Jonathan A. Eisen

Performance comparison of probe-capture enrichment sequencing of viruses in wastewater influent and settled solids from the California Central Valley

The paper compares two viral sequencing pipelines from wastewater influent and solids, finding that solids capture more DNA viruses while influent captures more RNA viruses, with probe-capture enrichment providing comparable results across fractions.

Eukaryotic MAGs recovered from deep metagenomic sequencing of the seagrass, Zostera marina, include a novel chytrid in the order Lobulomycetales

This study uses deep metagenomic sequencing to recover MAGs from Zostera marina, identifying a novel chytrid in the Lobulomycetales order and other eukaryotic lineages with genomic novelty.

Convergent lignocellulose degradation in terrestrial crabs is driven by distinct host genus-specific microbial communities

This study identifies genus-specific microbial communities in terrestrial crabs that enable lignocellulose degradation through convergent functional adaptations.

Microbiome Assembly in Zostera marina during early host development: An EcoFAB 2.0 Application for Aquatic Plant-Microbe Interactions

This paper uses EcoFAB 2.0 to study microbiome assembly in Zostera marina seedlings, identifying stage-specific microbial indicators and demonstrating controlled microbiome manipulation.

Skin microbiomes of frogs vary among individuals and body regions, revealing differences that reflect known patterns of chytrid infection

The study examines skin microbiome variation in frogs, finding that tank environments influence microbiomes more than individual identity, and identifying potential Bd-inhibitory bacteria.

Genomic streamlining of seagrass-associated Colletotrichum sp. may be related to its adaptation to a marine monocot host

This study presents the genome of a seagrass-associated Colletotrichum sp. and finds it has a streamlined genome with fewer genes and gene families compared to related species, possibly linked to its marine ecological niche.

Phoronids and their tubes harbor distinct microbiomes compared to surrounding sediment

This study investigates the microbiomes of phoronids and their tubes, finding distinct microbial communities compared to surrounding sediment and suggesting potential roles in sulfur cycling.

Genomes from Bacteria Associated with the Canine Oral Cavity: a Test Case for Automated Genome-Based Taxonomic Assignment

The paper compares manual and automated taxonomic assignment methods for bacterial genomes from the canine oral cavity, finding GTDB to be less subjective and labor-intensive.

Recent Outbreaks of Shigellosis in California Caused by Two Distinct Populations of Shigella sonnei With Increased Virulence or Fluoroquinolone Resistance

The paper investigates two distinct Shigella sonnei populations in California outbreaks, identifying increased virulence and fluoroquinolone resistance as key factors.