Sign in

Matt Olm

@mattolm.bsky.social
2K followers 212 following 48 posts

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

PostsRepliesMedia
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.
1198
Reposted by Matt Olm
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
1133
Reposted by Matt Olm
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
26330
Reposted by Matt Olm
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...
15321
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
150
Reposted by Matt Olm
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
495
Reposted by Matt Olm
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…
053
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!
090
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!
0100
Matt Olm @mattolm.bsky.social · 28/04/2026
Congratulations, @jingqian.bsky.social ! A great talk and a well-deserved accomplishment!
030
Reposted by Matt Olm
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
263
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!
071
Reposted by Matt Olm
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 ...
241
Reposted by Matt Olm
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
097
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.
192
Reposted by Matt Olm
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.
18432
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!
160
Reposted by Matt Olm
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
22613
Reposted by Matt Olm
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
57938
Reposted by Matt Olm
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
96113
Reposted by Matt Olm
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… 🧵
1162
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.
1220
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...
03739
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!
1217
Reposted by Matt Olm
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
1214
Reposted by Matt Olm
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]
414067
Reposted by Matt Olm
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...
513674
Reposted by Matt Olm
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.
11110
Reposted by Matt Olm
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...
141
Reposted by Matt Olm
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.”
172
Reposted by Matt Olm
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...
551189766
Reposted by Matt Olm
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
1737442
Reposted by Matt Olm
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).
2102
Reposted by Matt Olm
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…
2176
Reposted by Matt Olm
Jacob Schreiber @jmschreiber91.bsky.social · 15/01/2025
EXTREMELY cool and demonstrates clearly the promise of deep learning + bio. www.nature.com/articles/s41...
nature.com
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...
419648
Reposted by Matt Olm
Austin Richardson @agdr.org · 13/12/2024
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...
A screenshot of a webpage titled "Taxonomy Time Machine" showing the taxonomic lineage and descendants of the Influenza A Virus
0217
Reposted by Matt Olm
Conor (Conchúr) Meehan @conmeehan.bsky.social · 08/01/2025
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...
zenodo.org
Guidelines of the Ad Hoc Committee on Mitigating Changes in Prokaryotic Nomenclature
These are the guidelines issued by the Ad Hoc Committee on Mitigating Changes in Prokaryotic Nomenclature (CoMiCProN). The guidelines are ratified at CoMiCProN meetings. Mission Statement. CoMiCProN i...
63014
Matt Olm @mattolm.bsky.social · 03/01/2025
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...
doi.org
Metagenomic immunoglobulin sequencing reveals IgA coating of microbial strains in the healthy human gut - Nature Microbiology
Metagenomic immunoglobulin sequencing (MIg-seq) uncovered patterns of IgA antibody binding of bacterial strains in the healthy human gut microbiome.
33712
Matt Olm @mattolm.bsky.social · 03/01/2025
Thanks for the shout-out, Dan!
030
Reposted by Matt Olm
Nature Microbiology @natmicrobiol.nature.com · 02/01/2025
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...
nature.com
Metagenomic immunoglobulin sequencing reveals IgA coating of microbial strains in the healthy human gut - Nature Microbiology
Metagenomic immunoglobulin sequencing (MIg-seq) uncovered patterns of IgA antibody binding of bacterial strains in the healthy human gut microbiome.
18027
Matt Olm @mattolm.bsky.social · 14/12/2024
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!
0249
Matt Olm @mattolm.bsky.social · 13/12/2024
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!
5381
Reposted by Matt Olm
Michael Fischbach @mfgrp.bsky.social · 11/12/2024
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
23693294
Matt Olm @mattolm.bsky.social · 06/12/2024
Experiment was 70% successful again, but this time with friends! Here's to 100% success in the new year! @jingqian.bsky.social
060
Reposted by Matt Olm
Ran Blekhman @blekhman.bsky.social · 05/12/2024
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/
0276
Matt Olm @mattolm.bsky.social · 02/12/2024
Fish brains host microbes- could human brains host them too? I shared my "inherently skeptical", but intrigued, thoughts in this fun article.
1106
Reposted by Matt Olm
Alex Crits-Christoph @acritschristoph.bsky.social · 02/12/2024
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?
bsky.app
182
Matt Olm @mattolm.bsky.social · 25/11/2024
Our lab's first IgA experiment was 70% successful. Here's to making the next one 100%! @jingqian.bsky.social
180
Reposted by Matt Olm
Katherine Xue @ksxue.bsky.social · 19/11/2024
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
kxuelab.com
Xue lab at UC Irvine
Ecology and evolution in the human gut microbiome
24390115
Matt Olm @mattolm.bsky.social · 19/11/2024
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?
583