Emily C.P. Weiss

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.

Seeing how microbes are organized within a community can inspire hypotheses about how species interact with each other. We used HiPR-FISH spatial imaging to look at the distribution of microbes within five distinct microbial communities growing on the surface of aged cheeses.

We are interested in neuroactive metabolites that influence animal behavior. Some fungi have horizontally transferred neuroactive metabolite pathways between species. We used a horizontal gene transfer detection pipeline to screen for novel fungal genes tied to neuroactivity.

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.

Some human proteins are encoded by genes with repetitive sequences, which, if they expand, damage the nervous system and cause disorders like Huntington’s disease. We found animals with similar proteins that have more repeats than we’ve ever seen in healthy people.

We previously released a draft genome assembly for the lone star tick, A. americanum. We've now predicted genes from this assembly to use for downstream functional characterization and comparative genomics efforts.

Peptigate predicts bioactive peptides from transcriptomes. It integrates existing tools to predict sORF-encoded peptides, cleavage peptides, and RiPPs, then annotates them for bioactivity and other properties. We welcome feedback on expanding its capabilities.