Exploring microbial mysteries at META 2015

Julie Segre

Microbes are a hot topic at the moment, which helps explain the high level of excitement going into Synthesis + Selection of Host-Microbe Systems, a summer research symposium that took place July 31-Aug. 2 in Eugene. But the University of Oregon’s Microbial Ecology and Theory of Animals (META) Center for Systems Biology, which presented the conference, deserves a good deal of the credit say those who are familiar with the symposium and the META Center, one of 13 systems biology centers funded by the National Institutes of Health.

Judith Eisen

“There are relatively few conferences that focus on host-associated microbial communities and META is unique in that it can put together a small conference with a specific focus and a single track of high-quality scientific talks,” said Curtis Huttenhower, an associate professor of computational biology and bioinformatics at Harvard University who served as last year’s keynote speaker at the symposium. “(Director) Karen Guillemin worked hard to track the symposium this year toward systems and synthetic biology and saying ‘What can we do to quantitatively model microbial ecosystems and microbial communities? and ‘What can we do to program or change or intervene in them?”

Now in just its third year of operations, the META Center continues to build an international reputation as a hub for innovative microbiome research and the symposium is a part of the Center’s growing renown. The conference drew some 160 attendees — including microbiologists and other scientists such as Huttenhower from around the world. Additionally, there were UO faculty members from other departments, undergraduates, graduate students and curious community members.

For the second year in a row Nancy’s Yogurt sponsored the event. Although yogurt companies do not typically offer financial support to research conferences, Guillemin appealed to the firm based on a shared interest in microbes (Nancy’s was among the first yogurt makers to introduce yogurt made with probiotic microbial cultures to a mainstream market). As an added bonus, Nancy’s provided yogurt at the symposium.

At the opening night reception, the sense of anticipation was palpable as attendees filtered into the Hilton Eugene lobby, escaping the heat on a day when the high temperature hit 102 degrees.

“I’m excited to hear some talks,” said Brett Davis, a graduate student in the Masters Internship Program for Bioinformatics and Genetics.

“I think there’s a lot to learn here,” agreed Ryan Jiskra, a classmate in the same program. “I think most people don’t realize that we’rJulie Hale and Travis Wilese colonized by more bacteria than we are human cells by an order of magnitude … your flora is so important to your health.”

Davis and Jiskra were looking forward to the keynote address from Julie Segre, a senior investigator with the National Institutes of Health whose research examines bacteria and microbes of the skin microbiome and tracks hospital-acquired infections. Her address “Genomic Epidemiology,” focused on the use of genome sequencing to track antibiotic resistant bacteria in hospitals and drew a full house to one of the Hilton conference center ballrooms.

“A lot of attention has been focused on pathogens and we do need to care about pathogens, but the emergence of antibiotic resistance is something that is less of a biological question but a cultural imperative,” Segre said calling for an end to the “metaphor of warfare” when it comes to understanding the microbes all around us.

“We do want to keep antibiotics in our pockets, but we’ve given that away too cheaply and used them to protect us from things we don’t need to be protected from,” she said, referring to the problem of antibiotic resistant bacteria due to the inappropriate use of antibiotics.

Last year’s META symposium, titled Modeling our Microbial Selves, was focused on understanding the mutually beneficial coexistence of humans and their symbiotic bacteria. This year’s event, Synthesis + Selection, sought to explore how host-microbe systems function by learning how they can be built from scratch and how they respond to natural and experimentally imposed selective pressures — forces that alter the behavior and fitness of living organisms.

“I would say that the first symposium was a bit more of an exploration of what the META Center is (exploring the concept of Modeling our Microbial Selves in terms of experimental, computational, and theoretical modeling), Guillemin said. “While this one was more forward looking to where the META Center might want to go in the future into areas of synthetic biology and experimental evolution.”

From its inception, one of the distinguishing characteristics of the META Center has been its focus not just on identifying microbes, but on zeroing in on how microbes function as a part of a system.

“A lot of the work that’s being done (in microbiome research) is very descriptive work,” Guillemin said. “So while it’s possible to describe what bacteria are on your elbow and on your shoulder there’s been a bottleneck in terms of being able to understand ‘What does that mean?’ ‘Why does it matter?’ ‘How does this impact your health?’”

Interdisciplinarity is another key ingredient of the Center, says META’s Bill Cresko, one of 12 affiliated researchers from four different departments and four institutes and an associate professor of biology at the UO.

“The center brings together researchers from different disciplines that historically wouldn’t have talked to one another, this is really where the advances in the life sciences are coming from as we move forward,” Cresko explained. “It’s different branches, a molecular biologist and an evolutionary geneticist now coming back together and saying ‘Wow, if we actually combine our approaches here we get new insights and new discoveries about a system.’”

That interdisciplinarity was on display at the symposium. University of Texas chemist Jason Shear gave one of the most anticipated presentations on the second day of the conference. He spoke about his work using a 3D printer and the fluid-trapping techniques of microfluidics to print synthetic microscopic bacterial communities on slides and examine how those microbes interact. A talk by Stanford biologist Tadashi Fukami highlighted previous META presentations and detailed Fukami’s research examining how species assemble into ecological communities.Students on opening night

As with last year’s symposium, presentations intentionally did not include time for questions and answers, and speakers instead participated in panel discussions designed to stimulate discussion. Connections to last year’s event could also be seen in shorter presentations by postdocs and graduate students tied to last year’s marquee speakers. Alexander Eng, a University of Washington graduate student in the lab of genome sciences professor Elhanan Borenstein, gave a short talk on research using an algorithm to design minimal microbial communities. Stephen Nayfach, a graduate student at the University of California San Francisco who works with computational biologist Katie Pollard, gave a short presentation on gene content and “biogeography” of microbial species.

Undergraduate students were also featured in the symposium as part of META’s training and outreach initiatives. The center aims to increase training opportunities and encourage diversity through the Alaska Oregon Research Training Alliance (AORTA). The program builds on ties with the University of Alaska and provides Native Americans and Alaska Natives with the opportunity to participate in research and training during an intensive summer outreach program at the UO.

Poster session

One of the AORTA participants, Adam Paskvan, discussed his research during the symposium poster session. A senior from the University of Alaska Fairbanks studying chemistry with a concentration in biochemistry, Paskvan examined two different genera of bacteria isolated from the gut of a zebrafish. Like other students in the program he devised and carried out the research project on his own, with only the guidance of his mentors, Dave Anderson and Jeneva Anderson, both postdoctoral scholars in the Institute of Molecular Biology.

“I hadn’t used a lot of these (research) techniques before,” Paskvan said, contrasting the smaller Alaska lab he was accustomed to with the Guillemin lab where he conducted his research. “When we arrived we didn’t really know what we would be studying. We found some preliminary data and went from there. Dave and Jeneva were amazing mentors.”

AORTA Team

The META symposium tied into a half-day interdisciplinary workshop examining the ethics and philosophy of microbiology. Presented by UO biology professor Brendan Bohannan and Nicolae Morar, an assistant professor of philosophy and environmental studies, the workshop had a significant crossover audience with the META Symposium. It featured anthropologists, philosophers and biophysicists discussing philosophical and ethical questions such as “What does it mean to be a multicellular organism?”