Researchers have come up with a groundbreaking way to identify a vital group of gut microbes that are typically found in humans and play a significant role in maintaining health. They believe this discovery opens up exciting avenues for personalized nutrition and tailored treatments aimed at addressing chronic diseases linked to imbalances in the gut microbiome, such as diabetes, inflammatory bowel disease, and cancer.
A team of researchers at Rutgers University-New Brunswick, alongside international partners, has developed a new approach to pinpointing the essential gut microbes found in humans that are critical for health.
The findings, published in Cell, suggest that this discovery paves the way for innovative strategies in precision nutrition and personalized medical treatments designed to manage chronic conditions tied to gut microbiome imbalances, including diabetes, inflammatory bowel disease, and cancer.
The core microbiome includes a collection of microbes present in the digestive system that are vital for functions such as digestion, immune response, and mental wellness. When this core microbiome is diminished or lost, it can lead to a state known as dysbiosis, which is marked by an imbalance between helpful and harmful microbes in the gut. Dysbiosis has been associated with various chronic ailments, such as inflammatory bowel disease, metabolic issues, neurological disorders, chronic kidney disease, and some cancers.
Research has demonstrated that transferring beneficial fecal microbiota from a healthy colon to a diseased colon can improve these conditions, strongly suggesting that maintaining a core microbiome is essential for good health.
The fundamental structure of the core microbiome comprises two different groups of bacteria known as the Foundation Guild and the Pathobiont Guild. These groups engage in dynamic and stable interactions that are critical for sustaining human health. By employing artificial intelligence models, the Two Competing Guilds approach can analyze various populations unaffected by factors like ethnicity, geography, or disease types, and predict personalized responses to immunotherapy across a range of conditions.
The scientific community has yet to agree on what specifically makes up the core microbiome or on the most accurate ways to identify its key microbial members.
Traditional microbiome analysis methods typically define the core microbiome through commonly shared taxonomic units, such as species or genus, in human populations. Nevertheless, this categorization may fall short in detail. For instance, within a single species, certain strains can be either beneficial or harmful. While the well-known gut bacterium E. coli includes mostly benign strains, E. coli O157 is known to cause serious foodborne illnesses.
This new study addresses these challenges by utilizing high-quality genomes directly assembled from metagenomic sequencing datasets. Each genome is assigned a universal unique identifier for tracking its ecological behavior. This genome-specific strategy provides high-resolution analysis, minimizing noise, and includes genomes of novel, unclassifiable bacteria that are not limited by incomplete databases.
“Our research identifies the bacteria in the gut that remain interconnected regardless of challenges the body faces, like changes in diet or illness,” explained Liping Zhao, the Eveleigh-Fenton Chair of Applied Microbiology and a professor in the Department of Biochemistry and Microbiology at Rutgers School of Environmental and Biological Sciences. “By focusing on these resilient and interconnected microbes, we’ve devised a method to identify the most crucial microorganisms for sustaining our health.”
This method successfully identified two contrasting groups of core gut bacteria: the beneficial Foundation Guild and the potentially harmful but necessary Pathobiont Guild.
The Foundation Guild plays a vital role in structuring and stabilizing the entire gut microbiome. These bacteria help break down dietary fibers and produce short-chain fatty acids (SCFAs) like butyrate, which promote gut health by reinforcing the gut barrier, reducing inflammation, and acting as an energy source for colon cells. SCFAs are also essential for curbing harmful bacteria.
On the other hand, while the Pathobiont Guild is necessary in small amounts for immune education and vigilance, an overgrowth of these microbes can lead to disease progression.
The balance between these two guilds is like a seesaw—when the Foundation Guild is in charge, gut health prevails. However, if the Pathobiont Guild becomes dominant, dysbiosis may ensue, potentially leading to inflammation and exacerbating various chronic conditions.
“Our model aids in identifying these core bacterial groups and demonstrates how they can be fostered to keep their dominance,” Zhao added. “This opens new avenues for personalized nutrition and targeted therapies aimed at restoring balance within the gut microbiome.”
By focusing on the fiber-degradation genes of the Foundation Guild, personalized dietary guidelines could be developed to encourage these critical microbes’ ecological dominance.
The Two Competing Guilds model not only presents a fresh method but also sets a new benchmark for recognizing the members of the core microbiome. By asserting that members of the core microbiome must be consistently connected across diverse environments, the model enhances microbiome research standards, as per Zhao.
Zhao and his team intend to carry out a series of trials to enhance personalized therapies aimed at restoring the ecological dominance of the Foundation Guild in patients experiencing severe dysbiosis. By applying the Two Competing Guilds model in clinical circumstances, they aspire to translate their research into practical therapies that can substantially improve patient outcomes, even in cases previously deemed irreversible.
This study was a collaborative venture involving experts from Rutgers, Shanghai Jiao Tong University, Tufts University Medical School, and other institutions. The research was financially supported by several entities, including the New Jersey Institute for Food, Nutrition, and Health at Rutgers, the Canadian Institute for Advanced Research (CIFAR), Notitia Biotechnologies Company, and the Eveleigh-Fenton Endowed Chair Fund.
