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Researchers are delving deeper into the gut microbiome for answers about organisms other than bacteria

There’s far more to the gut microbiome than bacteria. Fungi, viruses and archaea all play roles in the human gut community, but are seldom part of the microbiome discussion.
These constituent organisms won’t be overlooked during Sunday’s AGA Committee Sponsored Symposium Microbiome Active Learning Session 200: The Nonbacterial Gut Microbiome in Health and Disease.

“The focus has always been on bacteria because it’s the low-hanging fruit in terms of sequencing,” said symposium moderator Gail Hecht, MD, AGAF, professor of medicine and microbiology/immunology, and chief of gastroenterology and nutrition at Loyola University Stritch School of Medicine, Chicago. “The initial technology could identify bacteria but has been slower to begin to identify other constituent organisms. In the past year, the technology has moved forward quickly enough that we are going to be able to get an analysis of bacteria, fungi, viruses and archaea.”

Sponsored by the AGA Center for Gut Microbiome Research and Education and the AGA Institute Council Microbiome & Microbial Diseases in the Gastrointestinal Tract Section, the symposium will feature a special wrinkle that makes it especially personal and uniquely “interactive.” Prior to the meeting, dozens of DDW® attendees submitted their own stool samples to the American Gut Project for analysis by 16S ribosomal RNA and shotgun metagenomic sequencing. This DDW-specific population will provide the core data for the symposium.

“American Gut has sequenced all the DNA in the DDW samples,” said founder Rob Knight, PhD, director of the Center for Microbiome Innovation and professor of pediatrics and computer science at the University of California, San Diego. He presented a similar session at DDW last year that focused on the bacterial microbiome.

“The primary goal of American Gut is to create as comprehensive a map of the human gut microbiome as we can, to bring in as many people from as many places and as many backgrounds as we can,” Dr. Knight said. “This session at DDW shows attendees just how complex and variable the microbiome really is.”

The roles of different organisms that make up the gut microbiome is far from clear. Some bacterial species are associated with disease and some with health, but most play an unknown role, according Gary Wu, MD, professor and co-director of the PennCHOP Microbiome Program at the University of Pennsylvania Perelman School of Medicine and the Children’s Hospital of Philadelphia.

“For example, there’s a huge interest in the role fungi play in inflammatory bowel disease [IBD],” Dr. Wu said. “Our lab and others have identified a specific fungal signature that is associated with IBD. We know there are certain types of immune receptors in the intestinal tract that respond particularly well to fungi, which suggests they may be important in health and disease. We just don’t know how right now.”

Another example Dr. Wu will discuss during the session involves archaea, which produce methane and are associated with constipation. But it’s not clear, Dr. Wu said, whether archaea growth and excessive methane production are the result of constipation, or if archaea and methane production play a role in the development of constipation.
“In this session, we will be looking at a completely different dimension of the microbes that live in the gut,” Dr. Wu said. “We are using much more advanced technology than has been available in the past to assess gut microbes that people may not know much about yet.”

Please refer to the DDW Mobile App or the Program section in Sunday’s DDW Daily News for additional details on this and other DDW® events.

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