Weissella ghanensis sp. nov., isolated from a Ghanaian cocoa fermentation

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.

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.

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.

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.

Predictive Microbial Community and Functional Gene Expression Profiles in Pineapple Peel Fermentation Using 16S rRNA Gene Sequences

Pineapple peel (PP) is a by-product with the potential to be used as a raw material for functional beverages. Traditional PP fermentation has so far paid little attention to the microbial community and its role in the fermentation process. As a result, the current research looked into the microbial communities and their roles during PP fermentation. A metagenomic approach based on the 16S rRNA sequencing data was used to assess the microbial communities. Subsequent analysis was performed using PICRUSt (phylogenetic investigation of communities by reconstruction of unobserved states) to analyze the microbial functions in the fermentation system. The microecology of the fermentation process in three samples was predominated by Firmicutes. Furthermore, the well-known probiotic genera Weissella, Lactobacillus, and Lactococcus were found to be predominating in the gumer, promic, and control samples, respectively. It was obvious that microenvironmental differences have an effect on the microbial composition of PP fermentation. Moreover, functional prediction revealed that carbohydrate metabolism was the most prevalent metabolic pathway during the fermentation process. Additionally, it was discovered that all of the bacteria found in the samples played significant roles in carbohydrate, amino acid, vitamin, and co-factor metabolism, which can be inferred to result in the production of beneficial metabolites.

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.

Dissecting industrial fermentations of fine flavour cocoa through metagenomic analysis

The global demand for fine-flavour cocoa has increased worldwide during the last years. Fine-flavour cocoa offers exceptional quality and unique fruity and floral flavour attributes of high demand by the world's elite chocolatiers. Several studies have highlighted the relevance of cocoa fermentation to produce such attributes. Nevertheless, little is known regarding the microbial interactions and biochemistry that lead to the production of these attributes on farms of industrial relevance, where traditional fermentation methods have been pre-standardized and scaled up. In this study, we have used metagenomic approaches to dissect on-farm industrial fermentations of fine-flavour cocoa. Our results revealed the presence of a shared core of nine dominant microorganisms (i.e. Limosilactobacillus fermentum, Saccharomyces cerevisiae, Pestalotiopsis rhododendri, Acetobacter aceti group, Bacillus subtilis group, Weissella ghanensis group, Lactobacillus_uc, Malassezia restricta and Malassezia globosa) between two farms located at completely different agro-ecological zones. Moreover, a community metabolic model was reconstructed and proposed as a tool to further elucidate the interactions among microorganisms and flavour biochemistry. Our work is the first to reveal a core of microorganisms shared among industrial farms, which is an essential step to process engineering aimed to design starter cultures, reducing fermentation times, and controlling the expression of undesirable phenotypes.

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.

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.

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).

Phylogenetic Analyses of pheS, dnaA and atpA Genes for Identification of Weissella confusa and Weissella cibaria Isolated from a South African Sugarcane Processing Factory

A previous study reported on the isolation of 430 polysaccharide (gum)-producing bacteria from a South African sugarcane processing factory and the identification of isolates by comparative 16S rRNA gene sequencing. A large number of isolates (202) belonged to the genus Weissella and clustered with reference strains of Weissella cibaria and Weissella confusa. In this study, we identified 147 strains as W. cibaria and 55 as W. confusa based on phylogenetic analyses of pheS and dnaA gene sequences of representative isolates. We also included atpA gene sequence analysis of Weissella isolates as potential future phylogenetic marker to differentiate amongst strains of W. cibaria and W. confusa.

Weissella, a novel lactic acid bacteria isolated from wild Sumatran orangutans (Pongo abelii)

Aims

This study aimed to isolate and identify lactic acid bacteria (LAB) in wild Sumatran orangutans to provide more information about LAB diversity derived from Sumatran orangutan feces.

Materials and Methods

Fecal sampling from three female orangutans, around 35 years old, was carried out in the wild forest areas at the research station of Suaq Belimbing Gunung Leuser National Park located in the South Aceh district. Orangutan fecal samples were taken in the morning when the orangutans first defecated. The orangutans were above the tree, which is approximately 12-15 m from the ground where feces were found.

Results

Fermentation testing using the API 50 CHL Kit showed that OUL4 isolates were identified as Lactococcus lactis ssp. lactis with an identity value of 73.5%. Homology analysis demonstrated that the OUL4 isolates have 93% similarity to Weissella cibaria, and phylogenetic trees constructed using Mega 7.0 also showed that OUL4 isolates are related to W. cibaria.

Conclusion

These results show that there is a difference in identification between biochemical testing with API kits and molecular analyses on LAB isolates from wild Sumatran orangutans. Based on 16S rRNA gene homology, the OUL4 LAB isolates from wild Sumatran orangutans have 93% homology to W. cibaria.

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.

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.

Review: Diversity of Microorganisms in Global Fermented Foods and Beverages

Culturalable and non-culturable microorganisms naturally ferment majority of global fermented foods and beverages. Traditional food fermentation represents an extremely valuable cultural heritage in most regions, and harbors a huge genetic potential of valuable but hitherto undiscovered strains. Holistic approaches for identification and complete profiling of both culturalable and non-culturable microorganisms in global fermented foods are of interest to food microbiologists. The application of culture-independent technique has thrown new light on the diversity of a number of hitherto unknown and non-cultural microorganisms in naturally fermented foods. Functional bacterial groups ("phylotypes") may be reflected by their mRNA expression in a particular substrate and not by mere DNA-level detection. An attempt has been made to review the microbiology of some fermented foods and alcoholic beverages of the world.

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.

Responses of microbial community and acidogenic intermediates to different water regimes in a hybrid solid anaerobic digestion system treating food waste

This study investigated the effects of different water regimes in an acidogenic leach bed reactor (LBR) during 16-day batch mode food waste digestion. LBRs were operated under five water replacement ratios (WRRs) (100%, 75%, 50%, 25% and 5% in LBRs R1, R2, R3, R4 and R5, respectively) and methanogenic effluent (ME) addition with two leachate recirculation frequencies (once in 24 h and 12 h in LBRs R6 and R7, respectively). Results showed that 50-100% WRRs accelerated the hydrolysis and acidogenesis with butyrate as the dominant product (∼35% of COD); whereas 5-25% WRRs promoted propionate production. The ME recirculation enhanced protein decomposition and reduced ethanol production. Lactobacillus dominated in LBRs with water addition (R1-R5), while Clostridium and hetero-fermenting lactic acid bacteria dominated in LBR with ME addition (R7). The highest volatile solid degradation (82.9%) and methane yield (0.29 L-CH4/g VS) were obtained with ME addition at 0.7 d hydraulic retention time.

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)).

Weissella viridescens in meat products – a review

Although ubiquitous, bacteria of theWeissellagenus are not given sufficient attention. Many members of the genus were originally classified asLeuconostocorLactobacillus. With the development of molecular methods, these phylogenetically closely related bacteria formed a separate group, theWeissellagenus. Due to its heterofermentative metabolism,Weissellaspp. may cause considerable damage particularly in the meat industry. Slime formation and greening of meat products are sensory defects for which the technologically important speciesWeissella viridescensis responsible. This article summarizes basic information about the influence ofWeissella viridescenson meat processing.

Weissella diestrammenae sp. nov., isolated from the gut of a camel cricket (Diestrammena coreana)

A novel, Gram-stain-positive, non-motile, facultatively anaerobic, rod- or coccoid-shaped bacterium, designated strain ORY33T, was isolated from the gut of a camel cricket (Diestrammena coreana). The 16S rRNA gene sequence analysis showed that strain ORY33T belonged to the genus Weissella , with highest sequence similarity to Weissella koreensis S-5623T (97.7 %). The strain grew optimally at 30 °C and pH 7 in the presence of 0 % (w/v) NaCl. Catalase and oxidase activities were negative. The genomic DNA G+C content of strain ORY33T was 45.1 mol%. DNA–DNA hybridization values between strain ORY33T and closely related members of the genus Weissella were less than 27 %. The major fatty acids of strain ORY33T were C18 : 1ω9c, C16 : 0 and C14 : 0. Based on these phenotypic, phylogenetic and genotypic analyses, strain ORY33T represents a novel species belonging to the genus Weissella , for which the name Weissella diestrammenae sp. nov. is proposed. The type strain is ORY33T ( = KACC 16890T = JCM 18559T).

Weissella oryzae sp. nov., isolated from fermented rice grains

A taxonomic study was conducted on two Gram-reaction-positive, catalase-negative, irregular short-rod-shaped or coccoid lactic acid bacteria, designated strains SG25T and SG23, that were isolated from grains of fermented Japanese rice (Oryza sativa L. subsp. japonica). A phylogenetic analysis based on 16S rRNA gene sequence data clearly showed that the strains belonged to the genus Weissella and were most closely related to Weissella soli LMG 20113T (with a sequence similarity of 96.9 % for each novel strain). The peptidoglycan of each strain contained the amino acids glutamic acid, lysine, serine and alanine in a molar ratio of 1.0 : 1.2 : 0.5 : 3.0, respectively. On the basis of the unusual phenotypic characteristics of the novel strains and the low levels of DNA–DNA relatedness recorded between each novel strain and Weissella soli JCM 12536T, strains SG25T and SG23 represent a single novel species in the genus Weissella , for which the name Weissella oryzae sp. nov. is proposed. The type strain is SG25T ( = JCM 18191T  = DSM 25784T).

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

Six facultatively anaerobic, non-motile lactic acid bacteria were isolated from spontaneous cocoa bean fermentations carried out in Brazil, Ecuador and Malaysia. Phylogenetic analysis revealed that one of these strains, designated M75(T), isolated from a Brazilian cocoa bean fermentation, had the highest 16S rRNA gene sequence similarity towards Weissella fabaria LMG 24289(T) (97.7%), W. ghanensis LMG 24286(T) (93.3%) and W. beninensis LMG 25373(T) (93.4%). The remaining lactic acid bacteria isolates, represented by strain M622, showed the highest 16S rRNA gene sequence similarity towards the type strain of Fructobacillus tropaeoli (99.9%), a recently described species isolated from a flower in South Africa. pheS gene sequence analysis indicated that the former strain represented a novel species, whereas pheS, rpoA and atpA gene sequence analysis indicated that the remaining five strains belonged to F. tropaeoli; these results were confirmed by DNA-DNA hybridization experiments towards their respective nearest phylogenetic neighbours. Additionally, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry proved successful for the identification of species of the genera Weissella and Fructobacillus and for the recognition of the novel species. We propose to classify strain M75(T) ( = LMG 26217(T)  = CCUG 61472(T)) as the type strain of the novel species Weissella fabalis sp. nov.

Carnobacterium iners sp. nov., a psychrophilic, lactic acid-producing bacterium from the littoral zone of an Antarctic pond

Two lactic acid-producing, Gram-stain-positive rods were isolated from a microbial mat actively growing in the littoral zone of an Antarctic lake (Forlidas Pond) in the Pensacola mountains and studied using a polyphasic taxonomic approach. The isolates were examined by phylogenetic analysis of the 16S rRNA gene, multilocus sequence analysis of pheS, rpoA and atpA, and biochemical and genotypic characteristics. One strain, designated LMG 26641, belonged to Carnobacterium alterfunditum and the other strain, designated LMG 26642(T), could be assigned to a novel species, with Carnobacterium funditum DSM 5970(T) as its closest phylogenetic neighbour (99.2 % 16S rRNA gene sequence similarity). Carnobacterium iners sp. nov. could be distinguished biochemically from other members of the genus Carnobacterium by the lack of acid production from carbohydrates. DNA-DNA relatedness confirmed that strain LMG 26642(T) represented a novel species, for which we propose the name Carnobacterium iners sp. nov. (type strain is LMG 26642(T)  = CCUG 62000(T)).

Identification of lactic acid bacteria isolated during traditional fura processing in Ghana

Fura is a millet-based spontaneously fermented dumpling produced and consumed in parts of West Africa, particularly Nigeria, Burkina Faso and Ghana. From eight traditional fura production sites in northern Ghana, 862 lactic acid bacteria were isolated and identified to species level using a combination of genotypic and phenotypic methods including (GTG)(5)-based PCR fingerprinting and 16S rRNA gene sequencing, multiplex PCR by means of recA gene sequence comparison, conventional morphological characteristics and carbohydrate fermentation profiling. During millet dough fermentation, pH decreased from 5.6-6.4 to 4.1-3.7 and total lactic acid bacteria (LAB) counts increased from 4.4-5.3 to 7.9-9.2 log(10) (cfu/g). The initial stages of the fermentation were characterized by co-dominance of homo- and heterofermentative species of Pediococcus acidilactici, Weisella confusa, Lactobacillus fermentum, Lactobacillus reuteri, Lactobacillus salivarius, and Lactobacillus paraplantarum whereas L. fermentum was dominating at the end of the fermentation. L. fermentum was predominant in all fermentations (p < 0.05) and a high uniformity was observed among production sites regarding the dominance of L. fermentum. L. fermentum and W. confusa were isolated in all production sites and almost at all fermentation stages indicating that they are indigenous to traditional fura processing. The other LAB bacteria species which comprised a minor proportion of the total LAB occurred occasionally and in an irregular pattern among the production sites.

Weissella sp. outbreaks in commercial rainbow trout (Oncorhynchus mykiss) farms in Brazil

The genus Weissella contains 14 bacterial species that usually occur in nutrient-rich environments and in fermented foods and beverages. Outbreaks of hemorrhagic septicemia were reported in three commercial rainbow trout (Oncorhynchus mykiss) farms in Brazil in 2008 and 2009. Seventy-seven Gram-positive isolates were obtained from 41 diseased fish from these farms. The bacterial strains were identified as Weissella at the genus level using biochemical tests, Weissella genus-specific PCR, and 16S rRNA sequencing. To evaluate potential routes of infection, rainbow trout juveniles were experimentally infected with the pathogen. In addition, the resistance of the pathogen to five antibiotics was tested, and provisional epidemiological cut-off values were calculated using the normalized resistance interpretation (NRI). All isolates presented similar phenotypic profiles and positive reactions for Weissella genus-specific PCR. The 16S rRNA sequences of the Brazilian strains showed 100% similarity with sequences of Chinese isolates that previously were identified as the first case of Weissella sp. infection in fish. The disease was successfully reproduced in the laboratory by intraperitoneal injection, immersion, and cohabitation between diseased and healthy fish. All isolates were resistant to sulfonamide, and based on NRI analysis, one, two, and three isolates were classified as non-wild-type (NWT) for erythromycin, oxytetracycline, and norfloxacin, respectively. This is the first description of multiple cases of Weissella sp. infection in rainbow trout farms outside of China, of infectious routes for the disease, and of provisional epidemiological cut-off values for resistance of these bacteria to four antibiotics.

Interesting starter culture strains for controlled cocoa bean fermentation revealed by simulated cocoa pulp fermentations of cocoa-specific lactic acid bacteria

Among various lactic acid bacterial strains tested, cocoa-specific strains of Lactobacillus fermentum were best adapted to the cocoa pulp ecosystem. They fermented glucose to lactic acid and acetic acid, reduced fructose to mannitol, and converted citric acid into lactic acid and 2,3-butanediol.

Spontaneous organic cocoa bean box fermentations in Brazil are characterized by a restricted species diversity of lactic acid bacteria and acetic acid bacteria

Spontaneous organic cocoa bean box fermentations were carried out on two different farms in Brazil. Physical parameters, microbial growth, bacterial species diversity [mainly lactic acid bacteria (LAB) and acetic acid bacteria (AAB)], and metabolite kinetics were monitored, and chocolates were produced from the fermented dry cocoa beans. The main end-products of the catabolism of the pulp substrates (glucose, fructose, and citric acid) by yeasts, LAB, and AAB were ethanol, lactic acid, mannitol, and/or acetic acid. Lactobacillus fermentum and Acetobacter pasteurianus were the predominating bacterial species of the fermentations as revealed through (GTG)(5)-PCR fingerprinting of isolates and PCR-DGGE of 16S rRNA gene PCR amplicons of DNA directly extracted from fermentation samples. Fructobacillus pseudoficulneus, Lactobacillus plantarum, and Acetobacter senegalensis were among the prevailing species during the initial phase of the fermentations. Also, three novel LAB species were found. This study emphasized the possible participation of Enterobacteriaceae in the cocoa bean fermentation process. Tatumella ptyseos and Tatumella citrea were the prevailing enterobacterial species in the beginning of the fermentations as revealed by 16S rRNA gene-PCR-DGGE. Finally, it turned out that control over a restricted bacterial species diversity during fermentation through an ideal post-harvest handling of the cocoa beans will allow the production of high-quality cocoa and chocolates produced thereof, independent of the fermentation method or farm.

Weissella fabaria sp. nov., from a Ghanaian cocoa fermentation

Two lactic acid bacteria, strains 257T and 252, were isolated from traditional heap fermentations of Ghanaian cocoa beans. 16S rRNA gene sequence analysis of these strains allocated them to the genus Weissella, showing 99.5 % 16S rRNA gene sequence similarity towards Weissella ghanensis LMG 24286T. Whole-cell protein electrophoresis, fluorescent amplified fragment length polymorphism fingerprinting of whole genomes and biochemical tests confirmed their unique taxonomic position. DNA–DNA hybridization experiments towards their nearest phylogenetic neighbour demonstrated that the two strains represent a novel species, for which we propose the name Weissella fabaria sp. nov., with strain 257T (=LMG 24289T =DSM 21416T) as the type strain. Additional sequence analysis using pheS gene sequences proved useful for identification of all Weissella–Leuconostoc–Oenococcus species and for the recognition of the novel species.

Weissella beninensis sp. nov., a motile lactic acid bacterium from submerged cassava fermentations, and emended description of the genus Weissella

Four Gram-positive, catalase-negative, short rod-shaped or coccoid, heterofermentative lactic acid bacterial strains (2L24P13(T), 1L48P15, 1L24P31 and 1L24P34) with unusual phenotypic and genotypic properties were isolated from submerged fermenting cassava on MRS agar. All strains were motile, grew at 15 degrees C, produced dl-lactic acid from glucose with gas formation and produced ammonia from arginine. Acid was produced from d-fructose, d-galactose, d-glucose, lactose, maltose, d-mannose, melibiose, d-raffinose, sucrose, N-acetylglucosamine and d-mannitol, but not from d-arabinose or xylose. 16S rRNA gene sequence analysis revealed that the strains belonged to the genus Weissella and were most closely related to Weissella ghanensis LMG 24286(T). Low DNA-DNA reassociation values were obtained between the isolates and W. ghanensis DSM 19935(T). Based on the genetic and phenotypic results, the strains are considered to represent a novel species, for which the name Weissella beninensis sp. nov. is proposed. The type strain is 2L24P13(T) (=DSM 22752(T)=LMG 25373(T)).