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Matt Olm @mattolm.bsky.social · 28d

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

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Matt Olm @mattolm.bsky.social · Aug 30

Wow so impressive!

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Matt Olm @mattolm.bsky.social · Aug 22

Today marks one year since I opened my lab at CU Boulder! Grateful for the amazing group we’ve assembled and thrilled about the research progress we’ll be sharing soon 🤞

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Matt Olm @mattolm.bsky.social · Jul 17

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

Nature Microbiology @natmicrobiol.nature.com · Jul 16

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 - Nature Microbiology

A comprehensive genomic analysis reveals species- and strain-level heterogeneity in carbohydrate utilization potential across bifidobacteria of human origin.

www.nature.com

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Reposted by Matt Olm

Alex Crits-Christoph @acritschristoph.bsky.social · Jul 13

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

Tom Booth @boothicus.bsky.social · Jul 9

🏺

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

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Reposted by Matt Olm

Tami Lieberman @contaminatedsci.bsky.social · May 1

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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Reposted by Matt Olm

Florian Trigodet @floriantrigodet.bsky.social · Apr 28

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 🧵

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

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Reposted by Matt Olm

Trenton Dailey-Chwalibóg @trenton.phd · Mar 25

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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Reposted by Matt Olm

Trenton Dailey-Chwalibóg @trenton.phd · Mar 25

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

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Reposted by Matt Olm

Alex Crits-Christoph @acritschristoph.bsky.social · Mar 5

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...

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Reposted by Matt Olm

WESA @wesa.fm · Feb 21

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

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Reposted by Matt Olm

Alex Crits-Christoph @acritschristoph.bsky.social · Feb 4

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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Reposted by Matt Olm

Karthik Anantharaman @karthik-a.bsky.social · Jan 30

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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Reposted by Matt Olm

Luis Pedro Coelho @luispedrocoelho.bsky.social · Jan 29

#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…

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

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Reposted by Matt Olm

Jacob Schreiber @jmschreiber91.bsky.social · Jan 15

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

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

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Reposted by Matt Olm

Austin Richardson @agdr.org · Dec 13

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

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Reposted by Matt Olm

Conor (Conchúr) Meehan @conmeehan.bsky.social · Jan 8

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...

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

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Matt Olm @mattolm.bsky.social · Jan 5

Thanks for the shout-out, Noah!

Matt Olm @mattolm.bsky.social · Jan 3

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)

IgA Metagenomic Immunoglobulin Sequencing (MIG-Seq)

IgA, the most highly produced human antibody, is continually secreted into the gut to shape the intestinal microbiota. Methodological limitations have critically hindered defini...

doi.org

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Matt Olm @mattolm.bsky.social · Jan 3

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)

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Matt Olm @mattolm.bsky.social · Jan 3

We found discrete IgA binding levels, consistency in microbial IgA binding across people (columns), & intriguing trends in IgA binding across species (rows). We spent hours staring at this first ever comprehensive genome-resolved view of IgA binding; so much insight and so much to learn! (3/5)

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Matt Olm @mattolm.bsky.social · Jan 3

IgA is the main antibody secreted by mucosal surfaces and it binds ~15% of human gut microbes. Binding can be both beneficial or detrimental to microbes, and there's lots we don't know about who IgA binds and how it sculpts the microbiome. We developed MIg-Seq to answer some of these questions (2/5)

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Matt Olm @mattolm.bsky.social · Jan 3

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

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Matt Olm @mattolm.bsky.social · Jan 3

Thanks for the shout-out, Dan!

Dan Sprockett @danielsprockett.bsky.social · Jan 3

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 - 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

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Reposted by Matt Olm

Nature Microbiology @natmicrobiol.nature.com · Jan 2

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...

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

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