MICROBIAL COMMUNITIES: A BIOTECHNOLOGY STUDY WITH SINGLE-CELL SEQUENCING

Microorganisms are the most abundant life forms on Earth, yet an estimated 90-99% remain uncharacterized due to the limitations of traditional culturing methods in laboratory settings. Emerging methodologies now allow for the direct analysis of microbial communities in their natural environments, bypassing the need for cultivation. Single-cell sequencing, in particular, enables the genomic characterization of individual cells, offering the potential to uncover new genomes from uncultivated strains and to detect intraspecies variations. While early studies primarily focused on eukaryotic cells, easier to sort with automated platforms, research on prokaryotic communities remains in its early stages. Initial trials using mock communities have highlighted key challenges in prokaryotic single-cell sequencing, including issues with lysis, cell counting, and sorting. In this study, we apply single-cell sequencing to a simple anaerobic microbial community. Additionally, a comparison between single-cell sequencing and the widely-used shotgun metagenomic approach will be presented, offering insights into the strengths and limitations of each technique in microbial characterization. The results obtained from single-cell sequencing and metagenomics serve distinct but complementary purposes in studying microbial communities. Metagenomics provides a broad overview of the taxonomic composition, offering insights into the overall community structure and potential functions. In contrast, single-cell sequencing focuses on the detailed characteristics of individual microorganisms, enabling a more precise understanding of both dominant and rare strains not only of their taxonomy but also of their functional traits. Integrating these approaches allow for a comprehensive characterization of microbiota with the granularity of single-cell resolution. With ongoing advancements, single-cell sequencing is poised to become a more routine and accessible tool, complementing traditional metagenomic approaches to revolutionise our understanding of microbial ecosystems. By enabling precise exploration of microbial diversity, interactions, and functional roles at the single-cell level, this technology offers unprecedented detail and clarity.