Former graduate student Albane Ruaud recently saw her machine learning tool published in PLoS Comp Bio: Ruaud A, Pfister N, Ley RE, Youngblut ND. Interpreting tree ensemble machine learning models with endoR. PLoS Computational Biology Dec 14;18(12):e1010714. (2022). Use endoR to...
Last week, Jessica (Jess) Sutter successfully defended her thesis titled “Phylogeny, pangenomics, and predicted functional diversity of maize rhizosphere Pseudomonas”. The work of Jess investigates a phenomenon observed in a study of the maize rhizosphere microbiome in a field study...
Our new paper on the evolutionary histories of the human gut microbiota is out in Science. The work was led by Taichi Suzuki and Liam Fitzstevens along with the Ley lab team: Victor Schmidt, Hagay Enav, Kelsey Huus, and Mirabeau...
Congratulations to Ruth Ley, who was awarded a certificate in recognition of her induction into the Leopoldina Academy during the annual ceremony held in Halle (Saale). This solidifies Ruth’s membership that began in 2020 and is another accolade to add...
Our new pre-print is up on bioRxiv! Led by Nicholas Youngblut, this work presents ResMiCo, a powerful tool for optimising metagenome assemblies. Metagenome assembly is increasing in popularity due to decreasing Illumina sequencing costs and easier library preparation methods. Unfortunately,...
While inositol lipids are ubiquitous in eukaryotes and have finely tuned roles in cellular signalling and membrane homoeostasis, bacterial inositol lipids were previously thought to be limited largely to PI-DAG synthesis in Actinobacteria as discribed for the obligate intracellular pathogen...
“It’s time to make the survey of humanity’s ‘second genome’ more complete.” A perspective piece on how to fill in the microbiome map by Ruth E. Ley. “This week marks the tenth anniversary of the first big survey of microbial...
Congratulations to Prof. Ruth Ley who has joined the Board of Trustees of the Jung Foundation! The Jung Foundation for Science and Research was established in 1967 by Ernst Emil Jung to promote science and social commitment. Since 1975, the foundation...
Yesterday, Jacobo successfully defended his thesis titled “Insights into the human gut microbiome and its link with obesity and cardiometabolic diseases”. During the last 4.5 years in the Ley Lab he has developed new methods and computational approaches to study...
Congratulations to Lara Berg for successfully completing her Masters degree in the Ley Lab! For her thesis, Lara charaterised strain-level metabolic and syntrophic variations in the dominant human gut methanogen, Methanobrevibacter smithii. Using M. smithii samples obtained from stool samples...
This week saw the release of our latest pre-print on bioRxiv! Titled Silent recognition of flagellins from human gut commensal bacteria by Toll-like receptor 5, this work was led by postdoc Sara Clasen and describes a mechanism for how the...
Congratulations are in order for Paul OG Jorzik, who has successfully completed his Master’s degree. Paul completed his thesis in the Ley Lab where he worked on the development of novel genetic systems for non-model human gut-associated bacteria. Congratulations Paul!
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A new review article was published today from postdoc Hagay Enav and Ruth Ley, discussing strain level colonisation of the developing infant gut microbiome. While the establishment of the infant microbiome has long been an area of interest, recent technological...
We are pleased and very proud to announce that postdoctoral researcher Taichi Suzuki has accepted a joint assistant professor position between the College of Health Solutions and Biodesign Institute at the Arizona State University and will be starting his own...
New article on microbiome engineering published in Cell (https://www.sciencedirect.com/science/article/abs/pii/S0092867421014975?via%3Dihub) in which our project leader and microbiome engineering expert James Marsh and Ruth E. Ley address the recent Cell issue by Jin et al. (https://www.sciencedirect.com/science/article/abs/pii/S0092867421015415) and discuss innovative tools for editing...
Congratulations to postdoctoral researcher Kelsey Huus who was awarded an EMBO fellowship to run the µHEAT study (‘Microbial-Human Ecology and Temperature’), which aims to understand interactions between the gut microbiome and the human immune system in the context of vaccination....
In our new publication in Environmental Microbiology, we explore the use of genome-level phylogenies and also genome-derived functional information for assessing alpha and beta diversity. Given the large number of microbial genomes that are now available, we sought to assess...
In our new preprint (Ruaud et al., 2022), we introduce endoR: an R-package to interpret machine learning models. We also present the application of endoR to human gut metagenomes to identify associations between H2 producers and methanogens in the human...