Jason Shapiro

🦠🧍‍♀️From bacterial to human immunity.

We report in @science.org the discovery of a human homolog of SIR2 antiphage proteins that participates in the TLR pathway of animal innate immunity.
Co-led wt @enzopoirier.bsky.social by D. Bonhomme and @hugovaysset.bsky.social

www.science.org/doi/10.1126/...

We are on the lookout for postdocs for two different projects at the intersection of ecology, evolution, and the human microbiome.

See thread for more information and reach out!

Congrats!

New #Rstats blog post: Plot Data Along a Genome with karyoploteR. Demos: genome density, per-base coverage, structural variation, GWAS Manhattan plots, combine multiple data types, gene expression results from DESeq2, epigenetic regulation from ENCODE doi.org/10.59350/dqs...

PBEEE/Quebec Merit Scholarship for Foreign Postdocs and Visiting Research Student and Visiting Researchers **Note that the FRQ is in the process of revamping their webpages. We will update links soon as we can with the current 2025 year's information. Be sure to check back to see if any eligibility or docu...

Are you a recent PhD (or soon to be PhD) from outside Canada looking to do a postdoc in Quebec?

Get in touch if you are excited about microbes, evolution, ecology, genomics (or all of the above!) and I'd be happy to help develop a project together!

www.mcgill.ca/gps/funding/...

We have a new 3-year postdoc position in our group at the @hifmb.de to study plasmids and plasmids systems of the marine environment to survey their utility in microbial responses to environmental change.

Please see the official job ad here, and spread the word:

jobs.awi.de/Vacancies/20...

The Wadsworth Center is expanding it's research focus on #virology /vector-borne diseases!
www.asmcareerconnections.org/job/research-scientist-5-g-31/78488664/
This is a unicorn assistant prof equivalent position with 12-month hard money salary and no teaching commitments (!)
Reposts appreciated 🙏

Metabolites are not genes — avoiding the misuse of pathway analysis in metabolomics - Nature Metabolism Pathway analysis, originally developed for gene expression data, has been adapted for metabolomics. However, owing to the unique characteristics and constraints of metabolites compared with genes, pat...

Metabolites are not genes — avoiding the misuse of pathway analysis in metabolomics

www.nature.com/articles/s42...

Efficient and robust search of microbial genomes via phylogenetic compression Nature Methods - Phylogenetic compression achieves performant and lossless compression of massive collections of microbial genomes, facilitating fast BLAST-like search and versatile alignment tasks.

Our latest paper, in which @brinda.eu (along with @zaminiqbal.bsky.social and others) introduces phylogenetic compression for storage and search of enormous microbial genome libraries, was published today in @naturemethods.bsky.social:

rdcu.be/eg4OA

1/

I'm delighted to share a useful FREE web-based app portal of powerful bioinformatics tools for microbial genomes and shotgun microbiome sequences!

It's called Micromics and is built by Middle Author Bioinformatics, led by co-founder @ironark.bsky.social
omix.midauthorbio.com

Reference-free variant calling with local graph construction with ska lo (SKA) Abstract. The study of genomic variants is increasingly important for public health surveillance of pathogens. Traditional variant calling methods from who

Our extension to ska, 'ska lo' (for 'left-out') which can additionally, and still very quickly, find indels and SNPs closers than the k-mer distance is now out: academic.oup.com/mbe/advance-...
This addresses a long standing challenge for reference-free variant callers

Integration of 168,000 samples reveals global patterns of the human gut microbiome The Human Microbiome Compendium is a unified database of publicly available human gut microbiome 16S samples, built with the integrated data from hundreds of independent projects. The compendium is us...

Today we report a new compendium of human gut microbiomes with >168,000 samples

By analyzing this massive dataset, we discovered distinct microbiome patterns across the globe, and show we can predict where a person lives just from their gut bacteria

Now out in Cell:

www.cell.com/cell/fulltex...

Congrats!

Application review for the 2025 Gordon Research Conference on Microbial Population Biology begins on Jan 20. Maximize your chance of acceptance and $ support by submitting your application with a poster abstract before that date! Details: www.grc.org/microbial-po...

Bright green spots are phages (viruses), bacteria are the faint rods in light blue.

We developed a microscopy-based technique🔬 to measure attachment of viruses #phages to host cells. 🦠

The paper was posted online today:
www.pnas.org/doi/10.1073/...

#phagesky #microsky

The first review article from my lab, helmed by @celiasouque.bsky.social, "From Petri Dishes to Patients to Populations: Scales and Evolutionary Mechanisms Driving Antibiotic Resistance" is now online and open access at Annual Reviews Microbiology:
www.annualreviews.org/content/jour...

Expanding the diversity of origin of transfer-containing sequences in mobilizable plasmids - Nature Microbiology Characterization of known plasmid oriT features facilitates identification of 21 oriT-containing sequence families which, alongside candidate sequence validation, expands our understanding of plasmid ...

Our paper on identifying novel origins of transfer by conjugation is out! One can now expand the known oriTs from 1% to 80% in species like Acinetobacter baumannii. This contributes to unravel hitcher plasmid mobility beyond model elements. #microsky www.nature.com/articles/s41...

A "starter pack" image for my Evolutionary Biologists pack

Seeing a bunch of new followers, so I just tidied up my Evolutionary Biologists starter pack—mostly trying to represent folks' fields right, and get in some topical journals/societies

Hope it's useful, but I'd also love to see packs from other folks, to better cover the field

go.bsky.app/TUNHbNu

Prediction of strain level phage–host interactions across the Escherichia genus using only genomic information - Nature Microbiology Phage–host interactions are computationally predicted using only genomic information, highlighting future research directions and enabling generation of custom phage cocktails.

Out in Nature Microbiology, we predicted phage-bacteria interactions in E. coli species using only genomic information.

Adsorption, not defense systems, is the main driver at this scale (relevant for a phage therapy context), leading to tailored cocktails!

www.nature.com/articles/s41...
🧵👇

I'm hiring a postdoc! To use substitution models to understand protein evolution and/or improve phylogenetic methods. evol.mcmaster.ca/brian/evoldi...

New preprint up! We sequenced hundreds of samples from across one of Earth's oldest living organisms - the Pando aspen clone - to understand how mutations accumulate and spread in long-lived clonal organisms. Our results were…surprising. 1/30

Tried to put together a Microbial Evolution starter pack, but there were so many great people I didn't want to leave out it turned into 3 starter packs

Comment or DM me if you were missed or would like to be added!

A thread (1/3)

go.bsky.app/6pkuYhi

Note - if you are interested in the amazing Lake Arrowhead Microbial Genomes meeting but cannot attend in person, there is a highly reduced cost virtual option to participate. See www.eventbrite.com/e/lake-arrow...

🚨Im looking for postdocs to join me at Montana State!

One position will focus on phage-host-microbe interactions in Lyme disease

The other will sequence phage populations recovered from ticks/mice

Interested? Send me a CV & cover letter! Job ads soon

🧫🦠🧪

Solving genomic puzzles: computational methods for metagenomic binning Abstract. Metagenomics involves the study of genetic material obtained directly from communities of microorganisms living in natural environments. The fiel

Solving genomic puzzles: computational methods for metagenomic binning

Want to know more about finding #phage and #bacteria in #metagenomes?

💻🧬🦠#phagesky

academic.oup.com/bib/article/...

gcplyr: an R package for microbial growth curve data analysis - BMC Bioinformatics Background Characterization of microbial growth is of both fundamental and applied interest. Modern platforms can automate collection of high-throughput microbial growth curves, necessitating the deve...

Glad to see this out! gcplyr is an R package that makes it easy to wrangle and analyze microbial growth curve data. In the paper, I highlight what it adds compared to other software

(a new version is up too! update to get the latest features)

#microbiomesky #MicroSky 🧬🖥️🦠🔬

doi.org/10.1186/s128...

Assistant Professor - Global Change Biology- Department of Integrative Biology University of California, Berkeley is hiring. Apply now!

Job alert!! Join Integrative Biology at UC Berkeley. We are hiring an Assistant Professor in the area of global change biology with emphasis on the Ecology and Evolution of Host-Microbe Interactions (pathogens, mutualists, microbiomes).

aprecruit.berkeley.edu/JPF04476

captcha image with 3x3 grid of animals featuring 3 elephants, 3 dogs with sunglasses, two mice, and a frog. test image at top is an elephant with a sign that reads "frog"

I didn't know I could enjoy a CAPTCHA test this much

Island biogeography theory provides a plausible explanation for why larger vertebrates and taller humans have more diverse gut microbiomes Abstract. Prior work has shown a positive scaling relationship between vertebrate body size, human height, and gut microbiome alpha diversity. This observa

Do taller people have more diverse gut microbiomes?

Yes!

Why??? Check out our latest study in the ISME Journal: t.co/vOnTficVN3

Amazing first-paper by postbac in the lab Kat Ramos! with Alex Carr, Ken Locey, and @cdiener.com

@isbsci.bsky.social

Check out our new paper in collaboration with Travis Wheeler's group out today in NAR Genomics & Bioinformatics! Editors choice!

VIBES: a workflow for annotating and visualizing viral sequences integrated into bacterial genomes

#microsky
#phagesky
🧫🧪🔬

doi.org/10.1093/narg...