Molecular identification of honey entomological origin based on bee mitochondrial 16S rRNA and COI gene sequences

Hydroxy Fatty Acid Synthesis-Related mRNA as the Biomarker for Detecting Mislabeling of Honey Entomological Origin

The authentication of the entomological origin of honey is a widespread concern, necessitating the prompt establishment of an effective approach for distinguishing between Apis cerana cerana honey (ACH) and Apis mellifera ligustica honey (AMH). Hydroxy fatty acids (HFAs) found in honey are bee-derived components synthesized by the mandibular glands of worker bees. We previously discovered significant variations in the hydroxy fatty acid composition between ACH and AMH, suggesting their potential as indicators for identifying the authenticity of the entomological origin of honey. Herein, we identified differentially expressed genes associated with HFA synthesis by conducting transcriptome sequencing of the mandibular glands of AC and AM honeybees. Subsequently, we proposed a method for the relative quantitative analysis of bee-derived RNA components using real-time fluorescence quantitative polymerase chain reaction, which was supplemented by multivariate statistical analysis to further discern differences in HFA synthesis-related mRNA between ACH and AMH. The results showed that the mRNAs of FAXDC2 (fatty acid hydroxylase domain-containing protein 2) and FAS (fatty acid synthase) may serve as indicators to discern the entomological origin of honey. This study presents two novel biomarkers for detecting mislabeling of the entomological origin in ACH and AMH based on variations in bee-derived components.

An innovative molecular approach towards the cost-effective entomological authentication of honey

Honey authentication and traceability are crucial not only for economic purposes but also for ensuring safety. However, the widespread adoption of cutting-edge technologies in practical applications has been hampered by complex, time-consuming sample pre-treatment processes, the need for skilled personnel, and substantial associated expenses. This study aimed to develop a simple and cost-effective molecular technique to verify the entomological source of honey. By utilizing newly designed primers, we successfully amplified the mitochondrial 16S ribosomal RNA gene of honey bees from honey, confirming the high quality of the extracted DNA. Employing RFLP analysis with AseI endonuclease, species-specific restriction patterns were generated for honey derived from six closely related honey bees of the Apis genus. Remarkably, this method was proven equally effective in identifying heat-treated and aged honey by presenting the same RFLP profiles as raw honey. As far as we know, this is the initial research of the simultaneous differentiation of honey from closely related honey bee species using the restriction endonuclease AseI and mitochondrial 16S rRNA gene fragments. As a result, it holds tremendous potential as a standardized guideline for regulatory agencies to ascertain the insect origins of honey and achieve comprehensive traceability.

A comprehensive review of the current trends and recent advancements on the authenticity of honey

The authenticity of honey currently poses challenges to food quality control, thus requiring continuous modernization and improvement of related analytical methodologies. This review provides a comprehensively overview of honey authenticity challenges and related analytical methods. Firstly, direct and indirect methods of honey adulteration were described in detail, commenting the existing challenges in current detection methods and market supervision approaches. As an important part, the integrated metabolomic workflow involving sample processing procedures, instrumental analysis techniques, and chemometric tools in honey authenticity studies were discussed, with a focus on their advantages, disadvantages, and scopes. Among them, various improved microscale extraction methods, combined with hyphenated instrumental analysis techniques and chemometric data processing tools, have broad application potential in honey authenticity research. The future of honey authenticity determination will involve the use of simplified and portable methods, which will enable on-site rapid detection and transfer detection technologies from the laboratory to the industry.

The Chemical Composition of Scaptotrigona mexicana Honey and Propolis Collected in Two Locations: Similarities and Differences

The chemical composition of stingless bee honey and propolis depends on the plant sources they are derived from, and thus reflects the flora available in the vicinity of the hives, the preferences of the bee species, and the climate (altitude and temperature). To understand the relative influence of these factors, we studied the composition of honey and propolis of the stingless bee Scaptotrigona mexicana. Samples from 24 colonies were analyzed: 12 each from two S. mexicana meliponaries located in the state of Chiapas in southern Mexico, approximately 8.5 km apart, Tuxtla Chico and Cacahoatán. The chemical composition of honey and propolis was studied using nuclear magnetic resonance (NMR) and gas chromatography-mass spectrometry (GC-MS), respectively. The antioxidant activity of propolis was also studied. Chemometric analyses were applied. The Tuxtla Chico honey samples contained higher concentrations of glucose and fructose, while the Cacahoatán samples displayed a rich composition of di- and trisaccharides. These differences can be attributed to the distinct nectar sources utilized by the bees at each location. Propolis compositions in the two locations also demonstrated qualitative differences, indicating a specific choice of resins by the bees. The observed substantial variations in the chemical composition of propolis and honey of S. mexicana from two locations relatively close to each other supports the assumption that bee species cannot be considered the most important factor in determining their chemistry.

Honey Quality Control: Review of Methodologies for Determining Entomological Origin

Honey is a widely consumed natural product, and its entomological origin can significantly influence its market value. Therefore, traceability of the entomological origin of honey should also be considered in honey quality control protocols. Although several methods exist, such as physicochemical characterization and bioactivity profiling of honey of different entomological origins, the most promising three methods for entomological authentication of honey include protein-based identification, chemical profiling, and a DNA-based method. All of these methods can be applied for reliable identification of the entomological origin of honey. However, as the honey is a complex matrix, the inconsistency of the results obtained by these methods is a pragmatic challenge, and therefore, the use of each method in all the cases is questionable. Most of these methodologies can be used for authentication of newly harvested honey and it is worth understanding the possibility of using these methods for authentication of relatively old samples. Most probably, using DNA-based methods targeting small fragments of DNA can provide the best result in old samples, however, the species-specific primers targeting short fragments are limited and not available for all species. Therefore, using universal primers in combination with a DNA metabarcoding approach can be a good solution that requires further investigation. This present article describes the applications of different methods, their pros, and their cons to identify honey based on entomological origin.

Towards DNA-Based Methods Analysis for Honey: An Update

Honey is a natural product widely consumed all over the world due to its relationship with healthy benefits. Additionally, environmental and ethical issues have a higher weight in the consumer's choice to buy honey as a natural product. Following the high demand of this product, several approaches have been suggested and developed aiming at the assessment of honey's quality and authenticity. Target approaches, such as pollen analysis, phenolic compounds, sugars, volatile compounds, organic acids, proteins, amino acids, minerals, and trace elements, showed an efficacy, particularly concerning the honey origin. However, a special highlight is given to DNA markers, due to their useful applicability in environmental and biodiversity studies, besides the geographical, botanical, and entomological origins. Different DNA target genes were already explored for addressing diverse sources of honey DNA, with DNA metabarcoding attaining a relevant importance. This review aims to describe the latest advances on DNA-based methods applied in honey related studies, identifying the research needs for the development of new and additional required methodologies, and to select the most adequate tools for future research projects.

Metabarcoding of eDNA for tracking the floral and geographical origins of bee honey

Authentic honey products have a high commercial value and are often falsified via adulteration. Metabarcoding of environmental DNA (eDNA) from bacterial, floral, and entomological sources has recently been proposed as a useful tool for identifying and authenticating floral and geographical origins of bee honey. In this study, eDNA metabarcoding was applied to reveal the bacterial, plant, and honey bee DNA signatures of 48 commercial honey products from six different geographical origins. Bacterial DNA composition in commercial honey showed different relative abundance of Paenibacillus and Bacillus in geographically different samples, and high abundance of Methylobacterium in chestnut honey implying potential use of bacterial DNA composition for honey authentication. Using the chloroplast trnL (UAA) as a DNA marker, floral origins of commercial honey were investigated. Based on floral DNA signatures, 12 monofloral honey samples were identified among the 45 samples tested. Targeted amplicon sequencing of cytochrome oxidase I (COI) gene from entomological DNA identified three different Apis mellifera sequence variants, specific to geographic origin of honey, suggesting that COI can be implemented as a DNA marker to trace the origin of honey. Therefore, the current study demonstrated the potential of eDNA based metabarcoding as a robust tool for evaluating commercial bee honey by exploring their floral and geographical origins.

Physicochemical characteristics, antioxidant properties and bacterial profiling of three Malaysian honey varieties: a study using multivariate analysis

BACKGROUND

The physicochemical characteristics, antioxidant properties, and bacterial profiles of Heterotrigona itama, Apis dorsata, and Apis mellifera honey of Malaysian origin were studied and the results were assessed using Pearson correlation analysis and canonical correspondence analysis (CCA).

RESULTS

The analysis showed that the Mellifera honey was characterized by high total sugar content (717.5 g kg^-1 ); the Itama honey was characterized by high free acidity (347.5 meq kg^-1 ); and the Dorsata honey was characterized by high radical scavenging activity (RSA; 69.3%RSA), total phenolic content (TPC; 1284.5 mg GAE kg^-1 ) and hydroxymethylfurfural (HMF; 51.5 mg kg^-1 ). Pearson correlation analysis showed that the TPC was positively correlated with HMF as well as RSA. The bacterial profile of Mellifera honey was significantly less diverse than Itama and Dorsata honey. Mellifera and Itama honey seemed to harbour a significant abundance of lactic acid bacteria, with relative abundance of 0.339 and 0.195, which suggests that it possesses probiotic potential. The Dorsata honey, however, contained pathogenic Clostridium genus, constituting 5% of its bacterial profile.

CONCLUSION

The characteristic properties of the three investigated honey, Itama, Dorsata, and Mellifera were identified. The distinctive characteristics of the honey varieties informed the development of appropriate processing strategies for retaining the beneficial qualities of raw honey. It is hoped that the results of this study will shine light on Malaysian honey in a highly competitive global market. © 2022 Society of Chemical Industry.

Honey Environmental DNA Can Be Used to Detect and Monitor Honey Bee Pests: Development of Methods Useful to Identify Aethina tumida and Galleria mellonella Infestations

Environmental DNA (eDNA) contained in honey derives from the organisms that directly and indirectly have been involved in the production process of this matrix and that have played a role in the hive ecosystems where the honey has been produced. In this study we set up PCR-based assays to detect the presence of DNA traces left in the honey by two damaging honey bee pests: the small hive beetle (Aethina tumida) and the greater wax moth (Galleria mellonella). DNA was extracted from 82 honey samples produced in Italy and amplified using two specific primer pairs that target the mitochondrial gene cytochrome oxidase I (COI) of A. tumida and two specific primer pairs that target the same gene in G. mellonella. The limit of detection was tested using sequential dilutions of the pest DNA. Only one honey sample produced in Calabria was positive for A. tumida whereas about 66% of all samples were positively amplified for G. mellonella. The use of honey eDNA could be important to establish early and effective measures to contain at the local (e.g., apiary) or regional scales these two damaging pests and, particularly for the small hive beetle, to prevent its widespread diffusion.

DNA-Based Method for Traceability and Authentication of Apis cerana and A. dorsata Honey (Hymenoptera: Apidae), Using the NADH dehydrogenase 2 Gene

Honey is a widely used natural product and the price of honey from Apis cerana (ACH) and A. dorsata (ADH) is several times more expensive than the one from A. mellifera (AMH), thus there are increasing fraud issues reported in the market by mislabeling or mixing honeys with different entomological origins. In this study, three species-specific primers, targeting the NADH dehydrogenase 2 (ND2) region of honeybee mitochondrial DNA, were designed and tested to distinguish the entomological origin of ACH, ADH, and AMH. Molecular analysis showed that each primer set can specifically detect the ND2 region from the targeted honeybee DNA, but not from the others. The amplicon size for A. cerana, A. dorsata and A. mellifera were 224, 302, and 377 bp, respectively. Importantly, each primer set also specifically produced amplicons with expected size from the DNA prepared from honey samples with different entomological origins. The PCR adulteration test allowed detection of 1% of AMH in the mixture with either ACH or ADH. Furthermore, real-time PCR and melting curve analysis indicated the possible discrimination of origin of honey samples. Therefore, we provide the newly developed PCR-based method that can be used to determine the entomological origin of the three kinds of honey.

Honey authenticity: analytical techniques, state of the art and challenges

Honey is a high-value, globally consumed, food product featuring a high market price strictly related to its origin. Moreover, honey origin has to be clearly stated on the label, and quality schemes are prescribed based on its geographical and botanical origin. Therefore, to enhance food quality, it is of utmost importance to develop analytical methods able to accurately and precisely discriminate honey origin. In this study, an all-time scientometric evaluation of the field is provided for the first time using a structured keyword on the Scopus database. The bibliometric analysis pinpoints that the botanical origin discrimination was the most studied authenticity issue, and chromatographic methods were the most frequently used for its assessment. Based on these results, we comprehensively reviewed analytical techniques that have been used in honey authenticity studies. Analytical breakthroughs and bottlenecks on methodologies to assess honey quality parameters using separation, bioanalytical, spectroscopic, elemental and isotopic techniques are presented. Emphasis is given to authenticity markers, and the necessity to apply chemometric tools to reveal them. Altogether, honey authenticity is an ever-growing field, and more advances are expected that will further secure honey quality.

Employing DNA metabarcoding to determine the geographical origin of honey

Unfavourable climatic conditions force Iranian beekeepers to translocate over large distances in the course of the year. However, irrespective of the main place of production, the honey is always labeled with the name of the beekeepers' hometown, which leads consequently to mislabeled products. The present study investigates the capability of DNA metabarcoding to locate the geographical origin of honey. The molecular markers (ITS2 and rbcL) allowed identification of 926 plant species in studied samples. A comprehensive review of floristic reference books specified 34 key species that could be used to successfully determine the geographical origin in 91.4% of samples. These key species were usually present in honey with tiny amounts and thus, conventional palynology might not be able to detect them. The present investigation indicates that although ITS2 is able to detect more species than rbcL, utilizing a combination of both markers provides more robust evidence of geographical origin.

An Alternative, High Throughput Method to Identify Csd Alleles of the Honey Bee

Applying instrumental insemination in closely related honey bee colonies often leads to frequent lethality of offspring causing colony collapse. This is due to the peculiarities of honey bee reproductive biology, where the complementary sex determination (csd) gene drives sex determination within a haplodiploid system. Diploid drones containing homozygous genotypes are lethal. Tracking of csd alleles using molecular markers prevents this unwanted event in closed breeding programs. Our approach described here is based on high throughput sequencing (HTS) that provides more data than traditional molecular techniques and is capable of analysing sources containing multiple alleles, including diploid individuals as the bee queen. The approach combines HTS technique and clipping wings as a minimally invasive method to detect the complementary sex determiner (csd) alleles directly from honey bee queens. Furthermore, it might also be suitable for screening alleles of honey harvested from hives of a closed breeding facility. Data on alleles of the csd gene from different honey bee subspecies are provided. It might contribute to future databases that could potentially be used to track the origin of honey. With the help of tracking csd alleles, more focused crossings will be possible, which could in turn accelerate honey bee breeding programmes targeting increase tolerance against varroosis as well.

Shotgun sequencing of honey DNA can describe honey bee derived environmental signatures and the honey bee hologenome complexity

Honey bees are large-scale monitoring tools due to their extensive environmental exploration. In their activities and from the hive ecosystem complex, they get in close contact with many organisms whose traces can be transferred into the honey, which can represent an interesting reservoir of environmental DNA (eDNA) signatures and information useful to analyse the honey bee hologenome complexity. In this study, we tested a deep shotgun sequencing approach of honey DNA coupled with a specifically adapted bioinformatic pipeline. This methodology was applied to a few honey samples pointing out DNA sequences from 191 organisms spanning different kingdoms or phyla (viruses, bacteria, plants, fungi, protozoans, arthropods, mammals). Bacteria included the largest number of species. These multi-kingdom signatures listed common hive and honey bee gut microorganisms, honey bee pathogens, parasites and pests, which resembled a complex interplay that might provide a general picture of the honey bee pathosphere. Based on the Apis mellifera filamentous virus genome diversity (the most abundant detected DNA source) we obtained information that could define the origin of the honey at the apiary level. Mining Apis mellifera sequences made it possible to identify the honey bee subspecies both at the mitochondrial and nuclear genome levels.

Untargeted and Targeted Discrimination of Honey Collected by Apis cerana and Apis mellifera Based on Volatiles Using HS-GC-IMS and HS-SPME-GC-MS

Fraudulent acts regarding honey authenticity that use Apis mellifera honey as a substitute for Apis cerana honey have garnered considerable concern in China and triggered a trust crisis from consumers. In this study, untargeted metabolomics analysis was carried out based on volatile fractions in honey from A. cerana and A. mellifera using headspace gas chromatography-ion mobility spectrometry (HS-GC-IMS). Honey from A. cerana and A. mellifera was discriminated by HS-GC-IMS profiling, principal component analysis, and orthogonal partial least-squares discrimination analysis. Tentative markers were identified from p-values and the variable importance in projection analysis and confirmed using the retention index, mass fragments, and reference standards by gas chromatography-mass spectrometry (GC-MS). A targeted method was established using the headspace solid phase coupled with microextraction GC-MS (HS-SPME-GC-MS) to quantitate the markers. The results demonstrated that the developed untargeted and targeted metabolomics approach performed well when discriminating honey from A. cerana and A. mellifera.

A next generation sequencing approach for targeted Varroa destructor (Acari: Varroidae) mitochondrial DNA analysis based on honey derived environmental DNA

Honey contains DNA from many different organisms that are part of hive micro-environmental niches and honey bee pathospheres. In this study, we recovered and sequenced mite mitochondrial DNA (mtDNA) from honey from different locations around the world (Europe, Asia, Africa, North and South America). DNA extracted from 17 honey samples was amplified with eight primer pairs targeting three mite mtDNA genes, obtaining 88 amplicons that were sequenced with an Ion Torrent sequencing platform. A bioinformatic pipeline compared produced reads with Varroa spp. mtDNA sequence entries available in GenBank and assigned them to different mitotypes. In all honey samples, the highest percentage of reads was attributed to the K1 lineage, including a few variants derived from it, in addition to J1 reads observed in the two South American samples and C1-1 reads obtained from the Chinese honey. This study opens new possibilities to analyse mite lineages and variants and monitor their geographical and temporal distribution, simplifying surveillance against this damaging honey bee parasite.

Towards honey authentication: Differentiation of Apis mellifera subspecies in European honeys based on mitochondrial DNA markers

Honey is the natural sweet substance produced by Apis mellifera honeybees in Europe. Depending on the country/region, the A. mellifera subspecies native to Europe belong to three different lineages: A (A. m. iberiensis), M (A. m. iberiensis and A. m. mellifera) and C (A. m. ligustica and A. m. carnica). In this work, two DNA-based approaches were developed with the aim of entomological authentication of European honeys. A cytb specific PCR assay was proposed to identify A-lineage honeybees, while a second method based on real-time PCR coupled to high resolution melting analysis targeting the COI gene was developed to differentiate C- and M-lineages honeybees. The proposed methodologies were validated successfully with honeys of known origin and applied to the entomological authentication of 20 commercial samples from different European countries. The results highlight the predominance of honeys from C-lineage honeybees in Europe, except in Iberian Peninsula countries (honey from A-lineage honeybees).

Shotgun metagenomics of honey DNA: Evaluation of a methodological approach to describe a multi-kingdom honey bee derived environmental DNA signature

Honey bees are considered large-scale monitoring tools due to their environmental exploration and foraging activities. Traces of these activities can be recovered in the honey that also may reflect the hive ecological micro-conditions in which it has been produced. This study applied a next generation sequencing platform (Ion Torrent) for shotgun metagenomic analysis of honey environmental DNA (eDNA). The study tested a methodological framework to interpret DNA sequence information useful to describe the complex ecosystems of the honey bee colony superorganism, its pathosphere and the heterogeneity of the agroecological environments and environmental sources that left DNA marks in the honey. Analysis of two honeys reported sequence reads from five main organism groups (kingdoms or phyla): arthropods (that mainly included reads from Apis mellifera, several other members of the Hymenotpera, in addition to members of the Diptera, Coleoptera and Lepidoptera, as well as aphids and mites), plants (that clearly confirmed the botanical origin of the two honeys, i.e. orange tree blossom and eucalyptus tree blossom honeys), fungi and bacteria (including common hive and honey bee gut microorganisms, honey bee pathogens and plant pathogens), and viruses (which accounted for the largest number of reads in both honeys, mainly assigned to Apis mellifera filamentous virus). The shotgun metagenomic approach that was used in this study can be applied in large scale experiments that might have multiple objectives according to the multi-kingdom derived eDNA that is contained in the honey.

Entomological signatures in honey: an environmental DNA metabarcoding approach can disclose information on plant-sucking insects in agricultural and forest landscapes

Honeydew produced from the excretion of plant-sucking insects (order Hemiptera) is a carbohydrate-rich material that is foraged by honey bees to integrate their diets. In this study, we used DNA extracted from honey as a source of environmental DNA to disclose its entomological signature determined by honeydew producing Hemiptera that was recovered not only from honeydew honey but also from blossom honey. We designed PCR primers that amplified a fragment of mitochondrial cytochrome c oxidase subunit 1 (COI) gene of Hemiptera species using DNA isolated from unifloral, polyfloral and honeydew honeys. Ion Torrent next generation sequencing metabarcoding data analysis assigned Hemiptera species using a customized bioinformatic pipeline. The forest honeydew honeys reported the presence of high abundance of Cinara pectinatae DNA, confirming their silver fir forest origin. In all other honeys, most of the sequenced reads were from the planthopper Metcalfa pruinosa for which it was possible to evaluate the frequency of different mitotypes. Aphids of other species were identified from honeys of different geographical and botanical origins. This unique entomological signature derived by environmental DNA contained in honey opens new applications for honey authentication and to disclose and monitor the ecology of plant-sucking insects in agricultural and forest landscapes.