Gut Bacteria Interactions Mapped in Comprehensive New Study

Bolor Buyanbadrakh, postdoctoral fellow at the Department of Chemistry
Photo Credit: Simon Jönsson

Scientific Frontline: Extended "At a Glance" Summary: Gut Microbiome Interactions

The Core Concept: Researchers have systematically mapped over 1,200 interactions among 36 representative human gut bacterial species to understand how they promote or inhibit each other's growth.

Key Distinction/Mechanism: The study reveals that negative (inhibitory) interactions dominate, largely due to bacteria altering their environment by increasing acidity (lowering pH); however, specific cooperative mechanisms were also identified, such as the use of extracellular vesicles or pH modification to support other species.

Major Frameworks/Components:

• Inhibitory Dominance: Most interactions are competitive, primarily driven by environmental acidification.
• Vesicle-Mediated Cooperation: Clostridium perfringens promotes the growth of Mediterraneibacter gnavus via the release of extracellular vesicles.
• pH Counteraction: Veillonella parvula increases environmental pH, counteracting acidification and enabling the growth of acid-sensitive species like Parabacteroides merdae.

Branch of Science: Microbiology, Molecular Biology, and Chemistry.

Future Application: The dataset and mechanistic insights provide a foundation for rationally predicting and manipulating microbiome composition for health benefits.

Why It Matters: Understanding these complex microbial communities is essential because they are directly linked to human digestion, immune function, and resistance to infection.

Photo Credit: Simon Jönsson

Understanding how bacteria influence one another is essential for understanding how microbial communities are formed and maintained. Researchers at Umeå University have now systematically mapped interactions among common gut bacteria, creating one of the most comprehensive datasets of its kind. Published in Nature Communications, the study reveals that inhibitory interactions dominate, while also identifying mechanisms through which some bacteria promote the growth of others.

The human gut contains hundreds of microbial species that form complex communities linked to digestion, immune function, and resistance to infection. Despite their importance, the interactions among many microbial species remain poorly understood.

By testing more than 1,200 interactions among 36 representative gut bacterial species, the researchers created one of the most comprehensive datasets of its kind.

The results showed that most interactions were negative, meaning that one species limited the growth of another. A major reason was that bacteria altered their environment, particularly by changing its pH, making it more acidic.

“Our results show that competition is a dominant feature of the gut microbiome. At the same time, we found specific examples of cooperation and identified the molecular mechanisms behind them,” says Bolor Buyanbadrakh, a postdoctoral fellow at the Department of Chemistry at Umeå University and the first author of the study.

One finding was that Clostridium perfringens promotes the growth of Mediterraneibacter gnavus through the release of extracellular vesicles, tiny particles released by bacteria that can carry molecules between cells. The study provides evidence that such vesicles can directly influence the growth of another bacterial species.

The researchers also discovered that Veillonella parvula can increase the pH of its surroundings, counteracting acidification caused by other bacteria. This change allowed acid-sensitive species, such as Parabacteroides merdae, to grow more effectively, even in more complex microbial communities.

André Mateus, assistant professor at the Department of Chemistry
Photo Credit: Mattias Pettersson

“Understanding how bacteria influence each other is essential if we want to predict or eventually manipulate microbiome composition in a rational way. Our work provides both a large interaction dataset and mechanistic insights that move the field in that direction,” says André Mateus, an assistant professor at the Department of Chemistry, team leader at the Laboratory for Molecular Infection Medicine Sweden (MIMS), and senior author of the study.

By revealing both competitive and cooperative mechanisms among gut bacteria, the study provides a foundation for predicting how microbial communities form and change over time.

Additional information: The study was carried out through a collaboration among researchers at the Department of Chemistry, the Department of Molecular Biology, the Laboratory for Molecular Infection Medicine Sweden (MIMS), and the Umeå Centre for Microbial Research (UCMR) at Umeå University. In addition to the Mateus group, the work involved the research groups of Madeleine Ramstedt, Sun Nyunt-Wai, and Björn Schröder. 

Funding: The study was supported by funding from the Swedish Research Council, the European Research Council (ERC), the Knut and Alice Wallenberg Foundation, Kempestiftelserna, and Jeanssons stiftelser.

Published in journal: Nature Communications

Title: Systematic profiling of growth interactions in human gut microbiome species

Authors: Bolor Buyanbadrakh, Elisabeth Baland, Paula Lambeck, Lucía Pérez Jiménez, Sandra M. Holmberg, Fabiola Puértolas-Balint, Eric Toh, Sun Nyunt Wai, Bjoern O. Schroeder, Madeleine Ramstedt, Shaochun Zhu, and André Mateus

Source/Credit: Umeå University | Simon Öhman Jönsson

Edited by: Scientific Frontline

Reference Number: mcb082226_01

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