Nov. 10, 2020
When CALIT2 held its first microbiome symposium in 2013, microbiologist Karen Nelson, president of the J. Craig Venter Institute, shared with the audience her vision for the nascent field of microbiome research. “We’re just starting to understand what these microbes do,” said Nelson, who led the genetic sequencing of the first human gut microbiome in 2006. She added: “I think we’re in the early stages of understanding what the microbiome means to health and disease. Now that we have technologies available … I think we’re going to be making significant inroads.”
Nelson, who later was elected to the National Academy of Sciences, was right. Improved sequencing techniques and lower costs have opened the floodgates to a boom in research on microbiomes, the communities of microorganisms that live in the environment and in humans.
Essential to human and environmental health, researchers now know that microbiomes govern the complex relationships between human health and disease. It is estimated that there are more than 1,000 different kinds of microorganisms living inside our bodies, containing 300 times more genes than our human cells.
Outside of the body, microbe communities regenerate soil nutrients, purify drinking water and stabilize the atmosphere. Each year, scientists better understand the degree to which microbiomes impact everything around them.
But in 2013, the field, especially in the area of human microbiomes, was relatively unexplored. Pierre Baldi, UC Irvine Distinguished Professor of computer science and director of the campus’s Institute for Genomics and Bioinformatics, along with CALIT2 Founding Director Larry Smarr, initiated the idea for a conference to bring together local experts. They called it Microbiome Connections. “The idea came up during various conversations between the two of us,” Baldi says. “We thought it was important because the field was relatively new at the time and [it was] clearly a new, significant direction of research. We wanted to be among the first.”
G.P. Li, CALIT2 Irvine division director, supported the idea immediately. “From a CALIT2 point of view, we always talk about digital transformation of health, energy, the environment and culture,” Li says. “At first, this was a health issue. Later, we added the environmental piece. But from the beginning, we saw the alignment with CALIT2’s mission to use information and communication technology for the digital transformations necessary to improve people’s lives.”
The conference, now an annual affair held in the fall, has grown in size and expertise. Registration more than doubled over the last seven years, from 116 attendees in 2013 to 260 last year. While the original conference featured only human microbiome experts, the event now features a full roster of topics connected to both human and environmental microbiomes.
Subject matter has included microbial biogeography, biofilm formation, marine bacteria, wild herbivores and dietary toxins, antibiotic resistance, health care infections and sustainable sanitation, among dozens of other topics.
A day-long workshop was added in 2017, and now, a poster session has been added, too. The SoCal Microbiome Conference, as it is now called, has outgrown the CALIT2 auditorium, its home for the past seven years, and will move to the Beckman Center. Originally scheduled for this September, the next conference will be held in fall 2021 instead due to the worldwide virus pandemic.
Microbiome research is growing by leaps and bounds on campus as well. While human and environmental microbiomes have traditionally been studied separately, UCI researchers have begun to bridge the gap. In 2017, UCI funded a new microbiome initiative with the goal of bringing together human and environmental microbiome collaborators.
The brainchild of two campus researchers – Jennifer Martiny, ecology and evolutionary biology professor; and Katrine Whiteson, assistant professor of molecular biology and biochemistry – the initiative seeks not only to encourage collaboration but also to train a new generation of interdisciplinary microbiome scientists.
The annual conference now falls under the purview of the Microbiome Initiative. “But we still always run everything by Pierre and Larry and get their blessing,” Whiteson says.
“There’s a huge amount of interest in learning how to do this kind of science,” adds Whiteson, who for several years was the only human microbiome researcher on campus. When she started her campus lab in 2014, she says, she was inundated with requests for collaboration, most of which she didn’t have the bandwidth to accommodate. Elizabeth Bess, assistant professor of chemistry, joined the effort a couple of years ago, and two new human-focused microbiome researchers will be added in biosciences by fall quarter.
The Microbiome Initiative hosts a series of training workshops as well as a weekly consulting hour that helps develop new projects, connect labs across disciplines and collect preliminary data. More than 90 individual researchers attended at least one consulting session last year seeking help with microbiome-related projects.
The initiative also sponsors a monthly update meeting, pilot project awards, fellowships for researchers and assistance with grant writing.
Growth in the field and on campus recently spawned the Microbiome Centers Consortium, also spearheaded by Martiny and Whiteson. Founded last year, the consortium serves as a network for university and national laboratory microbiome centers to promote collaboration and share intellectual and technical strengths.
“Around the time that Katrine and I started the microbiome initiative, we started realizing that there were lots of other universities that had these microbiome initiatives,” Martiny says. “And we were curious: how were they doing things?”
Twenty-eight initial member institutions attended the inaugural meeting at UCI last year; since then, the number of consortium centers has exploded to more than 80 and increases almost every month. A second annual meeting was scheduled in Chicago this June but has been postponed, again because of the coronavirus.
“It’s still early days for the consortium,” says Whiteson, “but we’ve been in touch with people from all over the world. Getting these tips and tricks from other microbiome centers about how they’re doing things is really, really helpful.”
The annual conference with roots at CALIT2 continues to grow in size and stature. “There was a lot of very forward-thinking science from the beginning because of the way Pierre and Larry put it together,” Whiteson says. “Our goal with the conference is to continue to highlight Southern California microbiome scientists. Southern California is a leader in this area, so we really attempt to showcase the great work going on in the region.”
– Anna Lynn Spitzer