Matt Olm

📢 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.

One simple trick that statisticians hate If you don't like the results, just ignore the control group

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… 🧵

Overall, after a year, I’m really happy with where the lab’s at. It feels like we’ve gone from a blank room (and empty hard drive) to a functioning research ecosystem. Can’t wait to start publishing to share our results with the world, and I’m so thankful to all my amazing lab members!

Another surprise is actually the sheer number of meetings. But they’re also more varied and interesting than I expected; a mix of mentoring, working on research problems, and discussing new ideas with potential collaborators all the time.

Work/life balance is also better than I expected. Having a toddler at home probably helps with this though, as I don’t really have the option to work late even if I wanted to! There have only been once or twice where deadlines have forced a short period of late nights and grueling hours.

Transitioning from doing research myself to mentoring others in completing that research has been more challenging than expected, but it’s amazing to get to see data appear without doing any of the hard work of generating it!

Overall it’s a total joy, and in almost every way just as fun as I had hoped it would be 😀. Getting to satisfy my curiosity on a daily basis while contributing to the global scientific enterprise and working with the next generation of scientists is just an incredible way to spend my days.

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...

Thanks, @zaminiqbal.bsky.social - very glad to see this out! A great contribution

Wow so impressive!

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]

Assemblies of long-read metagenomes suffer from diverse errors Genomes from metagenomes have revolutionised our understanding of microbial diversity, ecology, and evolution, propelling advances in basic science, biomedicine, and biotechnology. Assembly algorithms...

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.

Maternal balanced energy-protein supplementation reshapes the maternal gut microbiome and enhances carbohydrate metabolism in infants: a randomized controlled trial Nature Communications - Here, in a sub-study of the MISAME-III randomized controlled trial, the authors show that maternal balanced energy-protein supplementation during pregnancy and lactation...

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 pauses its Ph.D. admissions process amid research funding uncertainty A spokesperson for the University told WESA Friday that the school has "temporarily paused additional Ph.D. offers of admission," while Pitt works to understand how proposed federal funding cuts could...

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).

Gut microbiota strain richness is species specific and affects engraftment - Nature Strain richness of gut microbiota ecosystems is a key characteristic underpinning engraftment in faecal microbiota transplantation, and could improve the design of defined live biotherapeutic…

#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…

De novo designed proteins neutralize lethal snake venom toxins - Nature Deep learning methods have been used to design proteins that can neutralize the effects of three-finger toxins found in snake venom, which could lead to the development of safer and more accessible an...

EXTREMELY cool and demonstrates clearly the promise of deep learning + bio.

www.nature.com/articles/s41...

A screenshot of a webpage titled "Taxonomy Time Machine" showing the taxonomic lineage and descendants of the Influenza A Virus

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...

Thanks for the shout-out, Noah!

In my new lab at CU Boulder we are exploring how IgA binding shifts in infancy and states of disease, and the extent to which IgA actively shapes the human microbiota. Wet-lab protocol at doi.org/10.17504/pro...; bioinformatics code at github.com/MrOlm/MIGSeq.... Thanks for reading! (5/5)

We also found that there are specific genes linked to binding (indicating that microbes in the mucosa are typically targeted) (Fig. 3), that IgA-bound microbes have lower replication rates (Fig. 4), and that IgA binding is highly integrated with other components of the immune system (Fig. 5) (4/5)