Fructophilic Lactic Acid Bacteria, a Unique Group of Fructose-Fermenting Microbes

Convergent reductive evolution in bee-associated lactic acid bacteria

Distantly related organisms may evolve similar traits when exposed to similar environments or engaging in certain lifestyles. Several members of the Lactobacillaceae (LAB) family are frequently isolated from the floral niche, mostly from bees and flowers. In some floral LAB species (henceforth referred to as bee- associated), distinctive genomic (e.g., genome reduction) and phenotypic (e.g., preference for fructose over glucose or fructophily) features were recently documented. These features are found across distantly related species, raising the hypothesis that specific genomic and phenotypic traits evolved convergently during adaptation to the floral environment. To test this hypothesis, we examined representative genomes of 369 species of bee-associated and non-bee-associated LAB. Phylogenomic analysis unveiled seven independent ecological shifts towards the floral niche in LAB. In these bee-associated LAB, we observed pervasive, significant reductions of genome size, gene repertoire, and GC content. Using machine leaning, we could distinguish bee-associated from non-bee-associated species with 94% accuracy, based on the absence of genes involved in metabolism, osmotic stress, or DNA repair. Moreover, we found that the most important genes for the machine learning classifier were seemingly lost, independently, in multiple bee-associated lineages. One of these genes, adhE , encodes a bifunctional aldehyde-alcohol dehydrogenase associated with the evolution of fructophily, a rare phenotypic trait that was recently identified in many floral LAB species. These results suggest that the independent evolution of distinctive phenotypes in bee- associated LAB has been largely driven by independent loss of the same set of genes.

Importance

Several lactic acid bacteria (LAB) species are intimately associated with bees and exhibit unique biochemical properties with potential for food applications and honeybee health. Using a machine-learning based approach, our study shows that adaptation of LAB to the bee environment was accompanied by a distinctive genomic trajectory deeply shaped by gene loss. Several of these gene losses occurred independently in distantly related species and are linked to some of their unique biotechnologically relevant traits, such as the preference of fructose over glucose (fructophily). This study underscores the potential of machine learning in identifying fingerprints of adaptation and detecting instances of convergent evolution. Furthermore, it sheds light onto the genomic and phenotypic particularities of bee-associated bacteria, thereby deepening the understanding of their positive impact on honeybee health.

Bee-Associated Beneficial Microbes-Importance for Bees and for Humans

Bees are one of the best-known and, at the same time, perhaps the most enigmatic insects on our planet, known for their organization and social structure, being essential for the pollination of agricultural crops and several other plants, playing an essential role in food production and the balance of ecosystems, being associated with the production of high-value-added inputs, and a unique universe in relation to bees' microbiota. In this review, we summarize information regarding on different varieties of bees, with emphasis on their specificity related to microbial variations. Noteworthy are fructophilic bacteria, a lesser-known bacterial group, which use fructose fermentation as their main source of energy, with some strains being closely related to bees' health status. The beneficial properties of fructophilic bacteria may be extendable to humans and other animals as probiotics. In addition, their biotechnological potential may ease the development of new-generation antimicrobials with applications in biopreservation. The concept of "One Health" brings together fundamental and applied research with the aim of clarifying that the connections between the different components of ecosystems must be considered part of a mega-structure, with bees being an iconic example in that the healthy functionality of their microbiota is directly and indirectly related to agricultural production, bee health, quality of bee products, and the functional prosperity for humans and other animals. In fact, good health of bees is clearly related to the stable functionality of ecosystems and indirectly relates to humans' wellbeing, a concept of the "One Health".

Eupransor demetentiae gen. nov., sp. nov., a novel fructophilic lactic acid bacterium from bumble bees

Strain LMG 33000T was isolated from a Bombus lapidarius gut sample. It shared the highest percentage 16S rRNA sequence identity, average amino acid identity, and amino acid identity of conserved genes with Convivina intestini LMG 28291T (95.86 %, 69.9 and 76.2 %, respectively), and the highest percentage OrthoANIu value with Fructobacillus fructosus DSM 20349T (71.4 %). Phylogenomic analyses by means of 107 or 120 conserved genes consistently revealed Convivina as nearest neighbour genus. The draft genome of strain LMG 33000T was 1.44 Mbp in size and had a DNA G+C content of 46.1 mol%. Genomic and physiological analyses revealed that strain LMG 33000T was a typical obligately fructophilic lactic acid bacterium that lacked the adhE and aldh genes and that did not produce ethanol during glucose or fructose metabolism. In contrast, Convivina species have the adhE and aldh genes in their genomes and produced ethanol from glucose and fructose metabolism, which is typical for heterofermentative lactic acid bacteria. Moreover, strain LMG 33000T exhibited catalase activity, an unusual characteristic among lactic acid bacteria, that is not shared with Convivina species. Given its position in the phylogenomic trees, and the difference in genomic percentage G+C content and in physiological and metabolic characteristics between strain LMG 33000T and Convivina species, we considered it most appropriate to classify strain LMG 33000T into a novel genus and species within the Lactobacillaceae family for which we propose the name Eupransor demetentiae gen. nov., sp. nov., with LMG 33000T (=CECT 30958T) as the type strain.

Lactic acid bacteria as an eco-friendly approach in plant production: Current state and prospects

Since the late nineteenth century, the agricultural sector has experienced a tremendous increase in chemical use in response to the growing population. Consequently, the intensive and indiscriminate use of these substances caused serious damage on several levels, including threatening human health, disrupting soil microbiota, affecting wildlife ecosystems, and causing groundwater pollution. As a solution, the application of microbial-based products presents an interesting and ecological restoration tool. The use of Plant Growth-Promoting Microbes (PGPM) affected positive production, by increasing its efficiency, reducing production costs, environmental pollution, and chemical use. Among these microbial communities, lactic acid bacteria (LAB) are considered an interesting candidate to be formulated and applied as effective microbes. Indeed, these bacteria are approved by the European Food Safety Authority (EFSA) and Food and Drug Administration (FDA) as Qualified Presumption of Safety statute and Generally Recognized as Safe for various applications. To do so, this review comes as a road map for future research, which addresses the different steps included in LAB formulation as biocontrol, bioremediation, or plant growth promoting agents from the isolation process to their field application passing by the different identification methods and their various uses. The plant application methods as well as challenges limiting their use in agriculture are also discussed.

Extensive remodeling of sugar metabolism through gene loss and horizontal gene transfer in a eukaryotic lineage

BACKGROUND

In yeasts belonging to the subphylum Saccharomycotina, genes encoding components of the main metabolic pathways, like alcoholic fermentation, are usually conserved. However, in fructophilic species belonging to the floral Wickerhamiella and Starmerella genera (W/S clade), alcoholic fermentation was uniquely shaped by events of gene loss and horizontal gene transfer (HGT).

RESULTS

Because HGT and gene losses were first identified when only eight W/S-clade genomes were available, we collected publicly available genome data and sequenced the genomes of 36 additional species. A total of 63 genomes, representing most of the species described in the clade, were included in the analyses. Firstly, we inferred the phylogenomic tree of the clade and inspected the genomes for the presence of HGT-derived genes involved in fructophily and alcoholic fermentation. We predicted nine independent HGT events and several instances of secondary loss pertaining to both pathways. To investigate the possible links between gene loss and acquisition events and evolution of sugar metabolism, we conducted phenotypic characterization of 42 W/S-clade species including estimates of sugar consumption rates and fermentation byproduct formation. In some instances, the reconciliation of genotypes and phenotypes yielded unexpected results, such as the discovery of fructophily in the absence of the cornerstone gene (FFZ1) and robust alcoholic fermentation in the absence of the respective canonical pathway.

CONCLUSIONS

These observations suggest that reinstatement of alcoholic fermentation in the W/S clade triggered a surge of innovation that goes beyond the utilization of xenologous enzymes, with fructose metabolism playing a key role.

A comparative genomic analysis of Fructobacillus evanidus sp. nov. from bumble bees

The increase in studies on bee microbiomes is prompted by concerns over global pollinator declines. Bumble bees host core and non-core microbiota which may contribute to increased lifetime fitness. The presence of Fructobacillus in the gut microbiomes of bumble bee workers, or the replacement of core symbionts with Fructobacillus bacteria, has been considered a marker of dysbiosis. A phylogenomic analysis and functional genomic characterization of the genomes of 21 Fructobacillus isolates from bumble bees demonstrated that they represented four species, i.e. Fructobacillus cardui, Fructobacillus fructosus, Fructobacillus tropaeoli, and the novel species Fructobacillus evanidus sp. nov. Our results confirmed and substantiated the presence of two phylogenetically and functionally distinct Fructobacillus species clades that differ in genome size, percentage G + C content, the number of coding DNA sequences and metabolic characteristics. Clade 1 and clade 2 species differed in amino acid and, to a lesser extent, in carbohydrate metabolism, with F. evanidus and F. tropaeoli genomes featuring a higher number of complete metabolic pathways. While Fructobacillus genomes encoded genes that allow adhesion, biofilm formation, antibacterial activity and detoxification, other bacteria isolated from the bumble bee gut appeared better equipped to co-exist with the bumble bee host. The isolation and identification of multiple Fructobacillus species from several bumble bee gut samples in the present study also argued against a specific partnership between Fructobacillus species and their bumble bee hosts.

Fructobacillus fructosus OS-1010 strain stimulates intestinal cells to secrete exosomes that activate muscle cells

Fructobacillus is a lactic-acid bacterium recently identified in fructose-rich environments. Fructobacillus is also known to exhibit unusual growth characteristics due to an incomplete gene encoding alcohol/acetaldehyde hydrogenase, which results in an imbalance in the nicotinamide adenine mononucleotide (NAD+)/NADN levels. Recently, the addition of d-fructose to the culture medium of Fructobacillus strains increased the intracellular nicotinamide mononucleotide (NMN) content. In the present study, we evaluated the functionality of Fructobacillus that produces high levels of NMN, using one substrain (Fructobacillus fructosus OS-1010). Therefore, in this study, we examined its functionality in the interaction between intestinal cells and muscle cells. The results showed that supernatant derived from intestinal epithelial cells (Caco-2 cells) treated with F. fructosus OS-1010 activated muscle cells (C2C12 cells). Further analysis revealed that Caco-2 cells treated with F. fructosus OS-1010 secreted exosomes known as extracellular vesicles, which activated the muscle cells. Furthermore, pathway analysis of the target genes of miRNA in exosomes revealed that pathways involved in muscle cell activation, including insulin signaling and cardiac muscle regulation, neurotrophic factors, longevity, and anti-aging, can be activated by exosomes. In other words, F. fructosus OS-1010 could activate various cells such as the skin and muscle cells, by secreting functional exosomes from the intestinal tract.

Synergistic effect of the coculture of Leuconostoc pseudomesenteroides and Lactococcus lactis, isolated from honeybees, on the generation of plant-based dairy alternatives based on soy, pea, oat, and potato drinks

The production of plant-based dairy alternatives has been majorly focused on the improvement of sensorial, technological and nutritional properties, to be able to mimic and replace milk-based fermented products. The presence of off-flavours and antinutrients, the lack of production of dairy-like flavours or the metabolic inaccessibility of plant proteins are some of the challenges to overcome to generate plant-based dairy alternatives. However, in the present study, it is demonstrated how the synergistic effect of two LAB strains, when cocultured, can simultaneously solve those challenges when fermenting in four different plant-based raw materials: soy, pea, oat, and potato drinks (SPOP). The fermentation was performed through the mono- and co-culture of the two LAB strains isolated from Apis mellifera (honeybee): Leuconostoc pseudomesenteroides NFICC 2004 and Lactococcus lactis NFICC 2005. Firstly, the coculture of both strains demonstrated to increase the acidification rate of the four plant matrices. Moreover, L. pseudomesenteroides (LP) demonstrated to in situ produce high concentrations of mannitol when fructose was present as C-source. Furthermore, L. pseudomesenteroides, which encoded for PII-proteinase, demonstrated to break down SPOP proteins, releasing free amino acids that were used by L.lactis (LL) for growth and metabolism. Lastly, the analysis of their co-metabolic volatile performance showed the principal ability of removal of the main off-flavours found in SPOP, such as hexanal, 1-octen-3-ol, 2-pentylfuran, pentanal, octanal, heptanal, and nonanal, mainly led by L. pseudomesenteroides, as well as the production of dairy-like flavours, such as diacetyl and 3-methyl-1-butanol, triggered by L. lactis metabolism. Overall, these findings endorsed the use of honeybee isolated strains as starter cultures, demonstrated the potential of coupling genotypes and phenotypes of multiple strains to improve the organoleptic properties suggesting a potential of combining plant-based matrices for the generation of future high-quality plant-based dairy alternatives.

Recent trends in lactic acid-producing microorganisms through microbial fermentation for the synthesis of polylactic acid

Polylactic acid (PLA) is a range of unique bioplastics that are bio-based and biodegradable. PLA is currently driving market expansion for lactic acid (LA) due to its high demand as a building block in production. One of the most practical and environmentally benign techniques for synthesising PLA is through enzymatic polymerisation of microbial LA monomers. However, microbial LA fermentation does have some limitations. Firstly, it requires the use of a nutritionally rich medium. Secondly, LA production can be disrupted by bacteriophage infection or other microorganisms. Lastly, the yield can be low due to the formation of by-products through heterofermentative pathway. Considering the potential use of PLA as a replacement for conventional petrochemical-based polymers in industrial applications, researchers are focused on exploring the diversity of LA-producing microorganisms from various niches. Their goal is to study the functional properties of these microorganisms and their ability to produce industrially valuable metabolites. This review highlights the advantages and disadvantages of lactic acid-producing microorganisms used in microbial fermentation for PLA synthesis.

Analysis of the bacterial and fungal populations in South African sorghum beer (umqombothi) using full-length 16S rRNA amplicon sequencing

There is a need to profile microorganisms which exist pre-and-post-production of umqombothi, to understand its microbial diversity and the interactions which subsequently influence the final product. Thus, this study sought to determine the relative microbial abundance in umqombothi and predict the functional pathways of bacterial and fungal microbiota present. Full-length bacterial 16S rRNA and internal transcribed spacer (ITS) gene sequencing using PacBio single-molecule, real-time (SMRT) technology was used to assess the microbial compositions. PICRUSt2 was adopted to infer microbial functional differences. A mixture of harmful and beneficial microorganisms was observed in all samples. The microbial diversity differed significantly between the mixed raw ingredients (MRI), customary beer brew (CB), and optimised beer brew (OPB). The highest bacterial species diversity was observed in the MRI, while the highest fungal species diversity was observed in the OPB. The dominant bacterial species in the MRI, CB, and OPB were Kosakonia cowanii, Apilactobacillus pseudoficulneus, and Vibrio alginolyticus, respectively, while the dominant fungal species was Apiotrichum laibachii. The predicted functional annotations revealed significant (p < 0.05) differences in the microbial pathways of the fermented and unfermented samples. The most abundant pathways in the MRI were the branched-chain amino acid biosynthesis super pathway and the pentose phosphate pathway. The CB sample was characterised by folate (vitamin B9) transformations III, and mixed acid fermentation. Biotin (vitamin B7) biosynthesis I and L-valine biosynthesis characterised the OPB sample. These findings can assist in identifying potential starter cultures for the commercial production of umqombothi. Specifically, A. pseudoficulneus can be used for controlled fermentation during the production of umqombothi. Likewise, the use of A. laibachii can allow for better control over the fermentation kinetics such as carbohydrate conversion and end-product characteristics, especially esters and aroma compounds.

Convivina is a specialised core gut symbiont of the invasive hornet Vespa velutina

We provide a culturomics analysis of the cultivable bacterial communities of the crop, midgut and hindgut compartments, as well as the ovaries, of the invasive insect Vespa velutina, along with a cultivation-independent analysis of samples of the same nest through 16S rRNA amplicon sequencing. The Vespa velutina bacterial symbiont community was dominated by the genera Convivina, Fructobacillus, Lactiplantibacillus, Lactococcus, Sphingomonas and Spiroplasma. Lactococcus lactis and Lactiplantibacillus plantarum represented generalist core lactic acid bacteria (LAB) symbionts, while Convivina species and Fructobacillus fructosus represented highly specialised core LAB symbionts with strongly reduced genome sizes. Sphingomonas and Spiroplasma were the only non-LAB core symbionts but were not isolated. Convivina bacteria were particularly enriched in the hornet crop and included Convivina intestini, a species adapted towards amino acid metabolism, and Convivina praedatoris sp. nov. which was adapted towards carbohydrate metabolism.

Antimicrobial Properties, Functional Characterisation and Application of Fructobacillus fructosus and Lactiplantibacillus plantarum Isolated from Artisanal Honey

Honey is a valuable reservoir of lactic acid bacteria (LAB) and, particularly, of fructophilic LAB (FLAB), a relatively novel subgroup of LAB whose functional potential for human and food application has yet to be explored. In this study, FLAB and LAB strains have been isolated from honeys of different floral origins and selected for their broad antimicrobial activity against typical foodborne pathogenic bacteria and spoilage filamentous fungi. The best candidates, two strains belonging to the species Lactiplantibacillus plantarum and Fructobacillus fructosus, were submitted to partial characterisation of their cell free supernatants (CFS) in order to identify the secreted metabolites with antimicrobial activity. Besides, these strains were examined to assess some major functional features, including in vitro tolerance to the oro-gastrointestinal conditions, potential cytotoxicity against HT-29 cells, adhesion to human enterocyte-like cells and capability to stimulate macrophages. Moreover, when the tested strains were applied on table grapes artificially contaminated with pathogenic bacteria or filamentous fungi, they showed a good ability to antagonise the growth of undesired microbes, as well as to survive on the fruit surface at a concentration that is recommended to develop a probiotic effect. In conclusion, both LAB and FLAB honey-isolated strains characterised in this work exhibit functional properties that validate their potential use as biocontrol agents and for the design of novel functional foods. We reported antimicrobial activity, cytotoxic evaluation, probiotic properties and direct food application of a F. fructosus strain, improving the knowledge of this species, in particular, and on FLAB, more generally.

Metagenomics and metabolomics of Toddy, an Indian fermented date palm beverage

Toddy is a popular fermented palm beverage of India. No scientific information on shotgun metagenomics and metabolomics are available on toddy of India till date. Hence, we choose the fermented date palm beverage, locally called khejur toddy, of West Bengal and Jharkhand states of India, to profile microbial community, their targeted and untargeted metabolites to study the putative bio-functional genes corresponding to regulatory metabolic pathways. Shotgun-based metataxonomic analyses revealed the existence of all domains where bacteria were the most abundant domain (94.48%) followed by eukaryotes (3.38%), viruses (1.53%) and archaea (0.61%). Overall, 54 phyla, 363 families, 1087 genera and 1885 species were observed and identified. Bacillota (49.3%) was the most abundant bacterial phylum. At species level, several species of bacteria and yeasts were detected in toddy samples which included Leuconostoc mesenteroides,Leuconostoc citreum,Lactobacillus helveticus,Lactiplantibacillus plantarum,Lactococcus lactis, Acetobacter malorum, Gluconobacter japonicus, Gluconacetobacter liquefaciens, Fructobacillus durionis, Zymomonas mobilis and yeastsSaccharomyces cerevisiae, Hanseniaspora uvarumandHanseniaspora guilliermondii. Toddy metagenome was also compared with metagenome of pulque, the Mexican fermented fresh sap ofAgave, which was retrieved from NCBI database, and also with metagenomic data of some amplicon-based previous studies on toddy and African fermented palm drink for similarity, dissimilarity and uniqueness among them. Predictive biosynthesis of ethanol, acetic acid, butanoate, linalool, staurosporine, prodigiosin, folic acid, riboflavin, etc. were annotated by KEGG/COG database. Clustered regularly interspaced short palindromic repeats (CRISPR) analysis detected 23 arrays (average length 23.69 bp ± 4.28). Comprehensive Antibiotic Resistance Database (CARD) analysis did not show the presence of any momentous antibiotic resistance gene among the major microbial members. Metabolomics analysis detected many primary and secondary metabolites. We believe this is the first report on complete shotgun metagenomics, and metabolomics of fermented palm drink of India as well as Eastern India.

On the Molecular Selection of Exopolysaccharide-Producing Lactic Acid Bacteria from Indigenous Fermented Plant-Based Foods and Further Fine Chemical Characterization

Exopolysaccharides (EPSs) produced by lactic acid bacteria present a particular interest for the food industry since they can be incorporated in foods via in situ production by selected starter cultures or applied as natural additives to improve the quality of various food products. In the present study, 43 strains were isolated from different plant-based fermented foods and identified by molecular methods. The species found were distinctively specific according to the food source. Only six Lactiplantibacillus plantarum strains, all isolated from sauerkraut, showed the ability to produce exopolysaccharide (EPS). The utilization of glucose, fructose and sucrose was explored with regard to EPS and biomass accumulation by the tested strains. Sucrose was clearly the best carbon source for EPS production by most of the strains, yielding up to 211.53 mg/L by strain Lactiplantibacillus plantarum ZE2, while biomass accumulation reached the highest levels in the glucose-based culture medium. Most strains produced similar levels of EPS with glucose and fructose, while fructose was utilized more poorly for biomass production, yielding about 50% of biomass compared to glucose for most strains. Composition analysis of the EPSs produced by strain Lactiplantibacillus plantarum ZE2 from glucose (EPS-1) and fructose (EPS-2) revealed that glucose (80-83 mol%) and protein (41% w/w) predominated in both analyzed EPSs. However, the yield of EPS-1 was twice higher than that of EPS-2, and differences in the levels of all detected sugars were found, which shows that even for the same strain, EPS yield and composition vary depending on the carbon source. These results may be the basis for the development of tailored EPS-producing starter cultures for food fermentations, as well as technologies for the production of EPS for various applications.

Potential role of the gut microbiota of bumblebee Bombus pyrosoma in adaptation to high-altitude habitats

The gut microbiota affects the health and overall fitness of bumblebees. It can enhance the host's ecological range by leveraging their metabolic capacities. However, the diversity of the gut microbiota and adaptive functional evolution in high-altitude regions remain unclear. To explore how the gut microbiota helps the host adapt to high-altitude environments, we analyzed the differences in diversity and function of the gut microbiota between high- and low-altitude regions through full-length 16S rRNA sequencing. Our results show that high-altitude regions have a lower abundance of Fructobacillus and Saccharibacter compared to low-altitude regions. Additionally, some individuals in low-altitude regions were invaded by opportunistic pathogens. The gut microbiota in high-altitude regions has a greater number of pathways involved in "Protein digestion and absorption" and "Biosynthesis of amino acids," while fewer carbohydrate pathways are involved in "digestion and absorption" and "Salmonella infection." Our finding suggests that plateau hosts typically reduce energy metabolism and enhance immunity in response to adverse environments. Correspondingly, the gut microbiota also makes changes, such as reducing carbohydrate degradation and increasing protein utilization in response to the host. Additionally, the gut microbiota regulates their abundance and function to help the host adapt to adverse high-altitude environments.

A Comprehensive Review of Bioactive Compounds from Lactic Acid Bacteria: Potential Functions as Functional Food in Dietetics and the Food Industry

Lactic acid bacteria (LAB) are beneficial microbes known for their health-promoting properties. LAB are well known for their ability to produce substantial amounts of bioactive compounds during fermentation. Peptides, exopolysaccharides (EPS), bacteriocins, some amylase, protease, lipase enzymes, and lactic acid are the most important bioactive compounds generated by LAB activity during fermentation. Additionally, the product produced by LAB is dependent on the type of fermentation used. LAB derived from the genera Lactobacillus and Enterococcus are the most popular probiotics at present. Consuming fermented foods has been previously connected to a number of health-promoting benefits such as antibacterial activity and immune system modulation. Furthermore, functional food implementations lead to the application of LAB in therapeutic nutrition such as prebiotic, immunomodulatory, antioxidant, anti-tumor, blood glucose lowering actions. Understanding the characteristics of LAB in diverse sources and its potential as a functional food is crucial for therapeutic applications. This review presents an overview of functional food knowledge regarding interactions between LAB isolated from dairy products (dairy LAB) and fermented foods, as well as the prospect of functioning LAB in human health. Finally, the health advantages of LAB bioactive compounds are emphasized.

Philodulcilactobacillus myokoensis gen. nov., sp. nov., a fructophilic, acidophilic, and agar-phobic lactic acid bacterium isolated from fermented vegetable extracts

Lactic acid bacteria are commonly in the fermentation industry and pose potential positive effects on health. In this study, a new lactic acid bacterium was isolated from fermented vegetable extracts in Myoko, Niigata, Japan. This bacterium is fructophilic, acidophilic, and hard to grow on agar medium. The isolate is Gram-stain-positive, non-spore-forming, non-motile, rod-shaped, and catalase-negative. Growth occurred at pH 3.5-5.5, with optimal growth at pH 4.5-5.0. The cells formed colonies on a solid MRS medium with 20% (w/v) sucrose and 0.8% (w/v) gellan gum under anaerobic conditions. The bacterium was able to grow on up to 50% (w/v) sucrose but not on d-glucose. Moreover, 16S rRNA gene sequence analysis revealed that the strain was most closely related to Apilactobacillus ozensis (93.1% sequence similarity). The values of average nucleotide identity, digital DNA-DNA hybridization, average amino acid sequence identity, and amino acid identity of conserved genes were calculated between the isolated strain (type strain is WR16-4T = NBRC 115064T = DSM 112857T) and its phylogenetically closest type strains. The average nucleotide identity values (73.36-78.28%) and DNA-DNA hybridization values (16.3-32.9%) were significantly lower than the threshold values for species boundaries. The average amino acid sequence identity values (53.96-60.88%) were significantly below the threshold boundary of genus demarcation (68%). The amino acid identity of conserved genes values compared to strain WR16-4T were the genera Apilactobacillus, Nicoliella spurrieriana SGEP1_A5T, Acetilactobacillus jinshanensis HSLZ-75T, and Fructilactobacillus were 62.51-63.79%, 62.87%, 62.03%, and 58.00-61.04%, respectively. The 16S rRNA gene and core genome phylogenetic trees suggested that this novel strain was most closely related to the type strain of A. jinshanensis HSLZ-75T. Based on the physiological, morphological, and phenotypical characteristics of strain WR16-4T, we propose its classification as a novel genus, Philodulcilactobacillus myokoensis gen. nov., sp. nov.

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.

Postbiotic Metabolite of Lactiplantibacillus plantarum PD18 against Periodontal Pathogens and Their Virulence Markers in Biofilm Formation

Alternative methods to reduce infectious diseases caused by bacterial pathogens and their virulence factors, biofilm formations, have arisen to reduce the pressure on existing or currently developed disinfectants and antimicrobial agents. The current strategies for reducing the severity of periodontal pathogen-caused disease by using beneficial bacteria and their metabolites are highly desirable. Probiotic strains of lactobacilli related to foods from Thai-fermented foods were selected and their postbiotic metabolites (PM) were isolated with inhibitory activity on periodontal pathogens and their biofilm formation. The PM from Lactiplantibacillus plantarum PD18 (PD18 PM) with the highest antagonistic effect against Streptococcus mutans, Porphyromonas gingivalis, Tannerella forsythia and Prevotella loescheii was selected from 139 Lactobacillus isolates. The minimal inhibitory concentration (MIC) and minimum biofilm inhibitory concentration (MBIC) values of PD18 PM against the pathogens ranged from 1:2 to 1:4. The PD18 PM demonstrated the ability to prevent the biofilm formation of S. mutans and P. gingivalis by showing a significant reduction in viable cells, high percentages of biofilm inhibition at 92.95 and 89.68%, and the highest effective contact times at 5 and 0.5 min, respectively. L. plantarum PD18 PM showed potential as a promising natural adjunctive agent to inhibit periodontal pathogens and their biofilms.

Metataxonomic insights in the distribution of Lactobacillaceae in foods and food environments

Members of the family Lactobacillaceae, which now includes species formerly belonging to the genera Lactobacillus and Pediococcus, but also Leuconostocaceae, are of foremost importance in food fermentations and spoilage, but also as components of animal and human microbiota and as potentially pathogenic microorganisms. Knowledge of the ecological distribution of a given species and genus is important, among other things, for the inclusion in lists of microorganisms with a Qualified Presumption of Safety or with beneficial use. The objective of this work is to use the data in FoodMicrobionet database to obtain quantitative insights (in terms of both abundance and prevalence) on the distribution of these bacteria in foods and food environments. We first explored the reliability of taxonomic assignments using the SILVA v138.1 reference database with full length and partial sequences of the 16S rRNA gene for type strain sequences. Full length 16S rRNA gene sequences allow a reasonably good classification at the genus and species level in phylogenetic trees but shorter sequences (V1-V3, V3-V4, V4) perform much worse, with type strains of many species sharing identical V4 and V3-V4 sequences. Taxonomic assignment at the genus level of 16S rRNA genes sequences and the SILVA v138.1 reference database can be done for almost all genera of the family Lactobacillaceae with a high degree of confidence for full length sequences, and with a satisfactory level of accuracy for the V1-V3 regions. Results for the V3-V4 and V4 region are still acceptable but significantly worse. Taxonomic assignment at the species level for sequences for the V1-V3, V3-V4, V4 regions of the 16S rRNA gene of members of the family Lactobacillaceae is hardly possible and, even for full length sequences, and only 49.9 % of the type strain sequences can be unambiguously assigned to species. We then used the FoodMicrobionet database to evaluate the prevalence and abundance of Lactobacillaceae in food samples and in food related environments. Generalist and specialist genera were clearly evident. The ecological distribution of several genera was confirmed and insights on the distribution and potential origin of rare genera (Dellaglioa, Holzapfelia, Schleiferilactobacillus) were obtained. We also found that combining Amplicon Sequence Variants from different studies is indeed possible, but provides little additional information, even when strict criteria are used for the filtering of sequences.

Analysis of Microbial Diversity and Metabolites in Sauerkraut Products with and without Microorganism Addition

The microbial compositions and metabolites of fermented sauerkraut with and without the addition of microorganisms have been compared. The OTU clustering, nonvolatile compounds, volatile compounds and associations between bacterial taxa and metabolites were analyzed by 16S rRNA high-throughput sequencing technology, ultra performance liquid chromatography (UPLC), gas chromatography ion mobility mass spectrometry (GC-IMS) and the O2PLS model studies. The results showed that at the phylum level, the microbial species in the four sauerkraut types consisted mainly of the phyla Firmicutes and Proteobacteria, but different modes of microbial addition formed their own unique microbial communities. There were significant differences in the microbial communities among different northeast China sauerkraut samples, and different microbial communities exerted similar effects to inhibit Firmicutes production. At the genus level, sauerkraut without added microorganisms had the lowest microbial diversity. A total of 26 amino acids and 11 organic acids were identified and were more abundant in nonmicrobially fermented sauerkraut; 88 volatile organic compounds were identified in the 4 types of sauerkraut, with the microbially fermented sauerkraut being richer in alcohols, esters and acids. Different brands of sauerkraut contain their own unique flavor compounds. Cystine and tyrosine, ascorbic acid and acetic acid, and alcohols and esters are closely related to a wide range of microorganisms in sauerkraut. Elucidating the correlations among microbiota and metabolites will help guide future improvements in sauerkraut fermentation processes.

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.

Genomic diversity in Fructobacillus spp. isolated from fructose-rich niches

The Fructobacillus genus is a group of obligately fructophilic lactic acid bacteria (FLAB) that requires the use of fructose or another electron acceptor for their growth. In this work, we performed a comparative genomic analysis within the genus Fructobacillus by using 24 available genomes to evaluate genomic and metabolic differences among these organisms. In the genome of these strains, which varies between 1.15- and 1.75-Mbp, nineteen intact prophage regions, and seven complete CRISPR-Cas type II systems were found. Phylogenetic analyses located the studied genomes in two different clades. A pangenome analysis and a functional classification of their genes revealed that genomes of the first clade presented fewer genes involved in the synthesis of amino acids and other nitrogen compounds. Moreover, the presence of genes strictly related to the use of fructose and electron acceptors was variable within the genus, although these variations were not always related to the phylogeny.

Fructilactobacillus cliffordii sp. nov., Fructilactobacillus hinvesii sp. nov., Fructilactobacillus myrtifloralis sp. nov., Fructilactobacillus carniphilus sp. nov. and Fructobacillus americanaquae sp. nov., five novel lactic acid bacteria isolated from insects or flowers of Kangaroo Island, South Australia

Six strains, KI11_D11^T, KI4_B1, KI11_C11^T, KI16_H9^T, KI4_A6^T and KI3_B9^T, were isolated from insects and flowers on Kangaroo Island, South Australia. On the basis of 16S rRNA gene phylogeny, strains KI11_D11^T, KI4_B1, KI11_C11^T, KI16_H9^T, KI4_A6^T were found to be closely related to Fructilactobacillus ixorae Ru20-1^T. Due to the lack of a whole genome sequence for this species, whole genome sequencing of Fructilactobacillus ixorae Ru20-1^T was undertaken. KI3_B9^T was found to be closely related to Fructobacillus tropaeoli F214-1^T. Utilizing core gene phylogenetics and whole genome analyses, such as determination of AAI, ANI and dDDH, we propose that these six isolates represent five novel species with the names Fructilactobacillus cliffordii (KI11_D11^T= LMG 32130^T = NBRC 114988^T), Fructilactobacillus hinvesii (KI11_C11^T = LMG 32129^T = NBRC 114987^T), Fructilactobacillus myrtifloralis (KI16_H9^T= LMG 32131^T = NBRC 114989^T) Fructilactobacillus carniphilus (KI4_A6^T = LMG 32127^T = NBRC 114985^T) and Fructobacillus americanaquae (KI3_B9^T = LMG 32124^T = NBRC 114983^T). Chemotaxonomic analyses detected no fructophilic characters for these strains of member of the genus Fructilactobacillus. KI3_B9^T was found to be obligately fructophilic, similarly to its phylogenetic neighbours in the genus Fructobacillus. This study represents the first isolation, to our knowledge, of novel species in the family Lactobacillaceae from the Australian wild.

Fructose-induced topographical changes in fructophilic, pseudofructophilic and non-fructophilic lactic acid bacterial strains with genomic comparison

Fructophilic Lactic Acid Bacteria (FLAB), Fructobacillus fructosus DPC7238 and pseudofructophilic Leuconostoc mesenteroides DPC7261 and non-FLAB Limosilactobacillus reuteri DSM20016 strains were studied for their growth and morphological evolution as a function of increased fructose concentrations (0, 25, and 50% w/v) in the media. A comparison of the genomics of these strains was carried out to relate observed changes and understand fructose-rich adaptations. The viability of FLAB strains were reduced by approx. 50% at a 50% fructose concentration, while the Limosilactobacillus reuteri strain was reduced to approx. 98%. Electron microscopy demonstrated that FLAB strain, Fructobacillus. fructosus and pseudofructophilic Leuc. mesenteroides, were intact but expanded in the presence of high fructose in the medium. Limosilactobacillus reuteri, on the other hand, ruptured as a result of excessive elongation, resulting in the formation of cell debris when the medium contained more than 25% (w/v) fructose. This was entirely and quantitatively corroborated by three-dimensional data obtained by scanning several single cells using an atomic force microscope. The damage caused the bacterial envelope to elongate lengthwise, thus increasing width size and lower height. The cell surface became comparatively smoother at 25% fructose while rougher at 50% fructose, irrespective of the strains. Although Fructobacillus fructosus was highly fructose tolerant and maintained topological integrity, it had a comparatively smaller genome than pseudofructophilic Leuc. mesenteroides. Further, COG analysis identified lower but effective numbers of genes in fructose metabolism and transport of Fructobacillus fructosus, essentially needed for adaptability in fructose-rich niches.

Beehives possess their own distinct microbiomes

BACKGROUND

Honeybees use plant material to manufacture their own food. These insect pollinators visit flowers repeatedly to collect nectar and pollen, which are shared with other hive bees to produce honey and beebread. While producing these products, beehives accumulate a considerable number of microbes, including bacteria that derive from plants and different parts of the honeybees' body. Whether bacteria form similar communities amongst beehives, even if located in close proximity, is an ecologically important question that has been addressed in this study. Specific ecological factors such as the surrounding environment and the beekeeping methods used can shape the microbiome of the beehive as a whole, and eventually influence the health of the honeybees and their ecosystem.

RESULTS

We conducted 16S rRNA meta-taxonomic analysis on honey and beebread samples that were collected from 15 apiaries in the southeast of England to quantify the bacteria associated with different beehives. We observed that honeybee products carry a significant variety of bacterial groups that comprise bee commensals, environmental bacteria and symbionts and pathogens of plants and animals. Remarkably, this bacterial diversity differs not only amongst apiaries, but also between the beehives of the same apiary. In particular, the levels of the bee commensals varied significantly, and their fluctuations correlated with the presence of different environmental bacteria and various apiculture practices.

CONCLUSIONS

Our results show that every hive possesses their own distinct microbiome and that this very defined fingerprint is affected by multiple factors such as the nectar and pollen gathered from local plants, the management of the apiaries and the bacterial communities living around the beehives. Based on our findings, we suggest that the microbiome of beehives could be used as a valuable biosensor informing of the health of the honeybees and their surrounding environment.

Dynamics of microbial populations and metabolites of fermenting saps throughout tapping process of ron and oil palm trees in Côte d'Ivoire

Palm wine fermentation is a complex microbial process that evolves with tapping times. The dynamics in microbiota and metabolites throughout palm wine tapping days is still not established, which are critical for the distinctive characteristics of palm wine taste and quality, and thus the mastery of the daily quality fluctuation during tapping. We analyzed the changes in microbial community structure by amplicon sequencing of bacterial 16S rRNA gene and fungal internal transcribed spacer (ITS) region, and metabolite profile changes using mass spectrometry in palm wine collected over 25-30 days tapping of ron (Borassus aethiopum) and oil palms (Elaeis guineensis) from Côte d'Ivoire. The stage-wise collected palm wine samples showed distinct changes in microbial diversity and pH, supporting microbial community dynamics during palm wine tapping. Results highlighted the dominance of Saccharomyces cerevisiae in early stages and the emergence of non-Saccharomyces yeasts, particularly Hanseniaspora spp. in the later stages of oil palm wine tapping, vice versa in the case of ron palm wine tapping, with a unique presence of Saccharomycodes in the later stages (15-30 days). Fructophilic lactic acid bacteria (FLAB), mainly Fructobacillus and Leuconostoc, encountered in both types of palm wine tapping showed a decline at later stages of oil palm wine tapping. In this type of palm wine, acetic acid bacteria with genera Acetobacter and Glucanoacetobacter, by surpassing Lactobacillus in the last stage become dominant, whereas Lactobacillus remained dominant in ron palm wine throughout tapping days. The decline in the relative abundance of gevotroline and essential amino acids during the later stages of palm wine tapping (15-25 days) supports the difference in the health benefits of the palm wine obtained from different days of tapping, indicating that early stages of tapping is more nutritional and healthy than the later stages. The microbial dynamics may be a potential indicator of metabolite changes during palm sap fermentation, thus contributing to establish particular features of palm wines in different stages of tapping. This understanding of microbial ecology and chemical composition changes during palm wine tapping can be used as biomarkers to assess palm wine's quality and help to design an optimum starter culture.

Biofunctional soy-based sourdough for improved rheological properties during storage

Frozen dough storage, along with its thawing process, negatively affects the quality of the final product. Thus, fermentation with selected cultures and the enrichment of wheat-based dough using a specific soy powder could optimize the viscoelastic quality of frozen dough and increase its nutritional characteristics. Based on these aspects, the present study's objective was to examine the effects of soy powder addition to wheat flour with single cultures of Fructilactobacillus florum DSM 22689 or Saccharomyces cerevisiae and coculture with these two microorganisms for 72 h of fermentation. Additionally, the fermentation process was monitored, and viscoelastic behavior and physical-chemical analyses of the fermented sourdough before and after frozen storage were assessed, as soy protein has been proposed to hinder water migration throughout frozen storage. As observed, soy powder, an essential functional ingredient, had a favorable impact on the water-starch-gluten system, and enhanced the viscoelastic behavior before and after 4 weeks of frozen storage.

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.

Fructobacillus cardui sp. nov., isolated from a thistle (Carduus nutans) flower

A Fructobacillus strain was isolated from the flower of a nodding thistle (Carduus nutans) collected in Bavaria, Germany. The strain is Gram-positive, rod-shaped, non-motile, non-sporulating, catalase- and oxidase-negative, and facultatively anaerobic. Growth can be detected at 10-37 °C and pH 4 to 9. The genome size is about 1.56 Mbp and the G+C content is 43.76 mol%. Assignment to the genus Fructobacillus was done by average nucleotide identity (ANI), 16S rRNA gene sequence and multilocus sequence analyses. Calculations of ANI and digital DNA-DNA hybridization values indicate a novel species with Fructobacillus tropaeoli DSM 23246^T (93.58% ANI and 57.9 % dDDH) being its closest relative. Therefore, a new species named Fructobacillus cardui sp. nov. with TMW 2.2452^T (=DSM 113480^T=CECT 30515^T) as type strain is proposed.

Apilactobacillus apisilvae sp. nov., Nicolia spurrieriana gen. nov. sp. nov., Bombilactobacillus folatiphilus sp. nov. and Bombilactobacillus thymidiniphilus sp. nov., four new lactic acid bacterial isolates from stingless bees Tetragonula carbonaria and Austroplebeia australis

Four strains, SG5_A10T, SGEP1_A5T, SG4_D2T, and SG4_A1T, were isolated from the honey or homogenate of Australian stingless bee species Tetragonula carbonaria and Austroplebeia australis. Based on 16S rRNA gene phylogeny, core gene phylogenetics, whole genome analyses such as determination of amino acid identity (AAI), cAAI of conserved genes, average nucleotide identity (ANI), and digital DNA–DNA hybridization (dDDH), chemotaxonomic analyses, and the novel isolation sources and unique geography, we propose three new species and one genus with the names Apilactobacillus apisilvae sp. nov. (SG5_A10T = LMG 32133T = NBRC 114991T), Bombilactobacillus thymidiniphilus sp. nov. (SG4_A1T = LMG 32125T = NBRC 114984T), Bombilactobacillus folatiphilus sp. nov. (SG4_D2T = LMG 32126T = NBRC 115004T) and Nicolia spurrieriana sp. nov. (SGEP1_A5T = LMG 32134T = NBRC 114992T). Three out of the four strains were found to be fructophilic, where SG5_A10T and SGEP1_A5T belong to obligately fructophilic lactic acid bacteria, and SG4_D2T representing a new type denoted here as kinetically fructophilic. This study represents the first published lactic acid bacterial species associated with the unique niche of Australian stingless bees.

Mosquito sex and mycobiota contribute to fructose metabolism in the Asian tiger mosquito Aedes albopictus

BACKGROUND

Plant floral nectars contain natural sugars such as fructose, which are a primary energy resource for adult mosquitoes. Despite the importance of carbohydrates for mosquito metabolism, a limited knowledge is available about the pathways involved in sugar assimilation by mosquitoes and their associated microbiota. To this end, we used ¹³C-metabolomic and stable isotope probing approaches coupled to high-throughput sequencing to reveal fructose-related mosquito metabolic pathways and the dynamics of the active gut microbiota following fructose ingestion.

RESULTS

Our results revealed significant differences in metabolic pathways between males and females, highlighting different modes of central carbon metabolism regulation. Competitive and synergistic interactions of diverse fungal taxa were identified within the active mycobiota following fructose ingestion. In addition, we identified potential cross-feeding interactions between this. Interestingly, there is a strong correlation between several active fungal taxa and the presence of fructose-derived metabolites.

CONCLUSIONS

Altogether, our results provide novel insights into mosquito carbohydrate metabolism and demonstrate that dietary fructose as it relates to mosquito sex is an important determinant of mosquito metabolism; our results also further highlight the key role of active mycobiota interactions in regulating the process of fructose assimilation in mosquitoes. This study opens new avenues for future research on mosquito-microbiota trophic interactions related to plant nectar-derived sugars. Video abstract.

Probiotication of Nutritious Fruit and Vegetable Juices: An Alternative to Dairy-Based Probiotic Functional Products

Fruits and vegetables are widely known to be rich in nutrients, antioxidants, vitamins, dietary fiber, minerals, and a bioactive molecule, making them an essential component of a balanced diet with multiple documented positive effects on human health. The probiotication of plant-based juices for the production of functional and nutraceutical food serves as a healthy alternative to dairy probiotics. They are cholesterol free, lack several dairy allergens, and also encourage ingestion for people with lactose intolerance. This review highlights valuable claims regarding the efficacy of different probiotic strains on various diseases. A comprehensive nutrition comparison and the preference of plant-based over dairy probiotic drinks is also discussed, supported with updated market trends of probiotic drinks (dairy and non-dairy based). An extensive compilation of current plant-based probiotic drinks that are available in markets around the world is listed as a reference. The fermentability of carbon sources by probiotic microorganisms is crucial in addressing the development of plant-based drinks. Therefore, the pathway involved in metabolism of sucrose, glucose, fructose, and galactose in fruit and vegetable juice was also underlined. Finally, the key factors in monitoring the quality of probiotic products such as total soluble solids, sugar consumption, titratable acidity, pH, and stability at low storage temperatures were outlined.

Elevated Temperature May Affect Nectar Microbes, Nectar Sugars, and Bumble Bee Foraging Preference

Floral nectar, an important resource for pollinators, is inhabited by microbes such as yeasts and bacteria, which have been shown to influence pollinator preference. Dynamic and complex plant-pollinator-microbe interactions are likely to be affected by a rapidly changing climate, as each player has their own optimal growth temperatures and phenological responses to environmental triggers, such as temperature. To understand how warming due to climate change is influencing nectar microbial communities, we incubated a natural nectar microbial community at different temperatures and assessed the subsequent nectar chemistry and preference of the common eastern bumble bee, Bombus impatiens. The microbial community in floral nectar is often species-poor, and the cultured Brassica rapa nectar community was dominated by the bacterium Fructobacillus. Temperature increased the abundance of bacteria in the warmer treatment. Bumble bees preferred nectar inoculated with microbes, but only at the lower, ambient temperature. Warming therefore induced an increase in bacterial abundance which altered nectar sugars and led to significant differences in pollinator preference.

Investigation of the probiotic and metabolic potential of Fructobacillus tropaeoli and Apilactobacillus kunkeei from apiaries

Honeybee products have been among important consumer products throughout history. Microbiota has attracted attention in recent years due to both their probiotic value and industrial potential. Fructophilic lactic acid bacteria (FLAB), whose field of study has been expanding rapidly in the last 20 years, are among the groups that can be isolated from the bee gut. This study aimed to isolate FLAB from the honeybees of two different geographic regions in Turkey and investigate their probiotic, metabolic and anti-quorum sensing (anti-QS) potential. Metabolic properties were investigated based on fructose toleration and acid and diacetyl production while the probiotic properties of the isolates were determined by examining pH, pepsin, pancreatin resistance, antimicrobial susceptibility, and antimicrobial activity. Anti-QS activities were also evaluated with the Chromobacterium violaceum biosensor strain. Two FLAB members were isolated and identified by the 16S rRNA analysis as Fructobacillus tropaeoli and Apilactobacillus kunkeei, which were found to be tolerant to high fructose, low pH, pepsin, pancreatin, and bile salt environments. Both isolates showed anti-QS activity against the C. violaceum biosensor strain and no diacetyl production. The daily supernatants of the isolates inhibited the growth of Enterococcus faecalis ATCC 29212 among the selected pathogens. The isolates were found resistant to kanamycin, streptomycin, erythromycin, and clindamycin. In the evaluation of the probiotic potential of these species, the negative effect of antibiotics and other chemicals to which honeybees are directly or indirectly exposed draws attention within the scope of the "One Health" approach.

Biotechnological Processes Simulating the Natural Fermentation Process of Bee Bread and Therapeutic Properties-An Overview

Recent signs of progress in functional foods and nutraceuticals highlighted the favorable impact of bioactive molecules on human health and longevity. As an outcome of the fermentation process, an increasing interest is developed in bee products. Bee bread (BB) is a different product intended for humans and bees, resulting from bee pollen's lactic fermentation in the honeycombs, abundant in polyphenols, nutrients (vitamins and proteins), fatty acids, and minerals. BB conservation is correlated to bacteria metabolites, mainly created by Pseudomonas spp., Lactobacillus spp., and Saccharomyces spp., which give lactic acid bacteria the ability to outperform other microbial groups. Because of enzymatic transformations, the fermentation process increases the content of new compounds. After the fermentation process is finalized, the meaningful content of lactic acid and several metabolites prevent the damage caused by various pathogens that could influence the quality of BB. Over the last few years, there has been an increase in bee pollen fermentation processes to unconventional dietary and functional supplements. The use of the chosen starters improves the bioavailability and digestibility of bioactive substances naturally found in bee pollen. As a consequence of enzymatic changes, the fermentation process enhances BB components and preserves them against loss of characteristics. In this aspect, the present review describes the current biotechnological advancements in the development of BB rich in beneficial components derived from bee pollen fermentation and its use as a food supplement and probiotic product with increased shelf life and multiple health benefits.

Antimicrobial Activity from Putative Probiotic Lactic Acid Bacteria for the Biological Control of American and European Foulbrood Diseases

The balance of the gut microbiome is important for the honey bee’s growth and development, immune function and defense against pathogens. The use of a beneficial bacteria-based strategy for the prevention and biocontrol of American foulbrood (AFB) and European foulbrood (EFB) diseases in honey bees offers interesting prospects. Lactic acid bacteria (LAB) are common inhabitants of the gastrointestinal tract of the honey bee. Among LABs associated with bee gut microbiota, Lactiplantibacillus plantarum (previously Lactobacillus plantarum) and Apilactobacillus kunkeei (formerly classified as Lactobacillus kunkeei) are two of the most abundant species. In this study, four Lactiplantibacillus plantarum strains and four Apilactobacillus kunkeei strains, isolated from the gastrointestinal tract of honey bee (Apis mellifera L.) were selected for their in vitro inhibition ability of Paenibacillus larvae ATCC 9545 and Melissococccus plutonius ATCC 35311. In addition, these LABs have been characterized through some biochemical and functional characteristics: cell surface properties (hydrophobicity and auto-aggregation), carbohydrates assimilation and enzymatic activities. The antimicrobial, biochemical and cell surface properties of these LABs have been functional to their candidature as potential probiotics in beekeeping and for the biocontrol of AFB and EFB diseases.

Bacteriocin-mediated inhibition of some common pathogens by wild and mutant Lactobacillus species and in vitro amplification of bacteriocin encoding genes

Lactobacilli are the most common probiotics used in food and other industries because of their capability of producing bacteriocins. Bacteriocins are compounds that are used to kill pathogenic microorganisms. As most bacteria have become resistant to synthetic antibacterial tools, the importance of using probiotics as antibacterial agents has increased. This work was done to check the bacteriocin effect on some common pathogens and the influence of mutation on the bacteriocin activity of Lactobacilli was also investigated. Four strains were isolated, identified from meat and pickles samples via culturing methods, staining, biochemical tests, and ribotyping. Preliminary tests, including Gram staining and catalase test, were done for the confirmation of Lactobacillus species. All strains were gram-positive and catalase-negative. Antibacterial activity was checked against Pseudomonas aeruginosa, Staphylococcus aureus, Bacillus thuringiensis, Escherichia coli, and Salmonella enteritis via agar well diffusion method. The mutations were done using ethidium bromide and the influence of wild and mutants were also checked. Interestingly, mutants developed more virulence than wild ones. It was also observed that they all were sensitive to pepsin. Protein estimation was done via Bradford method. Ribotyping of GCU-W-PS1 revealed 99 % homology with Lactobacillus plantarum and GCU-W-MS1 to Lactobacillus curvatus (99 % homology). Curvacin A, sakacin P, and plantaricin A genes were also amplified using specific primers. Gene sequence showed the presence of curvacin A gene in GCU-W-MS1. It was concluded that lactic acid bacteria could be used as antibacterial tools against common pathogens.

First report on metabarcoding analysis of gut microbiome in Island Flying Fox (Pteropushypomelanus) in island populations of Malaysia

Flying fox (Pteropushypomelanus) belongs to the frugivorous bats, which play a crucial role in maintaining proper functioning of an ecosystem and conservation of the environment. Bats are well-known carriers of pathogenic viruses, such as BatCov RaTG13 from the coronavirus family that share 90.55% with SARS-CoV-2, the pathogen causing recent global pandemic coronavirus disease 19 (COVID-19). However, bats' possible role as a carrier of pathogenic bacteria is less explored. Here, using metabarcoding analysis through high-throughput sequencing, we explored the gut microbiome composition of different island populations on the east and west coasts of Peninsula Malaysia. The 16S rRNA gene in samples from Redang Island, Langkawi Island, Pangkor Island and Tinggi Island was amplified. Bacterial community composition and structure were analysed with α and β diversity metrics. A total of 25,658 operational taxonomic units at 97% similarity were assigned to eight phyla, 44 families, 61 genera and 94 species of microbes. The Proteobacteria was the dominant phylum in all populations. Meanwhile, the genera Enterobacter, Pseudomonas and Klebsiella, isolated in this study, were previously found in the rectum of other fruit bats. Our analyses suggest that Redang Island and Langkawi Island have high bacteria diversity. Thus, we found geographic locality is a strong predictor of microbial community composition and observed a positive correlation between ecological features and bacterial richness.

Phylogenomic and comparative genomic analyses of Leuconostocaceae species: identification of molecular signatures specific for the genera Leuconostoc, Fructobacillus and Oenococcus and proposal for a novel genus Periweissella gen. nov

The genera Convivina, Fructobacillus, Leuconostoc, Oenococcus and Weissella, which formed the family Leuconostocaceae, have recently been merged within the family Lactobacillaceae. Using genome sequences for 47 of the 52 named species from these genera, we report here comprehensive phylogenomic and comparative analyses on protein sequences from these species using multiple approaches. In a phylogenomic tree based on concatenated sequences of 498 core proteins from these five genera, and in a 16S rRNA gene tree, members of the genera Fructobacillus, Leuconostoc and Oenococcus formed distinct strongly supported clades. In contrast, Weissella species grouped into two distinct unrelated clades designated as the ‘Weissella main clade’ and ‘Weissella clade 2’. The presence of these clades is also seen in a matrix of pairwise average amino acid identity based on core protein sequences. In parallel, comparative genomic studies on protein sequences from Leuconostocaceae genomes have identified 46 conserved signature indels (CSIs) in diverse proteins that are unique characteristics of the different observed species clades. Of these identified CSIs, five, five and 13 CSIs are uniquely present in members of the genera Fructobacillus, Leuconostoc and Oenococcus, respectively. We also report here six and five CSIs that are exclusively present in the species from the Weissella main clade and Weissella clade 2, respectively, providing independent evidence supporting their distinctness from each other. The remaining 12 identified CSIs are commonly shared by some or all of the species from the genera Convivina, Fructobacillus and Leuconostoc, clarifying their interrelationships. The identified CSIs provide novel and reliable means for the identification/circumscription of members of the genera Fructobacillus, Leuconostoc and Oenococcus as well as the two Weissella species clades in molecular terms. Based on the strong phylogenetic and molecular evidence presented here, we propose that the genus Weissella be limited to only the species from the Weissella main clade, whereas the species forming Weissella clade 2 should be transferred to a new genus Periweissella gen. nov.

Dominance of Fructose-Associated Fructobacillus in the Gut Microbiome of Bumblebees (Bombus terrestris) Inhabiting Natural Forest Meadows

Simple Summary

A vast array of microorganisms colonize invertebrates and vertebrates. Most of these microbes reside in the digestive tract, where they constitute the intestinal (gut) microbiome. Some microbes are commensal, coexisting with their host without causing harm, while others can be mutualistic or pathogenic. Mutualistic microorganisms perform many health-related functions such as promoting digestion and acquisition of nutrients; hormone regulation; maintenance and control of the immune system; regulation of homeostasis and stress physiology of the body; insecticide resistance; production of certain vitamins; and providing protection against pathogenic microorganisms, parasites, and diseases. Bee-specific bacterial genera such as Lactobacillus, Snodgrassella, and Gilliamella dominate the gut communities of many bumblebees. This study confirmed Lactobacillus, Snodgrassella, and Gilliamella as dominant gut bacteria of the buff-tailed bumblebee Bombus terrestris in the agricultural landscape. However, we show that the guts of B. terrestris from natural forest habitats can be dominated by fructose-associated Fructobacillus spp. Our findings may have important implications for understanding the ecological role of bumblebees and the reasons for the decline of key pollinators.

Abstract

Bumblebees are key pollinators in agricultural landscapes. However, little is known about how gut microbial communities respond to anthropogenic changes. We used commercially produced colonies of buff-tailed bumblebees (Bombus terrestris) placed in three habitats. Whole guts (midgut, hindgut, and rectum) of B. terrestris specimens were dissected from the body and analyzed using 16S phylogenetic community analysis. We observed significantly different bacterial community composition between the agricultural landscapes (apple orchards and oilseed rape (Brassica napus) fields) and forest meadows, whereas differences in gut communities between the orchards and oilseed rape fields were nonsignificant. Bee-specific bacterial genera such as Lactobacillus, Snodgrassella, and Gilliamella dominated gut communities of B. terrestris specimens. In contrast, the guts of B. terrestris from forest meadows were dominated by fructose-associated Fructobacillus spp. Bacterial communities of workers were the most diverse. At the same time, those of males and young queens were less diverse, possibly reflecting greater exposure to the colony’s inner environment compared to the environment outside the colony, as well as bumblebee age. Our results suggest that habitat quality, exposure to environmental microbes, nectar quality and accessibility, and land use significantly affect gut bacterial composition in B. terrestris.

Microbial communities associated with honey bees in Brazil and in the United States

Honey bee colony losses worldwide call for a more in-depth understanding of the pathogenic and mutualistic components of the honey bee microbiota and their relation with the environment. In this descriptive study, we characterized the yeast and bacterial communities that arise from six substrates associated with honey bees: corbicular pollen, beebread, hive debris, intestinal contents, body surface of nurses and forager bees, comparing two different landscapes, Minas Gerais, Brazil and Maryland, United States. The sampling of five hives in Brazil and four in the USA yielded 217 yeast and 284 bacterial isolates. Whereas the yeast community, accounted for 47 species from 29 genera, was dominated in Brazil by Aureobasidium sp. and Candida orthopsilosis, the major yeast recovered from the USA was Debaryomyces hansenii. The bacterial community was more diverse, encompassing 65 species distributed across 31 genera. Overall, most isolates belonged to Firmicutes, genus Bacillus. Among LAB, species from Lactobacillus were the most prevalent. Cluster analysis evidenced high structuration of the microbial communities, with two distinguished microbial groups between Brazil and the United States. In general, the higher difference among sites and substrates were dependents on the turnover effect (~ 93% of the beta diversity), with a more pronounced effect of nestedness (~ 28%) observed from Brazil microbiota change. The relative abundance of yeasts and bacteria also showed the dissimilarity of the microbial communities between both environments. These results provide a comprehensive view of microorganisms associated with A. mellifera, highlighting the importance of the environment in the establishment of the microbiota associated with honey bees.

Fructose-coated Ångstrom silver prevents sepsis by killing bacteria and attenuating bacterial toxin-induced injuries

Serious infection caused by multi-drug-resistant bacteria is a major threat to human health. Bacteria can invade the host tissue and produce various toxins to damage or kill host cells, which may induce life-threatening sepsis. Here, we aimed to explore whether fructose-coated Ångstrom-scale silver particles (F-AgÅPs), which were prepared by our self-developed evaporation-condensation system and optimized coating approach, could kill bacteria and sequester bacterial toxins to attenuate fatal bacterial infections.

Methods: A series of in vitro assays were conducted to test the anti-bacterial efficacy of F-AgÅPs, and to investigate whether F-AgÅPs could protect against multi-drug resistant Staphylococcus aureus (S. aureus)- and Escherichia coli (E. coli)-induced cell death, and suppress their toxins (S. aureus hemolysin and E. coli lipopolysaccharide)-induced cell injury or inflammation. The mouse models of cecal ligation and puncture (CLP)- or E. coli bloodstream infection-induced lethal sepsis were established to assess whether the intravenous administration of F-AgÅPs could decrease bacterial burden, inhibit inflammation, and improve the survival rates of mice. The levels of silver in urine and feces of mice were examined to evaluate the excretion of F-AgÅPs.

Results: F-AgÅPs efficiently killed various bacteria that can cause lethal infections and also competed with host cells to bind with S. aureus α-hemolysin, thus blocking its cytotoxic activity. F-AgÅPs inhibited E. coli lipopolysaccharide-induced endothelial injury and macrophage inflammation, but not by directly binding to lipopolysaccharide. F-AgÅPs potently reduced bacterial burden, reversed dysregulated inflammation, and enhanced survival in mice with CLP- or E. coli bloodstream infection-induced sepsis, either alone or combined with antibiotic therapy. After three times injections within 48 h, 79.18% of F-AgÅPs were excreted via feces at the end of the 14-day observation period.

Conclusion: This study suggests the prospect of F-AgÅPs as a promising intravenous agent for treating severe bacterial infections.

Detection Bioactive Metabolites of Fructobacillus fructosus Strain HI-1 Isolated from Honey Bee's Digestive Tract Against Paenibacillus larvae

American foulbrood is a devastating disease of honey bee, causing economic loss in the beekeeping industry. The disease mainly causes reduction in honey bee populations which negatively affect the honey bee's major role as natural pollinators of significant crops and wildflowers. Thus, it is crucial to develop safe efficient strategies to control the disease and to improve bee colony health. Using lactic acid bacteria (LAB) as an alternative to chemical treatments is a promising novel technique for tackling honey bee diseases and improving their immunity. The endogenous LAB isolates were recovered from honey bee gut samples collected from different apiaries in two Egyptian governorates and screened for antagonistic activities against Paenibacillus larvae (pathogen of AFB disease). The results showed that 53.3% of tested LAB isolates (n = 120) exhibited antagonistic activities against P. larvae. The minimum inhibitory concentration and minimum bactericidal concentration of the most potent LAB isolate (with an inhibition zone of 44 mm) were 100 and 125 µL/mL, respectively. 16S rRNA sequencing identified the most potent isolate as Fructobacillus fructosus HI-1. The bioactive metabolites of F. fructosus were extracted with ethyl acetate and fractionated on thin-layer chromatography (TLC); also, bioactive fractions were detected. Heptyl 2-methylbutyrate, di-isobutyl phthalate, D-turanose, heptakis (trimethylsilyl), di-isooctyl phthalate, and hyodeoxycholic acid compounds were identified in the bioactive fractions. The result explores the promising administration of probiotic metabolites to control honey bee AFB disease, as a natural tool to substitute antibiotics and chemicals in disease-controlling strategies.

Strain diversity of plant-associated Lactiplantibacillus plantarum

Lactiplantibacillus plantarum (formerly Lactobacillus plantarum) is a lactic acid bacteria species found on plants that is essential for many plant food fermentations. In this study, we investigated the intraspecific phenotypic and genetic diversity of 13 L. plantarum strains isolated from different plant foods, including fermented olives and tomatoes, cactus fruit, teff injera, wheat boza and wheat sourdough starter. We found that strains from the same or similar plant food types frequently exhibited similar carbohydrate metabolism and stress tolerance responses. The isolates from acidic, brine‐containing ferments (olives and tomatoes) were more resistant to MRS adjusted to pH 3.5 or containing 4% w/v NaCl, than those recovered from grain fermentations. Strains from fermented olives grew robustly on raffinose as the sole carbon source and were better able to grow in the presence of ethanol (8% v/v or sequential exposure of 8% (v/v) and then 12% (v/v) ethanol) than most isolates from other plant types and the reference strain NCIMB8826R. Cell free culture supernatants from the olive‐associated strains were also more effective at inhibiting growth of an olive spoilage strain of Saccharomyces cerevisiae. Multi‐locus sequence typing and comparative genomics indicated that isolates from the same source tended to be genetically related. However, despite these similarities, other traits were highly variable between strains from the same plant source, including the capacity for biofilm formation and survival at pH 2 or 50°C. Genomic comparisons were unable to resolve strain differences, with the exception of the most phenotypically impaired and robust isolates, highlighting the importance of utilizing phenotypic studies to investigate differences between strains of L. plantarum. The findings show that L. plantarum is adapted for growth on specific plants or plant food types, but that intraspecific variation may be important for ecological fitness and strain coexistence within individual habitats.

Challenges associated with spray drying of lactic acid bacteria: Understanding cell viability loss

Lactic acid bacteria (LAB) cultures used in food fermentation are often dried to reduce transportation costs and facilitate handling during use. Dried LAB ferments are generally lyophilized to ensure high cell viability. Spray drying has come to the forefront as a promising technique due to its versatility and lower associated energy costs. Adverse conditions during spray drying, such as mechanical stress, dehydration, heating, and oxygen exposure, can lead to low LAB cell viability. This reduced viability has limited spray drying's industrial applications thus far. This review aims to demonstrate the operations and thermodynamic principles that govern spray drying, then correlate them to the damage suffered by LAB cells during the spray-drying process. The particularities of spray drying that might cause LAB cell death are detailed in this review, and the conclusion may enhance future studies on ways to improve cell viability.

Global cocoa fermentation microbiome: revealing new taxa and microbial functions by next generation sequencing technologies

This review provides an overview of the application of next-generation sequencing (NGS) technologies for microbiome analysis of cocoa beans fermentation. The cocoa-producing regions where NGS has been applied include Brazil, Ghana, Ivory Coast, Cameroon, Nicaragua, and Colombia. The data collected were processed by principal component analysis (PCA) and Venn diagrams to perform a multivariate association between microbial diversity and cocoa-producing regions. NGS studies have confirmed the dominance of three major microbial groups revealed by culture-dependent approaches, i.e., lactic acid bacteria, acetic acid bacteria, and yeasts. However, a more complex microbial diversity has been revealed, comprising sub-dominant populations, late-growing species, and uncultivable microorganisms. A total of 99 microbial genera and species were for the first time reported in cocoa beans fermentation, such as Brevibacillus sp., Halomonas meridiana, Methylobacterium sp., Novosphingobium sp., and Paenibacillus pabuli. PCA and Venn diagrams showed that species composition is rarely fixed and often experiences fluctuations of varying degrees and at varying frequencies between different cocoa-producing regions. Understanding these differences will provide further directions for exploring the functional and metabolic activity of rare and abundant taxa, as well as their use as starter cultures to obtain high-quality cocoa beans.

Mining indigenous honeybee gut microbiota for Lactobacillus with probiotic potential

The present study was done to explore the diversity of lactic acid bacteria (LAB) associated with the gastrointestinal tract (GIT) of honeybee species endemic to northeastern Pakistan. Healthy worker bees belonging to Apis mellifera, A. dorsata, A. cerana and A. florea were collected from hives and the surroundings of a major apiary in the region. The 16S rRNA amplicon sequencing revealed a microbial community in A. florea that was distinct from the others in having an abundance of Lactobacillus and Bifidobacteria. However, this was not reflected in the culturable bacteria obtained from these species. The isolates were characterized for safety parameters, and 20 LAB strains deemed safe were evaluated for resistance to human GIT stresses like acid and bile, adhesion and adhesiveness, and anti-pathogenicity. The five most robust strains, Enterococcus saigonensis NPL780a, Lactobacillus rapi NPL782a, Lactobacillus kunkeei NPL783a, and NPL784, and Lactobacillus paracasei NPL783b, were identified through normalized Pearson (n) principal components analysis (PCA). These strains were checked for inhibition of human pathogens, antibiotic resistance, osmotic tolerance, metabolic and enzymatic functions, and carbohydrate utilization, along with antioxidative and cholesterol-removing potential. The findings suggest at least three strains (NPL 783a, 784 and 782a) as candidates for further in vitro and in vivo investigations of their potential health benefits and application as novel probiotic adjuncts.

Selection of Lactic Acid Bacteria Species and Strains for Efficient Trapping of Drosophila suzukii

Simple Summary

The spotted wing drosophila (SWD) is an invasive fruit fly that causes serious economic damage to many fruit crops. Monitoring is the first step for any management program to determine the characteristics of a pest. For this purpose, there are no efficient baits registered to date. Certain bacteria release chemical compounds that attract SWD. We studied the bacterial impact on the enhanced attractiveness of a commercial bait (Droskidrink^®) under field and laboratory conditions. At first, Oenococcus oeni belonging to lactic acid bacteria (LAB) was found to release chemical compounds that were highly attractive for SWD. The attractiveness of Droskidrink^® bait was increased by O. oeni culture, resulting in a higher capture rate of SWD in traps. Therefore, our findings suggest the use of the bacterial culture inside the commercial SWD baits. The use of these kinds of baits can minimize the risk of pest outbreaks in fruit orchards in both domestic and wild environments. Our pest management approach is farmer-friendly in all aspects, as well as the food sector.

Abstract

(1) Monitoring of Drosophila suzukii is based on the use of effective traps and baits. The current baits are insufficient to provide efficient monitoring. The use of bacteria as bio-catalyzers to produce bioactive volatiles may improve flies’ attraction. Thus, we conducted this work to improve Droskidrink^® bait’s attractiveness using lactic acid bacteria. (2) Different baits that were based on the use of Droskidrink^® were assessed for flies’ attraction in a Droso-Trap^® in a vineyard. Oenococcus oeni, Pediococcus spp., and Lactobacillus spp. were used. The performance of the most attractive species, O. oeni, inoculated into Droskidrink^® was assessed in laboratory tests. The responses of female flies to volatiles produced by Droskidrink^® with O. oeni strains were recorded by electroantennography. (3) Preliminary field assessment of baits recorded O. oeni as the most attractive species. Three strain groups showed adaptation to test conditions. Volatiles extracted by the headspace of baits inoculated with O. oeni, elicited electroantennographic responses from fly antennae. (4) Droskidrink^® inoculated with O. oeni is a highly attractive bait for monitoring. These findings will be useful for improving the attractiveness of D. suzukii commercial baits based on the utilization of LAB volatiles in a strain-dependent manner.