Using housekeeping gene cpn60 as a marker for microbial community profiling and viability assessment

While high-throughput metagenomic sequencing has revolutionized the study of microbial communities, it remains surprisingly difficult to determine which microbes in a community are “alive” versus “dead” using current techniques. Microbial viability is fundamental to an understanding of the biology of the microbiome, as the functions of a microbial community are defined by its viable members. This limits our understanding of microbiome structures and their transmission between humans and our surroundings. Currently, several sequencing-based methods have been attempted to address this issue, yet these methods struggle with accuracy and scalability in complex communities.
In this study, we introduced a novel protein-coding marker gene approach using the cpn60 gene for comprehensive microbial community profiling and functional activity assessment through metagenomic and metatranscriptomic sequencing. We first constructed an extensive database integrating cpn60 protein and enriched cpn60 nucleotide sequences, expanding on the existing cpnDB nucleotide database. We used cpn60 protein IDs for protein-based taxonomy inference in the Human Microbiome Project II dataset and found strong agreement between cpn60-protein-based taxonomy and shotgun metagenomic results. This would suggest cpn60 being a discriminative marker for taxonomy profiling. Furthermore, we explored the potential of cpn60 protein expression in metatranscriptomic data as an indicator of bacterial species’ transcriptional activity. The cpn60-protein-based analysis correlated positively with growth rates estimated using the bPTR method, suggesting cpn60 proteins as robust markers for microbial community viability characterization. These insights underscore the feasibility of cpn60 in crafting taxonomic profiles from shotgun metagenomics data and in representing species activities within microbial communities through the integration of metatranscriptomic data. Employing marker genes emerges as a promising strategy to forge efficient and cost-effective viability assessments for microbial community samples.
This study contributes a promising new approach enhancing our ability to assess the functional activity of microbial communities through advanced metagenomic profiling and providing insights into the dynamics of microbial life in various ecosystems.