Adair L. Borges, Atanas Radkov, and Peter S. Thuy-Boun
Published: Dec 19, 2022
This pub details a process for phage amplification and concentration, DNA extraction, and HPLC and MS analysis of phage nucleosides. We optimized the approach with model phages known to use non-canonical nucleosides in their DNA, but plan to apply it for other phages.
Adair L. Borges, Rachel J. Dutton, Elizabeth A. McDaniel, Taylor Reiter, and Emily C.P. Weiss
Published: Mar 11, 2023
How do you approach getting a microbiome set up in a new lab? We’re sharing protocols for how we collected, stocked, and sequenced a set of cheese rind microbiomes and generated a high-quality metagenomics resource for future computational studies.
Januka Athukoralage, Adair L. Borges, and Taylor Reiter
Published: Mar 14, 2023
We struggled to isolate enough phage mRNA for HPLC as we searched for new nucleoside chemistries. Ribodepleting the abundant extracted rRNA introduced contaminating DNA, and we were still left with more bacterial mRNA than phage transcripts. We suggest an alternative approach.
Adair L. Borges, Rachel J. Dutton, Elizabeth A. McDaniel, Atanas Radkov, Taylor Reiter, and Emily C.P. Weiss
Published: Jul 19, 2023
We sampled cheese microbial communities to discover bacteriophages with unusual genome chemistries. We isolated 114 bacterial host strains and 17 phages, and identified one phage with a probable arabinose hypermodification of hydroxymethylcytosine.
Adair L. Borges, Feridun Mert Celebi, Kira E. Poskanzer, and Taylor Reiter
Published: Aug 25, 2023
We implemented a lightweight method to identify viruses in 342 human brain bulk and single-cell sequencing data sets, and identified two glioblastoma cells from a single patient that contained deltapolyomavirus sequences.