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Joint Berkeley Initiative for Microbiome Science

Joint Berkeley Initiative for Microbiome Science

  • About
    • Leadership
    • Scientific Advisory Board
    • Partners
    • News
  • Community
    • People
    • Spotlights
  • Education
    • Graduate Courses
    • Undergraduate Courses
    • Seminars and Events
  • Connect
    • Contact
  • Opportunities
    • Current Openings
    • Graduate Opportunities
    • Post-Baccalaureate Opportunities
    • Undergraduate Opportunities

News

Sequencing Salamanders

The Rosenblum lab reports host and habitat influences on the microbial communities living on salamanders. Published December 16, 2021 in FEMS Microbiology Ecology: https://doi.org/10.1093/femsec/fiab162



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Genome Editing in Communities

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.



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New Data Sharing Initiative

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



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Predicting Persistence

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



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Better Together: CRAGE + CRISPR

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



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Microbial Arms Races

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



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Fungi Around the World

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



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Adding Branches to the Tree of Life

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



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Expanding Phage Collections

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



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Iron Metabolism in Drought

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



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Protists in the Microbiome

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



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New Single-Cell Sequencing Pipeline

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



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Ploidy Problems

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



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Biofilms in Oral Bacteria

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



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Functional Genetics of a Gut Commensal

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



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Finding Bacterial Killer Genes

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



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Farming Practices Affect Mycorrhizae

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



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Complex Mutualisms

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



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Water Quality

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



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Cataloguing Metagenomes

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



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Bacterial Genome Editing

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



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Stressed Sorghum

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



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Drought Effects on Redwood Microbiome

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



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Automating Bioengineering

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/ 



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Mini-Cas in Mega-Phages

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 



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