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Matt Olm

@mattolm.bsky.social
2K followers 212 following 51 posts

Assistant Professor at CU Boulder Studying the human microbiome www.colorado.edu/lab/olm

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Matt Olm @mattolm.bsky.social · 07/10/2026
Sharable link: rdcu.be/9D1PAYzgMhea Coverage from NYT: www.nytimes.com/2026/10/07/s... Coverage from NPR: www.npr.org/2026/10/07/n... Coverage from Stanford: med.stanford.edu/news/all-new...
nytimes.com
Was the Human Gut Healthier in Ancient Times? (Gift Article)
The microbiome isn’t what it used to be in many parts of the world. The shift may be affecting the well-being of people in industrialized countries.
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Matt Olm @mattolm.bsky.social · 07/10/2026
An amazing collaboration between the Sonnenburg lab and Good lab at Stanford, the Tsimane Health and Life History Project (tsimane.anth.ucsb.edu), and the Tsimane and Hadza communities who made this possible.
tsimane.anth.ucsb.edu
The UNM-UCSB Tsimane Health and Life History Project
The UNM-Tsimane Health and Life History Project
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Matt Olm @mattolm.bsky.social · 07/10/2026
My final postdoc project is out today in Nature! We show microbes co-migrated with humans out of Africa; three independent methods agree, and timing matches archaeological / genetic evidence (Fig. 4c). Seeing Fig. 4c for 1st time was one of my most memorable "eureka" moments! doi.org/10.1038/s415...
doi.org
Prehistoric global migration of vanishing gut microbes with humans - Nature
Microbial species disappearing from industrialized populations have evolved with humans over millennia and migrated worldwide with them—this may have consequences for human health.
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Matt Olm @mattolm.bsky.social · 29/09/2026
Thanks to my student Asher Albrecht for presenting the paper at our journal club today!
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Matt Olm @mattolm.bsky.social · 29/09/2026
This is an interesting paper! Starting with a really big screen to look for GPCR activation by microbes, and ending with a convincing story by which microbes make acetylcholine in the gut to promote IgA production, ultimately leading to better colonization. www.nature.com/articles/s41...
nature.com
Commensal-derived acetylcholine enhances mucosal immune education - Nature
A diet–microbiome–host axis strengthens mucosal immune defences and reinforces host–microbiota mutualism.
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Alex Crits-Christoph @acritschristoph.bsky.social · 24/09/2026
Many people are obviously interested in this report in the context of Claude's capabilities. Given that it was guided by experts, and that another human team had already made more progress on a similar system, I think this case study does not say much about Claude's current independent capabilities
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Matt Olm @mattolm.bsky.social · 18/09/2026
Terrible news! RockRockRock will always live on in my heart. Photo attached of us there in 2018 (no idea what we were celebrating that made us take a photo) and of Kira there a few months ago (of course I made her pose at the sign).
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Jim Shaw @jimshaw.bsky.social · 15/09/2026
The sylph metagenome profiler is v1.0.0! sylph-docs.github.io A new DB format + approach --> huge performance gains: GTDB-R232 (200k species) now takes < 5 GB of RAM and ~30s (2GB fq.gz). Huge thanks to @benjwoodcroft.bsky.social and his ongoing performance efforts (github.com/wwood/weebill)
sylph-docs.github.io
Documentation for sylph - ultrafast, precise metagenomic profiling
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Matt Olm @mattolm.bsky.social · 08/09/2026
Congratulations!! My youngest just turned 3 months- hope mat leave went / is going well!
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Tami Lieberman @contaminatedsci.bsky.social · 08/09/2026
Two announcements regarding AccuSNV, which calls high precision SNVs across microbial genomes: Version 1.1 is now incredibly easy to install, run, and perform downstream analyses with (see image of typical output!). The manuscript was also published this summer in Genome Research! Links next...
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Matt Olm @mattolm.bsky.social · 06/08/2026
I may have Apple fan-boyed a little too hard on the office setup
An office with lots of Apple products
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Alex Crits-Christoph @acritschristoph.bsky.social · 08/07/2026
What are your favorite papers that linked patients, traced outbreaks, or distinguished epidemiological hypotheses on the careful basis of just a few SNVs? Like ~ <20? Bacterial best, viruses OK too
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Matt Olm @mattolm.bsky.social · 11/06/2026
What a dream team!
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bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 21/05/2026
IgA Targeting in the Infant Gut Is Modulated by Diet and Increasingly Directed Towards Persistent Species www.biorxiv.org/content/10.64898/20…
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Matt Olm @mattolm.bsky.social · 20/05/2026
Last week my lab welcomed two fantastic new grad students (Asher and Arya), today @jingqian.bsky.social and Parsa submitted our first two manuscripts to journals + bioRxiv, and tomorrow my wife and I head to hospital to deliver baby #2 and I start paternity leave. What an exciting start to summer!
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Matt Olm @mattolm.bsky.social · 03/05/2026
Congratulations to Dr. Emily Yeo on being the first student to graduate from my lab at CU Boulder! She transferred into my lab in Fall 2025, and the amazing work she did this past year will be published in the coming months. I couldn't ask for a better first student. We'll miss you Emily!
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Matt Olm @mattolm.bsky.social · 28/04/2026
Congratulations, @jingqian.bsky.social ! A great talk and a well-deserved accomplishment!
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Tyler Barnum @tylerbarnumphd.bsky.social · 01/04/2026
What if universities used undergraduates to make biological reagents? No, I don’t mean melting the students. I mean training people in biomanufacturing to reduce research costs. Thread + diagram, hopefully thought-provoking
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Matt Olm @mattolm.bsky.social · 06/03/2026
Excited to share great work from @jingqian.bsky.social , now a second year graduate student in my lab, from research she conducted at her previous position at Shanghai Jiao Tong University!
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Jing Qian @jingqian.bsky.social · 06/03/2026
Excited to share our new paper in @natmed.nature.com ! We evaluated AMR governance across all 193 countries to inform the 2026 Global Action Plan update. A massive collaborative effort - proud to contribute to this critical global health challenge. 🥳 doi.org/10.1038/s415...
doi.org
Evaluation of antimicrobial resistance governance across 193 countries to inform the 2026 Global Action Plan update - Nature Medicine
An evaluation across 193 countries for the 2026 Global Action Plan update showed that countries with strong multisectoral governance and early surveillance adoption achieved long-term improvements in ...
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Loïs Maignien, PhD. @loimai.bsky.social · 16/02/2026
Interested in developing your skills in microbial 'omics? Consider joining us in Brest 🇫🇷, Oct. 10-24 for two weeks of intensive lectures an tutorial from top faculties and TA! maignienlab.gitlab.io/ebame/ Bonus: beautiful seascape and friendly spirit!
maignienlab.gitlab.io
EBAME workshop
EBAME - Computational Microbial Ecogenomics Workshop
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Matt Olm @mattolm.bsky.social · 16/01/2026
I've long respected Peer Bork's work as top- tier in the field and always hoped to get to chat with him at a conference someday. Very sad to see this.
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Matt Olm @mattolm.bsky.social · 09/01/2026
Really great answer and thanks for taking the time to respond! I agree a super interesting field and love to see work like the paper you just published making the picture more and more clear over time
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Matt Olm @mattolm.bsky.social · 09/01/2026
Cool paper! Thanks for sharing. As an outside observer I’ve always wondered if the microbes in breast milk could all be from the skin around the nipple (infant oral microbiome + adult skin), or if there’s evidence they’re resident in breast tissue / come from elsewhere. Any thoughts as an expert?
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Alex Crits-Christoph @acritschristoph.bsky.social · 24/12/2025
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)
Figure 2. Himar1 transposon variant screen on a cohort of 92 bacterial species.
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Matt Olm @mattolm.bsky.social · 13/12/2025
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!
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Luke Hillary @lukehillary.bsky.social · 27/11/2025
📢 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
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Alex Crits-Christoph @acritschristoph.bsky.social · 12/11/2025
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.
Figure 2. PET screen results and RB-TnSeq gene fitness results
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Darren Dahly @statsepi.bsky.social · 30/10/2025
A lifehack for turning "non-significant" results into pure gold? (ICYMI) statsepi.substack.com/p/one-simple...
statsepi.substack.com
One simple trick that statisticians hate
If you don't like the results, just ignore the control group
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Monika S. Fischer @mofisch.bsky.social · 29/10/2025
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… 🧵
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Matt Olm @mattolm.bsky.social · 28/10/2025
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!
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Matt Olm @mattolm.bsky.social · 28/10/2025
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.
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Matt Olm @mattolm.bsky.social · 28/10/2025
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.
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Matt Olm @mattolm.bsky.social · 28/10/2025
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!
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Matt Olm @mattolm.bsky.social · 28/10/2025
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.
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Matt Olm @mattolm.bsky.social · 28/10/2025
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.
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Matt Olm @mattolm.bsky.social · 17/10/2025
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...
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Matt Olm @mattolm.bsky.social · 10/09/2025
Thanks, @zaminiqbal.bsky.social - very glad to see this out! A great contribution
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Matt Olm @mattolm.bsky.social · 30/08/2025
Wow so impressive!
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Matt Olm @mattolm.bsky.social · 17/07/2025
I reviewed this paper a bit ago and have been waiting for it to come out. A great resource for us Bifidobacteria researchers!
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Alex Crits-Christoph @acritschristoph.bsky.social · 13/07/2025
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
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Tami Lieberman @contaminatedsci.bsky.social · 01/05/2025
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]
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Florian Trigodet @floriantrigodet.bsky.social · 28/04/2025
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 🧵
biorxiv.org
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...
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Trenton Dailey-Chwalibóg @trenton.phd · 25/03/2025
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.
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Trenton Dailey-Chwalibóg @trenton.phd · 25/03/2025
Just yesterday, we published a deep dive into the physiological effects of #BEP supplementation on both mom and baby: rdcu.be/ed5Wb 🥰
rdcu.be
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...
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Alex Crits-Christoph @acritschristoph.bsky.social · 05/03/2025
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...
statnews.com
There is no ‘amyloid cabal’ in Alzheimer’s research
“There exists no ‘amyloid cabal’” in Alzheimer’s research, neurologist Dennis Selkoe writes in response to Charles Piller’s “Doctored.”
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WESA @wesa.fm · 21/02/2025
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.
wesa.fm
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...
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Alex Crits-Christoph @acritschristoph.bsky.social · 04/02/2025
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
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Karthik Anantharaman @karthik-a.bsky.social · 30/01/2025
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).
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Luis Pedro Coelho @luispedrocoelho.bsky.social · 29/01/2025
#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! www.nature.com/articles/s41586…
nature.com
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…
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