Higher-order microbial interactions revealed by comparative metabolic modeling of synthetic communities with varying species composition

Abstract

Understanding how microbial interactions scale with community complexity is key to microbiome engineering and ecological theory. This study investigates emergent metabolic behaviors in controlled in vitro synthetic anaerobic communities of two, three, or four species: cellulolytic bacterium (Ruminiclostridium cellulolyticum), a hydrogenotrophic methanogen (Methanospirillum hungatei), an acetoclastic methanogen (Methanosaeta concilii), and a sulfate-reducing bacterium (Desulfovibrio vulgaris), representing core metabolic guilds in cellulose degradation and carbon conversion. We applied a systems biology framework combining proteogenomics, stoichiometric flux modeling, and SMETANA (Species Metabolic Coupling Analysis) to quantify syntrophic cooperation and competition across configurations. Cooperation peaked in tri-cultures and declined nonlinearly in more complex assemblies. Species roles shifted contextually. Ruminiclostridium cellulolyticum was the dominant donor, adjusting cellulase and hydrogenase expression by partner. Methanosaeta concilii became fully metabolite-dependent while enhancing methanogenesis. Desulfovibrio vulgaris improved syntrophic efficiency via redox and hydrogen turnover. In contrast, Methanospirillum hungatei’s metabolic centrality declined despite higher CH4 output, suggesting interaction strength depends more on compatibility than richness. Reduced interactions in the four-species community stemmed from a single configuration and need further validation. This study moves beyond descriptive work by quantitatively resolving how metabolic networks rewire across defined communities. By characterizing context-dependent flux shifts at multiple layers, we provide a framework for interpreting and engineering stable, functionally interdependent microbial ecosystems.