High-throughput sequencing (HTS) has become a central tool for biomedicine and ecology. Metagenomic and amplicon sequencing are driving rapid discovery and diagnosis of parasites and pathogens, as well as the characterization of host-associated microbiomes. Targeted and untargeted sequencing approaches are not only revolutionizing our capacity to study host defenses and responses to parasites and pathogens, but also functional interactions with the microbiome.

Beyond biomedical applications, HTS is revolutionizing our capability to noninvasively characterize natural biodiversity. For instance, metabarcoding enables analysis of environmental DNA shed by living organisms, offering a powerful method to study ecosystems without direct interference. These tools hold potential to advance our understanding of the interactions among parasites, pathogens, and microbiomes within their natural host environments. HTS is crucial for monitoring these interactions over time and predicting potential disease emergence and spillover, especially in the context of global environmental change.

The goal of this Research Topic is to demonstrate the potential of HTS in exploring the dynamics among parasite, pathogen, and microbiome communities in non-model host species. We seek research that takes an ecological approach to better understand within-host interactions in the context of natural environmental variation. Research may use metagenomics, transcriptomics, metabarcoding, or other HTS-based approaches, combined with analytical tools from ecology and molecular biology to investigate these interactions, and their relationships with environmental variables.

We welcome Original Research, Review, Mini Review, Methods or Perspective articles utilizing HTS approaches to address the following:

• Describing parasite communities within natural host populations;
• Identifying and characterizing interactions among parasites, or between parasites, microbiomes, and their hosts;
• Examining the influence of ecological variables on parasite communities, or on the interactions between parasites, microbiomes, and hosts.

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Frontiers in Microbiology

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