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Alex Crits-Christoph

@acritschristoph.bsky.social

Computational microbiologist I like to post about: microbial genomics, microbial ecology, evolution, micro+plant biotechnology, climate, symbiosis, virology, ag, sci publishing and policy

2160 Posts5103 Follower1898 Folgt
Nina Friedman@ngfriedman.bsky.social · 2d ago

Starting in Spring or Summer 2027 K99/R00 (under its new activity code KT1/R00) will only be available to US citizens, permanent residents, and non-citizen nationals. I am hearing this from many program officers, but NIH has yet to make an official statement to my knowledge.

Rauf Salamzade@raufs.bsky.social · 3d ago

We investigated and identified several skin-derived bacteria that antagonize common pathogenic species: www.nature.com/articles/s41... A cool highlight was that bacteria from feet, where fungi are particularly diverse, tended to be more broadly antifungal than those from other body sites! #microevo

Large-scale investigation for antimicrobial activity reveals newly-identified defensive species across the healthy skin microbiome - Nature Communications

Authors present the EPithelial Isolate Collection (EPIC), a large skin microbiome culture collection, uncovering new species, widespread antifungal activity, and hidden biosynthetic diversity, reveali...

nature.com

Zeke Hausfather@zekehausfather.com · 3d ago

I'm not sure folks have realized just how crazy the second half of 2026 and 2027 will be for global temperatures – on the back of a record-smashing El Niño event. Here is my latest estimate of where both years will end up compared to global temperatures since 1850.

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Sean Gibbons 🦠💩@gibbological.bsky.social · 3d ago

Exciting collaboration with @annabiosys.bsky.social's lab just went online. @isbscience.org metaSPLiT: a fast, efficient, and relatively low-cost method for single-cell transcriptomics in the human gut microbiome. 👇

bioRxiv Microbiology@biorxiv-microbiol.bsky.social · 5d ago

Phenotypic heterogeneity in the human gut microbiome revealed by subspecies-resolution single-cell transcriptomics https://www.biorxiv.org/content/10.64898/2026.07.30.741866v1

c0nc0rdance@c0nc0rdance.bsky.social · 4d ago

The headlines are still covering the cyclosporiasis outbreak from lettuce, but let's talk about a different summer, long ago. The headlines in Bavaria would have called it "summer diarrhea" & it was killing babies. Enter our hero, Professor Theodor Escherich of the Julius Hospital, Würzburg.

Signed portrait of Theodor Escherich, MD (1857-1911). Dr. Escherich was a German-Austrian pediatrician, best known for his discovery of the Escherichia coli bacterium
Aris Katzourakis@ariskatzourakis.bsky.social · 5d ago

Very interesting paper on smallpox sequences from when they were ibtrocuced to South America, capturing the complex evolutionary forces at play in the pathogen city of this virus. www.science.org/doi/10.1126/...

The genomic identity of early smallpox in South America

Smallpox was a major driver of population collapse in the Americas after European contact, yet the genetic identity of the causal strains remains unknown. Here, we report the first ancient smallpox ge...

science.org

Tami Lieberman@contaminatedsci.bsky.social · 5d ago

The manuscript describing SimPhyNI is now published! www.microbiologyresearch.org/content/jour... A few updates since last post, including some method tweaks that improve performance and speed. Also even easier to run. Try it for your microbial GWAS or epistasis needs!

High-precision binary trait association on phylogenetic trees

Traditional methods for identifying associations between genomic features and traits, or between pairs of genomic traits, struggle when applied to bacterial genomes. While several microbial genome-wid...

microbiologyresearch.org

Tami Lieberman@contaminatedsci.bsky.social · 7mo ago

Proud to announce SimPhyNI, a new tool for bacterial GWAS with higher precision and scalability than existing tools. Try it out and let us know what you think!!

AAUP@aaup.org · 6d ago

The AAUP is proud to endorse Dr. Abdul El-Sayed for U.S. Senate in the Michigan Democratic primary. Dr. El-Sayed is a fierce champion for debt-free & tuition-free higher education & will be an invaluable ally for academic freedom & higher education as a public good in Washington.

ENDORSEMENT: DR. ABDUL EL-SAYED 2026 MICHIGAN DEMOCRATIC PRIMARY
Romain Strock@romainstrock.bsky.social · 7d ago

Preprint alert: the final two chapters of my thesis are out! www.biorxiv.org/content/10.6... Bacteriocins in archaea and archaeocins in bacteria: a computational journey into the search for weaponry borrowed from another domain of life. A short 🧵

Bacteriocins in archaea and archaeocins in bacteria

Archaea and bacteria routinely live side by side in microbial communities and must interact at least on occasion. Whether such cross-Domain interactions are dominated by mutual disregard, co-operation...

biorxiv.org

Colette Delawalla, PhD@cdelawalla.bsky.social · 7d ago

The point is to make scientists think twice about publishing that paper that goes against the MAGA belief system, lest they too, be taken into the town square and assaulted with tomatoes. See? Whatever thing you think this is about...it isn't. Stop taking the bait!

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

My quote of the day Until this moment, Senator, I think I never really gauged your cruelty or your recklessness… Let us not assassinate this lad further, Senator. You’ve done enough. Have you no sense of decency, sir, at long last? Have you left no sense of decency? Joseph Welch

Alison Feder@alisonfeder.bsky.social · last wk.

A few months ago, @elena-romero.bsky.social published a paper showing that HIV escape from broadly neutralizing antibody 10-1074 is driven by very recurrent mutation. In her latest, she asks - just how soft are the signatures of these sweeps? www.biorxiv.org/content/10.6...

Haplotype and diversity signatures of ultra-soft selective sweeps in HIV-1

Many urgent medical and agricultural challenges are driven by resistance evolution via soft selective sweeps of multiple simultaneous mutations. Standard approaches to detect these mutations involve g...

biorxiv.org

Alan McNally@alanmcn1.bsky.social · last wk.

Peer review as it should be. From an ASM journal. Fine maybe the decision makes you go “ugh” but brilliantly inciteful and constructive review comments that undoubtedly make the paper better.

Nature Reviews Microbiology@natrevmicro.nature.com · 2w ago

New online! Eggerthella lenta: metabolism, pathogenesis and therapeutic implications

Eggerthella lenta: metabolism, pathogenesis and therapeutic implications

Nature Reviews Microbiology, Published online: 23 July 2026; doi:10.1038/s41579-026-01344-5Advancing microbiome research beyond well-studied bacterial species is key to understanding the full functional diversity and potential of the human gut microbiome. In this Review, Turnbaugh and colleagues explore the unique metabolism and pathogenic potential of Eggerthella lenta, supporting the feasibility and utility of studying diverse human-associated bacterial species.

dlvr.it

Yang Liu@yangliu-lmb.bsky.social · last wk.

When we talk with AI researchers, one question comes up most frequently: do you have datasets focused on mutations at key protein positions? Until now, building libraries for that usually meant a lot of DNA synthesis. We developed HGT-DGR as a faster and cheaper way to make them.

bioRxivpreprint@biorxivpreprint.bsky.social · 2w ago

Continuous target-specific mutagenesis and rapid gene evolution by diversity-generating retroelements in Escherichia coli https://www.biorxiv.org/content/10.64898/2026.07.21.739853v1

Nadine Ziemert@nadineziemert.bsky.social · last wk.

Looking for BGCs in large metagenomic datasets? Our new biorxiv preprint introduces metaSMASH, a scalable fork of antiSMASH designed specifically for metagenome-scale BGC detection and analysis : www.biorxiv.org/cgi/content/... Thanks @canerbagci.bsky.social and @kblin.bsky.social ❤️

metaSMASH: Scalable Biosynthetic Gene Cluster Detection for Large Metagenomic Assemblies

antiSMASH is widely used for biosynthetic gene cluster (BGC) detection and annotation, but its standard workflow is poorly suited to large metagenomic assemblies, where massive contig counts create severe runtime bottlenecks and complicate downstream result exploration. We present metaSMASH, a re-engineered fork of antiSMASH for metagenome-scale BGC analysis. metaSMASH preserves the original antiSMASH detection and annotation logic while introducing streaming, memory-bounded execution, record-level parallelisation, optional output filtering, and an interactive dashboard for large result sets. Across 25 benchmark metagenome datasets, metaSMASH reproduced identical BGC detection results while dramatically reducing computational cost. Relative to the default antiSMASH configuration, metaSMASH was a geometric-mean 38x faster. It also outperformed an ad hoc chunked antiSMASH workflow: in the default configuration it achieved a geometric-mean 2.9x speed-up and 1.7x lower peak memory, and with extended-analysis modules enabled it was 2.7x faster and used 3.1x less memory while completing all datasets, whereas the ad hoc workflow ran out of memory on the two largest assemblies. By substantially reducing the computational burden of large-scale metagenome analysis without sacrificing result equivalence, metaSMASH makes routine mining of assembled metagenomes more practical and provides a scalable foundation for natural product discovery from complex microbial communities. ### Competing Interest Statement The authors have declared no competing interest. German Center for Infection Research, TTU Novel Antibiotics 09.716 Volkswagen Foundation, 0072511-00

biorxiv.org

Carl T. Bergstrom@carlbergstrom.com · 2w ago

17. How could you write this paragraph and also reach the conclusions that the report reaches? It beggars belief. The entire document is a set of soundbites, some right, many wrong, all designed to appeal to the Vought/Vance/Thiel axis and utterly disconnected to the point of absolute incoherence.

Papers and patents are not the ultimate ends of progress, but way stations in the training of better scientists, engineers, and technicians. Science is not simply about the equipment, which any laboratory with enough capital can purchase, nor the instructions, which can be shared on a sheet of paper. Our true competitive advantage lies in the process knowledge embodied by America’s talent. Without skilled practitioners who pass their craft to those who follow, the engine stalls.
Alex Crits-Christoph@acritschristoph.bsky.social · 2w ago

There are a lot of very wrong things in the OSTP report, but this one is just silly for multiple reasons? The average tenure of an employee at unicorn tech and biotech startups in SF is just 2-4 years. www.inc.com/business-ins... (Maybe just a bit higher post 2022 slump?)

Here's the Average Tenure for Tech Workers in Silicon Valley's Top 15 Companies

A new report shows that software and internet companies had the highest employee turnover in 2017, compared with other major industries.

inc.com

Carl T. Bergstrom@carlbergstrom.com · 2w ago

15. I keep coming back to this line. It is willful misrepresentation of our federal funding agencies' mission beyond discovery: developing that R&D workforce (and a pipeline of ideas) that flow into the private sector so beloved to our author. We employ trainEES because trainING is what we do.

Frequent turnover fragments efforts and slows progress. As science funders have noted, no technology company would entrust its core R&D to a workforce composed primarily of temporary trainees, yet this is the standard model in academic research.62 A more balanced approach would expand stable, well-compensated career paths for staff scientists, engineers, and technicians, roles critical to sustained institutional capability.