A new method for soil microbiome analysis developed by researchers from the Faculty of Biology UW

01 10 2025

A study by a research team led by Klaudia Dębiec-Andrzejewska from the Institute of Microbiology, Faculty of Biology at the University of Warsaw, with the participation of Marcin Musiałowski and in collaboration with scientists from the University of Agriculture in Krakow, has been published in Scientific Reports. The paper presents the development and validation of a novel two-step method for soil microbiome analysis based on DNA sequencing – Two-Step Metabarcoding (TSM).

Traditional studies of soil microbiomes typically rely on universal 16S rDNA primers, which provide a general overview of microbial community composition. However, this approach can introduce substantial biases and often fails to detect rare or hard-to-amplify bacterial groups.

In the newly proposed approach, a two-step sequencing procedure was applied:

• in the first step, universal 16S rDNA primers were used to obtain an initial overview of the microbial community and to identify the dominant taxonomic groups,
• in the second step, primers specific to the identified dominant groups (including Actinobacteria, Acidobacteria, Firmicutes, Alphaproteobacteria, and Planctomycetes) were employed to generate more detailed data on microbial diversity.

The results obtained with the TSM method were compared both with those generated using only universal primers and with shotgun metagenomic sequencing, which is not affected by primer-related biases. The study demonstrated that TSM enables the identification of a larger number of taxa, improves biodiversity metrics, and shows greater consistency with shotgun metagenomic data.

The newly developed method is more accurate yet less expensive and easier to implement than full metagenomic sequencing. It represents a promising tool for assessing soil biodiversity, with potential applications in agriculture, environmental protection, and ecosystem monitoring.