the evolution of the acid fitness island in the genus Escherichia. In addition we use output from simulations and a set of known genomic islands from the literature to show that xenoGI can accurately identify genomic islands and place them on a phylogenetic tree.\n\nConclusionsxenoGI is an effective tool for studying the history of genomic island insertions in a clade of microbes. It identifies genomic islands, and determines which branch they inserted on within the phylogenetic tree for the clade. Such information is valuable because it helps us understand the adaptive path that has produced living species. Given the large and growing number of sequenced microbial genomes, this sort of analysis will become increasingly useful in the future.

bioinformatics↗