Characterization of strains of Weissella fabalis sp. nov. and Fructobacillus tropaeoli from spontaneous cocoa bean fermentations

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.

The Weissella and Periweissella genera: up-to-date taxonomy, ecology, safety, biotechnological, and probiotic potential

Bacteria belonging to the genera Weissella and Periweissella are lactic acid bacteria, which emerged in the last decades for their probiotic and biotechnological potential. In 2015, an article reviewing the scientific literature till that date on the taxonomy, ecology, and biotechnological potential of the Weissella genus was published. Since then, the number of studies on this genus has increased enormously, several novel species have been discovered, the taxonomy of the genus underwent changes and new insights into the safety, and biotechnological and probiotic potential of weissellas and periweissellas could be gained. Here, we provide an updated overview (from 2015 until today) of the taxonomy, ecology, safety, biotechnological, and probiotic potential of these lactic acid bacteria.

Motility in Periweissella Species: Genomic and Phenotypic Characterization and Update on Motility in Lactobacillaceae

The genus Weissella and the recently described genus Periweissella, to which some previously named Weissella species have been reclassified as a result of a taxogenomic assessment, includes lactic acid bacteria species with high biotechnological and probiotic potential. Only one species, namely, Periweissella (P.) beninensis, whose type strain has been shown to possess probiotic features, has so far been described to be motile. However, the availability of numerous genome sequences of Weissella and Periweissella species prompted the possibility to screen for the presence of the genetic determinants encoding motility in Weissella and Periweissellas spp. other than P. beninensis. Herein, we performed a comprehensive genomic analysis to identify motility-related proteins in all Weissella and Periweissella species described so far, and extended the analysis to the recently sequenced Lactobacillaceae spp. Furthermore, we performed motility assays and transmission electron microscopy (TEM) on Periweissella type strains to confirm the genomic prediction. The homology-based analysis revealed genes coding for motility proteins only in the type strains of P. beninensis, P. fabalis, P. fabaria and P. ghanensis genomes. However, only the P. beninensis type strain was positive in the motility assay and displayed run-and-tumble behavior. Many peritrichous and long flagella on bacterial cells were visualized via TEM, as well. As for the Lactobacillaceae, in addition to the species previously described to harbor motility proteins, the genetic determinants of motility were also found in the genomes of the type strains of Lactobacillus rogosae and Ligilactobacillus salitolerans. This study, which is one of the first to analyze the genomes of Weissella, Periweissella and the recently sequenced Lactobacillaceae spp. for the presence of genes coding for motility proteins and which assesses the associated motility phenotypes, provides novel results that expand knowledge on these genera and are useful in the further characterization of lactic acid bacteria.

Microbial symbionts are shared between ants and their associated beetles

The transmission of microbial symbionts across animal species could strongly affect their biology and evolution, but our understanding of transmission patterns and dynamics is limited. Army ants (Formicidae: Dorylinae) and their hundreds of closely associated insect guest species (myrmecophiles) can provide unique insights into interspecific microbial symbiont sharing. Here, we compared the microbiota of workers and larvae of the army ant Eciton burchellii with those of 13 myrmecophile beetle species using 16S rRNA amplicon sequencing. We found that the previously characterized specialized bacterial symbionts of army ant workers were largely absent from ant larvae and myrmecophiles, whose microbial communities were usually dominated by Rickettsia, Wolbachia, Rickettsiella and/or Weissella. Strikingly, different species of myrmecophiles and ant larvae often shared identical 16S rRNA genotypes of these common bacteria. Protein-coding gene sequences confirmed the close relationship of Weissella strains colonizing army ant larvae, some workers and several myrmecophile species. Unexpectedly, these strains were also similar to strains infecting dissimilar animals inhabiting very different habitats: trout and whales. Together, our data show that closely interacting species can share much of their microbiota, and some versatile microbial species can inhabit and possibly transmit across a diverse range of hosts and environments.

Comparative genomic analysis of Periweissella and the characterization of novel motile species

The genus Periweissella was proposed as a novel genus in the Lactobacillaceae in 2022. However, the phylogenetic relationship between Periweissella and other heterofermentative lactobacilli, and the genetic and physiological properties of this genus remain unclear. This study aimed to determine the phylogenetic relationship between Periweissella and the two closest genera, Weissella and Furfurilactobacillus, by the phylogenetic analysis and calculation of (core gene) pairwise average amino acid identity. Targeted genomic analysis showed that fructose bisphosphate aldolase was only present in the genome of Pw. cryptocerci. Mannitol dehydrogenase was found in genomes of Pw. beninensis, Pw. fabaria, and Pw. fabalis. Untargeted genomic analysis identified the presence of flagellar genes in Periweissella but not in other closely related genera. Phenotypes related to carbohydrate fermentation and motility matched the genotypes. Motility genes were organized in a single operon and the proteins shared a high amino acid similarity in the genus Periweissella. The relatively low similarity of motility operons between Periweissella and other motile lactobacilli indicated the acquisition of motility by the ancestral species. Our findings facilitate the phylogenetic, genetic, and phenotypic understanding of the genus Periweissella.ImportanceThe genus Periweissella is a heterofermentative genus in the Lactobacillaceae which includes predominantly isolates from cocoa fermentations in tropical climates. Despite the relevance of the genus in food fermentations, genetic and physiological properties of the genus are poorly characterized and genome sequences became available only after 2020. This study characterized strains of the genus by functional genomic analysis, and by determination of metabolic and physiological traits. Phylogenetic analysis revealed that Periweissella is the evolutionary link between rod-shaped heterofermentative lactobacilli and the coccoid Leuconostoc clade with the genera Weissella and Furfurilactobacillus as closest relatives. Periweissella is the only heterofermentative genus in the Lactobacillaceae which comprises predominantly motile strains. The genomic, physiological, and metabolic characterization of Periweissella may facilitate the potential use of strains of the genus as starter culture in traditional or novel food fermentations.

Probiotic Potential and Safety Assessment of Type Strains of Weissella and Periweissella Species

Although numerous strains belonging to the Weissella genus have been described in the last decades for their probiotic and biotechnological potential, others are known to be opportunistic pathogens of humans and animals. Here, we investigated the probiotic potential of two Weissella and four Periweissella type strains belonging to the species Weissella diestrammenae, Weissella uvarum, Periweissella beninensis, Periweissella fabalis, Periweissella fabaria, and Periweissella ghanensis by genomic and phenotypic analyses, and performed a safety assessment of these strains. Based on the results of the survival to simulated gastrointestinal transit, autoaggregation and hydrophobicity characteristics, as well as adhesion to Caco-2 cells, we showed that the P. beninensis, P. fabalis, P. fabaria, P. ghanensis, and W. uvarum type strains exhibited a high probiotic potential. The safety assessment, based on the genomic analysis, performed by searching for virulence and antibiotic resistance genes, as well as on the phenotypic evaluation, by testing hemolytic activity and antibiotic susceptibility, allowed us to identify the P. beninensis type strain as a safe potential probiotic microorganism. IMPORTANCE A comprehensive analysis of safety and functional features of six Weissella and Periweissella type strains was performed. Our data demonstrated the probiotic potential of these species, indicating the P. beninensis type strain as the best candidate based on its potential probiotic features and the safety assessment. The presence of different antimicrobial resistance profiles in the analyzed strains highlighted the need to establish cutoff values to perform a standardized safety evaluation of these species, which, in our opinion, should be mandatory on a strain-specific basis.

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.

Bacteriobiota and Chemical Changes during the Ripening of Traditional Fermented "Pirot 'Ironed' Sausage"

"Pirot 'ironed' sausage" (Pis) is a traditional, fermented sausage, made from different types of meat (beef and chevon), without additives or starter cultures. The physical-chemical properties (pH, water activity, fats, moisture, and protein contents) were examined in the initial meat batter stuffing and during ripening. Total bacterial diversity was examined at different time points using both culturable (traditional) and non-culturable (NGS sequencing) approaches. During the ripening, a decrease in pH value, a_w, and moisture content was observed, as well as an increase in protein and fat content. At least a two-fold significant decrease was noted for colorimetric values during the ripening period. The dominance of Proteobacteria and Firmicutes was observed in the non-culturable approach in all studied samples. During the ripening process, an increase in Firmicutes (from 33.5% to 63.5%) with a decrease in Proteobacteria (from 65.4% to 22.3%) was observed. The bacterial genera that were dominant throughout the ripening process were Lactobacillus, Photobacterium, Leuconostoc, Weissella, and Lactococcus, while Carnobacterium, Brochothrix, and Acinetobacter were found also, but in negligible abundance. Among the culturable bacteria, Latilactobacillus sakei (Lactobacillus sakei) and Leuconostoc mesenteoides were present in all stages of ripening.

The Weissella Genus: Clinically Treatable Bacteria with Antimicrobial/Probiotic Effects on Inflammation and Cancer

Weissella is a genus earlier considered a member of the family Leuconostocaceae, which was reclassified into the family Lactobacillaceae in 1993. Recently, there have been studies emphasizing the probiotic and anti-inflammatory potential of various species of Weissella, of which W. confusa and W. cibaria are the most representative. Other species within this genus include: W. paramesenteroides, W. viridescens, W. halotolerans, W. minor, W. kandleri, W. soli, W. ghanensis, W. hellenica, W. thailandensis, W. fabalis, W. cryptocerci, W. koreensis, W. beninensis, W. fabaria, W. oryzae, W. ceti, W. uvarum, W. bombi, W. sagaensis, W. kimchi, W. muntiaci, W. jogaejeotgali, W. coleopterorum, W. hanii, W. salipiscis, and W. diestrammenae. Weissella confusa, W. paramesenteroides, W. koreensis, and W. cibaria are among the few species that have been isolated from human samples, although the identification of these and other species is possible using metagenomics, as we have shown for inflammatory bowel disease (IBD) and healthy controls. We were able to isolate Weissella in gut-associated bacteria (post 24 h food deprivation and laxatives). Other sources of isolation include fermented food, soil, and skin/gut/saliva of insects/animals. With the potential for hospital and industrial applications, there is a concern about possible infections. Herein, we present the current applications of Weissella on its antimicrobial and anti-inflammatory mechanistic effects, the predisposing factors (e.g., vancomycin) for pathogenicity in humans, and the antimicrobials used in patients. To address the medical concerns, we examined 28 case reports focused on W. confusa and found that 78.5% of infections were bacteremia (of which 7 were fatal; 1 for lack of treatment), 8 were associated with underlying malignancies, and 8 with gastrointestinal procedures/diseases of which 2 were Crohn’s disease patients. In cases of a successful resolution, commonly administered antibiotics included: cephalosporin, ampicillin, piperacillin-tazobactam, and daptomycin. Despite reports of Weissella-related infections, the evolving mechanistic findings suggest that Weissella are clinically treatable bacteria with emerging antimicrobial and probiotic benefits ranging from oral health, skin care, obesity, and inflammatory diseases to cancer.

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.

Novel Insights Into the Phylogeny and Biotechnological Potential of Weissella Species

In this study, the genomes of the Weissella (W.) beninensis, W. diestrammenae, W. fabalis, W. fabaria, W. ghanensis, and W. uvarum type strains were sequenced and analyzed. Moreover, the ability of these strains to metabolize 95 carbohydrates was investigated, and the genetic determinants of such capability were searched within the sequenced genomes. 16S rRNA gene and genome-based-phylogeny of all the Weissella species described to date allowed a reassessment of the Weissella genus species groups. As a result, six distinct species groups within the genus, namely, W. beninensis, W. kandleri, W. confusa, W. halotolerans, W. oryzae, and W. paramesenteroides species groups, could be described. Phenotypic analyses provided further knowledge about the ability of the W. beninensis, W. ghanensis, W. fabaria, W. fabalis, W. uvarum, and W. diestrammenae type strains to metabolize certain carbohydrates and confirmed the interspecific diversity of the analyzed strains. Moreover, in many cases, the carbohydrate metabolism pathway and phylogenomic species group clustering overlapped. The novel insights provided in our study significantly improved the knowledge about the Weissella genus and allowed us to identify features that define the role of the analyzed type strains in fermentative processes and their biotechnological potential.

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.

Community scale in-situ rapid biological reduction and resource recovery of food waste

In this study, a community-scale in-situ rapid biological reduction (IRBR) system was applied to achieve the rapid disposal and resource recovery of food waste (FW). A total of 5263 kg FW was processed in the 35 days of stably operation, during which 84.37% total mass reduction and 43.30% volatile solid removal were achieved, and the odor had been effectively controlled. Microbial sequencing results showed that aerobic and facultative thermophilic bacteria were major bacterial community, and vigorous metabolism of both carbohydrate and amino acid were maintained during the IRBR process. The final products have the potential to be recycled as organic fertilizers or bio-solid fuel to realize resource recovery. The results of economic analysis showed that the IRBR system had lower FW disposal costs due to the high automation. These results suggested that the IRBR system was an environmentally friendly, economical and practical method for the FW rapid treatment.

Influence of thermal assistance on the biodegradation of organics during food waste bio-drying: Microbial stimulation and energy assessment

Recently, bio-drying was highlighted in the drying pretreatment of high-moisture organic wastes for their energy recovery. In this study, to investigate the influences of thermal assistance on microbial stimulation and energy utilization in organic degradation, thermally assisted bio-drying (TB) was conducted on food waste (FW) and was compared with conventional bio-drying (CB) and thermal drying (TD). As expected, more water was removed in TB, which exhibited no lag phenomenon and intensified microbial activity. Corresponding with the stimulated enzyme activity, more readily degradable carbohydrates, lipids and lignocellulose were decomposed in TB than those in CB, and lipid degradation generated a significant proportion of the total bio-heat generated (43.13%-45.83%). Furthermore, according to the microbial analysis (qPCR and 16S rRNA gene sequencing), Bacillus was found to be the dominant genus involved in the degradation of organics during TB and CB. In the initial phase, rather than Weissella, as in CB, Ureibacillus was notable in TB for the degradation of readily degradable substrates. In the late phase, Pseudoxanthomonas and Saccharomonospora were enriched for degrading lignocellulose. In addition, heat balance and life-cycle energy assessment demonstrated that a small amount of thermal heat (11.96%) upgraded bio-drying with high energy efficiency. Compared with the CB and TD processes, the TB trial consumed less thermal energy (0.58 MJ/kg H₂O) and achieved a higher energy output/input ratio (3.64). This research suggests that thermal assistance is a promising approach to enhancing FW bio-drying, which exhibits efficient drying performance and great potential for energy recovery.

Functional role of yeasts, lactic acid bacteria and acetic acid bacteria in cocoa fermentation processes

Cured cocoa beans are obtained through a post-harvest, batchwise process of fermentation and drying carried out on farms in the equatorial zone. Fermentation of cocoa pulp-bean mass is performed mainly in heaps or boxes. It is made possible by a succession of yeast, lactic acid bacteria (LAB) and acetic acid bacteria (AAB) activities. Yeasts ferment the glucose of the cocoa pulp into ethanol, perform pectinolysis and produce flavour compounds, such as (higher) alcohols, aldehydes, organic acids and esters. LAB ferment the glucose, fructose and citric acid of the cocoa pulp into lactic acid, acetic acid, mannitol and pyruvate, generate a microbiologically stable fermentation environment, provide lactate as carbon source for the indispensable growth of AAB, and contribute to the cocoa and chocolate flavours by the production of sugar alcohols, organic acids, (higher) alcohols and aldehydes. AAB oxidize the ethanol into acetic acid, which penetrates into the bean cotyledons to prevent seed germination. Destruction of the subcellular seed structure in turn initiates enzymatic and non-enzymatic conversions inside the cocoa beans, which provides the necessary colour and flavour precursor molecules (hydrophilic peptides, hydrophobic amino acids and reducing sugars) for later roasting of the cured cocoa beans, the first step of the chocolate-making.

Weissella: An Emerging Bacterium with Promising Health Benefits

Weissella strains have been the subject of much research over the last 5 years because of the genus' technological and probiotic potential. Certain strains have attracted the attention of the pharmaceutical, medical, and food industries because of their ability to produce antimicrobial exopolysaccharides (EPSs). Moreover, Weissella strains are able to keep foodborne pathogens in check because of the bacteriocins, hydrogen peroxide, and organic acids they can produce; all listed have recognized pathogen inhibitory activities. The Weissella genus has also shown potential for treating atopic dermatitis and certain cancers. W. cibaria, W. confusa, and W. paramesenteroides are particularly of note because of their probiotic potential (fermentation of prebiotic fibers) and their ability to survive in the gastrointestinal tract. It is important to note that most of the Weissella strains with these health-promoting properties have been shown to be save safe, due to the absence or the low occurrence of virulence or antibiotic-resistant genes. A large number of scientific studies continue to report on and to support the use of Weissella strains in the food and pharmaceutical industries. This review provides an overview of these studies and draws conclusions for future uses of this rich and previously unexplored genus.

The bacterial diversity of raw Moroccon camel milk

Dromedary camel milk is generally considered a valuable and marketable commodity but its production suffers from poor hygienic conditions that result in low microbiological quality and the presence of various pathogens. The objective of the present study was to provide a detailed report of the bacterial species level composition of Moroccan raw camel milk samples that can serve as a starting point for the selection of starter cultures to facilitate a change in manufacturing practices to an improved and safer production system. The composition of the bacterial community in four freshly collected raw camel milk samples was analyzed by performing a large-scale isolation campaign combined with 16S rRNA gene amplicon sequencing. A total of 806 isolates were obtained from four raw camel milk samples using ten combinations of growth media and incubation conditions. Subsequent isolate dereplication using MALDI-TOF mass spectrometry and identification of representative isolates through sequence analysis of protein encoding and 16S rRNA genes revealed the presence of established and novel dairy lactic acid bacteria, as well as bacteria that are considered indicators of poor hygienic conditions and psychrotrophic spoilage organisms. The large numbers of Lactococcus and Enterococcus isolates obtained present an interesting resource for starter culture selection.

Curing of Cocoa Beans: Fine-Scale Monitoring of the Starter Cultures Applied and Metabolomics of the Fermentation and Drying Steps

Starter culture-initiated cocoa fermentation processes can be applied to improve the quality of cured cocoa beans. However, an accurate monitoring of the microbial strains inoculated in fresh cocoa pulp-bean mass to assess their contribution to the cocoa bean curing process is still lacking. In the present study, eight different cocoa fermentation processes were carried out with Trinitario cocoa in vessels in Costa Rica to assess the contribution of two candidate yeast starter culture strains, namely Saccharomyces cerevisiae IMDO 050523 and Pichia kudriavzevii IMDO 020508, inoculated in combination with Limosilactobacillus fermentum IMDO 0611222 and Acetobacter pasteurianus IMDO 0506386. A multiphasic approach, consisting of culture-dependent selective plating and incubation, rRNA-PCR-DGGE community profiling of agar plate washes, and culture-independent high-throughput amplicon sequencing, combined with a metabolite target analysis of non-volatile and volatile organic compounds (VOCs), was performed on samples from the fermentation and/or drying steps. The different starter culture mixtures applied effectively steered the cocoa fermentation processes performed. Moreover, the use of an amplicon sequence variant (ASV) approach, aligning these ASVs to the whole-genome sequences of the inoculated strains, allowed the monitoring of these inoculated strains and their differentiation from very closely related variants naturally present in the background or spontaneous fermentation processes. Further, traits such as malolactic fermentation during the fermentation step and acetoin and tetramethylpyrazine formation during the drying step could be unraveled. Finally, the yeast strains inoculated influenced the substrate consumption and metabolite production during all starter culture-initiated fermentation processes. This had an impact on the VOC profiles of the cured cocoa beans. Whereas the P. kudriavzevii strain produced a wide range of VOCs in the cocoa pulp, the S. cerevisiae strain mostly influenced the VOC composition of the cured cocoa beans.

Micromonospora fluminis sp. nov., isolated from mountain river sediment

During a bioprospection of bacteria with antimicrobial activity, the actinomycete strain A38^T was isolated from a sediment sample of the Carpintero river located in the Gran Piedra Mountains, Santiago de Cuba province (Cuba). This strain was identified as a member of the genus Micromonospora by means of a polyphasic taxonomy study. Strain A38^T was an aerobic Gram-positive filamentous bacterium that produced single spores in a well-developed vegetative mycelium. An aerial mycelium was absent. The cell wall contained meso-diaminopimelic acid and the whole-cell sugars were glucose, mannose, ribose and xylose. The major cellular fatty acids were isoC_15:0, 10 methyl C_17:0, anteiso-C_17:0 and iso-C_17:0. The predominant menaquinones were MK-10(H₄) and MK-10(H6). Phylogenetic analysis of 16S rRNA gene sequences revealed that this strain was closely related to Micromonospora tulbaghiae DSM 45142^T (99.5 %), Micromonospora citrea DSM 43903^T (99.4 %), Micromonospora marina DSM 45555^T (99.4 %), Micromonospora maritima DSM 45782^T (99.3 %), Micromonospora sediminicola DSM 45794^T (99.3 %), Micromonospora aurantiaca DSM 43813^T (99.2 %) and Micromonospora chaiyaphumensis DSM 45246^T (99.2 %). The results of OrthoANIu analysis showed the highest similarity to Micromonospora chalcea DSM 43026^T (96.4 %). However, the 16S rRNA and gyrB gene sequence-based phylogeny and phenotypic characteristics provided support to distinguish strain A38^T as a novel species. On the basis of the results presented here, we propose to classify strain A38^T (=LMG 30467^T=CECT 30034^T) as the type strain of the novel species Micromonospora fluminis sp. nov.

Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory

This review provides a state-of-the-art description of the performance of Sanger cycle sequencing of the 16S rRNA gene for routine identification of bacteria in the clinical microbiology laboratory. A detailed description of the technology and current methodology is outlined with a major focus on proper data analyses and interpretation of sequences. The remainder of the article is focused on a comprehensive evaluation of the application of this method for identification of bacterial pathogens based on analyses of 16S multialignment sequences. In particular, the existing limitations of similarity within 16S for genus- and species-level differentiation of clinically relevant pathogens and the lack of sequence data currently available in public databases is highlighted. A multiyear experience is described of a large regional clinical microbiology service with direct 16S broad-range PCR followed by cycle sequencing for direct detection of pathogens in appropriate clinical samples. The ability of proteomics (matrix-assisted desorption ionization-time of flight) versus 16S sequencing for bacterial identification and genotyping is compared. Finally, the potential for whole-genome analysis by next-generation sequencing (NGS) to replace 16S sequencing for routine diagnostic use is presented for several applications, including the barriers that must be overcome to fully implement newer genomic methods in clinical microbiology. A future challenge for large clinical, reference, and research laboratories, as well as for industry, will be the translation of vast amounts of accrued NGS microbial data into convenient algorithm testing schemes for various applications (i.e., microbial identification, genotyping, and metagenomics and microbiome analyses) so that clinically relevant information can be reported to physicians in a format that is understood and actionable. These challenges will not be faced by clinical microbiologists alone but by every scientist involved in a domain where natural diversity of genes and gene sequences plays a critical role in disease, health, pathogenicity, epidemiology, and other aspects of life-forms. Overcoming these challenges will require global multidisciplinary efforts across fields that do not normally interact with the clinical arena to make vast amounts of sequencing data clinically interpretable and actionable at the bedside.

Overview of exopolysaccharides produced by Weissella genus - A review

Exopolysaccharides (EPS) from lactic acid bacteria (LAB) are much diversed in structure, composition and applications which also adding a great commercial potential due to its generally recognized as safe (GRAS) status. LAB genus such as Lactobacillus, Leuconostoc, Streptococcus, Weissella, Lactococcus are known to produce EPS. Among this genus, Weissella is enormously reported for diversity and high production of EPS with wide range of industrial applications and bio-functional properties. This review summarize in detail about the Weissella EPS from genus to functional application. Physico-chemical characterization from production, purification step to structural elucidation of Weissella EPS is comprehensively discussed along with their properties. Weissella genus has revealed various EPS with significant functional potentials, making massive application in food and pharma industries as viscosifiers, biothickener, emulsifiers and stabilizers. In addition to this, biological properties of these EPS revealed multiple health promoting properties which can be explored for further applications in food and pharmaceutical sectors.

Weissella sagaensis sp. nov., isolated from traditional Chinese yogurt

Three Gram-stain-positive bacterial strains, designated X0750^T, X0278 and X0401, isolated from traditional yogurt in Tibet Autonomous Region, PR China, were characterized by a polyphasic approach, including sequence analyses of the 16S rRNA gene and three housekeeping genes (pheS, rpoA and recA), determination of average nucleotide identity (ANI) and average amino acid identity (AAI), in silico DNA-DNA hybridization (isDDH), fatty acid methyl ester (FAME) analysis and phenotypic characterization. Strain X0750^T was phylogenetically related to the type strains of Weissella hellenica, Weissella bombi, Weissella paramesenteroides, Weissella jogaejeotgali, Weissella thailandensis, Weissella oryzae, Weissella cibaria and Weissella confusa, having 94.4-100 % 16S rRNA gene sequence similarities, 76.7-90.0 % pheS gene sequence similarities, 88.9-99.4 % rpoA gene sequence similarities and 77.6-92.8 % recA gene sequence similarities, respectively. ANI, isDDH and AAI values between strain X0750^T and type strains of phylogenetically related species were less than 90.4, 40.9 and 92.8 % respectively, confirming that strain X0750^T represents a novel species within the genus Weissella. Based upon the data obtained in the present study, a novel species, Weissella sagaensis sp. nov., is proposed and the type strain is X0750^T(=NCIMB 15192^T=CCM 8924^T=LMG 31184^T=CCTCC AB 2018403^T).

Weissella cryptocerci sp. nov., isolated from gut of the insect Cryptocercus kyebangensis

A taxonomic study of a Gram-stain-positive, rod-shaped, non-motile, non-spore-forming, catalase-negative bacterium, isolated from the gut of an insect, Cryptocercus kyebangensis collected from the mountainous area of Seoraksan, Yangyang-gun, Republic of Korea, was conducted. Its 16S rRNA gene sequence showed high similarity values to Weissella ghanensis LMG 24286^T (95.9 %), Weissella beninensis 2L24P13^T (95.9 %), Weissella fabalis M75^T (95.7 %) and Weissella fabaria 257^T (95.7 %). The phylogenetic tree indicated that the novel organism formed a cluster with W. ghanensis LMG 24286^T, W. beninensis 2L24P13^T, W. fabalis M75^T and W. fabaria 257^T. The G+C content was 41.1 mol% on the basis of the whole-genome sequence. Polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, two unidentified aminophospholipids, one unidentified phospholipid and four unidentified lipids. The major cellular fatty acids were C_18 : 1 ω9c, C_16 : 0, C_14 : 0, summed feature 8 (C_18 : 1ω7c and/or C_18 : 1ω6c) and summed feature 8 (C_16 : 1 ω7c and/or C_16 : 1 ω6c). The cell-wall peptidoglycan was of A4α type with the interpeptide bridge of Gly-d-Glu. Based on these results, strain 26KH-42^T could be classified as a novel species of the genus Weissella, for which the name Weissellacryptocerci sp. nov. is proposed. The type strain is 26KH-42^T (=KACC 18423^T=NBRC 113066^T).

Actinomadura roseirufa sp. nov., producer of semduramicin, a polyether ionophore

The taxonomic position of 'Actinomadura roseorufa' LMG 30035^T, a semduramicin-producing mutant of strain ATCC 53666^P, which was isolated from a soil sample collected in Yamae Village, Kamamoto, Japan, was clarified in the present study using a polyphasic approach. This Gram-positive, aerobic actinomycete formed a well-developed, extensively branched, non-fragmenting substrate and aerial mycelia which differentiated into single, smooth-appearing spores. Based on analysis of nearly complete 16S rRNA gene sequence, strain LMG 30035^T was found to be closely related to the type strains of Actinomadura fibrosa ATCC 49459^T (98.88 %) and Actinomadura formosensis JCM 7474^T (98.82 %) (pairwise similarity values in parentheses). Digital DNA-DNA hybridisation experiments revealed unambiguously that strain LMG 30035^T represents a novel Actinomadura species (OrthoANIu values less than 83.1 %; dDDH values less than 27.2 % with type strains of validly named Actinomadura species). Analysis of the cell wall revealed the presence of meso-diaminopimelic acid in the peptidoglycan. The whole-cell sugars were glucose, madurose, galactose, ribose and rhamnose. The major polar lipids included phosphatidylinositol and diphosphatidylglycerol. The predominant menaquinones were MK-9(H₆), MK-9(H₈), MK-9(H₄) and MK-9(H₂). The major fatty acids were C_16 : 00, 10-methyl C_18 : 0, C_18 : 1  ω9c and C_18 : 00. The DNA G+C content of its genome was 72.5 mol%. In summary, these characteristics distinguish strain LMG 30035^T from validly named species of the genus Actinomadura, and therefore, we propose to classify this strain formally as the novel species Actinomadura roseirufa sp. nov. with LMG 30035^T (=CECT 9808^T,=ATCC 53664^T) as the type strain.

Linking cocoa varietals and microbial diversity of Nicaraguan fine cocoa bean fermentations and their impact on final cocoa quality appreciation

Nicaraguan cocoa bean fermentations of several single local cocoa varieties originating from the same region (North Highlands of Nicaragua, San Jose de Bocay/El Cuá) were compared to fermentations of blended cocoa varietals from other producing regions of the country (Waslala and Nueva Guinea) making use of High Throughput Sequencing techniques, metabolite target analysis and sensory evaluation of cocoa liquor samples. A succession of the important cocoa-related yeasts Hanseniaspora uvarum/opuntiae, Saccharomyces cerevisiae and/or Pichia kudriavzevii was seen for single varietals and Nueva Guinea fermentations, while Kazachstania humilis dominated the mid and end phase of the Waslala cocoa fermentations. Tatumella species (mainly Tatumella terrea and Tatumella punctata) predominated the bacterial community at the onset of all fermentations followed by unusually late (generally 2 days into the fermentations) appearance of Lactobacillus fermentum relative to fermentations in other parts of the World. Acetobacter spp. were the main acetic acid bacteria during all fermentations, but also Gluconobacter spp. were involved in some single-variety fermentations. All fermentations proved complete as determined by metabolite analysis with bean sucrose being fully depleted and pulp sugars exhausted after 48-72 h of fermentation. From an organoleptic point of view, all Nicaraguan cocoas of this study reflected fine fruity (citrus or berry-like) flavours with distinct herbal or caramel notes. Floral notes were associated with the cases where P. kudriavzevii was involved in the later stages of fermentation. Intense citrus/fruity character was related to high pulp and bean citrate concentrations. Off-notes were found in some over-fermented batches where Bacillus spp. was detected. No relation between cut-test results and organoleptic appreciation was seen.

Genetic and technological characterization of lactic acid bacteria isolated from tropically grown fruits and vegetables

Phyllosphere microorganisms are common contaminants of fruit or vegetable containing foods. The aim of this study was to identify and characterize lactic acid bacteria isolated from fruits and vegetables from Reunion Island, regarding possible application in food. Among 77 isolates, a large diversity of species was observed, with isolates belonging to Lactobacillus plantarum (3 isolates), other species of Lactobacillus (3), Lactococcus lactis (13), Leuconostoc pseudomesenteroides (25), Leuconostoc lactis (1), Leuconostoc mesenteroides (7), Leuconostoc citreum (14), Weissella cibaria (4), Weissella confusa (4), other species of Weissella (2) and Fructobacillus tropaeoli (1). Several of these species, although belonging to lactic acid bacteria, are poorly characterized, because of their low occurrence in dairy products. Lactobacillus, Lactococcus, Leuconostoc and Weissella isolates were classified by (GTG)₅ fingerprinting in 3, 6, 21 and 10 genetic groups, respectively, suggesting a large intra-species diversity. Several Weissella and Lactobacillus isolates were particularly tolerant to acid and osmotic stress, whereas Lc. pseudomesenteroides 60 was highly tolerant to oxidative stress. Isolates of Weissella 30, 64 and 58, Leuconostoc 60 and 12b, Lactobacillus 75 and Fructobacillus 77 present relevant characteristics for their use as starters or as preservative cultures for fruits and vegetables.

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.

Temporal and Spatial Distribution of the Acetic Acid Bacterium Communities throughout the Wooden Casks Used for the Fermentation and Maturation of Lambic Beer Underlines Their Functional Role

Few data have been published on the occurrence and functional role of acetic acid bacteria (AAB) in lambic beer production processes, mainly due to their difficult recovery and possibly unknown role. Therefore, a novel aseptic sampling method, spanning both the spatial and temporal distributions of the AAB and their substrates and metabolites, was combined with a highly selective medium and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) as a high-throughput dereplication method followed by comparative gene sequencing for their isolation and identification, respectively. The AAB (Acetobacter species more than Gluconobacter species) proliferated during two phases of the lambic beer production process, represented by Acetobacter orientalis during a few days in the beginning of the fermentation and Acetobacter pasteurianus from 7 weeks until 24 months of maturation. Competitive exclusion tests combined with comparative genomic analysis of all genomes of strains of both species available disclosed possible reasons for this successive dominance. The spatial analysis revealed that significantly higher concentrations of acetic acid (from ethanol) and acetoin (from lactic acid) were produced at the tops of the casks, due to higher AAB counts and a higher metabolic activity of the AAB species at the air/liquid interface during the first 6 months of lambic beer production. In contrast, no differences in AAB species diversity occurred throughout the casks.IMPORTANCE Lambic beer is an acidic beer that is the result of a spontaneous fermentation and maturation process. Acidic beers are currently attracting attention worldwide. Part of the acidity of these beers is caused by acetic acid bacteria (AAB). However, due to their difficult recovery, they were never investigated extensively regarding their occurrence, species diversity, and functional role in lambic beer production. In the present study, a framework was developed for their isolation and identification using a novel aseptic sampling method in combination with matrix-assisted laser desorption ionization-time of flight mass spectrometry as a high-throughput dereplication technique followed by accurate molecular identification. The sampling method applied enabled us to take spatial differences into account regarding both enumerations and metabolite production. In this way, it was shown that more AAB were present and more acetic acid was produced at the air/liquid interface during a major part of the lambic beer production process. Also, two different AAB species were encountered, namely, Acetobacter orientalis at the beginning and Acetobacter pasteurianus in a later stage of the production process. This developed framework could also be applied for other fermentation processes.

Lactobacillus panisapium sp. nov., from honeybee Apis cerana bee bread

A novel facultatively anaerobic, Gram-stain-positive, non-motile, non-spore-forming, catalase-negative bacterium of the genus Lactobacillus, designated strain Bb 2-3^T, was isolated from bee bread of Apis cerana collected from a hive in Kunming, China. The strain was regular rod-shaped. Optimal growth occurred at 37 °C, pH 6.5 with 5.0 g l⁻¹ NaCl. The predominant fatty acids were C_18 : 1ω9c, C_16 : 0 and C_19 : 0 iso. Respiratory quinones were not detected. Seven glycolipids, three lipids, phosphatidylglycerol and diphosphatidylglycerol were detected. The peptidoglycan type A4α l-Lys-d-Asp was determined. Strain Bb 2-3^T was closely related to Lactobacillus bombicola DSM 28793^T, Lactobacillus apis LMG 26964^T and Lactobacillus helsingborgensis DSM 26265^T, with 97.8, 97.6 and 97.0 % 16S rRNA gene sequence similarity, respectively. A comparison of two housekeeping genes, rpoA and pheS, revealed that strain Bb 2-3^T was well separated from the reference strains of species of the genus Lactobacillus. The average nucleotide identity between strain Bb 2-3^T and the type strains of closely related species was lower than the 95–96 % threshold value for delineation of genomic prokaryotic species. The G+C content of the genomic DNA of strain Bb 2-3^T was 37.4 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic analyses, strain Bb 2-3^T is proposed to represent a novel species of the genus Lactobacillus, for which we propose the name Lactobacillus panisapium sp. nov. The type strain is Bb 2-3^T (=DSM 102188^T=ACCC 19955^T).

Why Are Weissella spp. Not Used as Commercial Starter Cultures for Food Fermentation?

Among other fermentation processes, lactic acid fermentation is a valuable process which enhances the safety, nutritional and sensory properties of food. The use of starters is recommended compared to spontaneous fermentation, from a safety point of view but also to ensure a better control of product functional and sensory properties. Starters are used for dairy products, sourdough, wine, meat, sauerkraut and homemade foods and beverages from dairy or vegetal origin. Among lactic acid bacteria, Lactobacillus, Lactococcus, Leuconostoc, Streptococcus and Pediococcus are the majors genera used as starters whereas Weissella is not. Weissella spp. are frequently isolated from spontaneous fermented foods and participate to the characteristics of the fermented product. They possess a large set of functional and technological properties, which can enhance safety, nutritional and sensory characteristics of food. Particularly, Weissella cibaria and Weissella confusa have been described as high producers of exo-polysaccharides, which exhibit texturizing properties. Numerous bacteriocins have been purified from Weissella hellenica strains and may be used as bio-preservative. Some Weissella strains are able to decarboxylate polymeric phenolic compounds resulting in a better bioavailability. Other Weissella strains showed resistance to low pH and bile salts and were isolated from healthy human feces, suggesting their potential as probiotics. Despite all these features, the use of Weissella spp. as commercial starters remained non-investigated. Potential biogenic amine production, antibiotic resistance pattern or infection hazard partly explains this neglecting. Besides, Weissella spp. are not recognized as GRAS (Generally Recognized As Safe). However, Weissella spp. are potential powerful starters for food fermentation as well as Lactococcus, Leuconostoc or Lactobacillus species.

Enhanced mannitol biosynthesis by the fruit origin strain Fructobacillus tropaeoli CRL 2034

Mannitol is a natural low-calorie sugar alcohol produced by certain (micro)organisms applicable in foods for diabetics due to its zero glycemic index. In this work, we evaluated mannitol production and yield by the fruit origin strain Fructobacillus tropaeoli CRL 2034 using response surface methodology with central composite design (CCD) as optimization strategy. The effect of the total saccharide (glucose + fructose, 1:2) content (TSC) in the medium (75, 100, 150, 200, and 225 g/l) and stirring (S; 50, 100, 200, 300 and 350 rpm) on mannitol production and yield by this strain was evaluated by using a 2² full-factorial CCD with 4 axial points (α = 1.5) and four replications of the center point, leading to 12 random experimental runs. Fermentations were carried out at 30 °C and pH 5.0 for 24 h. Minitab-15 software was used for experimental design and data analyses. The multiple response prediction analysis established 165 g/l of TSC and 200 rpm of S as optimal culture conditions to reach 85.03 g/l [95% CI (78.68, 91.39)] of mannitol and a yield of 82.02% [95% CI (71.98, 92.06)]. Finally, a validation experiment was conducted at the predicted optimum levels. The results obtained were 81.91 g/l of mannitol with a yield of 77.47% in outstanding agreement with the expected values. The mannitol 2-dehydrogenase enzyme activity was determined with 4.6-4.9 U/mg as the highest value found. To conclude, F. tropaeoli CRL 2034 produced high amounts of high-quality mannitol from fructose, being an excellent candidate for this polyol production.

Food Evolution: The Impact of Society and Science on the Fermentation of Cocoa Beans

Cocoa is part of the cultural heritage in many areas of South and Central America and has played an important role in the history of human culture there. The modern methods of cocoa bean production for the purpose of the manufacture of modern chocolate are tied to the origin and development of cocoa bean fermentation and processing methods and the science of microbiology. To date, however, there has not been a study that discusses the impacts of both science and culture on the evolution of cocoa beans and cocoa bean processing. This work provides both a detailed overview of the evolution and historical development of cocoa, from its earliest forms to modern chocolate manufacturing, an in-depth discussion of the biochemistry of cocoa bean fermentation, as well as a compilation of primary research studies with details on fermentation methods, the scientific bases of interactions in microbial fermentations, and methods for their investigation, as well as metabolites that are produced. As a result, we present here the major microorganisms among all the ones that have been identified in previous studies. This database will aid researchers seeking standardized inoculants to drive cocoa bean fermentation, as well as serve as a guide for inventorying and assessing other food evolution-related studies regarding traditional and artisanal-based food systems.

Weissella jogaejeotgali sp. nov., isolated from jogae jeotgal, a traditional Korean fermented seafood

Strain FOL01T was isolated from traditionally fermented Korean jogae jeotgal (fermented clams). Phylogenetic sequence analysis of the 16S rRNA gene from FOL01T revealed that it is closely related to Weissella thailandensis FS61-1T and Weissella paramesenteroides ATCC 33313T with 99.39 % and 98.50 % 16S rRNA gene sequence similarities, respectively. API and VITEK analyses showed that strain FOL01T could be separated from its nearest phylogenetic relatives with respect to carbohydrate fermentation and antibiotic resistance. Subsequent amplified rRNA gene restriction analysis of 16S rRNA genes and HaeIII-restriction enzyme profiling of genomic DNAs revealed different band patterns. In addition, DNA-DNA hybridization of genomic DNAs showed 63.9 % relatedness. Analysis of the composition of cellular fatty acids confirmed that strain FOL01T differs from its close relatives and supports the proposal to assign this organism to a novel species of the genus Weissella. Based on these results, strain FOL01T could be classified as a novel species of the genus Weissella, for which the name Weissella jogaejeotgali sp. nov. is proposed. The type strain is FOL01T ( = KCCM 43128T = JCM 30589T).

The genus Weissella: taxonomy, ecology and biotechnological potential

Bacteria assigned to the genus Weissella are Gram-positive, catalase-negative, non-endospore forming cells with coccoid or rod-shaped morphology (Collins et al., 1993; Björkroth et al., 2009, 2014) and belong to the group of bacteria generally known as lactic acid bacteria. Phylogenetically, the Weissella belong to the Firmicutes, class Bacilli, order Lactobacillales and family Leuconostocaceae (Collins et al., 1993). They are obligately heterofermentative, producing CO2 from carbohydrate metabolism with either d(-)-, or a mixture of d(-)- and l(+)- lactic acid and acetic acid as major end products from sugar metabolism. To date, there are 19 validly described Weissella species known. Weissella spp. have been isolated from and occur in a wide range of habitats, e.g., on the skin and in the milk and feces of animals, from saliva, breast milk, feces and vagina of humans, from plants and vegetables, as well as from a variety of fermented foods such as European sourdoughs and Asian and African traditional fermented foods. Thus, apart from a perceived technical role of certain Weissella species involved in such traditional fermentations, specific Weissella strains are also receiving attention as potential probiotics, and strain development of particularly W. cibaria strains is receiving attention because of their high probiotic potential for controlling periodontal disease. Moreover, W. confusa and W. cibaria strains are known to produce copius amounts of novel, non-digestible oligosaccharides and extracellular polysaccharides, mainly dextran. These polymers are receiving increased attention for their potential application as prebiotics and for a wide range of industrial applications, predominantly for bakeries and for the production of cereal-based fermented functional beverages. On the detrimental side, strains of certain Weissella species, e.g., of W. viridescens, W. cibaria and W. confusa, are known as opportunistic pathogens involved in human infections while strains of W. ceti have been recently recongnized as etiological agent of "weissellosis," which is a disease affecting farmed rainbow trouts. Bacteria belonging to this species thus are important both from a technological, as well as from a medical point of view, and both aspects should be taken into account in any envisaged biotechnological applications.

Bifidobacterium commune sp. nov. isolated from the bumble bee gut

Bifidobacteria were isolated from the gut of Bombus lapidarius, Bombus terrestris and Bombus hypnorum bumble bees by direct isolation on modified trypticase phytone yeast extract agar. The MALDI-TOF MS profiles of four isolates (LMG 28292(T), R-53560, R-53124, LMG 28626) were found to be identical and did not cluster with the profiles of established Bifidobacterium species. Analysis of the 16S rRNA gene sequence of strain LMG 28292(T) revealed that LMG 28292(T) is most closely related to the Bifidobacterium bohemicum type strain (96.8%), which was also isolated from bumble bee gut specimens. The hsp60 gene of strain LMG 28292(T) shows 85.8% sequence similarity to that of the B. bohemicum type strain. The (GTG)5-PCR profiles and the hsp60 sequences of all four isolates were indistinguishable; however, three different phenotypes were observed among the four isolates by means of the API 50CHL microtest system. Based on the phylogenetic, genotypic and phenotypic data, we propose to classify the four isolates within the novel species Bifidobacterium commune sp. nov., with LMG 28292(T) (= DSM 28792(T)) as the type strain.

Bombella intestini gen. nov., sp. nov., an acetic acid bacterium isolated from bumble bee crop

In the frame of a bumble bee gut microbiota study, acetic acid bacteria (AAB) were isolated using a combination of direct isolation methods and enrichment procedures. MALDI-TOF MS profiling of the isolates and a comparison of these profiles with profiles of established AAB species identified most isolates as Asaia astilbis or as ‘Commensalibacter intestini’, except for two isolates (R-52486 and LMG 28161T) that showed an identical profile. A nearly complete 16S rRNA gene sequence of strain LMG 28161T was determined and showed the highest pairwise similarity to Saccharibacter floricola S-877T (96.5 %), which corresponded with genus level divergence in the family Acetobacteraceae . Isolate LMG 28161T was subjected to whole-genome shotgun sequencing; a 16S–23S rRNA internal transcribed spacer (ITS) sequence as well as partial sequences of the housekeeping genes dnaK, groEL and rpoB were extracted for phylogenetic analyses. The obtained data confirmed that this isolate is best classified into a new genus in the family Acetobacteraceae . The DNA G+C content of strain LMG 28161T was 54.9 mol%. The fatty acid compositions of isolates R-52486 and LMG 28161T were similar to those of established AAB species [with C18 : 1ω7c (43.1 %) as the major component], but the amounts of fatty acids such as C19 : 0 cyclo ω8c, C14 : 0 and C14 : 0 2-OH enabled to differentiate them. The major ubiquinone was Q-10. Both isolates could also be differentiated from the known genera of AAB by means of biochemical characteristics, such as their inability to oxidize ethanol to acetic acid, negligible acid production from melibiose, and notable acid production from d-fructose, sucrose and d-mannitol. In addition, they produced 2-keto-d-gluconate, but not 5-keto-d-gluconate from d-glucose. Therefore, the name Bombella intestini gen nov., sp. nov. is proposed for this new taxon, with LMG 28161T ( = DSM 28636T = R-52487T) as the type strain of the type species.

Weissella uvarum sp. nov., isolated from wine grapes

Two bacterial strains (B18BM42(T) and B18NM6) were recovered during a study of bacterial diversity on wine grapes (Vitis vinifera L.) from the Nemea region in Greece. Phylogenetic analysis based on 16S rRNA gene sequences placed the two strains within the genus Weissella, and found them to be most closely related to Weissella minor NRIC 1625(T) followed by Weissella viridescens NRIC 1536(T) (99.1 and 98.9% sequence similarity, respectively). The level of DNA-DNA relatedness between strains B18NM42(T) and W. minor NRIC 1625(T) or W. viridescens NRIC 1536(T) was 31.9 and 35.0%, respectively. The two novel strains could be genetically differentiated from their closest relatives by REA-PFGE (restriction enzyme analysis-pulse field gel electrophoresis), RAPD (randomly amplified polymorphic DNA) and rep-PC R analyses (repetitive sequence-based PCR). Physiological examination showed that the novel strains can be distinguished from phylogenetically related species by their ability to grow at 42 °C and by certain carbohydrate fermentations. Based on the evidence above, the affiliation of the two strains to a novel species with the proposed name Weissella uvarum sp. nov. is suggested. The type strain is B18NM42(T) ( =DSM 28060(T) =NCCB 100484(T)).

Bacteriophages of leuconostoc, oenococcus, and weissella

Leuconostoc (Ln.), Weissella, and Oenococcus form a group of related genera of lactic acid bacteria, which once all shared the name Leuconostoc. They are associated with plants, fermented vegetable products, raw milk, dairy products, meat, and fish. Most of industrially relevant Leuconostoc strains can be classified as either Ln. mesenteroides or Ln. pseudomesenteroides. They are important flavor producers in dairy fermentations and they initiate nearly all vegetable fermentations. Therefore, bacteriophages attacking Leuconostoc strains may negatively influence the production process. Bacteriophages attacking Leuconostoc strains were first reported in 1946. Since then, the majority of described Leuconostoc phages was isolated from either dairy products or fermented vegetable products. Both lytic and temperate phages of Leuconostoc were reported. Most of Leuconostoc phages examined using electron microscopy belong to the Siphoviridae family and differ in morphological details. Hybridization and comparative genomic studies of Leuconostoc phages suggest that they can be divided into several groups, however overall diversity of Leuconostoc phages is much lower as compared to, e.g., lactococcal phages. Several fully sequenced genomes of Leuconostoc phages have been deposited in public databases. Lytic phages of Leuconostoc can be divided into two host species-specific groups with similarly organized genomes that shared very low nucleotide similarity. Phages of dairy Leuconostoc have rather limited host-ranges. The receptor binding proteins of two lytic Ln. pseudomesenteroides phages have been identified. Molecular tools for detection of dairy Leuconostoc phages have been developed. The rather limited data on phages of Oenococcus and Weissella show that (i) lysogeny seems to be abundant in Oenococcus strains, and (ii) several phages infecting Weissella cibaria are also able to productively infect strains of other Weissella species and even strains of the genus Lactobacillus.

Acetobacter sicerae sp. nov., isolated from cider and kefir, and identification of species of the genus Acetobacter by dnaK, groEL and rpoB sequence analysis

Five acetic acid bacteria isolates, awK9_3, awK9_4 ( = LMG 27543), awK9_5 ( = LMG 28092), awK9_6 and awK9_9, obtained during a study of micro-organisms present in traditionally produced kefir, were grouped on the basis of their MALDI-TOF MS profile with LMG 1530 and LMG 1531(T), two strains currently classified as members of the genus Acetobacter. Phylogenetic analysis based on nearly complete 16S rRNA gene sequences as well as on concatenated partial sequences of the housekeeping genes dnaK, groEL and rpoB indicated that these isolates were representatives of a single novel species together with LMG 1530 and LMG 1531(T) in the genus Acetobacter, with Acetobacter aceti, Acetobacter nitrogenifigens, Acetobacter oeni and Acetobacter estunensis as nearest phylogenetic neighbours. Pairwise similarity of 16S rRNA gene sequences between LMG 1531(T) and the type strains of the above-mentioned species were 99.7%, 99.1%, 98.4% and 98.2%, respectively. DNA-DNA hybridizations confirmed that status, while amplified fragment length polymorphism (AFLP) and random amplified polymorphic DNA (RAPD) data indicated that LMG 1531(T), LMG 1530, LMG 27543 and LMG 28092 represent at least two different strains of the novel species. The major fatty acid of LMG 1531(T) and LMG 27543 was C18 : 1ω7c. The major ubiquinone present was Q-9 and the DNA G+C contents of LMG 1531(T) and LMG 27543 were 58.3 and 56.7 mol%, respectively. The strains were able to grow on D-fructose and D-sorbitol as a single carbon source. They were also able to grow on yeast extract with 30% D-glucose and on standard medium with pH 3.6 or containing 1% NaCl. They had a weak ability to produce acid from d-arabinose. These features enabled their differentiation from their nearest phylogenetic neighbours. The name Acetobacter sicerae sp. nov. is proposed with LMG 1531(T) ( = NCIMB 8941(T)) as the type strain.

The microbial diversity of traditional spontaneously fermented lambic beer

Lambic sour beers are the products of a spontaneous fermentation that lasts for one to three years before bottling. The present study determined the microbiota involved in the fermentation of lambic beers by sampling two fermentation batches during two years in the most traditional lambic brewery of Belgium, using culture-dependent and culture-independent methods. From 14 samples per fermentation, over 2000 bacterial and yeast isolates were obtained and identified. Although minor variations in the microbiota between casks and batches and a considerable species diversity were found, a characteristic microbial succession was identified. This succession started with a dominance of Enterobacteriaceae in the first month, which were replaced at 2 months by Pediococcus damnosus and Saccharomyces spp., the latter being replaced by Dekkera bruxellensis at 6 months fermentation duration.

Acetobacter lambici sp. nov., isolated from fermenting lambic beer

An acetic acid bacterium, strain LMG 27439T, was isolated from fermenting lambic beer. The cells were Gram-stain-negative, motile rods, catalase-positive and oxidase-negative. Analysis of the 16S rRNA gene sequence revealed the strain was closely related to Acetobacter okinawensis (99.7 % 16S rRNA gene sequence similarity with the type strain of this species), A. ghanensis (99.6 %), A. syzygii (99.6 %), A. fabarum (99.4 %) and A. lovaniensis (99.2 %). DNA–DNA hybridization with the type strains of these species revealed moderate DNA–DNA hybridization values (31–45 %). Strain LMG 27439T was unable to grow on glycerol or methanol as the sole carbon source, on yeast extract with 10 % ethanol or on glucose-yeast extract medium at 37 °C. It did not produce acid from l-arabinose, d-galactose or d-mannose, nor did it produce 2-keto-d-gluconic acid, 5-keto-d-gluconic acid or 2,5-diketo-d-gluconic acid from d-glucose. It did not grow on ammonium as the sole nitrogen source and ethanol as the sole carbon source. These genotypic and phenotypic data distinguished strain LMG 27439T from established species of the genus Acetobacter , and therefore we propose this strain represents a novel species of the genus Acetobacter . The name Acetobacter lambici sp. nov. is proposed, with LMG 27439T ( = DSM 27328T) as the type strain.

Gluconobacter cerevisiae sp. nov., isolated from the brewery environment

Three strains, LMG 27748T, LMG 27749 and LMG 27882 with identical MALDI-TOF mass spectra were isolated from samples taken from the brewery environment. Analysis of the 16S rRNA gene sequence of strain LMG 27748T revealed that the taxon it represents was closely related to type strains of the species Gluconobacter albidus (100 % sequence similarity), Gluconobacter kondonii (99.9 %), Gluconobacter sphaericus (99.9 %) and Gluconobacter kanchanaburiensis (99.5 %). DNA–DNA hybridization experiments on the type strains of these species revealed moderate DNA relatedness values (39–65 %). The three strains used d-fructose, d-sorbitol, meso-erythritol, glycerol, l-sorbose, ethanol (weakly), sucrose and raffinose as a sole carbon source for growth (weak growth on the latter two carbon sources was obtained for strains LMG 27748T and LMG 27882). The strains were unable to grow on glucose-yeast extract medium at 37 °C. They produced acid from meso-erythritol and sucrose, but not from raffinose. d-Gluconic acid, 2-keto-d-gluconic acid and 5-keto-d-gluconic acid were produced from d-glucose, but not 2,5-diketo-d-gluconic acid. These genotypic and phenotypic characteristics distinguish strains LMG 27748T, LMG 27749 and LMG 27882 from species of the genus Gluconobacter with validly published names and, therefore, we propose classifying them formally as representatives of a novel species, Gluconobacter cerevisiae sp. nov., with LMG 27748T ( = DSM 27644T) as the type strain.