Dear Microbiome Researchers, We would like to invite you to the next session of the NFDI4Microbiota Coffee Talk Series on Strain tracking across metagenomic samples with SameStr by Daniel Podlesny (EMBL) Abstract: Microbial communities are integral to human health, yet fundamental questions about their establishment, stability, resilience, and transmission remain incompletely understood. For instance, microbes are passed on to offspring and interconnected through social interactions and food webs, but it remains unclear whether this results in lifelong persistence, adaptation, and stable transmission across generations. Although short-read metagenomics provides cost-effective and high-depth sequencing for studying these questions, it inherently fragments genomes, complicating the reconstruction of microbial genotypes and their tracking across hosts. To address this limitation, we developed SameStr, a bioinformatic program for strain-resolved metagenomics, enabling precise tracking of microbes across metagenomic samples. By leveraging Single Nucleotide Variants (SNVs) within species-specific marker genes, SameStr facilitates the detection and quantification of microbial transmission and persistence, as well as the observation of direct strain competition. To enhance accessibility, we have released SameStr as a Nextflow-based workflow available on GitHub and the NFDI4Microbiota CloWM platform. This allows users to conveniently deploy and execute the SameStr pipeline end-to-end locally, in cloud environments, or through the graphical user interface on CloWM. We have applied the workflow to analyze over 120,000 metagenomic samples, demonstrating its robustness and scalability. SameStr has enabled strain-resolved analysis of microbial dynamics with unprecedented phylogenetic resolution, shedding light on parent-infant microbial transmission in early childhood, longitudinal strain persistence in adults, and strain dynamics during therapeutic interventions, including Fecal Microbiota Transplantation (FMT) and probiotic administration. These analyses have uncovered taxonomic, clinical, and ecological factors critical to microbiome assembly, demonstrating the potential of SameStr to provide deeper insights into microbiome ecology and therapeutic strategies. Date & Time: 28 April 2025 14:30 - 15:30 CEST Zoom link: https://helmholtz-hzi-de.zoom-x.de/j/68764089023?pwd=cvlqk3FLgKyIyK3xkUy2... Meeting ID: 687 6408 9023 Passcode: 826218 We look forward to your participation and an engaging discussion. Best regards, The NFDI4Microbiota Team ________________________________ Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Vorsitzende des Aufsichtsrates: Frau MinDir'in Prof. Dr. Veronika von Messling, Bundesministerium für Bildung und Forschung Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für Wissenschaft und Kultur Wissenschaftlicher Geschäftsführer: Prof. Dr. Josef Penninger - Administrativer Geschäftsführer: Christian Scherf Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477 Unsere Hinweise zum Datenschutz finden Sie hier: https://www.helmholtz-hzi.de/de/service/datenschutz/