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

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.

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.

The control sample showed exclusive assignment to Rosa chinensis, supporting the validity of the analytical workflow. In both honey samples, plant-derived sequences were predominantly assigned to Helianthus annuus (common sunflower) and Eucalyptus grandis (rose gum), consistent with the regional flora. Key bacterial taxa included Paenibacillus larvae in one sample, Acinetobacter johnsonii in the other, and Apilactobacillus kunkeei, Bradyrhizobium sp., Sphingobium yanoikuyae, and Stutzerimonas stutzeri in both. Apis mellifera filamentous virus was detected in both samples.

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.