When we think of ecosystems, we imagine valleys and forests. But at the recent Multi-omics for Microbiomes conference, we learned that there are microbial ecosystems everywhere: growing on our teeth, catching the sun's rays while bobbing along in the ocean, and soaking up moisture in the soil that covers the forest floor.
"This conference was unusual in the way that it brought so many different disciplines together," said PNNL's Janet Jansson, the conference chair.
Soil lovers united at the Multi-omics for Microbiomes conference.
Co-hosted by Pacific Northwest National Laboratory's Microbiomes in Transition (MinT) Initiative and Department Of Energy's Environmental Molecular Sciences Laboratory (EMSL), this three-day event hosted nearly 200 scientists representing 12 countries. The conference, held in Pasco, Washington Aug. 1 to 3, brought together a diverse group of scientists and multiple sponsors. (These included Waters, ThermoFisher Scientific, TerraGenome, QIAGEN, Agilent, Bruker, Illumina, Bayer, Microorganisms, Soylent, and Phase Genomics.) The sponsors had fun giveaways for our scientists, such as stuffed DNA molecules.
Scientists presented their research either in one of two poster sessions or during one of six different oral sessions, which covered multiple topics: from human-associated microbiomes to advanced multi-omics methods. During the presentations, we learned about how scientists apply multi-omics approaches to understand complex microbial communities, design new technologies to increase our understanding of microbiomes, and develop computational tools to analyze and visualize -omics data.
"We're gonna talk about dirt. The microbes are hungry. They want their phosphorus. They want their nitrogen."
Home is where the microbes are
Scientists typically use multi-omics to study microbial communities in the gut and soil. Keynote speaker Rob Knight from the University of California, San Diego kicked off the gut discussion with a bang. "What if your gut came equipped with a time bomb?" he asked. "You'd want to know what made it tick and how to diffuse it."
Then Rosa Krajmalnik-Brown from Arizona State University talked about the gut-brain connection and how children with autism have less diversity in their gut microbiome compared to neurotypical children. But, she said, there's hope. "The amount of DNA that we have in our second genome, our microbiome, is something that we can change." Krajmalnik-Brown and her team have found that fecal transplants in autistic children have relieved some autism symptoms. Her talk came with a warning, however. "As exciting as this sounds," she said, "don't try this at home."
PNNL's Emily Graham explained how she studies microbial communities through space and time.
We left the world of the gut microbes behind when Melanie Mayes from Oakridge National Laboratory in Tennessee took the stage. "Big switch," she said. "We're gonna talk about dirt. The microbes are hungry. They want their phosphorus. They want their nitrogen." PNNL's Emily Graham and Malak Tfaily joined the soil-microbe conversation by talking about how PNNL studies microbial communities both right here near the Columbia River and as far away as the bogs and fens of Sweden.
Then we heard snippets about a variety of other ecosystems. Sonya Dyhrman from Columbia University took us to the ocean to talk about cyanobacteria called Trichodesmium. Stanford's Diana Proctor talked about communities on individual teeth: Each tooth has its own microbiome! And keynote speaker Bruce Hungate from Northern Arizona University listed a few abstract ecosystems: a tumor and a network that describes how opportunistic pathogens travel between people to spread disease.
The right microbe for the job
Identifying microbes in a new environment is only the beginning. Then researchers move on to more in-depth questions, such as what are these microbes actually doing? Dan Buckley from Cornell had an answer: Ask the microbes.
By using a technique called stable isotope probing, or SIP, scientists can watch labeled molecules travel from organism to organism. Using this method, "we can go beyond just who ate that carbon," Buckley said. "We want to know who ate it first and who ate it second." Many researchers at the conference also use SIP or SIP-like variations to watch nutrients travel through their communities.
Another hot topic was separating out molecules-like metabolites-from ecosystems. PNNL's Erin Baker talked about how her team's ion mobility mass spectrometry coupled with mass spectrometry system is starting to get promising results. It can isolate molecules that no other system can separate, she said.
Experiments that answer questions like "Who's there?" and "What are these microbes doing?" can get big. So some researchers talked about new methods to help biologists sort through their data.
PNNL's Lisa Bramer discussed a new framework that researchers can use to access their data. Using this technology, users can visualize their results as well as sort data and look for statistical trends. Bramer hopes this program will help scientists understand their data and come up with new biological questions.
Theodore Alexandrov, a researcher at the European Molecular Biology Laboratory, also shared a new bioinformatics platform he's helped develop. Using this platform, researchers can pull metabolites out of large datasets. The cloud-based platform allows users to quickly upload their data and start analysis.
Now it's time for the scientists to take all this new information back to their own labs. PNNL postdocs Peyton Smith and Taniya RoyChowdhury said they found the conference both useful and awe-inspiring. They acquired helpful hints for their own projects and learned about completely different research areas.
"That is the real hallmark of success," says Jansson. "When you come to a conference and then you leave with some new aspects of knowledge."
Stay tuned for the next Multi-omics for Microbiomes conference in the summer of 2019.