Matt Olm
@mattolm.bsky.social
Reposted by Matt Olm
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)
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)
December 24, 2025 at 3:03 PM
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)
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!
December 13, 2025 at 4:59 PM
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!
Reposted by 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
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
November 27, 2025 at 8:44 PM
📢 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
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
Reposted by Matt Olm
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.
We identified a plasmid vector for the strain and generated a large RB-TnSeq library, screening for genes impacting plastic degradation.
November 12, 2025 at 7:05 PM
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.
We identified a plasmid vector for the strain and generated a large RB-TnSeq library, screening for genes impacting plastic degradation.
Reposted by Matt Olm
A lifehack for turning "non-significant" results into pure gold?
(ICYMI)
statsepi.substack.com/p/one-simple...
(ICYMI)
statsepi.substack.com/p/one-simple...
One simple trick that statisticians hate
If you don't like the results, just ignore the control group
statsepi.substack.com
October 30, 2025 at 10:29 AM
A lifehack for turning "non-significant" results into pure gold?
(ICYMI)
statsepi.substack.com/p/one-simple...
(ICYMI)
statsepi.substack.com/p/one-simple...
Reposted by Matt Olm
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… 🧵
October 29, 2025 at 3:48 PM
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.
October 28, 2025 at 1:48 PM
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...
jobs.colorado.edu/jobs/JobDeta...
October 17, 2025 at 4:00 PM
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...
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!
New RESOURCE!
Integrative genomic reconstruction reveals heterogeneity in carbohydrate utilization across human gut bifidobacteria
@arzamasovalex.bsky.social @drlarsbode.bsky.social Andrei Osterman, Jeff Gordon & co
#microbiomesky #microsky
www.nature.com/articles/s41...
Integrative genomic reconstruction reveals heterogeneity in carbohydrate utilization across human gut bifidobacteria
@arzamasovalex.bsky.social @drlarsbode.bsky.social Andrei Osterman, Jeff Gordon & co
#microbiomesky #microsky
www.nature.com/articles/s41...
Integrative genomic reconstruction reveals heterogeneity in carbohydrate utilization across human gut bifidobacteria - Nature Microbiology
A comprehensive genomic analysis reveals species- and strain-level heterogeneity in carbohydrate utilization potential across bifidobacteria of human origin.
www.nature.com
July 17, 2025 at 1:44 AM
I reviewed this paper a bit ago and have been waiting for it to come out. A great resource for us Bifidobacteria researchers!
Reposted by Matt Olm
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
Missing phylogenetics, could be very interesting to genotype and/or assemble some of these pathogens if coverage is high enough
🏺
Previously a preprint now a paper led by the Copenhagen group- ancient DA extracted from 1313 ancient humans shows the dynamics of different infectious diseases across Eurasia over the last 37,000 years.
www.nature.com/articles/s41...
Previously a preprint now a paper led by the Copenhagen group- ancient DA extracted from 1313 ancient humans shows the dynamics of different infectious diseases across Eurasia over the last 37,000 years.
www.nature.com/articles/s41...
The spatiotemporal distribution of human pathogens in ancient Eurasia - Nature
Screening shotgun-sequencing data from ancient humans covering 37,000 years of Eurasian history uncovers the widespread presence of ancient bacterial, viral and parasite DNA and zoonotic pathogens coi...
www.nature.com
July 13, 2025 at 7:19 PM
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
Missing phylogenetics, could be very interesting to genotype and/or assemble some of these pathogens if coverage is high enough
Reposted by Matt Olm
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]
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]
May 1, 2025 at 6:41 PM
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]
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]
Reposted by Matt Olm
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 🧵
www.biorxiv.org/content/10.1...
and tell you just a little bit about it in the following 🧵
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...
www.biorxiv.org
April 28, 2025 at 8:08 AM
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 🧵
www.biorxiv.org/content/10.1...
and tell you just a little bit about it in the following 🧵
Reposted by Matt Olm
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.
March 25, 2025 at 11:58 AM
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.
Reposted by Matt Olm
Just yesterday, we published a deep dive into the physiological effects of #BEP supplementation on both mom and baby: rdcu.be/ed5Wb 🥰
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...
rdcu.be
March 25, 2025 at 11:58 AM
Just yesterday, we published a deep dive into the physiological effects of #BEP supplementation on both mom and baby: rdcu.be/ed5Wb 🥰
Reposted by Matt Olm
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...
www.statnews.com/2025/02/14/a...
March 5, 2025 at 10:55 PM
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...
www.statnews.com/2025/02/14/a...
Reposted by Matt Olm
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.
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...
www.wesa.fm
February 21, 2025 at 9:56 PM
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.
Reposted by Matt Olm
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
February 4, 2025 at 4:05 AM
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
Reposted by Matt Olm
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).
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).
January 30, 2025 at 1:57 AM
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).
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).
Reposted by Matt Olm
#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…
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…
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…
www.nature.com
January 29, 2025 at 3:56 AM
#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…
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…
Reposted by Matt Olm
EXTREMELY cool and demonstrates clearly the promise of deep learning + bio.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
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...
www.nature.com
January 15, 2025 at 8:25 PM
EXTREMELY cool and demonstrates clearly the promise of deep learning + bio.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Matt Olm
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...
🕰️ app: taxonomy.onecodex.com
📄 pre-print: www.biorxiv.org/content/10.1...
December 13, 2024 at 5:29 PM
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...
🕰️ app: taxonomy.onecodex.com
📄 pre-print: www.biorxiv.org/content/10.1...
Reposted by Matt Olm
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...
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...
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...
zenodo.org
January 8, 2025 at 9:43 AM
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...
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...
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.
doi.org
January 3, 2025 at 6:27 PM
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!
More cool strain-level findings from @mattolm.bsky.social -- kind of unbelievable that this hadn't been done yet!
"Metagenomic immunoglobulin sequencing reveals IgA coating of microbial strains in the healthy human gut"
www.nature.com/articles/s41...
"Metagenomic immunoglobulin sequencing reveals IgA coating of microbial strains in the healthy human gut"
www.nature.com/articles/s41...
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.
www.nature.com
January 3, 2025 at 6:03 PM
Thanks for the shout-out, Dan!
Reposted by Matt Olm
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...
by Justin Sonnenburg, Matt Olm, Sean Spencer & co
#microsky
www.nature.com/articles/s41...
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.
www.nature.com
January 2, 2025 at 5:38 PM
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...
by Justin Sonnenburg, Matt Olm, Sean Spencer & co
#microsky
www.nature.com/articles/s41...