Chao Yang
@chaooo.bsky.social
Associate Professor, Shanghai Institute of Materia Medica.
Bacterial genome evolution, genomic epidemiology, Vibrio
Bacterial genome evolution, genomic epidemiology, Vibrio
Reposted by Chao Yang
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...
www.nature.com/articles/s41...
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 ...
www.nature.com
December 17, 2025 at 6:53 PM
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...
www.nature.com/articles/s41...
Reposted by Chao Yang
Nature Reviews Genetics Focus issue: Eco-evolutionary genomics of microorganisms www.nature.com/collections/... 🧬🖥️🧪🦠 🧵 1/
December 16, 2025 at 5:00 PM
Nature Reviews Genetics Focus issue: Eco-evolutionary genomics of microorganisms www.nature.com/collections/... 🧬🖥️🧪🦠 🧵 1/
Reposted by Chao Yang
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 🧬 🧪 💊
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 🧬 🧪 💊
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...
journals.plos.org
December 13, 2025 at 9:46 AM
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 🧬 🧪 💊
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 🧬 🧪 💊
Reposted by Chao Yang
metaTraits: a large-scale integration of microbial phenotypic trait information
academic.oup.com/nar/advance-...
academic.oup.com/nar/advance-...
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
academic.oup.com
November 30, 2025 at 4:47 AM
metaTraits: a large-scale integration of microbial phenotypic trait information
academic.oup.com/nar/advance-...
academic.oup.com/nar/advance-...
Reposted by Chao Yang
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 👇
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...
doi.org
November 30, 2025 at 7:51 PM
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 👇
Reposted by Chao Yang
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...
www.nature.com/articles/s41...
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...
www.nature.com
August 27, 2025 at 11:04 AM
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...
www.nature.com/articles/s41...
Reposted by Chao Yang
Beautiful work on the emergence of the pandemic clone of V. parahaemolyticus
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...
www.nature.com/articles/s41...
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...
www.nature.com
August 27, 2025 at 11:21 AM
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
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...
www.nature.com/articles/s41...
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...
www.nature.com
August 27, 2025 at 1:06 PM
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
Reposted by Chao Yang
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...
doi.org/10.1016/j.ti...
July 24, 2025 at 2:04 AM
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...
doi.org/10.1016/j.ti...
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.
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.
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...
www.medrxiv.org
July 21, 2025 at 10:42 AM
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.
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.
Reposted by Chao Yang
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...
June 30, 2025 at 4:24 AM
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...
Reposted by Chao Yang
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...
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 ...
www.biorxiv.org
February 28, 2025 at 6:06 AM
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...