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
We look forward to your participation and an engaging discussion.
Best regards,
The NFDI4Microbiota Team