New microbiome tool: Gut bacteria cooperation vs. competition determines health

Scientists have discovered a new way to differentiate healthy microbiomes from diseased ones, based on gut bacteria interactions. They coin this method as the Ecological Network Balance Index (ENBI), which assesses whether microbial communities are dominated by competition or cooperation. 

Nutrition Insight speaks with study author Martin Blaser, M.D., the director of Rutgers Health’s Center for Advanced Biotechnology and Medicine in the US, who says the metric shows potential links to nutrition, metabolic health, and disease resilience. 

However, it requires scientists to further apply and validate ENBI before it can be used in R&D or personalized nutrition.

His team finds that ENBI can effectively distinguish healthy people from patients with various diseases, including colorectal cancer, when applied to existing data. This detection is especially valuable as the disease progresses, such as using it to measure shifts by analyzing stool samples.

Additionally, the Science study underscores that gut health is not just dependent on the types of bacteria present but also on the interactions they share. This suggests a shift in understanding gut diseases as a system, presenting the possibility of earlier detection and tailored interventions, and more effective microbiome-based therapies.

Researchers from US-based Rutgers University and Princeton University collaborated with Spain’s Universidad de Granada to create the ENBI using computational simulation.

“Good versus bad” bacteria?

Blaser says that traditional gut microbiome analyses mostly focus on diversity, or the number of “good versus bad bacteria.” However, diversity alone is not sufficient to define what is happening in the microbiome, as a dysbiotic community can be low or high in diversity.

“We define communities in terms of their net metabolic interactions — are the communities present in a net cooperative or are they competitive?”

Rod-shaped bacteria and spherical cocci represent different microbes that share the gut’s complex ecosystem (Image credits: Rutgers University).“We found that in healthy communities, competition dominated, but in dysbiotic communities, a group of cooperative organisms dominated — think of them like ‘little mafias’ grabbing all of the good resources. Competition keeps them in check,” he explains.

Applying ENBI in future therapy research

According to Blaser, who is also a professor of Medicine and Pathology & Laboratory Medicine, cooperation and competition patterns between microbes can reveal deeper understandings of diet response, metabolic health, and resilience to disease. However, there is not enough data to understand these details.

“ENBI is a research tool — the more researchers who use it, the faster we will be able to answer these questions,” notes Blaser.

Furthermore, he says this interaction-based metric might ultimately be used in nutrition R&D or consumer testing. “But the fundamental research we have done has to be applied further and translated into more real-world problems.”

“I look forward to seeing how other scientists apply this new way of looking at the microbiome.”

Studying microbe patterns

Study co-author Maria Gloria Dominguez-Bello, Henry Rutgers professor of Microbiome and Health, notes that diseases emerge when microbiomes reorganize themselves, as the findings show.

“In diseases such as inflammatory bowel disease, Clostridioides difficile infection, irritable bowel syndrome (IBS), and colorectal cancer, bacteria form more cooperative, tightly connected groups that can dominate and disrupt normal function.”

The bacteria were seen to behave in two main ways. One where a diverse, competitive state was associated with health, while the other was dominated by small, tightly connected groups of cooperating bacteria linked to disease. 

Senior author Bonachela adds that this pattern could help experts identify problems earlier. “In theory, it should be possible to measure it from just stool samples, which is a very non-invasive way to monitor gut health,” says the associate professor at the Rutgers School of Environmental and Biological Sciences.

Blaser says the tool needs further use for verification before applications for personalized nutrition.Lead author Roberto Corral López explains: “At first, we were just testing whether the model could reproduce basic features of real microbiomes. But very early on, we saw that it naturally produced two distinct patterns.”

This prompted the team to compare their simulations with patient DNA. And when they checked the data, they observed the same pattern, explains López, who is a postdoctoral associate at the Instituto Carlos I de Física Teórica y Computacional in Spain.

Question of probiotics and fecal transplant

The researchers believe their findings might also help explain why gut health therapies, such as probiotics or fecal microbiota transplants, are sometimes successful or fail.

“Treatments are typically based on the idea that you need particular bacteria to be there,” says Bonachela. “But if that is not the issue, if the issue is that key relationships are missing, then just adding the bacterium does not make a difference; it is necessary to recreate those relationships.”

“The interesting aspect of fecal transplants is not that you introduce the species then,” he adds. “It is that you introduce a whole community, and, therefore, you are keeping the interactions that allow that community to be healthy. It is not that certain bacteria need to be there. They need to be there with the right partners.”

Additionally, Corral López says that the research might make microbiome-based therapies more predictable.

“Right now, [fecal] donor selection is largely based on availability and basic health screening. Our work opens up the possibility of matching microbial communities based on how their interaction networks fit together, rather than just which species are present. That could help us design treatments that are tailored to each patient’s microbiome instead of relying on trial and error.”

The ENBI might make microbiome therapies more predictable.Bonachela adds: “We are trying to understand how these systems work so we can make a real difference in people’s lives.”

Gut health in headlines

Research on gut health is booming, presenting new opportunities for product development.

For instance, Cambridge researchers linked higher levels of the “hidden” gut bacteria group CAG-170 to better health, while low levels are associated with IBS, obesity, and other diseases. Another study found that common gut bacteria have a direct protein-level dialogue with the human immune system.

For infants, other experts mapped gut bacteria into an atlas, revealing opportunities for creating new, tailored probiotics. This includes diverse strains from 48 countries, some of which are not found in commercial probiotics, which they argue are outdated and not effective.

Meanwhile, global scientists recently established, for the first time, a clear definition of gut health: “A state of normal gastrointestinal function without active gastrointestinal disease and gut-related symptoms that affect quality of life.”

In addition, a lab study found that eight common food additives did not disrupt the gut microbiome at real doses.