Comparison of Metagenomics and Metatranscriptomics Tools: A Guide to Making the Right Choice
Metadatos
Afficher la notice complèteAuteur
Terrón Camero, Laura Carmen; Gordillo González, Fernando; Salas Espejo, Eduardo; Andrés León, EduardoEditorial
MDPI
Materia
16S Bracken Kraken2 Metagenomics Metatranscriptomics Nextflow Pipeline QIIME2 Shotgun sequencing
Date
2022-12-03Referencia bibliográfica
Terrón-Camero, L.C... [et al.]. Comparison of Metagenomics and Metatranscriptomics Tools: A Guide to Making the Right Choice. Genes 2022, 13, 2280. [https://doi.org/10.3390/genes13122280]
Patrocinador
regional Andalusian Government; POSTDOC_21 _00394Résumé
The study of microorganisms is a field of great interest due to their environmental (e.g., soil
contamination) and biomedical (e.g., parasitic diseases, autism) importance. The advent of revolutionary
next-generation sequencing techniques, and their application to the hypervariable regions
of the 16S, 18S or 23S ribosomal subunits, have allowed the research of a large variety of organisms
more in-depth, including bacteria, archaea, eukaryotes and fungi. Additionally, together with the
development of analysis software, the creation of specific databases (e.g., SILVA or RDP) has boosted
the enormous growth of these studies. As the cost of sequencing per sample has continuously decreased,
new protocols have also emerged, such as shotgun sequencing, which allows the profiling of
all taxonomic domains in a sample. The sequencing of hypervariable regions and shotgun sequencing
are technologies that enable the taxonomic classification of microorganisms from the DNA present
in microbial communities. However, they are not capable of measuring what is actively expressed.
Conversely, we advocate that metatranscriptomics is a “new” technology that makes the identification
of the mRNAs of a microbial community possible, quantifying gene expression levels and active
biological pathways. Furthermore, it can be also used to characterise symbiotic interactions between
the host and its microbiome. In this manuscript, we examine the three technologies above, and
discuss the implementation of different software and databases, which greatly impact the obtaining of
reliable results. Finally, we have developed two easy-to-use pipelines leveraging Nextflow technology.
These aim to provide everything required for an average user to perform a metagenomic analysis of
marker genes with QIMME2 and a metatranscriptomic study using Kraken2/Bracken.