The influence of methodological solutions on the results of metagenomic sequencing of bacterial communities
https://doi.org/10.52419/issn2072-2419.2025.3.563
Abstract
The term microbiome encompasses the totality of genes belonging to microorganisms (bacteria, viruses, fungi) that inhabit a particular environment. Sequencing a region of the 16S rRNA gene allows us to study the taxonomic composition of the microbiota, identifying bacteria and archaea, including those that are difficult to cultivate. However, this method still does not have a standardized procedure. The many available methodological options complicate the reproducibility of results and, as a rule, limit the comparability of results between independent studies using different methodologies, measurement and bioinformatics pipelines. Interpretation, discussion and visualization of animal microbiome research results are a complex task due to the lack of uniform standard parameters and reference data for collection and comparison. Standardized methodologies in the study of microorganism communities are needed to simplify and compare the results of different studies. This analysis presents the main reasons for discrepancies in the data obtained at all stages of the work. These include sampling (sampling location, method, sample transport and storage), nucleic acid extraction, 16S rRNA primer selection, amplification, library preparation, sequencing and bioinformatics pipeline. Challenges associated with metagenomic data-based taxonomic and functional profiling include issues of classification accuracy in the face of systematic database errors, difficulties in predicting functions and metabolic interactions in different microbial communities, and the lack of a unified methodological approach to conducting the study. Overcoming these obstacles will require interdisciplinary collaboration, development of computational tools and improvement of analytical methods.
About the Author
O. V. Prasolova
The Russian State Center for Animal Feed and Drug Standardization and Quality
Russian Federation
Russian Federation
Candidate of Sciences (Veterinary medicine), Leading researcher of the Molecular Biology Department
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Review
For citations:
Prasolova O.V. The influence of methodological solutions on the results of metagenomic sequencing of bacterial communities. International Journal of Veterinary Medicine. 2025;(3):563-568. (In Russ.) https://doi.org/10.52419/issn2072-2419.2025.3.563
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