Gene-specific selective sweeps are pervasive across human gut microbiomes - Nature Development and application of the integrated linkage disequilibrium score (iLDS) reveals both selective pressures impacting the human gut microbiome and the mechanisms by which gut bacteria adapt to ...

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/

A metabolic atlas of the Klebsiella pneumoniae species complex reveals lineage-specific metabolism and capacity for intra-species co-operation Why are there so many co-circulating Klebsiella pneumoniae clones? Using genomics and large-scale metabolic modelling of >7000 isolates, this study identifies structured, clone-specific metabolic spec...

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 Abstract. Microbes differ greatly in their organismal structure, physiology, and environmental adaptation, yet information about these phenotypic traits is

metaTraits: a large-scale integration of microbial phenotypic trait information

academic.oup.com/nar/advance-...

Life Identification Numbers: A bacterial strain nomenclature approach Unified strain taxonomies are needed for the epidemiological surveillance of bacterial pathogens and international communication in microbiological research. Core genome multilocus sequence typing (cg...

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 👇

Wave succession in the pandemic clone of Vibrio parahaemolyticus driven by gene loss - Nature Ecology & Evolution A combination of large-scale phylogenomic analysis, mouse lethality experiments and bacterial growth assays shows that gene loss in the putrescine utilization pathway has enhanced biofilm formation an...

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

Adaptive evolution and global spread of macrolide-resistant Bordetella pertussis during the post-pandemic pertussis resurgence Pertussis resurgence following the COVID-19 pandemic remains poorly understood. Here, we integrate global surveillance data with 8,117 Bordetella pertussis genomes from 35 countries to investigate the...

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...

Macrogenetic atlas of prokaryotes Macrogenetics investigates the patterns and predictors of intraspecific genetic variation across diverse taxa, offering a framework to address longstanding evolutionary hypotheses. Here, we present a ...

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...