Genome-based analysis reveals niche differentiation among Firmicutes in full-scale anaerobic digestion systems

Fermentative Firmicutes species are key players in anaerobic digestion; however, their niche differentiation based on carbohydrate utilization in full-scale systems remains unclear. In this study, we investigated niche differentiation among four major Firmicutes classes using a genome-centric approach, reconstructing 39 high-quality metagenome-assembled genomes. Limnochordia and Clostridia exhibited the broadest substrate versatility, utilizing 24% and 18% of the predicted substrates, respectively. Although common substrates were shared, each class demonstrated unique substrate preferences driven by distinct functional and metabolic differences. Limnochordia and Clostridia possess unique carbohydrate-active enzyme families, such as GH177 and CBM91, which enable xylan and arabinan degradation. Bacilli were abundant with the GH1 and GH3 families, which are critical for cellulose degradation. Overall, the Firmicutes classes showed low overlap in substrate use and functional profiles, confirming significant niche differentiation. Our results demonstrate that Firmicutes occupy distinct dietary niches supporting insights into bacterial coexistence in anaerobic digestion systems.