1) Want to know how much of your metagenome is eukaryotic? No references? No problem. We developed SingleM microbial fraction (SMF) and ran it on 250k metagenomes https://www.biorxiv.org/content/10.1101/2024.05.16.594470v1.

If you know what Eukaryotes are there, you can filter reads by mapping to their genomes. However, often you don’t know what’s in your sample, or the euk doesn’t have a genome.

#metagenomics #bioinformatics #genomics #microbiomes #microbialecology

Large-scale estimation of bacterial and archaeal DNA prevalence in metagenomes reveals biome-specific patterns

Metagenomes often contain many reads derived from eukaryotes. However, there is usually no reliable method for estimating the prevalence of non-microbial reads in a metagenome, forcing many analysis techniques to make the often-faulty assumption that…

^bioRxiv

Happy to see the first experimental project I led finally out in the world! With Jeremy Moore, Sydney Olsen, and Mike Travisano

We combined experimental evolution and mathematical modeling to ask: do bacteria evolve to swim away from phages?

1/n

https://doi.org/10.1101/2023.04.29.538831

#microbiology #evolution #ecology #phages #phage #bacteria #MicrobialEvolution #MicrobialEcology

Fight not flight: parasites drive the bacterial evolution of resistance, not avoidance

In the face of ubiquitous threats from parasites, hosts often evolve strategies to resist infection or to altogether avoid contact with parasites. At the microbial scale, bacteria frequently encounter viral parasites, bacteriophages.

^bioRxiv