Análise de dados de metagenômica obtidos de amostras de solo: caracterização taxonômica, do resistoma e do viruloma

Abstract

In recent decades, various technological advances and incentives directed towards scientific research have made Brazil stand out internationally in the field of agricultural production, in response to the growing global demand for food. Despite this, there is still significant neglect regarding the importance of soil microbial communities, whether due to a lack of information or underestimation of their crucial role, which results in management practices that fail to fully exploit the productive capacity of the soil. To change this scenario, a promising approach is through the use of advanced biotechnology techniques, such as metagenomic sequencing of soil samples. Analyses of data from this sequencing can reveal valuable information about the microorganisms present in the sample, thus enabling more efficient and sustainable management of agricultural soils. In this context, the aim here is to proceed with metagenomic data analyses from soil samples, using (raw) sequenced data made publicly available by Ordine et al. (2023). Specifically, the objectives are to: i) characterize the taxonomic profile of microbial communities, highlighting the diversity and abundance of microorganisms; ii) identify the resistome and virulome profiles, focusing on the abundance and diversity of antibiotic resistance genes (ARGs) and virulence factors (VFs); and iii) clarify the observed differences in the analyzed soil samples, considering the adopted management practices. To this end, various existing bioinformatics tools are applied in sequence to implement pipelines capable of performing unsupervised data analysis. In particular, this work implements two pipelines using the GNU Bash programming language, with one of them being designed for taxonomic classification and the other for characterizing antibiotic resistance genes (ARGs) and virulence factors (VFs). As a result of the execution of these pipelines, important genera for soil and plant health were identified, such as Bradyrhizobium, Nocardioides, and Pseudomonas. In turn, regarding the ARGs, relevant genes such as vanRO, rsmA, and RbpA were identified. Still, in the context of VFs, the presence of genes such as acpXL, hsiB1, and pilG were observed in the samples considered. Therefore, the results obtained confirm the validity of the implemented pipelines, which were designed for both taxonomic classification and characterization of the resistome and the virulome.