Biosciences News

Taking their cue from Nature, Berkeley Lab researchers have engineered living cells to act as a starting point, or “scaffold,” for the self-assembly of composite materials. The resulting engineered living materials (ELMs) represent a new class of material that may open the door to advanced applications in bioelectronics, biosensing, and smart materials.

Leading the effort was Caroline Ajo-Franklin, whose lab is part of the Molecular Foundry, a DOE Office of Science User Facility, and who holds a secondary appointment in the Molecular Biophysics and Integrated Bioimaging (MBIB) Division. A study describing the work was recently published in ACS Synthetic Biology.

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Understanding nutrient flows within microbial communities is important to a wide range of fields, including medicine, bioremediation, carbon sequestration, and sustainable biofuel development. Now, researchers have built the Web of Microbes, a unique database and visualization tool that lets scientists quickly see patterns in microbial food webs. The tool, which was created through a collaboration among biologists and computational researchers at Berkeley Lab, NERSC, and the Joint Genome Institute (JGI), offers insights that other metabolic pathway databases cannot. “While most existing databases focus on metabolic pathways or identifications, the Web of Microbes is unique in displaying information on which metabolites are consumed or released by an organism in an environment such as soil,” said Suzanne Kosina, lead author on the paper and senior research associate in Biosciences’ Environmental Genomics and Systems Biology (EGSB) Division.

Read more on the Computing Sciences website.

In Nature, researchers in Berkeley Lab’s Biosciences Area, the Gladstone Institutes, and the Chan-Zuckerberg Biohub presented nearly 61,000 microbial genomes that were computationally reconstructed from 3,810 publicly available human gut metagenomes, which are datasets of all the genetic material present in a microbiome sample. The metagenome-assembled genomes (MAGs) included 2,058 previously unknown species, bringing the number of known human gut species to 4,558 and increasing the phylogenetic diversity of sequenced gut bacteria by 50 percent. This work helps answer the question of why certain microbes have not been cultivated in the lab. Read more in the Berkeley Lab News Center.

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Researchers from Biosciences and the Computational Research Division (CRD) have formed a new integrated Computational Biosciences Group to develop tools for addressing a range of scientific problems that cross organizational lines. Members of the group include (pictured, from left): Héctor García Martin of the Biological Systems and Engineering and the Environmental Genomics and Systems Biology Divisions (BSE/EGSB), acting group lead Kris Bouchard (BSE), Chris Mungall (EGSB), Andrew Tritt of the Computational Research Division(CRD), Oliver Rübel (CRD), and Ben Brown (EGSB). Additional members not pictured are: Aydın Buluç (CRD), Silvia Crivelli (CRD), Hans Johansen (CRD), Talita Perciano (CRD), and Peter Zwart of the Molecular Biophysics and Integrated Bioimaging Division (MBIB).

Read more on the Computing Sciences website.

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.