unveiling the hidden repertoire of chemoreceptors from rare taxa in microbial communities

Chemoreception plays a pivotal role in the adaptability, survival, and ecological interactions of microbes. However, current work has been restricted to the study of chemotactic organisms isolated in the lab, limiting our ability to investigate the true biodiversity of chemoreceptors in complex microbial communities. We argue that due to the vast landscape of low abundance, chemosensitive microorganisms, they cannot be properly captured using conventional bulk metagenomics sequencing. Instead, we propose a novel long-read target capture sequencing approach based on a custom enrichment panel that accounts for all known chemoreceptor gene biodiversity along the entire prokaryotic phylogeny. Validation of this new method using rhizosphere, phyllosphere, soil, lake water, human gut, and animal rumen samples revealed a large hidden space of rare chemoreceptor genes. Hence, compared to standard metagenomics sequencing, our targeted approach can identify up to two orders of magnitude more chemoreceptor genes per sample, while improving the length and quality of gene assemblies.