I've said it before, but a major issue with the current peer review system is that reviewers think their goal is to "improve" a paper that has no critical flaws and can be published as is

🦠What are the early-life colonization & assembly dynamics of bacteriophages? Out today online in Cell Host & Microbe, our paper took a strain-resolved approach to investigate early phage colonizers. Article: doi.org/10.1016/j.chom…

Beyond thrilled that my postdoc paper from Howitt Lab on protists in the microbiota is out at Cell! This huge collaborative effort with the amazing Bhatt and Sonnenburg labs revealed exciting biology about fascinating, neglected gut eukaryotes! authors.elsevier.com/c/1iFQYL7PXmeTc

Milk to mucus:How B. fragilis colonizes the gut. Preview by Matt Olm noel mueller highlighting Dr Ekaterina Buzun Dr. Hiutung Chu 朱曉彤 @chulab.bsky.social work showing mechanism for HMO digestion by B.fragilis & demonstrating same pathway works on mucus to establish gut residency cell.com/cell-host-micr…

Very balanced and nicely written discussion on bugs in bioinformatics software. Bugs like this are much more common than most people realize

Just released version 3.5.0 of dRep (github.com/MrOlm/drep), which now allows skani (github.com/bluenote-1577/…) to be used as a comparison algorithm! (as well as removing a few dependencies that made installation annoying in some cases).

A fantastic postdoc position in bioinformatic microbiome research is available in The Sonnenburg Lab at Stanford! I'm leaving after 4 great years to start my lab at Boulder, and Justin is looking to fill my position. DM me or email Justin ([email protected]) for questions

New tool from Cultivarium: models to predict oxygen tolerance, temperature, salinity, and pH optima from a genome - without using pesky gene annotations. Very excited to share this resource. Quick explainer: 1/10

Excited to hear incoming CU Boulder professor Matt Olm’s talk on ‘Applying meta genomic sequencing to decipher the human infant gut microbiome.’

When you receive a peer-reviewer suggestion for your manuscript that you think is silly or unnecessary, but isn't harmful, how do you usually respond?

Happy to announce that our (me and Yun William Yu) metagenome profiler sylph (github.com/bluenote-1577/…) is now published in Nature Biotechnology! 1/5

Hospitalization throws the preterm gut microbiome off-key Cell Host & Microbe Matt Olm cell.com/cell-host-micr…

I just made a thread on BlueSky about our recent publication on IgA binding- check it out if interested bsky.app/profile/mattol…