Matt Olm

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.

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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)

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)

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)

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.

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!

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.

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...

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!

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!

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

Experiment was 70% successful again, but this time with friends! Here's to 100% success in the new year! @jingqian.bsky.social

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/

That sounds right to me. Any thoughts, @drsalinaslab.bsky.social ?

Agreed. The most convincing experiment for me was showing that the fish acquired live, genetically-modified fluorescent bacteria into their brains, but agree that more data with wild fish would be great

A brain microbiome in salmonids at homeostasis Salmonids have a resident bacterial community in the brain.

I generally agree with you (and the points you list in the next post), but what do you make of this paper that (imo) really substantially shows live microbes in the brains of fish? www.science.org/doi/10.1126/... I would not have predicted the results in this paper before reading it