Grateful to share our paper on gene-specific selective sweeps in human gut microbiomes, now out in Nature! It has been a joy to work with @rwolff.bsky.social, whose insights and hard work made this possible.
www.nature.com/articles/s41...
Nature Reviews Genetics Focus issue: Eco-evolutionary genomics of microorganisms www.nature.com/collections/... 🧬🖥️🧪🦠 🧵 1/
Absolutely stoked to have this published in @plosbiology.org
We looked at the metabolism of #Klebsiella pneumoniae 🦠🧫. We not only demonstrated lineage-specific #metabolism, but that lineages can cross-feed and support each other.
journals.plos.org/plosbiology/...
#MicroSky #microbiology 🧬 🧪 💊
metaTraits: a large-scale integration of microbial phenotypic trait information
academic.oup.com/nar/advance-...
Huge preprint if you are interested in bacterial strain taxonomy! The why and how of cgMLST LIN codes: An extensively revised and expanded version doi.org/10.1101/2024... I will summarize it for you in this thread 👇
Combination of large-scale phylogenomic analysis, mouse lethality experiments and bacterial growth assays shows sheds light on how a pandemic clone of Vibrio parahaemolyticus was able to spread worldwide
www.nature.com/articles/s41...
Beautiful work on the emergence of the pandemic clone of V. parahaemolyticus
Our “Less is more” story is out! 🚀 We reveal how gene loss shaped the adaptive evolution of pandemic Vibrio parahaemolyticus, highlight a potentially general mechanism across bacteria. Huge thanks @danielfalush.bsky.social @campy-bara.bsky.social @jaimemurtaza.bsky.social & all coauthors
How to get introgressed fragments in genomic data? Everything you always wanted to know you find in our review in @cp-trendsgenetics.bsky.social, led by Xin Huang:
doi.org/10.1016/j.ti...
Figure 4. Evolutionary dynamics and global dissemination of the MR-MT28 clone
Figure 3. Temporal dynamics of B. pertussis lineages (A), macrolide resistance (B), and antigenic (C) profiles
Figure 2. Global population structure and resistance and antigenic profiles of B. pertussis
Figure 1. Global pertussis case numbers and incidence rates since 2000
What drove the post-pandemic global pertussis upsurge? Immunity debt? Waning immunity? Other factors?
Our recent study highlights the key role of pathogen evolution.
We also identified the global spread of a drug-resistant clone, MR-MT28, which warrants coordinated global surveillance.
Molassodon! Excited to post my research group's first laboratory project. We identify a phenotype and a putative ecological strategy for the Molassodon ecospecies of Vibrio parahamolyticus, thanks to the hard work of our lab team led by @campy-bara.bsky.social www.biorxiv.org/content/10.1...
Delighted to present our Macrogenetics atlas of prokaryotes. www.biorxiv.org/content/10.1... This is a herculean effort from Chao Yang, which has a previous existence as a preprint first posted in 2018 "why panmictic bacteria are rare?" www.biorxiv.org/content/10.1...
