# COmmunity and Single Microbe Optimisation System (COSMOS)

## TL;DR

The COSMOS system helps design efficient microbial systems for bioprocessing by comparing single microbes and microbial communities.

## Contribution

COSMOS is a new computational framework that simulates and optimizes microbial systems for biosynthesis.

## Key findings

- COSMOS identified the Shewanella oneidensis–Klebsiella pneumoniae co-culture as optimal for 1,3-propanediol production under anaerobic conditions.
- Microbial communities show resilience in nutrient-limited environments.
- Computational tools like COSMOS can balance productivity and operational simplicity in bioprocessing.

## Abstract

Bioprocessing utilises microbial monocultures and communities to convert renewable resources into valuable products. While monocultures offer simplicity, communities provide metabolic diversity and cooperative biosynthesis. To systematically evaluate these systems, we developed COmmunity and Single Microbe Optimisation System (COSMOS), a dynamic computational framework that simulates and compares monocultures and co-cultures to determine optimal microbial systems tailored to a specific environment. COSMOS revealed key factors shaping biosynthetic performance, such as environmental conditions, microbial interactions, and carbon sources. Notably, it predicted the Shewanella oneidensis–Klebsiella pneumoniae co-culture as the most efficient producer of 1,3-propanediol under anaerobic conditions, aligning closely with experimental data, including optimal carbon source concentrations and inoculum ratios. Additional findings highlight the resilience of microbial communities in nutrient-limited processes and emphasise the role of computational tools in balancing productivity with operational simplicity. Overall, this study advances the rational design of microbial systems, paving the way for sustainable bioprocesses and circular bio-economies.