: Visualizing Microbiome Time Series Data in R.

Despite playing a key role in the health of their hosts, host-associated microbial communities demonstrate considerable variation over time. These communities comprise thousands of temporally dynamic taxa, which makes visualizing microbial time series data challenging. As such, a method to visualize both the proportional and absolute change in the relative abundance of multiple taxa across multiple subjects over time is needed.

Alkaline Urine in the Emergency Department Predicts Nitrofurantoin Resistance.

Background: The Proteeae group (i.e., Proteus species, Morganella morganii, and Providencia species) frequently causes urinary tract infections (UTIs) and is generally resistant to nitrofurantoin.

Community-led, integrated, reproducible multi-omics with anvi'o.

Big data abound in microbiology, but the workflows designed to enable researchers to interpret data can constrain the biological questions that can be asked. Five years after anvi’o was first published, this community-led multi-omics platform is maturing into an open software ecosystem that reduces constraints in ‘omics data analyses.