News

The Banfield and Doudna labs announce DART-ET-seq, a method for targeted DNA insertion in a community context. Published December 6, 2021 in Nature Microbiology: https://doi.org/10.1038/s41564-021-01014-7.

Announcement of the National Microbiome Data Collaborative Data Portal, a resource for hosting microbiome data that is accessible and usable across systems and studies: https://academic.oup.com/nar/article/50/D1/D828/6414581

New work from the Banfield Lab (Environmental Science, Policy, and Management) identifies traits of bacteria that help them to survive the infant gut. Published September 21st, 2021 in Cell Reports Medicine: https://doi.org/10.1016/j.xcrm.2021.100393

The Yoshikuni group (Lawrence Berkeley Lab) integrates chassis-independent recombinase-assisted genome engineering with CRISPR to rapidly profile the function of bacterial biosynthetic gene clusters. Published September 10th, 2021 in Cell Chemical Biology: https://doi.org/10.1016/j.chembiol.2021.08.009

A multi-year study from the Koskella lab (Integrative Biology) describes co-evolutionary arms races between bacteria and phages in natural microbial communities. Published in The American Naturalist:  https://doi.org/10.1086/717181

A new study from the Dawson lab (Integrative Biology) analyzes biogeographic patterns of free-living and host-associated fungi. Read more in Ecology Letters: https://doi.org/10.1111/ele.13886

Congratulations to the Banfield Lab (Environmental Science, Policy, and Management) for two new publications describing the diversity and metabolic capabilities of the largely uncultivated, ultra-small bacteria comprising the Candidate Phyla Radiation. Published July 13th, 2021 and August 17th, 2021 in mSystems: https://doi.org/10.1128/mBio.00521-21, https://doi.org/10.1128/mSystems.01205-20

Nikos Kyrpides (Joint Genome Institute) and colleagues compiled a database of nearly 200,000 bacteriophage genomes and predicted protein clusters. Published June 24, 2021 in Nature Microbiology: https://doi.org/10.1038/s41564-021-00928-6

Drought stress disrupts iron homeostasis in plant roots, leading to changes in root-associated microbial communities. Published by the Coleman-Derr lab (Plant and Microbial Biology) in Nature Communications, May 28, 2021: https://doi.org/10.1038/s41467-021-23553-7

A large-scale field experiment from the Firestone lab (Environmental Science, Policy, and Management) shows that distinct protist communities inhabit the rhizosphere in different plant developmental stages, shedding new light on an understudied component of the plant microbiome. Published April 28, 2021 in Microbiome: https://doi.org/10.1186/s40168-021-01042-9

New pipeline developed by Jan-Feng Cheng (Joint Genome Institute) and colleagues for single-cell sequencing of microbial eukaryotes. Published April 23, 2021 in iScience: https://www.cell.com/iscience/pdf/S2589-0042(21)00258-3.pdf

New work from the Coleman-Derr lab (Plant and Microbial Biology) evaluated the contributions of polyploidy and domestication to wheat microbiome composition. Published March 18, 2021 in PLOS One: https://doi.org/10.1371/journal.pone.0248030

The Zhang lab (Chemical and Biomolecular Engineering) identified biochemical mechanisms of adhesion and biofilm formations in Streptococcus mutans, a significant contributor to tooth decay in the human oral microbiota. Published March 4, 2021 in Nature Chemical Biology: https://doi.org/10.1038/s41589-021-00745-2

The Deutschbauer and Arkin groups (Lawrence Berkeley Lab) reported the results of transposon mutagenesis of Bacteroides thetaiotaomicron, a commensal bacterium in the human gut. Published March 2, 2021 in Cell Reports: https://doi.org/10.1016/j.celrep.2021.108789

A team led by Vivek Mutalik and Adam Arkin identified (Lawrence Berkeley Lab) identified producers and targets of tailocins in soil bacterial genomes. Published March 1, 2021 in ISME: https://doi.org/10.1038/s41396-021-00921-1

The Coleman-Derr lab (Plant and Microbial Biology) reported changes in microbiome composition, gene content, and activity of arbuscular mycorrhizal fungi across agricultural management strategies in the San Jaoquin Valley. Published December 11, 2020 in Applied and Environmental Microbiology: https://aem.asm.org/content/87/5/e02345-20.abstract

Soil microbiota mediate tradeoffs between development timing and heat stress in Caenorhabditis elegans, in a study by the Shapira lab (Integrative Biology) published November 13, 2020 in Microorganisms: https://www.mdpi.com/2076-2607/8/11/1781

New study from the Nelson lab (Civil and Environmental Engineering) assessed the effects of water quality metrics like chlorine levels and pH on microbial cell counts. Published November 10, 2020 in Environmental Science: Water Research & Technology: https://pubs.rsc.org/en/content/articlehtml/2020/ew/d0ew00809e

Catalog of metagenome-assembled genomes from a range of environments described by Emiley Eloe-Fadrosh and colleagues at the Joint Genome Institute. Published in Nature Biotechnology on November 9, 2020: https://doi.org/10.1038/s41587-020-00769-4

The Cheng group (Joint Genome Institute) developed CRAGE, a method for engineering large gene clusters into bacterial chromosomes. Published November 4, 2020 in PLOS One: https://doi.org/10.1371/journal.pone.0241867

Heat and drought stress affect the Sorghum microbiome in different ways, but both involve recruitment of Actinobacteria. Reported in Phytobiomes by the Coleman-Derr lab on October 7, 2020: https://apsjournals.apsnet.org/doi/pdf/10.1094/PBIOMES-07-20-0052-R

The Dawson lab (Integrative Biology) identified Actinobacteria enrichment in the microbiomes of redwood tree roots under dry conditions. Published October 1, 2020 in Molecular Ecology: https://doi.org/10.1111/mec.15666

Machine Learning Takes on Synthetic Biology: Algorithms Can Bioengineer Cells for You https://newscenter.lbl.gov/2020/09/25/machine-learning-takes-on-synthetic-biology-algorithms-can-bioengineer-cells-for-you/ 

Megaphages harbor mini-Cas proteins ideal for gene editing https://news.berkeley.edu/2020/07/16/megaphages-harbor-mini-cas-proteins-ideal-for-gene-editing/ https://science.sciencemag.org/content/369/6501/333.long 

New study from the Yelick group (Lawrence Berkeley Lab) showed that MetaHipMer, a new tool for coassembly of large metagenome sequence datasets, recovers more complete genomes with lower error rates than sample-by-sample assembly. Published July 1, 2020 in Scientific Reports: https://www.nature.com/articles/s41598-020-67416-5