10:37 a.m.
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
________________________________
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