The microbial diversity in Portuguese raw honeys remains largely uncharacterized, constituting a serious knowledge gap in one of the country's most important resources. This work provides an initial investigation with amplicon metabarcoding analysis of two Lavandula spp. from different geographical regions of Portugal and one Eucalyptus spp. honey. The results obtained allowed to identify that each honey harbors diverse microbiomes with taxa that can potentially affect bee and human health, cause spoilage, and highlight bad bee-hive management practices. We verified that prokaryotes had a tendency towards a more marked core bacterial and a relative homogenous taxa distribution, and that the botanical origin of honey is likely to have a stronger impact on the fungal community. Thus, the results obtained in this work provide important information that can be helpful to improve this critical Portuguese product and industry.
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