An international research team has sequenced and archived the world’s most comprehensive collection of human gut bacteria, identifying a total of 105 new species of bacteria that naturally populate the human gastrointestinal (GI) tract.
This new bacteria “data center” will allow future researchers to more easily identify and study the role of individual bacterial species across a variety of intestinal disorders, such as inflammatory bowel disease (IBD).
The study, “A human gut bacterial genome and culture collection for improved metagenomic analyses,” was published in the journal Nature Biotechnology.
The human GI tract is populated by a diverse and constantly changing group of microorganisms, also known as the gut microbiome, which is mainly made up of different types of bacteria. Still other microorganisms such as viruses and fungi also reside there.
Imbalances in the levels of these different organisms in the gut, particularly bacteria, have been shown to contribute to the development of different diseases such as IBD.
To identify microbial species within the GI tract, researchers often use a method called metagenomic sequencing. This method allows the sequencing of genetic information (DNA content) from mixed samples of several gut bacteria. However, this technique is often unable to differentiate between bacterial species or strains that are similar to each other, making it difficult to identify and research the roles of individual bacterial species in disease.
Because of the technical limitations of sequencing, there is still a lot that isn’t known regarding the different bacterial species that reside in the gut.
Researchers from the Wellcome Sanger Institute, Hudson Institute of Medical Research in Australia, and EMBL’s European Bioinformatics Institute worked together to build the Human Gastrointestinal Bacteria Culture Collection (HBC), a bank of GI bacterial isolates that can be used by scientists in future studies.
The international team first cultured and purified bacterial isolates from fecal samples of eight healthy adults from the United Kingdom and 12 from North America.
After sequencing a total of 737 individual bacterial strains, the researchers were able to identify 273 bacterial species in the feces of these subjects. These included 173 species that had not been previously sequenced and 105 that were newly identified.
Overall, this data has increased the information on human GI bacterial genomes by 37%, the researchers said.
They found that many of the newly discovered species occur frequently within the human population, meaning these may represent an important part of the human gut microbiome that needs to be further explored.
Next, the researchers combined the genetic data collected from the HBC with publicly available information from the National Center for Biotechnology Information (NCBI) genome database of 617 human gastrointestinal-associated bacterial genomes. Using this approach they created the Human Gastrointestinal Microbiota Genome Collection (HGG), the largest database of human gut bacteria.
“This study has led to the creation of the largest and most comprehensive public database of human health-associated intestinal bacteria,” Samuel Forster, PhD, a researcher at the Wellcome Sanger Institute and Hudson Institute of Medical Research, and lead author of the study, said in a press release. “The gut microbiome plays a major in health and disease. This important resource will fundamentally change the way researchers study the microbiome.”
“Our analysis demonstrates a 61.1% increase in classification potential with the HGG compared to the existing genomes,” the researchers wrote.
More importantly, researchers now have access to genome sequenced isolates of bacterial species that can be used for investigating the role of specific bacteria in human health and 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,” said Rob Finn, PhD, team leader at EMBL’s European Bioinformatics Institute and co-author of the study. “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.”
The availability of the HBC will also reduce the costs associated with new research studies focused on GI bacterial analysis.
“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. Ultimately, this will lead us towards developing new diagnostics and treatments for diseases such as gastrointestinal disorders, infections and immune conditions,” said Trevor Lawley, PhD, senior author of the study from the Wellcome Sanger Institute.