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

IgA Targeting in the Infant Gut Is Modulated by Diet and Increasingly Directed Towards Persistent Species https://www.biorxiv.org/content/10.64898/2026.05.19.726352v1

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!

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!

Congratulations, @jingqian.bsky.social ! A great talk and a well-deserved accomplishment!

Jing Qian@jingqian.bsky.social · 3mo ago

Honored that our work received the Best Abstract Award at the Lillian Fountain-Smith Nutrition Conference I also gave my first lightning talk, nervous but incredibly grateful for the experience. Thanks to @mattolm.bsky.social and to our lab for all the support 💛

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

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!

Jing Qian@jingqian.bsky.social · 5mo ago

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...

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...

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 ...

doi.org

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!

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.

Steven Salzberg@stevensalzberg.bsky.social · 7mo ago

very sad news. Peer Bork was one of the leaders of our field, a wonderful scientist, and he's much too young to be gone. www.embl.org/news/embl-an...

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)

bioRxiv Synthetic Biology@biorxiv-synthbio.bsky.social · 7mo ago

A scalable transposon mutagenesis system for non-model bacteria https://www.biorxiv.org/content/10.64898/2025.12.22.696024v1

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!

📢 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

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.

bioRxiv Microbiology@biorxiv-microbiol.bsky.social · 9mo ago

Functional genomics in a microbe that degrades and metabolizes PET plastic https://www.biorxiv.org/content/10.1101/2025.11.11.687616v1

A lifehack for turning "non-significant" results into pure gold? (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

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.

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...

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 · last yr.

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...

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 · last yr.

🏺 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...

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]

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...

biorxiv.org

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.

Nature Communications@natcomms.nature.com · last yr.

Maternal balanced energy-protein supplementation reshapes the maternal gut #microbiome and enhances carbohydrate metabolism in infants: a randomized controlled trial @trenton.phd @carllachat.bsky.social #nutrition #PublicHealth #metabolism www.nature.com/articles/s41...

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

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...

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.”

statnews.com

Jeremy Berg@jeremymberg.bsky.social · last yr.

It was distressing to see the skepticism about Alzheimer's disease research expressed at the Bhattahcharya hearing today. This has been fueled by Charles Piller's sensationalized (NOT sensational) reporting and book. 1/n

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...

wesa.fm

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).

#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…

nature.com

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...

nature.com