HolomiRA: a reproducible pipeline for miRNA binding site prediction in microbial genomes

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Bruscadin, Jennifer Jessica ; Cardoso, Taina Figueiredo ; Conteville, Liliane Costa ; da Silva, Juliana Virginio ; Ibelli, Adriana Mercia Guaratini ; Pena, Gabriel Alexander Colmenarez ; Porto, Thanny ; de Oliveira, Priscila Silva Neubern ; Andrade, Bruno Gabriel Nascimento ; Zerlotini, Adhemar ; Regitano, Luciana Correia de Almeida

• Tipo de documento: Artigo Científico
• Fonte: BMC Bioinformatics; v. 26, n. 1, p. 16-pg., 2025-10-01.

Resumo

BackgroundSmall RNAs, such as microRNAs (miRNAs), are candidates for mediating communication between the host and its microbiota, regulating bacterial gene expression and influencing microbiome functions and dynamics. Here, we introduce HolomiRA (Holobiome miRNA Affinity Predictor), a computational pipeline developed to predict target sites for host miRNAs in microbiome genomes. HolomiRA operates within a Snakemake workflow, processes microbial genomic sequences in FASTA format using freely available bioinformatics software and incorporates built-in data processing methods. The pipeline begins by annotating protein-coding sequences from microbial genomes using Prokka. It then identifies candidate regions, evaluates them for potential host miRNA binding sites and the accessibility of these target sites using RNAHybrid and RNAup software. The predicted results that meet the quality filter parameters are further summarized and used to perform a functional analysis of the affected genes using SUPER-FOCUS software.ResultsIn this paper, we demonstrate the use of the HolomiRA pipeline by applying it to publicly available metagenome-assembled genomes obtained from human feces, as well as from bovine feces and ruminal content. This approach enables the prediction of bacterial genes and biological pathways within microbiomes that could be influenced by host miRNAs. It also allows for the identification of shared or unique miRNAs, target genes, and taxonomies across phenotypes, environments, or host species.ConclusionsHolomiRA is a practical and user-friendly pipeline designed as a hypothesis-generating tool to support the prediction of host miRNA binding sites in prokaryotic genomes, providing insights into host-microbiota communication mediated by miRNA regulation. HolomiRA is publicly available on GitHub: https://github.com/JBruscadin/HolomiRA. (AU)

• Processo FAPESP: 19/04089-2 - O Hologenoma de Nelore: implicações na qualidade de carne e em eficiência alimentar
• Beneficiário: Luciana Correia de Almeida Regitano
• Modalidade de apoio: Auxílio à Pesquisa - Programa eScience e Data Science - Temático
• Processo FAPESP: 22/06281-0 - Interação microbioma-hospedeiro: prospecção e validação de biomarcadores de interesse agropecuário e descoberta de alvos terapêuticos em bovinos
• Beneficiário: Tainã Figueiredo Cardoso
• Modalidade de apoio: Auxílio à Pesquisa - Projeto Geração