New research from Ben-Gurion University of the Negev, just published in Nature Microbiology (https://doi.org/10.1038/s41564-026-02310-w), reveals that when microbes live together, they can sense one another and actively reduce competition by shifting toward different roles instead of all doing the same thing.
It shows that microbes do not just respond to their environment, they respond to each other. In fact, the identity of neighboring microbes can have a stronger effect on protein production than the food source itself.
The new study led by Dr. Sarah Moraïs under the supervision of Prof. Itzhak Mizrahi, has some profound implications for how we think about microbes and the microbiome and therefore how we could tweak them in the future.
This discovery potentially addresses a long-standing ecological problem: microorganisms do not live alone. In nature, many species coexist within the same community, even though based on their genomic potential they often appear expected to compete aggressively for similar resources, and in theory could eliminate one another. What they found suggests that microbes may actually detect each other’s presence and actively adjust their behavior to reduce competition and conflict. By shifting what they do, they may minimize direct overlap, improve coexistence, and enhance survival. This provides a potential mechanistic explanation for how diverse multi-species microbial communities can assemble and persist, despite the expectation of intense competition.
Never alone
Most of us think about microbes as individual species. This bacterium does one thing, that bacterium does another. But in reality, microbes are almost never alone.
They live in dense, crowded communities, in our gut, in the rumen of cows, in soil, in oceans, essentially everywhere. And like people sharing a workspace, they need to figure out how to coexist without everyone doing the same job, wasting energy, and competing for the same resources.
Moraïs and Mizrahi built small, controlled microbial communities using gut-associated bacteria. Instead of just tracking which microbes were present, they looked at which proteins each microbe produced, which indicate their function.
“A microbe is not defined only by its genome, which represents its potential, but also by its community. The same bacterium can behave very differently depending on who surrounds it,” notes Moraïs.
Dynamic systems
If microbes actively coordinate what they do in response to each other, then microbiomes are not just collections of species. They are dynamic, adaptive systems.
And that shift in perspective matters.
“In human health, it suggests that designing probiotics or microbiome-based therapies is not just about choosing the “right” microbes. It is about finding the right combinations, communities where microbes naturally divide tasks instead of competing or duplicating effort,” says Prof. Mizrahi, “In agriculture, especially in systems like the rumen where microbes control feed efficiency and methane emissions, understanding how communities organize themselves could help us guide them toward more productive and sustainable states.
“In biotechnology, it points toward a different strategy. Instead of engineering single “super microbes,” we can design ensembles of microbes, each doing part of the job, making the entire system more efficient and stable. And in microbiome restoration, it offers a new explanation for why some microbes fail to establish. It may not be that they are missing, but that their ecological “home” is missing. Rebuilding the right community context could allow them to return.”
Underlying rules
More broadly, their work suggests that microbial communities follow underlying rules. Division of labor and efficiency are not accidents. They emerge naturally from interactions. If those roles can be understood, then research can move from simply describing microbiomes to actually predicting, shaping, and engineering them.
Additional researchers included Michael Mazor, Itai Amit, Ido Grinshpan, Yehonatan Shelly, and Liron Levin from BGU and Philip Gerth, Anke Trautwein-Schult, Sandra Maaß, and Dörte Becher from the University of Greifswald.
The research was supported by the European Research Council (ERC 866530), the Israel Science Foundation–Swiss National Science Foundation (ISF–SNSF 1057/24), and the Israel Science Foundation (979/25).
No comments yet