We’re excited to share that our latest paper is now published in Frontiers in Bioinformatics: “N2SIMBA: from Network topology to SIMulation of interactions and BActerial abundance, using microbial consumer resource model.”
In this work, we introduce N2SIMBA, a modular simulation framework designed to generate realistic 16S rDNA-seq count tables starting from known microbial interaction networks. Since experimentally validated ground-truth interaction networks are rarely available, especially for complex bacterial communities, N2SIMBA provides a flexible in silico tool to systematically benchmark network inference methods.
The framework leverages the Microbial Consumer Resource Model to simulate microbial community dynamics through metabolite-mediated interactions, accounting for both competitive and promotional effects between taxa. By combining ecological modelling with sequencing count simulation, N2SIMBA enables users to study how community composition changes under different network topologies, environmental conditions, and perturbations.
We hope this framework will be useful for researchers interested in microbial ecology, systems biology, and the design of robust bacterial communities. New features and extensions are already under active development!.
Congratulations to Matteo Baldan, Giacomo Baruzzo, Piero Mariotto, Ada Rossato, Marco Cappellato, and Barbara Di Camillo for this work.
The paper is available at: https://doi.org/10.3389/fbinf.2026.1783447