Microbes fine-tune their protein production to make communities more efficient

14.09.2026

Microbial communities may be engineered at the protein-expression level because bacteria adjust their protein production in response to specific neighbors.

What is already known

Microbes form communities where many species must share limited resources and avoid direct competition, but most research has focused on how bacteria respond to non-living conditions such as nutrients or pH, rather than how they respond to neighboring microbes.

What this research adds

Researchers grew bacteria alone, in pairs, and in four-species groups on either fructose or plant fiber as the main energy source. Bacteria changed their protein production in response to which microbial neighbors were present. These partner-specific changes reduced duplicated functions across the community, and this reduced overlap was linked with higher community productivity.

Conclusions

The findings suggest that microbial communities may be engineered at the protein-expression level because bacteria adjust their protein production in response to specific neighbors.

Microbes form communities where many species must share limited resources and avoid direct competition. Now, researchers have found that bacteria fine-tune the proteins they make depending on neighboring microbes, helping communities use resources more efficiently.

The findings, published in Nature Microbiology, suggest that microbial communities may be engineered at the protein-expression level.

Most previous studies have focused on how bacteria respond to non-living conditions such as nutrients or pH, rather than how they respond to neighboring microbes. In particular, it was unclear whether bacteria change their protein production in response to specific microbial partners, and whether those changes help reduce competition.

Sarah Moraïs at Ben-Gurion University of the Negev in Israel and her colleagues set out to address that question by growing bacteria alone, in pairs, and in four-species groups on either fructose or plant fiber as the main energy source.

Partner-specific responses

Changing the energy source altered bacterial protein production, even when growth did not change much, showing that microbes adjust to match their food environment. But when bacteria were grown in communities, their protein production changed even more.

Bacterial responses were often partner-specific: the same species changed its protein production differently depending on which other species it was paired with. Some bacteria showed distinct responses to different partners, while others responded more similarly.

The changes were spread across many parts of metabolism rather than concentrated in one pathway, suggesting that each species has its own strategy for adjusting to different communities, the authors say.

Higher productivity

In most cases, bacterial communities had less functional overlap than species grown alone, which indicates that microbes tend to stop making some proteins when another community member could cover similar functions.

This reduced overlap was linked with higher community productivity, the researchers found.

The work does not prove that the same division of labor happens in real-world microbiotas. However, the authors say, “these principles can help guide future efforts to understand, predict and engineer microbial ecosystems across various applications, including health, agriculture and the environment.”