A Berkeley Lab team analyzed the genotypes and phenotypes of several Arthrobacter strains to correlate cellular functions to their location at varying depths within a single sediment core and in nearby groundwater. They found that Arthrobacter, as a genus, has remarkable flexibility in altering its suites of carbon degradation genes. This genomic variation was found to be linked to the individual strain’s environment and is the basis for Arthrobacter’s ability to break down a wide variety of complex carbon sources.
CRISPR enzymes are like super scissors: they cut, delete, and add genes to a specific kind of cell, one at a time. But now, UC Berkeley faculty and Biosciences Area researchers have figured out how to add or modify genes within a microbial community of many different species, coining the phrase, “community editing.”
Computer code co-developed by a scientist from Lawrence Berkeley National Laboratory (Berkeley Lab) and embraced by the global science community over two decades has been hailed by Nature as one of “ten computer codes that transformed science.”
Researchers in the Environmental Genomics and Systems Biology (EGSB) and Biological Systems and Engineering (BSE) Divisions at Berkeley Lab employed a large-scale functional genomics approach to systematically characterize Bacteroides thetaiotaomicron, a beneficial bacterium prevalent in the human gut. They performed hundreds of genome-wide fitness assays and identified new functions for 40 proteins, including antibiotic tolerance, polysaccharide degradation, and colonization of the GI tract in germ-free mice.
Viruses that infect bacteria, or phages, are continually evolving ways to target and exploit their specific hosts. Their bacterial hosts, in turn, are continually evolving means to evade the phages. These perpetual battles for survival yield incredibly diverse molecular arsenals that researchers are itching to study, yet doing so can be tedious and labor-intensive.
A team led by Berkeley Lab scientists has developed an efficient and inexpensive new method to gain insight into these defensive strategies. They reported in PLOS Biology that a combination of three recently developed techniques can reveal which bacterial receptors phages exploit to infect the cell, as well as what cellular mechanisms the bacteria use to respond to a phage infection.