Genome sequencing and analysis of the first complete genome of Lactobacillus kunkeei strain MP2, an Apis mellifera gut isolate

A review on recent taxonomic updates of gut bacteria associated with social bees, with a curated genomic reference database

Honeybees and bumblebees play a crucial role as essential pollinators. The special gut microbiome of social bees is a key factor in determining the overall fitness and health of the host. Although bees harbor relatively simple microbial communities at the genus level, recent studies have unveiled significant genetic divergence and variations in gene content within each bacterial genus. However, a comprehensive and refined genomics-based taxonomic database specific to social bee gut microbiomes remains lacking. Here, we first provided an overview of the current knowledge on the distribution and function of social bee gut bacteria, as well as the factors that influence the gut population dynamics. We then consolidated all available genomes of the gut bacteria of social bees and refined the species-level taxonomy, by constructing a maximum-likelihood core genome phylogeny and calculating genome-wide pairwise average nucleotide identity. On the basis of the refined species taxonomy, we constructed a curated genomic reference database, named the bee gut microbe genome sequence database (BGM-GDb). To evaluate the species-profiling performance of the curated BGM-GDb, we retrieved a series of bee gut metagenomic data and inferred the species-level composition using metagenomic intra-species diversity analysis system (MIDAS), and then compared the results with those obtained from a prebuilt MIDAS database. We found that compared with the default database, the BGM-GDb excelled in aligned read counts and bacterial richness. Overall, this high-resolution and precise genomic reference database will facilitate research in understanding the gut community structure of social bees.

Putative Role of Anti-microbial Peptide Recovered from Lactiplantibacillus spp. in Biocontrol Activity

Antimicrobial peptides (AMPs) stand as a promising alternative to conventional pesticides, leveraging a multifaceted approach to combat plant pathogens. This study focuses on identifying and characterizing the AMP produced by Lactiplantibacillus argentoratensis strain IT, demonstrating potent antibacterial activity against various harmful microorganisms. Evaluation of AMPs' antibacterial activity was conducted through an agar well diffusion assay, a reliable method for assessing secondary metabolite antimicrobial efficacy. The study unveils the antimicrobial potential of the purified extract obtained from Lactiplantibacillus argentoratensis IT, isolated from goat milk. Notably, the AMP exhibited robust antibacterial activity against phytopathogens affecting solanaceous crops, including the Gram-negative Ralstonia solanacearum. Expression conditions and purification methods were optimized to identify the peptide's mass and sequence, utilizing LC-MS and SDS-PAGE. This paper underscores the application potential of Lactiplantibacillus spp. IT as a biocontrol agent for managing bacterial infectious diseases in plants. Results indicate optimal AMP production at 37 °C, with a culture broth pH of 5 during fermentation. The obtained peptide sequence corresponded to peaks at 842.5 and 2866.4 m/z ratio, with a molecular weight of approximately 5 kDa according to tricine SDS-PAGE analysis. In conclusion, this study lays the foundation for utilizing Lactiplantibacillus spp. IT derived AMPs in plant biocontrol strategies, showcasing their efficacy against bacterial phytopathogens. These findings contribute valuable insights for advancing sustainable agricultural practices.

Characterization of Lactic Acid Bacteria Strains Isolated from Algerian Honeybee and Honey and Exploration of Their Potential Probiotic and Functional Features for Human Use

Using culture enrichment methods, 100 strains of bacilli of lactic acid bacteria (LAB) were isolated from honeybee Apis mellifera intermissa and fresh honey, collected from apiaries located in the north-east of Algeria. Amongst all of the isolated LAB, 19 selected strains were closely affiliated to four species-Fructobacillus fructosus (10), Apilactobacillus kunkeei (5), Lactobacillus kimbladii and/or Lactobacillus kullabergensis (4)-using phylogenetic and phenotypic approaches. The in vitro probiotic characteristics (simulated gastrointestinal fluids tolerance, autoaggregation and hydrophobicity abilities, antimicrobial activity and cholesterol reduction) and safety properties (hemolytic activity, antibiotic resistance and absence of biogenic amines) were evaluated. The results indicated that some strains showed promising potential probiotic properties. In addition, neither hemolytic activity nor biogenic amines were produced. The carbohydrate fermentation test (API 50 CHL) revealed that the strains could efficiently use a broad range of carbohydrates; additionally, four strains belonging to Apilactobacillus kunkeei and Fructobacillus fructosus were found to be exopolysaccharides (EPS) producers. This study demonstrates the honeybee Apis mellifera intermissa and one of her products as a reservoir for novel LAB with potential probiotic features, suggesting suitability for promoting host health.

Comparative genomics of Lactobacillaceae from the gut of honey bees, Apis mellifera, from the Eastern United States

Lactobacillaceae are an important family of lactic acid bacteria that play key roles in the gut microbiome of many animal species. In the honey bee (Apis mellifera) gut microbiome, many species of Lactobacillaceae are found, and there is functionally important strain-level variation in the bacteria. In this study, we completed whole-genome sequencing of 3 unique Lactobacillaceae isolates collected from hives in Virginia, USA. Using 107 genomes of known bee-associated Lactobacillaceae and Limosilactobacillus reuteri as an outgroup, the phylogenetics of the 3 isolates was assessed, and these isolates were identified as novel strains of Apilactobacillus kunkeei, Lactobacillus kullabergensis, and Bombilactobacillus mellis. Genome rearrangements, conserved orthologous genes (COG) categories and potential prophage regions were identified across the 3 novel strains. The new A. kunkeei strain was enriched in genes related to replication, recombination and repair, the L. kullabergensis strain was enriched for carbohydrate transport, and the B. mellis strain was enriched in transcription or transcriptional regulation and in some genes with unknown functions. Prophage regions were identified in the A. kunkeei and L. kullabergensis isolates. These new bee-associated strains add to our growing knowledge of the honey bee gut microbiome, and to Lactobacillaceae genomics more broadly.

Novel Candidate Microorganisms for Fermentation Technology: From Potential Benefits to Safety Issues

Fermentation is one of the oldest known production processes and the most technologically valuable in terms of the food industry. In recent years, increasing nutrition and health awareness has also changed what is expected from fermentation technology, and the production of healthier foods has started to come a little more forward rather than increasing the shelf life and organoleptic properties of foods. Therefore, in addition to traditional microorganisms, a new generation of (novel) microorganisms has been discovered and research has shifted to this point. Novel microorganisms are known as either newly isolated genera and species from natural sources or bacterial strains derived from existing bacteria. Although novel microorganisms are mostly studied for their use in novel food production in terms of gut-microbiota modulation, recent innovative food research highlights their fermentative effects and usability, especially in food modifications. Herein, Clostridium butyricum, Bacteroides xylanisolvens, Akkermansia muciniphila, Mycobacterium setense manresensis, and Fructophilic lactic acid bacteria (FLAB) can play key roles in future candidate microorganisms for fermentation technology in foods. However, there is also some confusion about the safety issues related to the use of these novel microorganisms. This review paper focuses on certain novel candidate microorganisms for fermentation technology with a deep view of their functions, benefits, and safety issues.

Draft Genome Sequences of 3 Strains of Apilactobacillus kunkeei Isolated from the Bee Gut Microbial Community

Apilactobacillus kunkeei is a fructophilic lactic acid bacterium found in fructose-rich environments such as flowers, fruits, fermented food, honey, and honeydew, as well as in the guts of fructose-feeding insects. We report here the draft genome sequences of three Apilactobacillus kunkeei strains isolated from the gut microbial community of three honeybees.

Apilactobacillus kunkeei is a fructophilic lactic acid bacterium found in fructose-rich environments such as flowers, fruits, fermented food, honey, and honeydew, as well as in the guts of fructose-feeding insects. We report here the draft genome sequences of three Apilactobacillus kunkeei strains isolated from the gut microbial community of three honeybees.

Potential Application of Apilactobacillus kunkeei for Human Use: Evaluation of Probiotic and Functional Properties

Apilactobacillus kunkeei is an insect symbiont with documented beneficial effects on the health of honeybees. It belongs to fructophilic lactic acid bacteria (FLAB), a subgroup of lactic acid bacteria (LAB) notably recognized for their safe status. This fact, together with its recurrent isolation from hive products that are traditionally part of the human diet, suggests its possible safe use as human probiotic. Our data concerning three strains of A. kunkeei isolated from bee bread and honeybee gut highlighted several interesting features, such as the presence of beneficial enzymes (β-glucosidase, β-galactosidase and leucine arylamidase), the low antibiotic resistance, the ability to inhibit P. aeruginosa and, for one tested strain, E. faecalis, and an excellent viability in presence of high sugar concentrations, especially for one strain tested in sugar syrup stored at 4 °C for 30 d. This datum is particularly stimulating, since it demonstrates that selected strains of A. kunkeei can be used for the probiotication of fruit preparations, which are often used in the diet of hospitalized and immunocompromised patients. Finally, we tested for the first time the survival of strains belonging to the species A. kunkeei during simulated gastrointestinal transit, detecting a similar if not a better performance than that showed by Lacticaseibacillus rhamnosus GG, used as probiotic control in each trial.

Interest of bacterial pangenome analyses in clinical microbiology

Thanks to the progress and decreasing costs in genome sequencing technologies, more than 250,000 bacterial genomes are currently available in public databases, covering most, if not all, of the major human-associated phylogenetic groups of these microorganisms, pathogenic or not. In addition, for many of them, sequences from several strains of a given species are available, thus enabling to evaluate their genetic diversity and study their evolution. In addition, the significant cost reduction of bacterial whole genome sequencing as well as the rapid increase in the number of available bacterial genomes have prompted the development of pangenomic software tools. The study of bacterial pangenome has many applications in clinical microbiology. It can unveil the pathogenic potential and ability of bacteria to resist antimicrobials as well identify specific sequences and predict antigenic epitopes that allow molecular or serologic assays and vaccines to be designed. Bacterial pangenome constitutes a powerful method for understanding the history of human bacteria and relating these findings to diagnosis in clinical microbiology laboratories in order to optimize patient management.

Alterations in honey bee gut microorganisms caused by Nosema spp. and pest control methods

BACKGROUND

Honey bees are associated with gut microorganisms essential for their nutrition and health. The composition of the microbial community can be used as a biological health indicator and is characterized using biomarker fatty acids. Commonly, gut microorganisms are exposed to pathogens and to an array of chemical and biological pest control methods.

RESULTS

We found a strong negative effect on microbial gut community composition when exposed to the bee pest control chemicals oxytetracycline, oxalic acid and imidacloprid, and when inoculated with the bee pest Nosema spp. and the potential bee pest biocontrol agent Lactobacillus plantarum. Results from the in vitro test with bee pest chemicals showed a differential response of Lactobacillus spp. At the community level, some taxonomic groups were more affected depending on treatment, but sharp changes in the microbial structure were caused by compounds generally considered as bee safe.

CONCLUSION

Our results show that pests such as Nosema spp. and pest control methods alter the composition of bee gut microorganisms, which may have severe consequences for pathogen defense, physiology and general honey bee health. In addition, L. plantarum has potential as a biocontrol agent against Nosema spp. © 2018 Society of Chemical Industry.

Novel solid-state fermentation of bee-collected pollen emulating the natural fermentation process of bee bread

Structure of lactic acid bacteria biota in ivy flowers, fresh bee-collected pollen (BCP), hive-stored bee bread, and honeybee gastrointestinal tract was investigated. Although a large microbial diversity characterized flowers and fresh BCP, most of lactic acid bacteria species disappeared throughout the bee bread maturation, giving way to Lactobacillus kunkeei and Fructobacillus fructosus to dominate long stored bee bread and honeybee crop. Adaptation of lactic acid bacteria was mainly related to species-specific, and, more in deep, to strain-specific features. Bee bread preservation seemed related to bacteria metabolites, produced especially by some L. kunkeei strains, which likely gave to lactic acid bacteria the capacity to outcompete other microbial groups. A protocol to ferment BCP was successfully set up, which included the mixed inoculum of selected L. kunkeei strains and Hanseniaspora uvarum AN8Y27B, almost emulating the spontaneous fermentation of bee bread. The strict relationship between lactic acid bacteria and yeasts during bee bread maturation was highlighted. The use of the selected starters increased the digestibility and bioavailability of nutrients and bioactive compounds naturally occurring in BCP. Our biotechnological protocol ensured a product microbiologically stable and safe. Conversely, raw BCP was more exposed to the uncontrolled growth of yeasts, moulds, and other bacterial groups.

Fructose-rich niches traced the evolution of lactic acid bacteria toward fructophilic species

Fructophilic lactic acid bacteria (FLAB) are found in fructose-rich habitats associated with flowers, fruits, fermented foods, and the gastrointestinal tract of several insects having a fructose-based diet. FLAB are heterofermentative lactobacilli that prefer fructose instead of glucose as carbon source, although additional electron acceptor substrates (e.g. oxygen) remarkably enhance their growth on glucose. As a newly discovered bacterial group, FLAB are gaining increasing interest. In this review, the ecological context in which these bacteria exist and evolve was resumed. The wide frequency of isolation of FLAB from fructose feeding insects has been deepened to reveal their ecological significance. Genomic, metabolic data, reductive evolution, and niche specialization of the main FLAB species have been discussed. Findings to date acquired are consistent with a metabolic model in which FLAB display a reliance on environmental niches and the degree of host specificity. In light of FLAB proximity to lactic acid bacteria generally considered to be safe, and due to their peculiar metabolic traits, FLAB may be successfully exploited in food and pharmaceutical applications.

The queen's gut refines with age: longevity phenotypes in a social insect model

BACKGROUND

In social insects, identical genotypes can show extreme lifespan variation providing a unique perspective on age-associated microbial succession. In honey bees, short- and long-lived host phenotypes are polarized by a suite of age-associated factors including hormones, nutrition, immune senescence, and oxidative stress. Similar to other model organisms, the aging gut microbiota of short-lived (worker) honey bees accrue Proteobacteria and are depleted of Lactobacillus and Bifidobacterium, consistent with a suite of host senescence markers. In contrast, long-lived (queen) honey bees maintain youthful cellular function with much lower expression of oxidative stress genes, suggesting a very different host environment for age-associated microbial succession.

RESULTS

We sequenced the microbiota of 63 honey bee queens exploring two chronological ages and four alimentary tract niches. To control for genetic and environmental variation, we quantified carbonyl accumulation in queen fat body tissue as a proxy for biological aging. We compared our results to the age-specific microbial succession of worker guts. Accounting for queen source variation, two or more bacterial species per niche differed significantly by queen age. Biological aging in queens was correlated with microbiota composition highlighting the relationship of microbiota with oxidative stress. Queens and workers shared many major gut bacterial species, but differ markedly in community structure and age succession. In stark contrast to aging workers, carbonyl accumulation in queens was significantly associated with increased Lactobacillus and Bifidobacterium and depletion of various Proteobacteria.

CONCLUSIONS

We present a model system linking changes in gut microbiota to diet and longevity, two of the most confounding variables in human microbiota research. The pattern of age-associated succession in the queen microbiota is largely the reverse of that demonstrated for workers. The guts of short-lived worker phenotypes are progressively dominated by three major Proteobacteria, but these same species were sparse or significantly depleted in long-lived queen phenotypes. More broadly, age-related changes in the honey bee microbiota reflect the regulatory anatomy of reproductive host metabolism. Our synthesis suggests that the evolution of colony-level reproductive physiology formed the context for host-microbial interactions and age-related succession of honey bee microbiota.

Inhibitory effect of biofilm-forming Lactobacillus kunkeei strains against virulent Pseudomonas aeruginosa in vitro and in honeycomb moth (Galleria mellonella) infection model

Biofilms correspond to complex communities of microorganisms embedded in an extracellular polymeric matrix. Biofilm lifestyle predominates in Pseudomonas aeruginosa, an opportunistic Gram negative pathogen responsible for a wide spectrum of infections in humans, plants and animals. In this context, anti-biofilm can be considered a key strategy to control P. aeruginosa infections, thereby more research in the field is required. On the other hand, Lactobacillus species have been described as beneficial due to their anti-biofilm properties and their consequent effect against a wide spectrum of pathogens. In fact, biofilm-forming Lactobacilli seem to be more efficient than their planktonic counterpart to antagonise pathogenic bacteria. In this work, we demonstrated that Lactobacillus kunkeei, a novel Lactobacillus species isolated from honeybee guts, can form biofilms in vitro. In addition, the L. kunkeei biofilm can, in turn, inhibit the formation of P. aeruginosa biofilms. Finally, we found that L. kunkeei strains attenuate infection of P. aeruginosa in the Galleria mellonella model, presumably by affecting P. aeruginosa biofilm formation and/or their stability. Since L. kunkeei presents characteristics of a probiotic, this work provides evidence arguing that the use of this Lactobacillus species in both animals (including insects) and humans could contribute to impair P. aeruginosa biofilm formation.

Metabolism of Fructophilic Lactic Acid Bacteria Isolated from the Apis mellifera L. Bee Gut: Phenolic Acids as External Electron Acceptors

Fructophilic lactic acid bacteria (FLAB) are strongly associated with the gastrointestinal tracts (GITs) of Apis mellifera L. worker bees due to the consumption of fructose as a major carbohydrate. Seventy-seven presumptive lactic acid bacteria (LAB) were isolated from GITs of healthy A. mellifera L. adults, which were collected from 5 different geographical locations of the Apulia region of Italy. Almost all of the isolates showed fructophilic tendencies: these isolates were identified as Lactobacillus kunkeei (69%) or Fructobacillus fructosus (31%). A high-throughput phenotypic microarray targeting 190 carbon sources was used to determine that 83 compounds were differentially consumed. Phenotyping grouped the strains into two clusters, reflecting growth performance. The utilization of phenolic acids, such as p-coumaric, caffeic, syringic, or gallic acids, as electron acceptors was investigated in fructose-based medium. Almost all FLAB strains showed tolerance to high phenolic acid concentrations. p-Coumaric acid and caffeic acid were consumed by all FLAB strains through reductases or decarboxylases. Syringic and gallic acids were partially metabolized. The data collected suggest that FLAB require external electron acceptors to regenerate NADH. The use of phenolic acids as external electron acceptors by the 4 FLAB showing the highest phenolic acid reductase activity was investigated in glucose-based medium supplemented with p-coumaric acid. Metabolic responses observed through a phenotypic microarray suggested that FLAB may use p-coumaric acid as an external electron acceptor, enhancing glucose dissimilation but less efficiently than other external acceptors such as fructose or pyruvic acid.IMPORTANCE Fructophilic lactic acid bacteria (FLAB) remain to be fully explored. This study intends to link unique biochemical features of FLAB with their habitat. The quite unique FLAB phenome within the group lactic acid bacteria (LAB) may have practical relevance in food fermentations. The FLAB phenome may have implications for the levels of hexose metabolism products in fermented foods, as well as food probiotication. Due to the harsh conditions of honeybees' GITs, these bacteria had to develop specific physiological and biochemical characteristics, such as tolerance to phenolic acids. The screening of FLAB strains based on metabolic pathways involving phenolic acids may allow the selection of starter cultures with both technological and functional beneficial attributes. Bioconversion of phenolic compounds may contribute to the aroma attributes and biofunctionality of fermented foods. Thus, the selection of FLAB strains as starter cultures with specific enzymatic activities involving phenolic acids may have a promising role in food fermentations.