This study reports the virome investigation of pollinator species and other floral visitors associated with plants from the south of Bahia: Aphis aurantii, Atrichopogon sp., Dasyhelea sp., Forcipomyia taiwana, and Trigona ventralis hoozana. Studying viruses in insects associated with economically important crops is vital to understand transmission dynamics and manage viral diseases that pose as threats for global food security. Using literature mining and public RNA next-generation sequencing data deposited in the NCBI SRA database, we identified potential vectors associated with Malvaceae plant species and characterized the microbial communities resident in these insects. Bacteria and Eukarya dominated the metagenomic analyses of all taxon groups. We also found sequences showing similarity to elements from several viral families, including Bunyavirales, Chuviridae, Iflaviridae, Narnaviridae, Orthomyxoviridae, Rhabdoviridae, Totiviridae, and Xinmoviridae. Phylogenetic analyses indicated the existence of at least 16 new viruses distributed among A. aurantii (3), Atrichopogon sp. (4), Dasyhelea sp. (3), and F. taiwana (6). No novel viruses were found for T. ventralis hoozana. For F. taiwana, the available libraries also allowed us to suggest possible vertical transmission, while for A. aurantii we followed the infection profile along the insect development. Our results highlight the importance of studying the virome of insect species associated with crop pollination, as they may play a crucial role in the transmission of viruses to economically important plants, such as those of the genus Theobroma, or they will reduce the pollination process. This information may be valuable in developing strategies to mitigate the spread of viruses and protect the global industry.

Theobroma cacao plantations are of significant economic importance worldwide, primarily for chocolate production. During the harvest and processing of cocoa beans, they are subjected to fermentation either by microorganisms present in the environment (spontaneous fermentation) or the addition of starter cultures, with different strains directly contributing distinct flavor and color characteristics to the beans. In addition to fungi and bacteria, viruses are ubiquitous and can affect the quality of the fermentation process by infecting fermenting organisms, destabilizing microbial diversity, and consequently affecting fermentation quality. Therefore, in this study, we explored publicly available metatranscriptomic libraries of cocoa bean fermentation in Limon Province, Costa Rica, looking for viruses associated with fermenting microorganisms. Libraries were derived from the same sample at different time points: 7, 20, and 68 h of fermentation, corresponding to yeast- and lactic acid bacteria-driven phases. Using a comprehensive pipeline, we identified 68 viral sequences that could be assigned to 62 new viral species and 6 known viruses distributed among at least nine families, with particular abundance of elements from the Lenarviricota phylum. Interestingly, 44 of these sequences were specifically associated with ssRNA phages (Fiersviridae) and mostly fungi-infecting viral families (Botourmiaviridae, Narnaviridae, and Mitoviridae). Of note, viruses from those families show a complex evolutionary relationship, transitioning from infecting bacteria to infecting fungi. We also identified 10 and 3 viruses classified within the Totiviridae and Nodaviridae families, respectively. The quantification of the virus-derived RNAs shows a general pattern of decline, similar to the dynamic profile of some microorganism genera during the fermentation process. Unexpectedly, we identified narnavirus-related elements that showed similarity to segmented viral species. By exploring the molecular characteristics of these viral sequences and applying Hidden Markov Models, we were capable of associating these additional segments with a specific taxon. In summary, our study elucidates the complex virome associated with the microbial consortia engaged in cocoa bean fermentation that could contribute to organism/strain selection, altering metabolite production and, consequently, affecting the sensory characteristics of cocoa beans.

The omics sciences represent a revolution for clinical studies, offering integrative approaches to analyzing biological data with unprecedented depth. From the discovery of the double-helix structure of DNA to the CRISPR-Cas9 gene editing tool, passing through the evolution of sequencing platforms and the exponential advance of computing power and in silico tools, omics has progressed in its role of leading innovative solutions for old challenges in health sciences. In this review, we describe different omics, the history of their techniques and technologies, data analysis and up-to-date visualization tools used for clinical data in research and health systems. We also discuss how omics are currently being applied in diagnosis, precision and personalized medicine. For the future, omics vow to underpin the majority of decisions made by health professionals, allowing individualized treatments based on Big Data and personal biological information.

MicroRNAs (miRNAs) are key post-transcriptional regulators involved in a wide range of biological processes in insects, yet little is known about their roles in stingless bees. Here, we present the first characterization of miRNAs in Melipona quadrifasciata using small RNAs (sRNAs) deep sequencing. A total of 193 high-confidence mature miRNAs were identified, including 106 M. quadrifasciata-exclusive sequences. Expression profiling revealed that mqu-miR-1 and mqu-miR-276 together accounted for over 70% of all miRNA reads, suggesting their central roles in development and reproduction. Comparative analyses showed a higher conservation of M. quadrifasciata miRNAs with other Hymenopterans, especially Apis mellifera and Bombus spp. Putative target genes were predicted using a consensus approach, and functional annotation indicated their involvement in diverse biological regulatory pathways. This work represents the first comprehensive identification of the miRNA repertoire in stingless bees using sRNAs and provides a valuable foundation for understanding miRNA-mediated gene regulation in this ecologically and economically important pollinator.

Predatory insects such as ladybirds, green lacewings, and an aphid-feeding gall midge have been commercialized and deployed worldwide to deal with the challenge of pest control. However, no information is available on their viruses which could interfere with the efficiency of biocontrol. To start filling this gap, this study employed an integrative bioinformatics approach starting from 21 publicly available RNA-seq libraries from 6 countries of 8 natural enemy species used to control aphids. A total of 41 putative novel viruses were identified and classified into 16 families and 1 genus. In addition, 13 known viruses were detected, including aphid and phytopathogenic viruses, and a virus from the invasive harlequin ladybird. The Aphid lethal paralysis virus was detected in several species at different trophic levels, including plants, aphid vectors, predatory insects, and insectivorous vertebrates. Thus, an ecosystem perspective on viruses across trophic levels is proposed because feeding may facilitate the spread of viruses between distant taxonomic species, such as invertebrate and vertebrate insectivorous predators. In conclusion, a simple assessment of the viral diversity in eight predatory insects of agricultural relevance, using a bioinformatics approach, has revealed a potential interspecies viral flux that deserves research attention. Further studies on viruses circulating in agricultural insect species are essential to improve biological control strategies based on trophic interactions, to conserve biodiversity, and to develop knowledge on the evolution of viral entities and their role as members of an agroecological system.