A game-changer in probiotics? Microbiome discovery could stimulate innovation

05 Feb 2019 --- Scientists are one step closer to uncovering how the gut microbiome affects our health, after isolating more than 100 previously unknown species of bacteria from healthy people’s intestines. The involved researchers have created what they say is the most “comprehensive public database of human health-associated intestinal bacteria to date.” It could provide a wealth of information on treating different disorders, as well as a diverse range of potential probiotics.

The research comes from the Wellcome Sanger Institute, Hudson Institute of Medical Research, Australia and the European Molecular Biology Laboratory's (EMBL) European Bioinformatics Institute.

Bacteria comprise about 2 percent of an individual’s body weight and the gut microbiome is a major bacterial site and an essential contributor to human health.

“Imbalances in our gut microbiome can contribute to diseases and complex conditions such as Inflammatory Bowel Disease, Irritable Bowel Syndrome allergies and obesity. However, as many species of gut bacteria are extremely difficult to grow in the laboratory, there is a huge gap in our knowledge of them,” the researchers report.

Published in Nature Biotechnology, the findings can help scientists detect faster and more accurately which bacteria are present in the human gut. This will also provide the foundation to develop new ways of treating diseases such as gastrointestinal disorders, infections and immune conditions.

As part of this study, researchers studied fecal samples from 20 people from the UK and Canada. They successfully grew and DNA sequenced 737 individual bacterial strains from these.

The researcher report that analysis of these isolates revealed 273 separate bacterial species, including 173 that had never previously been sequenced. Of these, 105 species had never even been isolated before.

“The gut microbiome plays a major part in health and disease. This important resource will fundamentally change the way researchers study the microbiome,” says Dr. Samuel Forster, first author on the paper from the Wellcome Sanger Institute and Hudson Institute of Medical Research, Australia.

“Despite the remarkable diversity of bacteria represented in the collection everything we have found existed within just 20 individuals,” Dr. Forster tells NutritionInsight. “The next step is to identify key groups of people where further culturing will capture the maximum bacterial diversity. This could be due to lifestyle, diet or other factors.”

“It is essential to continue to build these resources of bacterial isolates with matched genome sequences. As we do this, it will become increasingly possible to measure the diversity of bacteria within both healthy people and patient cohorts. This will provide enormous advances in the field of microbiome-based medicine,” he continues.

Standard methods to understand how the gut microbiome affect human health involve sequencing the DNA from mixed samples of gut bacteria to try to understand each component. However, these studies have been severely hampered by the lack of individually isolated bacteria and reference genomes from them.

The new culture collection and reference genomes will make it much cheaper and easier for researchers to determine which bacteria are present within communities of people and research their role in disease.

“For researchers trying to find out which species of bacteria are present in a person's microbiome, the database of reference genomes from pure isolates of gut bacteria is crucial,” notes Dr. Rob Finn, an author from EMBL's European Bioinformatics Institute. “Then if they want to test a hypothesis, for example, that a particular species is enriched in a certain disease, they can get the isolate itself from the collection and physically test in the laboratory if this species seems to be important.”

“This culture collection of individual bacteria will be a game-changer for basic and translational microbiome research. By culturing the unculturable, we have created a resource that will make microbiome analysis faster, cheaper and more accurate and will allow further study of their biology and functions,” explains Dr. Trevor Lawley, Senior author from the Wellcome Sanger Institute.

Ultimately, Lawley states that this approach will provide avenues for developing new diagnostics and treatments for diseases such as gastrointestinal disorders, infections and immune conditions.

Forster tells NutritionInsight that although significant further research is required to understand how diet can impact and change the microbiome, novel understandings on bacterial isolates have the potential to be “extremely informative for both the food and beverage industry.”

“With access to these bacterial isolates, it will now be possible to test their nutrient usage and metabolic potential,” Forster puts forward.

“This new resource provides a diverse range of potential probiotics that are now available for investigations. While there remains a long way to go in this research area, this resource represents the enormous potential to advance this field,” he says.

“Pre- and probiotics remain an active area of research. This field has made significant progress in the commercialization of bacterial preparations for wide-scale consumer administration. With this new bacterial resource, we now have the ability to focus on the vast array of novel bacterial species that may have key roles in the treatment of numerous diseases,” he concludes.

Additional reporting by Lucy Gunn

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