Microbial metabarcoding highlights different bacterial and fungal populations in honey samples from local beekeepers and market in north-eastern Italy

Identification of potential insect ecological interactions using a metabarcoding approach

Species interactions are challenging to quantify, particularly when they happen cryptically. Molecular methods have become a key tool to uncover these interactions when they leave behind a DNA trace from the interacting organism (e.g., pollen on a bee) or when the taxa are still present but morphologically challenging to identify (e.g., microbial or fungal interactions). The decreasing costs of sequencing makes the mass analysis of thousands of target species possible. However, the challenge has shifted to selecting molecular markers which maximize information recovery while analyzing these data at broad biological scales. In this manuscript we use model arthropod groups to compare molecular markers and their analysis across life stages. We develop protocols for two ecologically and economically devastating pests, the spongy moth (Lymantria dispar dispar) and the emerald ash borer (Agrilus planipennis), and a group of pollinators including bees and wasps which regularly deposit eggs in "bee hotels" where the larvae develop. Using Illumina MiSeq and Oxford Nanopore MinION platforms we evaluate seven primer pairs for five molecular markers which target plants, fungi, microbes, insects, and parasitic phyla (e.g., nematodes). Our data reveals hundreds of potential ecological interactions and establishes generalized methods which can be applied across arthropod host taxa with recommendations on the appropriate markers in different systems. However, we also discuss the challenge of differentiating co-occurring DNA signals and true ecological interactions, a problem only starting to be recognized as eDNA from the environment accumulates on living organisms.

Comparison of the Physicochemical Properties, Microbial Communities, and Hydrocarbon Composition of Honeys Produced by Different Apis Species

The chemical composition and quality of honey are influenced by its botanical, geographic, and entomological origins, as well as climatic conditions. In this study, the physicochemical characteristics, microbial communities, and hydrocarbon compounds of honey produced by Apis mellifera, Apis cerana, Apis laboriosa, Apis dorsata, and Apis florea were elucidated. The physicochemical profile of the honey exhibited significant differences across species, including moisture content (18.27-23.66%), fructose (33.79-38.70%), maltose (1.10-1.93%), electrical conductivity (0.37-0.74 mS/cm), pH (3.36-3.72), diastase activity (4.50-29.97 diastase number), and color (37.90-102.47 mm). Microbial analysis revealed a significant abundance of lactic acid bacteria, particularly the Apilactobacillus genus in A. laboriosa honey and the Lactobacillus in A. florea honey, indicating significant probiotic potential. Chemometric methods, principal component analysis, hierarchical cluster analysis, and orthogonal partial least squares discriminant analysis (OPLS-DA) were used to classify the honey samples based on the 12 beeswax-derived hydrocarbons. The OPLS-DA model demonstrated 100% accuracy in predicting the entomological origin of honey, indicating that specific hydrocarbons are reliable markers for honey classification.

Honey microbiota, methods for determining the microbiological composition and the antimicrobial effect of honey - A review

Honey is a natural product used since ancient times due to its taste, aroma, and therapeutic properties (antibacterial, antiviral, anti-inflammatory, and antioxidant activity). The purpose of this review is to present the species of microorganisms that can survive in honey and the effect they can have on bees and consumers. The techniques for identifying the microorganisms present in honey are also described in this study. Honey contains bacteria, yeasts, molds, and viruses, and some of them may present beneficial properties for humans. The antimicrobial effect of honey is due to its acidity and high viscosity, high sugar concentration, low water content, the presence of hydrogen peroxide and non-peroxidase components, particularly methylglyoxal (MGO), phenolic acids, flavonoids, proteins, peptides, and non-peroxidase glycopeptides. Honey has antibacterial action (it has effectiveness against bacteria, e.g. Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, and Acinetobacter, etc.), antifungal (effectiveness against Candida spp., Aspergillus spp., Fusarium spp., Rhizopus spp., and Penicillium spp.), antiviral (effectiveness against SARS-CoV-2, Herpes simplex virus type 1, Influenza virus A and B, Varicella zoster virus), and antiparasitic action (effectiveness against Plasmodium berghei, Giardia and Trichomonas, Toxoplasma gondii) demonstrated by numerous studies that are comprised and discussed in this review.

Honeydew Honey as a Reservoir of Bacteria with Antibacterial and Probiotic Properties

The purpose of this study was to isolate, identify, and evaluate the antibacterial and probiotic potential of bacteria from honeydew honey collected in Poland. Isolates (189 colonies from 10 honey samples) were evaluated for their antimicrobial activity against Staphylococcus aureus, Bacillus cereus, Escherichia coli, and Yersinia enterocolitica, and then identified by MALDI-TOF-MS. The isolates with the greatest antimicrobial properties were screened for their probiotic potential. The total number of bacteria isolated from honey did not exceed the value of 2.5 × 102 CFU/mL. The Bacillus pumilus/altitudinis, B. licheniformis, and Bacillus cereus groups were the dominant identified bacteria. Almost 16% of the isolates expressed antibacterial potential against three pathogenic bacteria, over 20% against two, while almost 34% of the isolates did not inhibit any. The survival rate of the isolates under gastrointestinal tract conditions was higher after 4 h of exposure to bile salts (>60% survival rate for 66.66% of the isolates), while at pH 2.0, it was lower (>50% survival rate for 44% of the isolates). The most resistant isolate B. pumilus/altitudinis survived at a rate of 77% at low pH and 108% with bile salts. These results confirmed that honeydew honey is a promising reservoir of bacteria that produces metabolites with antimicrobial and probiotic potential.

Underexplored food safety hazards of beekeeping products: Key knowledge gaps and suggestions for future research

These days, a growing consumer demand and scientific interest can be observed for nutraceuticals of natural origin, including apiculture products. Due to the growing emphasis on environmental protection, extensive research has been conducted on the pesticide and heavy metal contamination of bee products; however, less attention is devoted on other food safety aspects. In our review, scientific information on the less-researched food safety hazards of honey, bee bread, royal jelly, propolis, and beeswax are summarized. Bee products originating from certain plants may inherently contain phytotoxins, like pyrrolizidine alkaloids, tropane alkaloids, matrine alkaloids, grayanotoxins, gelsemium alkaloids, or tutin. Several case studies evidence that bee products can induce allergic responses to sensitive individuals, varying from mild to severe symptoms, including the potentially lethal anaphylaxis. Exposure to high temperature or long storage may lead to the formation of the potentially toxic 5-hydroxymethylfurfural. Persistent organic pollutants, radionuclides, and microplastics can potentially be transferred to bee products from contaminated environmental sources. And lastly, inappropriate beekeeping practices can lead to the contamination of beekeeping products with harmful microorganisms and mycotoxins. Our review demonstrates the necessity of applying good beekeeping practices in order to protect honeybees and consumers of their products. An important aim of our work is to identify key knowledge gaps regarding the food safety of apiculture products.

The first ITS1 profiling of honey samples from the Southeast Asian region Lombok, Bali and Banggi Island

Southern Asian flowers offer honeybees a diversity of nectar. Based on its geographical origin, honey quality varies. Traditional methods are less authentic than DNA-based identification. The origin of honey is determined by pollen, polyphenolic, and macro-microorganisms. In this study, amplicon sequencing targets macro-microorganisms in eDNA using the ITS1 region to explore honey's geographical location and authentication. The variety of honey samples was investigated using ITS1 with Illumina sequencing. For all four honey samples, raw sequence reads showed 979,380 raw ITS1 amplicon reads and 375 ASVs up to the phylum level. The highest total number of 202 ASVs up to phylum level identified Bali honey with 211,189 reads, followed by Banggi honey with 309,207 a total number of 111 ASVs, and Lombok represents only 63 ASVs up to phylum level with several read 458,984. Based on Shannon and Chao1, honey samples from Bali (B2) and (B3) exhibited higher diversity than honey from Lombok (B1) and green honey from Sabah (B4), while the Simpson index showed that Banggi honey (B4) had higher diversity. Honey samples had significant variance in mycobiome taxonomic composition and abundance. Zygosaccharomyces and Aspergillus were the main genera found in Lombok honey, with percentages of 68.81% and 29.76% respectively. Bali honey samples (B2 and B3) were identified as having a significant amount of the genus Aureobasidium, accounting for 40.81% and 25% of the readings, respectively. The microbiome composition of Banggi honey (B4) showed a high presence of Zygosaccharomyces 45.17% and Aureobasidium 35.24%. The ITS1 analysis effectively distinguishes between honey samples of different origins and its potential as a discriminatory tool for honey origin and authentication purposes.

The buzz about honey-based biosurveys

Approximately 1.8 million metric tonnes of honey are produced globally every year. The key source behind this output, the honey bee (Apis mellifera), works tirelessly to create the delicious condiment that is consumed worldwide. The honey that finds its way into jars on store shelves contains a myriad of information about its biogeographical origins, such as the bees that produced it, the botanical constituents, and traces of other organisms or pathogens that have come in contact with the product or its producer. With the ongoing threat of honey bee decline and overall global biodiversity loss, access to ecological information has become an key factor in preventing the loss of species. This review delves into the various molecular techniques developed to characterize the collective DNA harnessed within honey samples, and how it can be used to elucidate the ecological interactions between honey bees and the environment. We also explore how these DNA-based methods can be used for large-scale biogeographical studies through the environmental DNA collected by foraging honey bees. Further development of these techniques can assist in the conservation of biodiversity by detecting ecosystem perturbations, with the potential to be expanded towards other critical flying pollinators.

The quality of selected raw and pasteurized honeys based on their sensory profiles and consumer preferences

The purpose of this study was to determine the sensory profile of honeys based on the method of quantitative descriptive analysis and principal component analysis and assess consumer preferences of raw and pasteurized honeys. Samples of multi-floral honeys (from the store and apiary) were subjected to sensory analysis based on the method of ranking for taste preference, the method of scaling based on color, aroma, taste, and texture, and the method of differential descriptive analysis using 11 quality descriptors. The results were subjected to statistical analysis using the Principal Component Analysis method. The taste was found to be a descriptor that differentiates honey by origin. Consumers prefer the taste of pasteurized honeys. As a result of assessing the quality of honeys using the scaling method, it was found that: raw honeys are characterized by a lighter color than pasteurized honeys, store-bought honeys have a less noticeable aroma than honeys obtained from beekeepers, while samples of pasteurized honeys were judged to have a consistency more like that of typical honey. The sensory profiles obtained highlight the differences between pasteurized honeys and raw honeys.

A preliminary metabarcoding analysis of Portuguese raw honeys

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.

Characterization of the archaeal community in foods: The neglected part of the food microbiota

Despite the large number of studies conducted on archaea associated with extreme environments, the archaeal community composition in food products is still poorly known. Here, we investigated a new insight into exploring the archaeal community in several food matrices, with a particular focus on determining whether living archaea were present. A total of 71 samples of milk, cheese and its derived brine, honey, hamburger, clam, and trout were analyzed by high-throughput 16S rRNA sequencing. Archaea were detected in all the samples, ranging from 0.62 % of microbial communities in trout to 37.71 % in brine. Methanogens dominated 47.28 % of the archaeal communities, except for brine, which was dominated by halophilic taxa affiliated with the genus Haloquadratum (52.45 %). Clams were found to be a food with high richness and diversity of archaea and were targeted for culturing living archaea under different incubation time and temperature conditions. A subset of 16 communities derived from culture-dependent and culture-independent communities were assessed. Among the homogenates and living archaeal communities, the predominant taxa were distributed in the genera Nitrosopumilus (47.61 %) and Halorussus (78.78 %), respectively. A comparison of the 28 total taxa obtained by culture-dependent and culture-independent methods enabled their categorization into different groups, including detectable (8 out of 28), cultivable (8 out of 28), and detectable-cultivable (12 out of 28) taxa. Furthermore, using the culture method, the majority (14 out of 20) of living taxa grew at lower temperatures of 22 and 4 °C during long-term incubation, and few taxa (2 out of 20) were found at 37 °C during the initial days of incubation. Our results demonstrated the distribution of archaea in all analyzed food matrices, which opens new perspectives to expand our knowledge on archaea in foods and their beneficial and detrimental effects.

Honey characterization and identification of fructophilic lactic acid bacteria of fresh samples from Melipona beecheii, Scaptotrigona pectoralis, Plebeia llorentei, and Plebeia jatiformis hives

Stingless bees are essential to preser tropical ecosystems. They pollinate native flora, producing honey with properties for traditional health uses. Lactic acid bacteria spontaneously ferment honey in stingless bee honey (SBH). This study aims to determine the main physicochemical characteristics of Melipona beecheii, Scraptotrigona pectoralis, Plebeia jatiformis and Plebeia llorentei honey and to isolate and identify FLAB present in SBH samples. The physicochemical properties of SBH, such as color, pH, acidity, sugars, protein, total soluble solids, water activity, total polyphenols, and antioxidant activity, were determined since these parameters can be related to the presence of some bacteria groups, and with health benefits for humans and the hive ecosystems. FLAB harvested from honey, taken directly from storing pots of the hives, were identified by 16S ribosomal RNA sequencing and preserved for future biotechnological use due to their resistance to non-ionic osmotic stress. The results showed significant differences in the physicochemical characteristics of SBH samples. Seven FLAB from four stingless bee species were identified as Fructobacillus pseudoficulneus and F. tropaeoli. In addition, three other strains of Fructilactobacillus spp. were identified only at the genus level. All species showed the ability to grow under different carbon sources, resulting in negative hemolysis and sensitivity to cefuroxime, erythromycin, and chloramphenicol. To the best of our knowledge, this is the first time that the physicochemical and FLAB characterization of SBH from P. jatiformis and P. llorentei has been reported. Therefore, the future following research should be focused on the environmental, health and food biotechnological applications implications of FLAB from SBH.

Microbiome analysis of raw honey reveals important factors influencing the bacterial and fungal communities

Raw honeys contain diverse microbial communities. Previous studies have focused on isolating bacteria and fungi that are culturable, while missing a large proportion of the microbial community due to culture-based constraints. This study utilized next-generation sequencing (NGS) to analyze the composition of microorganisms in raw honey; these data can reveal environmental and physicochemical variables that are associated with different microbial communities. To examine the microbial composition (bacteria and fungi) of raw honey and analyze its association with physicochemical properties, four types of honey (monofloral, wildflower, manuka, and feral; n total = 36) were analyzed via amplicon metagenomics. The analyzed honey samples had relatively similar bacterial communities but more distinct and diverse fungal communities. Honey type was determined as a significant factor influencing alpha and beta diversity metrics of bacterial and fungal communities. For the bacterial communities, titratable acidity (TA) was associated with community richness and diversity. For the fungal communities, Brix, TA, and color were associated with community richness, while water activity and color were associated with community diversity. Additionally, important bacterial and fungal amplicon sequence variants (ASVs) that influenced the overall community were identified. Results from this study provide important insights into the microbial communities associated with different types of raw honey, which could improve our understanding of microbial dynamics in beehives, improve honey production, and prevent honeybee disease.

Beehive products as bioindicators of antimicrobial resistance contamination in the environment

The use of antimicrobials in agricultural, veterinary and medical practice exerts selective pressure on environmental microbiota, promoting the emergence and spread of antimicrobial resistance (AMR), a global concern for the One Health Initiative Task Force (OHITF). Honeybees have been studied as bioindicators of AMR in the environment, but little is known about beehive products like honey and pollen. The aim of this study was to assess the prevalence of AMR genes (ARGs) in beehive products and investigated their origins. Specifically, possible associations between ARGs, microbiota and other characteristics of different honey and pollen samples, including country of origin, flower type, type of commercial distribution and environmental factors, such as land use, weather and composition of the environment surrounding the beehives were investigated. We found that beehive products harboured ARGs conferring resistance to β-lactams, macrolides, (fluoro)quinolones and polymyxins. Most samples possessed resistance to multiple antimicrobial classes, with honey and pollen showing similar ARG profiles. Even if Lactobacillus and Acinetobacter genera were common in the microbial communities of both honey and pollen, Bacillus, Clostridium, and Bombella defined honey microbiota, while Pseudomonas and Vibrio were enriched in pollen. ErmB and bla_TEM-1 co-occurred with Lactobacillus and Fructobacillus, while positive associations between β-lactams and macrolides and anthropogenic environments (i.e. industrial and commercial areas and non-irrigated arable lands) were found. Altogether, our findings suggest that ARGs in honey and pollen might originate from the honeybee foraging environment, and that the beehive products can be used as bioindicators of the AMR environmental contamination.

Natural contaminants in bee pollen: DNA metabarcoding as a tool to identify floral sources of pyrrolizidine alkaloids and fungal diversity

The use of bee pollen as a food supplement has increased in recent years as it contains several nutrients and phytochemicals. However, depending on floral composition, bee pollen can be contaminated by pyrrolizidine alkaloids (PAs), PA N-oxides (PANOs) and toxigenic fungi found in plants, which may pose a potential health risk for consumers. Thus, a DNA metabarcoding approach based on internal transcribed spacer 2 (ITS2) region was used to identify the plant sources of 17 PAs/PANOs detected by a validated method in liquid chromatography coupled to mass spectrometry (LC-MS/MS), as well as floral and fungal diversity in 61 bee pollen samples. According to LC-MS/MS analysis, 67% of the samples contained PAs/PANOs with mean concentration of 339 µg/kg. The contamination pattern was characterised by lycopsamine- and senecionine-type PAs/PANOs. PA/PANO-producing plants were identified in 54% of the PA/PANO-contaminated samples analysed by DNA metabarcoding, which also allowed identifying the overall floral and fungal composition of 56 samples. To evaluate the performance of the molecular approach, a subset of 25 samples was analysed by classical palynology. Palynological analysis partially confirmed the results of DNA metabarcoding, which had a better performance in distinguishing pollens of different genera from Asteraceae (76%) and Brassicaceae (88%). However, the molecular analysis did not identify pollens from Castanea, Eucalyptus, Hedera and Salix, which were abundant in 11 samples according to palynology. On the other hand, the molecular analysis allowed identifying several fungal genera in 33 samples, including the toxigenic fungi Alternaria and Aspergillus, which were positively correlated to the plant genus Hypericum. Despite limitations in identifying some pollen types, these preliminary results suggest that the DNA metabarcoding could be applied in a multidisciplinary approach to give a picture of floral and fungal diversity, which can be sources of natural contaminants in bee pollen and would help to control its safety.

Genome and Pangenome Analysis of Lactobacillus hilgardii FLUB-A New Strain Isolated from Mead

The production of mead holds great value for the Polish liquor industry, which is why the bacterium that spoils mead has become an object of concern and scientific interest. This article describes, for the first time, Lactobacillus hilgardii FLUB newly isolated from mead, as a mead spoilage bacteria. Whole genome sequencing of L. hilgardii FLUB revealed a 3 Mbp chromosome and five plasmids, which is the largest reported genome of this species. An extensive phylogenetic analysis and digital DNA-DNA hybridization confirmed the membership of the strain in the L. hilgardii species. The genome of L. hilgardii FLUB encodes 3043 genes, 2871 of which are protein coding sequences, 79 code for RNA, and 93 are pseudogenes. L. hilgardii FLUB possesses three clustered regularly interspaced short palindromic repeats (CRISPR), eight genomic islands (44,155 bp to 6345 bp), and three (two intact and one incomplete) prophage regions. For the first time, the characteristics of the genome of this species were described and a pangenomic analysis was performed. The concept of the pangenome was used not only to establish the genetic repertoire of this species, but primarily to highlight the unique characteristics of L. hilgardii FLUB. The core of the genome of L. hilgardii is centered around genes related to the storage and processing of genetic information, as well as to carbohydrate and amino acid metabolism. Strains with such a genetic constitution can effectively adapt to environmental changes. L. hilgardii FLUB is distinguished by an extensive cluster of metabolic genes, arsenic detoxification genes, and unique surface layer proteins. Variants of MRS broth with ethanol (10-20%), glucose (2-25%), and fructose (2-24%) were prepared to test the strain's growth preferences using Bioscreen C and the PYTHON script. L. hilgardii FLUB was found to be more resistant than a reference strain to high concentrations of alcohol (18%) and sugars (25%). It exhibited greater preference for fructose than glucose, which suggests it has a fructophilic nature. Comparative genomic analysis supported by experimental research imitating the conditions of alcoholic beverages confirmed the niche specialization of L. hilgardii FLUB to the mead environment.