DNA traces the origin of honey by identifying plants, bacteria and fungi

Wirta, Helena; Abrego, Nerea; Miller, Kirsten E.; Roslin, Tomas; Vesterinen, Eero J.

doi:10.1038/s41598-021-84174-0

Cited by 38 publications

(58 citation statements)

References 75 publications

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“…In line with previous work (47,49), our pipeline revealed that the majority of DNA traces contained in honey samples did not belong to plants (Figure 3a). To better understand the importance of this diversity and their relationship with honeybees, we first used a text mining approach to categorize their relationship with honeybees based on current literature (See method and Sup.…”

Section: Non-invasive Characterisation Of the Hive Pathogens And The Dynamics Of Core And Non-core Honeybee Gut Microbiomesupporting

confidence: 91%

“…The assessment of the complex ecological niche that honeybees occupy has only recently begun to be examined through the use of shotgun metagenomics (47)(48)(49). In this study we have developed a direct approach for shotgun metagenomics (Direct-SM) and a bioinformatic pipeline to assess the species composition of honey samples.…”

Section: Discussionmentioning

confidence: 99%

“…Honey shotgun metagenomics has only recently been applied (47) and has been demonstrated to describe both the variety of the symbiotic and pathogenic organisms that honeybees come in contact with as well as the floral origin of honey (48,49).…”

Section: Introductionmentioning

confidence: 99%

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Bee foraging preferences, microbiota and pathogens revealed by direct shotgun metagenomics of honey

Galanis

Vardakas

Reczko

et al. 2021

Preprint

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Honeybees (Apis mellifera) continue to succumb to human and environmental pressures despite their crucial role in providing essential ecosystem services. Owing to their foraging and honey production activities, honeybees form complex relationships with species across all domains, such as plants, viruses, bacteria (symbiotic and pathogenic), and other hive pests, making honey a valuable biomonitoring tool for assessing their ecological niche. Thus, the application of honey shotgun metagenomics (SM) has paved the way for a detailed description of the species honeybees interact with, in order to better assess the multiple factors governing their health. Here, we describe the implementation of optimized honey DNA extraction methodology coupled to direct shotgun metagenomics (Direct-SM) analysis, and to a computationally optimised and validated pipeline for taxonomic classification of species detected in honey. By comparing honey collected across 3 harvesting seasons in a stable apiary, we show that Direct-SM can describe the variability of sampled plant species, revealing honeybee behavioural adaptation. In addition, we reveal that Direct-SM can non-invasively capture the diversity of species comprising the core and non-core bacterial communities of the gut microbiome. Finally, we show that this methodology is applicable for the monitoring of pathogens and particularly for the biomonitoring varroa infestation. These results suggest that Direct-SM can accurately and comprehensively describe honeybee ecological niches and can be deployed to assess bee health in the field.

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Section: Non-invasive Characterisation Of the Hive Pathogens And The Dynamics Of Core And Non-core Honeybee Gut Microbiomesupporting

confidence: 91%

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Bee foraging preferences, microbiota and pathogens revealed by direct shotgun metagenomics of honey

Galanis

Vardakas

Reczko

et al. 2021

Preprint

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“…The data used for our study derive from a previous paper [ 23 ], in which we ask whether the taxonomic contents of honey might be used to identify the country of origin [ 23 ]. In the current study, we approach the same data from a novel perspective, asking what the taxonomic and functional groups detected in honey will reveal about the honeybee’s role in its environment.…”

Section: Introductionmentioning

confidence: 99%

Reconstructing the ecosystem context of a species: Honey-borne DNA reveals the roles of the honeybee

et al. 2022

Self Cite

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To assess a species’ impact on its environment–and the environment’s impact upon a species–we need to pinpoint its links to surrounding taxa. The honeybee (Apis mellifera) provides a promising model system for such an exercise. While pollination is an important ecosystem service, recent studies suggest that honeybees can also provide disservices. Developing a comprehensive understanding of the full suite of services and disservices that honeybees provide is a key priority for such a ubiquitous species. In this perspective paper, we propose that the DNA contents of honey can be used to establish the honeybee’s functional niche, as reflected by ecosystem services and disservices. Drawing upon previously published genomic data, we analysed the DNA found within 43 honey samples from Northern Europe. Based on metagenomic analysis, we find that the taxonomic composition of DNA is dominated by a low pathogenicity bee virus with 40.2% of the reads, followed by bacteria (16.7%), plants (9.4%) and only 1.1% from fungi. In terms of ecological roles of taxa associated with the bees or taxa in their environment, bee gut microbes dominate the honey DNA, with plants as the second most abundant group. A range of pathogens associated with plants, bees and other animals occur frequently, but with lower relative read abundance, across the samples. The associations found here reflect a versatile the honeybee’s role in the North-European ecosystem. Feeding on nectar and pollen, the honeybee interacts with plants–in particular with cultivated crops. In doing so, the honeybee appears to disperse common pathogens of plants, pollinators and other animals, but also microbes potentially protective of these pathogens. Thus, honey-borne DNA helps us define the honeybee’s functional niche, offering directions to expound the benefits and drawbacks of the associations to the honeybee itself and its interacting organisms.

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“…NGS methods have recently been investigated to distinguish between closely related eukaryotic species [21,22] and to detect food origins [23], the presence of toxic species [24], allergens [25], as well as other cases of adulteration [20,26,27], both accidental and economically motivated. However, the application of NGS technology is not without limitations.…”

Section: Introductionmentioning

confidence: 99%

Utilizing Big Data to Identify Tiny Toxic Components: Digitalis

Hunter

Literman

Handy

2021

Foods

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The botanical genus Digitalis is equal parts colorful, toxic, and medicinal, and its bioactive compounds have a long history of therapeutic use. However, with an extremely narrow therapeutic range, even trace amounts of Digitalis can cause adverse effects. Using chemical methods, the United States Food and Drug Administration traced a 1997 case of Digitalis toxicity to a shipment of Plantago (a common ingredient in dietary supplements marketed to improve digestion) contaminated with Digitalis lanata. With increased accessibility to next generation sequencing technology, here we ask whether this case could have been cracked rapidly using shallow genome sequencing strategies (e.g., genome skims). Using a modified implementation of the Site Identification from Short Read Sequences (SISRS) bioinformatics pipeline with whole-genome sequence data, we generated over 2 M genus-level single nucleotide polymorphisms in addition to species-informative single nucleotide polymorphisms. We simulated dietary supplement contamination by spiking low quantities (0–10%) of Digitalis whole-genome sequence data into a background of commonly used ingredients in products marketed for “digestive cleansing” and reliably detected Digitalis at the genus level while also discriminating between Digitalis species. This work serves as a roadmap for the development of novel DNA-based assays to quickly and reliably detect the presence of toxic species such as Digitalis in food products or dietary supplements using genomic methods and highlights the power of harnessing the entire genome to identify botanical species.

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DNA traces the origin of honey by identifying plants, bacteria and fungi

Cited by 38 publications

References 75 publications

Bee foraging preferences, microbiota and pathogens revealed by direct shotgun metagenomics of honey

Bee foraging preferences, microbiota and pathogens revealed by direct shotgun metagenomics of honey

Reconstructing the ecosystem context of a species: Honey-borne DNA reveals the roles of the honeybee

Utilizing Big Data to Identify Tiny Toxic Components: Digitalis

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