All you want for christmas is.... transposon mutagenesis! Our new work at @cultivarium.bsky.social screening lots of transposon vectors in lots of bacteria, from @charliegilbert.bsky.social and team. Transposon and promoter modular parts available on Addgene (pooled library will be there soon too)

Just got back from an incredible trip to Aga Khan University in Karachi, Pakistan, where I led a 3-day workshop on microbiome bioinformatics. I was blown away by the students, the research facilities (both on the Karachi campus and at the rural Matiari field site), and the hospitality of my hosts!

📢 New preprint is out on bioRxiv 📢: How much does virome prep influence our view of the human gut virome? Short answer: a lot. Long answer: doi.org/10.1101/2025... Different methods lead to distinct community structures, richness, and major virus-host abundance patterns. 🧵 1/5

Very happy to share our recent work @cultivarium.bsky.social on genetic tools for Ideonella sakaiensis, a (Betaproteo-)bacterium that degrades PET plastic. We identified a plasmid vector for the strain and generated a large RB-TnSeq library, screening for genes impacting plastic degradation.

A lifehack for turning "non-significant" results into pure gold? (ICYMI) statsepi.substack.com/p/one-simple...

The one year anniversary of my arrival at UBC flew by a month ago. Thanks to fellow newPI and former grad school pal @mattolm.bsky.social for reminding me of one of the biggest lessons I’ve learned this past year: *make* time to reflect! Here are some reflections on my first year as a PI & prof… 🧵

I have officially been a professor for just over a year! I’ve been reflecting on what this first year has been like and wanted to share a few thoughts on how it compares to the expectations I had when I decided to pursue this career over a decade ago.

My fantastic department at CU Boulder is hiring a tenure-track Assistant Professor! This is a broad search spanning nearly all areas of biology. Applications are due Nov 13, 2025. Feel free to reach out to me with questions, and please share widely. jobs.colorado.edu/jobs/JobDeta...

I reviewed this paper a bit ago and have been waiting for it to come out. A great resource for us Bifidobacteria researchers!

Cool paper, I appreciate how they compare observed vs expected breadth of coverage. Missing phylogenetics, could be very interesting to genotype and/or assemble some of these pathogens if coverage is high enough

Do people in the same household share strains when they have the same species? How many cells transmit when a strain is shared? Can strain composition be dynamic when species composition is stable? We answer these and related questions for the facial skin microbiome in our latest paper. 🧵[1/10]

I am very happy (and anxious) to share with you our most recent work in which we evaluated four of the most popular long-read assemblers, www.biorxiv.org/content/10.1... and tell you just a little bit about it in the following 🧵

Many pregnant women in rural #BurkinaFaso struggle to eat enough to meet the demands of their growing babies. This leads to higher rates of #miscarriage, still- and #preterm birth, and intrauterine growth restriction.

Just yesterday, we published a deep dive into the physiological effects of #BEP supplementation on both mom and baby: rdcu.be/ed5Wb 🥰

Good thread and good accompanying article. The conceptualization of all Alzheimer's research as a monolith of closed minded thought based on fraud is just a myth that doesn't stand up to scrutiny www.statnews.com/2025/02/14/a...

The University of Pittsburgh confirmed Friday that there would be no new Ph.D. offers of admission while Pitt works to understand how reduced federal aid could impact the institution.

good news, finally submitted my grant to nsf on Technical biases in quantifying the inclusive fitness of minority alleles under diversifying selection in diverse microbial communities

Putting on my editor's hat for my yearly rant about scientists who do not review manuscripts enough for journals. As a quantitative approach, consider reviewing 3X the papers submitted by you or your lab in a calendar year (the number 3X comes from if you expect 3 reviews for your own papers).

#reading "Gut microbiota strain richness is species specific and affects engraftment" by Chen-Liaw et al. As usual, quoted text is from manuscript [slight edits], unquoted is mine These are idiosyncratic personal notes, not a comprehensive review! https://www.nature.com/articles/s41586…

EXTREMELY cool and demonstrates clearly the promise of deep learning + bio. www.nature.com/articles/s41...

NCBI's Taxonomy changes over time. We built Taxonomy Time Machine to track these changes: 🕰️ app: taxonomy.onecodex.com 📄 pre-print: www.biorxiv.org/content/10.1...

New specific comment on the use of newer scientific names for species. TL;DR a reminder that once a name is validly published, it can always be used. You don't *have* to use a new name just because someone published it. zenodo.org/records/1461...

Our technique for studying strain-level IgA binding in the microbiome is out now at @naturemicrobiol.bsky.social! Fascinated by IgA since Sean Spencer told me about it, here we make some fundamental discoveries about strain-level IgA dynamics in the healthy human gut (1/5) doi.org/10.1038/s415...

Thanks for the shout-out, Dan!

OUT NOW: Metagenomic immunoglobulin sequencing (MIg-seq) reveals IgA coating of microbial strains in the healthy human gut by Justin Sonnenburg, Matt Olm, Sean Spencer & co #microsky www.nature.com/articles/s41...

Bifidobacteria are the primary consumers of breast milk and very important in the infant gut. However, current methods for profiling them require custom implementation. @ben-braun.bsky.social tackled this during his rotation in my lab by creating a fast, robust, and user-friendly tool. Check it out!

Just finished my first semester teaching as a professor! I taught biostatistics in R- despite not knowing R before this class. Teaching while learning was a bit chaotic, but at least now I understand both ANOVA and cryptic R dependency error messages!

Today we report that an engineered skin bacterium, swabbed gently on the head of a mouse, can unleash a potent antibody response against a pathogen. Could lead to topical vaccines that are applied in a cream. @djenetbousbaine.bsky.social led the charge... @natureportfolio.bsky.social 1/55

Experiment was 70% successful again, but this time with friends! Here's to 100% success in the new year! @jingqian.bsky.social

One of my favorite visualizations, showing the sizes of host and microbial cells on the same scale, spanning several orders of magnitude From a review by Baker et al : pubmed.ncbi.nlm.nih.gov/37700024/

Fish brains host microbes- could human brains host them too? I shared my "inherently skeptical", but intrigued, thoughts in this fun article.

Here's a fake account for folks to report if you have a minute: bsky.app/profile/erct... I am kinda worried about how moderation will be work in the near future with bluesky. Already seeing an uptick in fake accounts, harassers, spam. Maybe people will start to limit responses to followed only?

Our lab's first IgA experiment was 70% successful. Here's to making the next one 100%! @jingqian.bsky.social

Hi friends new and old! I study how microbes interact and evolve in complex communities like the human gut microbiome.🦠🧬💩 I'm thrilled to share that I'm starting a lab at UC Irvine in April 2025 and am recruiting at all levels - please spread the word! kxuelab.com More about my work below...🧵1/n

It can take a lot of time to figure out if a bioinformatics program is useful and worth investing time in. Here's how I quickly decide if it's worth trying: ✅ Recommended by peers ✅ >100 GitHub stars ✅ Clear documentation ❌ Journal impact factor is irrelevant  Agree? What are your heuristics?

Something unexpected about starting a new lab: the amount of physical labor involved in unboxing and setting up all the equipment! Grateful for my students' enthusiasm and teamwork in getting everything up and running!

Some thoughts on this call to action: I am very optimistic on future applications of industrial and environmental microbiology for environmental remediation and sustainable bioproduction - it's a big interest of mine! - but some caveats to be realistic about: 1/n academic.oup.com/ismej/articl...

I had such a good time at the Rust Belt Microbiome Conference! Fantastic science, fantastic people, and so fun to be back in Pittsburgh for a few days.

Beautiful work - isolation of a crassphage, and turns out it is a phage-plasmid!

A fantastic postdoc position in bioinformatic microbiome research is available in Justin Sonnenburg's 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

And thank you to @mattolm.bsky.social and Noel Mueller for their insightful Preview of our work! www.cell.com/cell-host-mi...

Check out our latest paper on how human milk oligosaccharides trigger the B. fragilis colonization program, led by Katya Buzun, in the current issue of Cell Host & Microbe! 🧪🧫🦠#MicroSky www.cell.com/cell-host-mi...

Wow, this is a strong study without obvious issues to me, but such a confusing result, IDK what to even think Like someone decided to see if a treatment we don't understand mechanistically at all would cure a syndrome we don't understand mechanistically at all and somehow that actually worked!

Really impressed by this super fast, useful, and well-thought out program. It's great to see someone with true math and coding skills contributing to our microbial bioinformatics community!

Excited to share our new technique for studying IgA binding in the microbiome! Fascinated by IgA since joining the Sonnenburg Lab, this work beautifully leverages Dr. Sean Spencers's immunology & my metagenomics expertise to make fundamental discoveries about IgA in the gut doi.org/10.1101/2023...