A pilot proof-of-concept study of microbial and botanical diversity in honey samples from Necochea, Argentina

<h4>Introduction</h4>Honey is a complex biological matrix containing plant-derived, microbial, and viral components that reflect both environmental and hive-associated processes. Traditional methods for determining botanical origin, such as melissopalynology, have limitations in resolution and scope. In this context, untargeted shotgun metagenomics emerges as a promising integrative approach for comprehensive honey characterization.<h4>Methods</h4>This pilot study explored the feasibility of applying an untargeted shotgun metagenomic approach to honey samples from Necochea, Buenos Aires province, Argentina. Two honey samples and a pollen control sample from Rosa chinensis were subjected to DNA extraction, shotgun library preparation, and sequencing on an Illumina NextSeq 500 platform.<h4>Results</h4>The control sample showed exclusive assignment to <i>Rosa chinensis</i>, supporting the validity of the analytical workflow. In both honey samples, plant-derived sequences were predominantly assigned to <i>Helianthus annuus</i> (common sunflower) and <i>Eucalyptus grandis</i> (rose gum), consistent with the regional flora. Key bacterial taxa included <i>Paenibacillus larvae</i> in one sample, <i>Acinetobacter johnsonii</i> in the other, and <i>Apilactobacillus kunkeei, Bradyrhizobium</i> sp., <i>Sphingobium yanoikuyae</i>, and <i>Stutzerimonas stutzeri</i> in both. <i>Apis mellifera filamentous virus</i> was detected in both samples.<h4>Discussion</h4>Given the limited sample size, these findings should be interpreted as exploratory and hypothesis-generating. Nevertheless, this proof-of-concept supports the potential of untargeted metagenomics as an integrated tool for the simultaneous characterization of botanical origin, microbial communities, and viral content in honey, offering advantages over targeted amplicon-based approaches. Future studies with larger and systematically designed cohorts will be necessary to validate and extend these observations.