Biosciences Area

A Community-driven Data Science System to Advance Microbiome Research

The National Microbiome Data Collaborative will develop an open-access framework for harnessing microbiome data to accelerate discoveries

The National Microbiome Data Collaborative (NMDC), a new initiative aimed at empowering microbiome research, is gearing up its pilot phase after receiving $10 million of funding from the U.S. Department of Energy (DOE) Office of Science. Led by Lawrence Berkeley National Laboratory (Berkeley Lab), in partnership with Los Alamos (LANL), Oak Ridge (ORNL), and Pacific Northwest (PNNL) National Laboratories, the NMDC will leverage DOE’s existing data-science resources and high-performance computing systems to develop a framework that facilitates more efficient use of microbiome data for applications in energy, environment, health, and agriculture.

KDM5 Deficiency Alters Gut Microbiome, Social Behavior in Flies

Genome-wide association (GWAS) and familial studies have found mutations that disrupt the function of KDM5 proteins in patients with autism spectrum disorders and related intellectual disabilities. Biological Systems and Engineering (BSE) Division researchers Jian-Hua Mao, Antoine Snijders, and Susan Celniker, in collaboration with a team of scientists led by Xingyin Liu at Nanjing Medical University (NMU) in China, used genetic tools in Drosophila to delineate how KDM5 contributes to autism and intellectual disability.

Beetle’s Gut Microbiome is Nature’s Biorefinery

A study led by Eoin Brodie and Javier Ceja-Navarro in Berkeley Lab’s Earth and Environmental Sciences Area (EESA) provides new insights into how the wood-eating passalid beetle’s complex digestive tract and resident microbes are able to efficiently turn tough plant polymers like lignin and cellulose into food and fuel. By bringing together a team of experts—including collaborators at Pacific Northwest National Laboratory and Lawrence Livermore National Laboratory—and using advanced molecular biology tools combined with spectrometry and tiny sensors, they discovered that the beetle’s gut is made up of specialized compartments, each with a distinct microbiome, that work together in a manner similar to a factory production line. “The key innovation that nature has provided here is a way to combine biochemical processes that are otherwise incompatible,” said Brodie, deputy director of EESA’s Climate and Ecosystem Sciences Division, who has a secondary affiliation in Biosciences’ Environmental Genomics and Systems Biology (EGSB) Division. The study was published in Nature Microbiology.

Read more in the Berkeley Lab News Center.

Megaphages Discovered in Human Gut Bacteria

While sequencing gut bacteria from people in Bangladesh, Berkeley Lab’s Jillian Banfield discovered phages, viruses that infect and reproduce inside bacteria, twice as big as any previously found in humans. She and her colleagues found the snippets of megaphage DNA in a CRISPR segment of one type of bacteria, Prevotella, that is uncommon in people eating a high-fat, low-fiber Westernized diet. Banfield and her team named the clade of megaphages “Lak phage” after the Laksam Upazila area of Bangladesh where they were found.

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