Community assembly modeling of microbial evolution within Barrett's esophagus and esophageal adenocarcinoma.

Mathematical modeling of somatic evolution, a process impacting both host cells and microbial communities in the human body, can capture important dynamics driving carcinogenesis. Here we considered models for esophageal adenocarcinoma (EAC), a cancer that has dramatically increased in incidence over the past few decades in Western populations, with high case fatality rates due to late-stage diagnoses. Despite advancements in genomic analyses of the precursor Barrett's esophagus (BE), prevention of late-stage EAC remains a significant clinical challenge.

Identification of Volatile Compounds in Pennycress Protein Isolates Produced by Both Alkaline and Salt-Based Processes.

Volatile off-notes in ground pennycress seeds, ground defatted pennycress seed, and the final protein isolates (produced from the defatted seeds by alkaline or salt extraction) were identified and "quantified" relative to an internal standard. Volatiles contributing off-notes were identified based on mass spectra, retention indices, and aroma descriptors. The compounds that produced the strongest odors based on gas chromatography:olfactometry were identified as potential aroma impact compounds.

Integration of 168,000 samples reveals global patterns of the human gut microbiome.

The factors shaping human microbiome variation are a major focus of biomedical research. While other fields have used large sequencing compendia to extract insights requiring otherwise impractical sample sizes, the microbiome field has lacked a comparably sized resource for the 16S rRNA gene amplicon sequencing commonly used to quantify microbiome composition. To address this gap, we processed 168,464 publicly available human gut microbiome samples with a uniform pipeline.

Comparison of sampling and culture methods for the recovery of yeast from hospital surfaces.

Objective: To compare the recovery of yeast from hospital surfaces from two different collection methods: Eswab moistened with molecular water, and premoistened stick-mounted sponge.

Design: Comparison of collection methods for the recovery of yeast in the hospital environment.

Setting: This study took place at intensive care units of a large academic medical center.

Incomplete human reference genomes can drive false sex biases and expose patient-identifying information in metagenomic data.

As next-generation sequencing technologies produce deeper genome coverages at lower costs, there is a critical need for reliable computational host DNA removal in metagenomic data. We find that insufficient host filtration using prior human genome references can introduce false sex biases and inadvertently permit flow-through of host-specific DNA during bioinformatic analyses, which could be exploited for individual identification. To address these issues, we introduce and benchmark three host filtration methods of varying throughput, with concomitant applications across low biomass samples such as skin and high microbial biomass datasets including fecal samples.