Analysis of Temporal Changes in Growth and Gene Expression for Commensal Gut Microbes in Response to the Polyphenol Naringenin.

In this study, the effect of the flavanone naringenin on the growth and genetic expression of the commensal gut microbes, Ruminococcus gauvreauii, Bifidobacterium catenulatum, and Enterococcus caccae, was analyzed. Analysis of growth curves revealed that Ruminococcus gauvreauii was unaffected by naringenin, Bifidobacterium catenulatum was slightly enhanced by naringenin, and Enterococcus caccae was severely inhibited by naringenin. Changes in genetic expression due to naringenin were determined using single-molecule RNA sequencing. Analysis revealed the following responses to naringenin: Ruminococcus gauvreauii upregulated genes involved in iron uptake; Bifidobacterium catenulatum upregulated genes involved in cellular metabolism, DNA repair and molecular transport, and downregulated genes involved in thymidine biosynthesis and metabolism; Enterococcus caccae upregulated pathways involved in transcription and protein transport and downregulated genes responsible for sugar transport and purine synthesis. For the first time, changes in growth and gene expression for commensal gut bacteria in response to naringenin were documented.

Metagenomic profiling of historic Colorado Front Range flood impact on distribution of riverine antibiotic resistance genes.

Record-breaking floods in September 2013 caused massive damage to homes and infrastructure across the Colorado Front Range and heavily impacted the Cache La Poudre River watershed. Given the unique nature of this watershed as a test-bed for tracking environmental pathways of antibiotic resistance gene (ARG) dissemination, we sought to determine the impact of extreme flooding on ARG reservoirs in river water and sediment. We utilized high-throughput DNA sequencing to obtain metagenomic profiles of ARGs before and after flooding, and investigated 23 antibiotics and 14 metals as putative selective agents during post-flood recovery. With 277 ARG subtypes identified across samples, total bulk water ARGs decreased following the flood but recovered to near pre-flood abundances by ten months post-flood at both a pristine site and at a site historically heavily influenced by wastewater treatment plants and animal feeding operations. Network analysis of de novo assembled sequencing reads into 52,556 scaffolds identified ARGs likely located on mobile genetic elements, with up to 11 ARGs per plasmid-associated scaffold. Bulk water bacterial phylogeny correlated with ARG profiles while sediment phylogeny varied along the river's anthropogenic gradient. This rare flood afforded the opportunity to gain deeper insight into factors influencing the spread of ARGs in watersheds.