More than 100 completely new species of bacteria from healthy people’s intestines have been discovered, isolated, and revealed today in a study published by an international team of researchers studying the gut microbiome, with the goal of developing new approaches to treating gastrointestinal disorders, infections, and immune conditions.
“This important resource will fundamentally change the way researchers study the microbiome,” declared the study’s first author, Samuel Forster, PhD, of the Wellcome Sanger Institute and Hudson Institute of Medical Research in Australia.
The study, “A human gut bacterial genome and culture collection for improved metagenomic analyses,” was published today in Nature Biotechnology.
The team—consisting of scientists from Wellcome Sanger, Hudson Institute of Medical Research, Australia, and EMBL’s European Bioinformatics Institute—has created a collection of human intestinal bacteria that they assert is the largest and most comprehensive gathered to date.
The researchers have unveiled the Human Gastrointestinal Bacteria Culture Collection (HBC). The HBC is a comprehensive set of 737 whole-genome-sequenced bacterial isolates, representing 273 species (105 of them being novel species) from 31 families found in the human gastrointestinal microbiota.
The researchers studied fecal samples from 20 people from the UK and Canada, and successfully grew and DNA-sequenced 737 individual bacterial strains from these. An 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.
According to the researchers, their new culture collection and reference genomes will make it much cheaper and easier to determine which bacteria are present within communities of people, as well as to research their role in disease.
“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,” stated Trevor Lawley, PhD, a senior author of the study who is also at Wellcome Sanger. “Ultimately, this will lead us towards developing new diagnostics and treatments for diseases such as gastrointestinal disorders, infections and immune conditions.”
Standard methods to understand how the gut microbiome affects human health have involved sequencing the DNA from mixed samples of gut bacteria to try to understand each component. Such studies have been hampered by the lack of individually-isolated bacteria and reference genomes available from them.
“Genome-sequenced isolates enable functional capacity to be inferred from the genetic repertoire of the reference genomes. This eliminates the need to perform ultra-deep metagenomic sequencing and ensures that complete functional pathways are contained within individual bacterium,” the researchers explained.
“In addition to improved accuracy, this method also has the capacity to improve sensitivity for functional analysis, allowing detection of functions that, although not prevalent, may represent fundamental differences between study cohorts,” the investigators added.