Lab Perturbations Disrupt Cross-Feeding, Leading to Microbial Extinction

The diversity of microbial ecosystems, such as those found in soil, seawater, and the human gut, is astonishing. Yet scientists often struggle to replicate this diversity in laboratory settings: attempts to cultivate microorganisms frequently result in their death.

Researchers at the Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB) in Germany have recently shed new light on this long-standing challenge. Their study suggests that microbial survival depends not only on the needs of individual organisms but also on a hidden web of interdependencies—relationships that can be disrupted by even minor structural changes.

In a paper published in the Proceedings of the National Academy of Sciences, biodiversity researchers Dr. Thomas Clegg and Professor Dr. Thilo Gross propose a simplified view of microbial communities as networks built on cross-feeding—the exchange of metabolic by-products between different populations.

Each microbial species consumes certain nutrients while releasing by-products that serve as food for others. Using innovative methods from network theory (a mathematical framework originally developed in physics to analyze complex systems), Clegg and Gross modeled this metabolic web.

Their analysis revealed that in such a network, the loss of specific populations can destabilize the entire system, causing the microbial community to abruptly collapse into a state of lower diversity.

These collapses act as tipping points, resembling blackouts in power grids or supply chain breakdowns seen during the COVID-19 pandemic.

 Dr. Thomas Clegg, Study Lead Author, University of Oldenburg

According to the researchers, attempting to cultivate a microbial community in the laboratory often constitutes a significant disturbance. For example, if certain species from a natural microbial community are missing from a sample, their absence may prevent the production of vital metabolic by-products needed by other organisms.

By focusing on the structure of these interactions, the study offers new insight into why diversity is so hard to maintain in a lab setting.

Dr Thilo Gross, Professor, University of Oldenburg

While scientists have long suspected that microbial interdependencies are key to successful cultivation, this study is the first to show how these dynamics function at the level of entire communities.

The findings offer a new perspective on microbial resilience, highlighting that even in resource-rich environments like laboratory cultures, communities can collapse if their underlying relational networks are disrupted.

Crucially, the model also suggests that once a microbial community collapses, recovery may be difficult, even if the necessary resources are later reintroduced.

It is not just about what individual microbes need, but who they depend on. The whole community thrives, or collapses, together.

Dr. Thomas Clegg, Study Lead Author, University of Oldenburg