David Stern

Hybridization capture sequencing for Vibrio spp. and associated virulence factors | mBio The increasing prevalence of pathogenic Vibrio spp. in aquatic ecosystems, driven by climate change, is closely linked to a rise in cholera and vibriosis cases, emphasizing the need for improved envir...

Hybridization capture sequencing for Vibrio spp. and associated virulence factors | mBio journals.asm.org/doi/10.1128/...

Promising toolkit for binning and visualizing assembly graphs. The assembly graph is an underutilized source of binning information IMO
gbintk.readthedocs.io/en/latest/

Nice review of dynamic field theory in linguistics by the other Stern @secretly-stern.bsky.social

Delivery Mode Impacts Gut Bacteriophage Colonization During Infancy Cesarean section delivery is associated with altered early-life bacterial colonization and later adverse inflammatory outcomes. Although gut bacteriophages can alter the gut microbiome and host res...

Happy to see this one out. Lots of fun work identifying bacteriophages in gut metagenomes www.tandfonline.com/doi/full/10....

Deep Cuts to Medical Research Funds Could Hobble University Budgets (Gift Article) Grants from the National Institutes of Health come with additional money for overhead. Proposed funding cuts would leave colleges with large budget gaps.

“I think it’s going to destroy research universities in the short term, and I don’t know after that.” Story by @by-cjewett.bsky.social on the new NIH policy that will shrivel support for research. www.nytimes.com/2025/02/07/u...

skalo: using SKA split k-mers with coloured de Brujin graphs to genotype indels Insertions and deletions (indels) are important contributors to the genetic diversity and evolution of pathogens like Mycobacterium tuberculosis . However, accurately identifying them from genomic dat...

www.biorxiv.org/content/10.1...

Here we provide evidence of henipaviruses in North America with the discovery of Camp hill virus in the Northern Short-Tailed Shrew, Alabama. Early release article available from EID
wwwnc.cdc.gov/eid/article/... #virology

Venn diagram illustrating microbial diversity of bacteria and archaea captured by isolates, metagenome-assembled genomes (MAGs) from NCBI and IMG, and metagenomes from IMG. A large portion of microbial diversity, labeled as 'Microbial Dark Matter,' represents species not captured by isolates or MAGs. Image modified from https://www.science.org/doi/10.1126/sciadv.adq2166

Genomes assembled from #metagenomes (a.k.a. MAGs) are awesome and have revolutionized our ability to study uncultivated microbes

...BUT: they still don't capture a lot of the 🦠 species that are out there

New @jgi.doe.gov paper led by Dongying Wu and Natalia Ivanova: www.science.org/doi/10.1126/...

Discovery and analysis of an 841 kbp phage genome: the largest known to date Viruses represent the most abundant biological entities on Earth, with bacteriophages (or phages) specifically infecting bacteria. Typically, double-strand DNA phages possess genomes around 50 kilobas...

An 841kb phage genome!
cc @baym.lol
www.biorxiv.org/content/10.1...

Top panels: graphs showing increases in spillover events, extinction rates, and temperature anomalies over the last few centuries. Bottom panel: a map of 10 pandemics since the year 1900. Four were linked to agriculture, two to wildlife use, and one to climate change.

🚨😷🧪 NEW: A growing body of evidence shows that pandemics, biodiversity loss, and climate change are part of a broader polycrisis - but there are no simple solutions. A sweeping overview of "Pathogens and planetary change" for the first issue of @natrevbiodiv.bsky.social, out now 🔓 rdcu.be/d6lHl

Interesting work and dataset to investigate the genetic population structure and colonization history of Plasmodium vivax in Latin America, inferring multiple waves of pre/post colonial migration & evolutionary contributions from European and African populations.
🔗 journals.plos.org/plospathogen...

horizontal transfers of large sets of genes among key lineages could explain the sporadic distribution of saxitoxin production. A fun project to be a part of and hopefully a valuable addition to an interesting story.

identified the large (53 gene!) biosynthetic gene cluster underlying its production. After screening public genomes for homologous cluster components, we found exceptionally high rates of horizontal transfer of those genes among cyanobacteria and that..

Novel Toxin Biosynthetic Gene Cluster in Harmful Algal Bloom-Causing Heteroscytonema crispum: Insights into the Origins of Paralytic Shellfish Toxins Abstract. Caused by both eukaryotic dinoflagellates and prokaryotic cyanobacteria, harmful algal blooms are events of severe ecological, economic, and publ

Out now in @genomebiolevol.bsky.social! With colleagues at NBACC and PNNL, we helped answer a long-standing question about how widely-divergent cyanobacteria produce saxitoxin, a major cause of paralytic shellfish poisoning. We assembled a new genome for a producer of saxitoxin and ...

Relating ecological diversity to genetic discontinuity across bacterial species - Genome Biology Background Genetic discontinuity represents abrupt breaks in genomic identity among species. Advances in genome sequencing have enhanced our ability to track and characterize genetic discontinuity in ...

And it’s been a while since I dipped my toe into the questions of what ‘species’ might mean for bacteria, and how they relate to ecology. But still interests me! genomebiology.biomedcentral.com/articles/10....

Interesting new paper -- evolutionary adaptations in Bifidobacterium across a huge range of host species

www.biorxiv.org/content/10.1...

PSAURON: a tool for assessing protein annotation across a broad range of species Abstract. Evaluating the accuracy of protein-coding sequences in genome annotations is a challenging problem for which there is no broadly applicable solut

Check out our just-published AI-based (temporal convolutional network) system, PSAURON, for predicting eukaryotic proteins, from @markusjsommer.bsky.social. We used a similar method in BALROG, our bacterial gene finder. Note: the "P" is silent in PSAURON 🤣 academic.oup.com/nargab/artic...

Unicore identifies single-copy protein structures across genomes using Foldseek, bypassing slow structure predictions by utilizing 3Di predictions from ProstT5, enabling rapid phylogenetic inference at the tree-of-life scale. 1/n
📄 www.biorxiv.org/content/10.1...
💾 github.com/steineggerla...