Thursday, 16 November 2017 11:05

ASM Hosts National Microbiome Data Collaborative Workshop

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Published in ASM News

Dr. Chris Kellogg of the U.S. Geological Survey was among the attendees at the meeting of the National Microbiome Data Collaborative Colloquium, held at ASM Headquarters November 9-10, 2017. The meeting was organized by Ed DeLong of the University of Hawaii and Claire Fraser of the Institute for Genome Sciences, University of Maryland.

The first meeting was held at the Joint Genome Institute in February 2017, followed by a “town hall” at ASM Microbe 2017. The town hall, aimed at getting input from a broader group, was attended by more than 300 people, “more than we expected,” says Kellogg. “It was standing room only.”

Dr. Kellogg, a Research Microbiologist at the St. Petersburg Coastal and Marine Science Center, is part of the Microbiome Interagency Working Group that arose from the National Microbiome Initiative launched in May 2016. That initiative’s goals are to support fundamental research, develop new technologies, and engage more people in the field. “Many scientists working in microbiome research are not aware of similar or related efforts elsewhere,” says Kellogg. The MIWG is a way for federal agencies to work together, “leveraging the efforts” of the various agencies to collaborate and coordinate efforts, “[avoiding duplication] in budgets and programs,” she adds.

The NMDC was formed to address some of the issues facing microbiome researchers in reporting and analyzing their data. Microbiome research covers a very broad area of disciplines, institutions, and physical locations, and current methods generate very large datasets. Being able to access, analyze, and compare these datasets is a fundamental need for the field. “We are starting with DNA sequences,” says Kellogg, “leaving the omics—transcriptomics, protemics, metabolomics—aside for now. If we can’t get this right with the DNA, we have no hope with the rest of it.” Nonetheless, the plan is to make efforts scalable so that additional types of data can be accommodated.

The NMDC is open, so that anyone can join, and is currently hosted at https://jgi.doe.gov/join-national-microbiome-data-collaborative-trellis/ . The steps arising from the November meeting are aimed at standardizing protocols so that data can be more easily compared. The approach, says Kellogg, is to “look for best practices that can keep as much commonality as possible,” recognizing that different situations may require departures based on what actually can be made to work. In addition, any such standards still need to be flexible enough to accommodate the inevitable changes in technology that will happen over time.

Ease of use is key in developing tools and standards. Though the collaborative greatly needs “hardcore computational biologists,” says Kellogg, “designing things only for power users does not do well for wide adoption. Everyone is already busy enough, so we need to keep the barriers low if we want people to integrate [NMDC standards] into their work.”

One of the points that came up repeatedly during the discussions, according to ASM CEO Stefano Bertuzzi, is that “metadata is data.” Kellogg elaborates, pointing out that “what constitutes ‘metadata’ is a matter of perspective—maybe it’s better to start calling it associated data. It’s all data, and it needs to be treated as being important.” Among the ways that the Collaborative hopes to make microbiome data more useful is making sure that analyses are associated with data, enabling resources to be saved and shared. “People won’t be repeatedly using resources to redo the same analyses,” Kellogg says. “Analyze it once, and have the analyzed data available as well as the raw data.” Another way to be more efficient with resources, she adds, is to “move tools to data, rather than data to tools.” Some participants pointed out that as data sets grow in size, even downloading them starts to have significant costs in time and energy. “These sequencing datasets,” Kellogg says, “are enormous. The data all need to go into [the] repository, and we need to have tools that allow you to go in, analyze, and come back out. You don’t want to move the datasets.”

Most of the tools needed are already in existence, but need to be assessed, chosen, and tweaked to fit the needs of the microbiome community. It is anticipated that training resources such as Data Carpentry (http://www.datacarpentry.org/) and online communities like the microBEnet microbiology of the built environment network (https://www.microbe.net/) will help members of the Collaborative get up to speed on their skills for using and analyzing large datasets.

One of the highlights of the meeting, says Kellogg, was that there was “so much agreement on the major points, especially the need for standardization. There was broad agreement that now is the right time for this to happen, the tools are there, and the field is mature.” The plan going forward is for more town hall meetings at the Ocean Sciences Meeting in February 2018 then at ASM Microbe 2018 in June. A white paper is forthcoming, adds Kellogg. The participants are invested, and “now we can identify champions for different chunks of it” to move forward, she says.

USGS Microbiome Research Fact Sheet

 

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