Pediococcus spp.-mediated competition interaction within Daqu microbiota determines the temperature formation and metabolic profiles

Fermented microbiota is critical to the formation of microenvironment and metabolic profiles in spontaneous fermentation. Microorganisms generate a diverse array of metabolites concurrent with the release of heat energy. In the case of Daqu fermentation, the peak temperature exceeded 60°C, forming a typical high-temperature fermentation system known as high-temperature Daqu. However, microorganisms that cause the quality variation in Daqu and how they affect the functional microbiota and microenvironment in the fermentation process are not yet clear. This study adopted high-throughput sequencing and monitored the dynamic fluctuations of metabolites and environmental factors to identify the pivotal microorganism responsible for the alterations in interaction patterns of functional keystone taxa and quality decline in the fermentation system of different operational areas during the in situ fermentation process that had been mainly attributed to operational taxonomic unit (OTU)_22 (Pediococcus acidilactici). Additionally, we used isothermal microcalorimetry, plate inhibition experiments, and in vitro simulation fermentation experiments to explore the impact of Pediococcus spp. on heat generation, microorganisms, and metabolite profiles. Results showed the heat peak generated by Pediococcus spp. was significantly lower than that of Bacillus spp., filamentous fungi, and yeast. In addition, the preferential growth of P. acidilactici strain AA3 would obviously affect other strains to colonize through competition, and its metabolites made a significant impact on filamentous fungi. The addition of P. acidilactici strain AA3 in simulated fermentation would cause the loss of pyrazines and acids in metabolites. These evidences showed that the overgrowth of Pediococcus spp. greatly influenced the formation of high temperatures and compounds in solid-state fermentation systems. Our work illustrated the vital impact of interaction variability mediated by Pediococcus spp. for microbial assembly and metabolites, as well as in forming temperature. These results emphasized the functional role of Daqu microbiota in metabolites and heat production and the importance of cooperation in improving the fermentation quality.IMPORTANCEThe stable and high-quality saccharifying and fermenting starter in traditional solid-state fermentation was the prerequisite for liquor brewing. An imbalance of microbial homeostasis in fermentation can adversely impact production quality. Identification of such critical microorganisms and verifying their associations with other fermentation parameters pose a challenge in a traditional fermentation environment. To enhance the quality of spontaneous fermented products, strategies such as bioaugmentation or the control of harmful microorganisms would be employed. This work started with the differences in high-temperature Daqu metabolites to explore a series of functional microorganisms that could potentially contribute to product disparities, and found that the differences in interactions facilitated directly or indirectly by Pediococcus spp. seriously affected the development of microbial communities and metabolites, as well as the formation of the microenvironment. This study not only identified functional microbiota in Daqu that affected fermentation quality, but also demonstrated how microorganisms interact to affect the fermentation system, which would provide guidance for microbial supervision in the actual production process. Besides, the application of isothermal microcalorimetry in this study was helpful for us to understand the heat production capacity of microorganisms and their adaptability to the environment. This study presented a commendable framework for improving and controlling the quality of traditional fermentation and inspired further investigations in similar systems.

Tasting of traditional Polish fermented cucumbers: Microbiology, morpho-textural features, and volatilome

In the present study, naturally fermented and unpasteurized cucumbers (Cucumis sativus L.) collected from 4 producers located in different regions of Poland were studied. The fermented cucumbers were characterized by significant nutritional features in terms of polyphenols content and antioxidant activity. Microbiological analyses revealed active bacterial populations of lactococci, thermophilic cocci, lactobacilli, and coagulase-negative cocci. The microbiological characterization of cucumber and brine samples through metataxonomic analysis allowed the dominant species to be detected, being Lactococcus and Streptococcus in cucumbers, and Lactiplantibacillus, Leuconostoc, Pediococcus, Secundilactobacillus, and Lentilactobacillus in brine. The isolation activity offered a clear picture of the main active lactic acid bacteria at the end of fermentation, being Pediococcus parvulus and Lactiplantibacillus plantarum group. All the studied isolates showed a good attitude in fermenting a cucumber-based broth, thus suggesting their potential application as starter or adjunct cultures for guided cucumber fermentation. Moreover, for the same isolates, strong aminopeptidase activity (due to leucine arylamidase and valine arylamidase) was observed, with potential effect on the definition of the final sensory traits of the product. Only a few isolates showed the ability to produce exopolysaccharides in synthetic medium. Of note, the presence of the hdcA gene in some Pediococcus ethanolidurans isolates also confirmed the need for a thorough characterization of starter candidates to avoid undesired adverse effects on consumer's health. No isolate showed the production of bacteriocins against Listeria innocua used as surrogate for Listeria monocytogenes. Based on the results of Headspace Solid-Phase Microextraction-Gas Chromatography/Mass Spectrometry analysis, a rich and complex volatilome, composed by more than 80 VOCs, was recognized and characterized. In more detail, the detected compounds belonged to 9 main classes, being oxygenated terpenes, alcohols, terpenes, ketones, acids, aldehydes, esters, sulfur, and sesquiterpenes.

Novel Wild-Type Pediococcus and Lactiplantibacillus Strains as Probiotic Candidates to Manage Obesity-Associated Insulin Resistance

As the food and pharmaceutical industry is continuously seeking new probiotic strains with unique health properties, the aim of the present study was to determine the impact of short-term dietary intervention with novel wild-type strains, isolated from various sources, on high-fat diet (HFD)-induced insulin resistance. Initially, the strains were evaluated in vitro for their ability to survive in simulated gastrointestinal (GI) conditions, for adhesion to Caco-2 cells, for bile salt hydrolase secretion, for cholesterol-lowering and cellular cholesterol-binding ability, and for growth inhibition of food-borne pathogens. In addition, safety criteria were assessed, including hemolytic activity and susceptibility to antibiotics. The in vivo test on insulin resistance showed that mice receiving the HFD supplemented with Pediococcus acidilactici SK (isolated from human feces) or P. acidilactici OLS3-1 strain (isolated from olive fruit) exhibited significantly improved insulin resistance compared to HFD-fed mice or to the normal diet (ND)-fed group.

Autochthonous buffalo-gut origin Pediococcus pentosaceus RM119 decreased diarrhea and enhanced gut health, immunity in neonatal Murrah calves

This study assessed the effect of autochthonous probiotic Pediococcus pentosaceus RM119 on gut health, growth, and nutrient utilization in calves. Twelve buffalo calves (<15 d) were divided into two groups, control without probiotics, and probiotic group with P. pentosaceus RM119 @ 108 CFU/calf/d. The probiotic group showed a reduction (p < 0.05) in fecal score, diarrhea episodes and duration of diarrhea. The fecal pH, fecal ammonia was lower, whereas lactate was higher in probiotic group than control. There was a significant increase (p < 0.01) in the concentration of fecal acetate, propionate and butyrate levels in the probiotic supplemented group. The fecal lactobacilli and bifidobacterium were higher (p < 0.01), whereas, fecal coliform and clostridial count were lower (p < 0.01) in P. pentosaceus RM119 supplemented group. There was an improvement in reduced glutathione anti oxidant. Overall, buffalo-gut origin P. pentosaceus RM119 reduced the frequency and severity of diarrhea in neonatal buffalo calves and improved the gut health.

Interactions between polyphenols from Theobroma cacao and Lactobacillales to evaluate the potential of a combined strategy for intestinal free-fatty acid removal

Reducing the absorption of lipids in the gastrointestinal tract is one approach used to manage caloric intake in the fight against excessive weight. Biocompounds, such as polyphenols and probiotics, have been used in this regard. However, some studies have reported that polyphenols have both inhibitory and stimulatory effects on bacterial growth. This study aimed to investigate the resistance to polyphenol-rich extracts from Theobroma cacao L. of Lactobacillales isolated from the human fecal microbiota of lean volunteers (with high saturated fat consumption), to further the knowledge of the potential combination of these bioactive compounds. The strains were selected using an improved and affordable strategy that allowed the rapid screening of strains with fat-removing capacity. Among 1400 isolates, two strains, Lactobacillus sp. A1 and Pediococcus acidilactici E1, were selected due to their capacity to remove saturated fats from the culture media similar to the reference strain Lactobacillus sp. JBD301. Both isolated strains differed in their resistance to cocoa polyphenols: the extract did not affect the growth of strain A1, but reduced the growth of strain E1. However, the extract did not affect the level of in vitro fat removal by either strain, confirming the potential use of a combination of bacteria and polyphenols as a promising strategy for the intestinal removal of free fatty acids.

Beneficial features of pediococcus: from starter cultures and inhibitory activities to probiotic benefits

Pediococci are lactic acid bacteria (LAB) which have been used for centuries in the production of traditional fermented foods. There fermentative abilities were explored by the modern food processing industry in use of pediococci as starter cultures, enabling the production of fermented foods with distinct characteristics. Furthermore, some pediococci strains can produce bacteriocins and other antimicrobial metabolites (AMM), such as pediocins, which are increasingly being explored as bio-preservatives in various food matrices. Due to their versatility and inhibitory spectrum, pediococci bacteriocins and AMM are being extensively researched not only in the food industry, but also in veterinary and human medicine. Some of the pediococci were evaluated as potential probiotics with different beneficial areas of application associated with human and other animals' health. The main taxonomic characteristics of pediococci species are presented here, as well as and their potential roles and applications as starter cultures, as bio-preservatives and as probiotic candidates.

Biotechnological Innovations and Therapeutic Application of Pediococcus and Lactic Acid Bacteria: The Next-Generation Microorganism

Lactic acid bacteria represent a worthwhile organism within the microbial consortium for the food sector, health, and biotechnological applications. They tend to offer high stability to environmental conditions, with an indicated increase in product yield, alongside their moderate antimicrobial activity. Lack of endotoxins and inclusion bodies, extracellular secretion, and surface display with other unique properties, are all winning attributes of these Gram-positive lactic acid bacteria, of which, Pediococcus is progressively becoming an attractive and promising host, as the next-generation probiotic comparable with other well-known model systems. Here, we presented the biotechnological developments in Pediococcal bacteriocin expression system, contemporary variegated models of Pediococcus and lactic acid bacteria strains as microbial cell factory, most recent applications as possible live delivery vector for use as therapeutics, as well as upsurging challenges and future perspective. With the radical introduction of artificial intelligence and neural network in Synthetic Biology, the microbial usage of lactic acid bacteria as an alternative eco-friendly strain, with safe use properties compared with the already known conventional strains is expected to see an increase in various food and biotechnological applications in years to come as it offers better hope of safety, accuracy, and higher efficiency.

Safety and beneficial properties of bacteriocinogenic Pediococcus acidilactici and Pediococcus pentosaceus isolated from silage

The control of Listeria monocytogenes is a relevant goal for dairy products, a process that begins from the supply of feed and management of animals' health. In the present study, we evaluated the safety of two bacteriocinogenic Pediococcus strains and show that both can be considered as safe, based on their haemolytic activity, biogenic amine production and antibiotic resistance, all evaluated through phenotypical and biomolecular approaches. Both strains have shown potential as a producer of γ-aminobutiric acid (GABA) and carry an incomplete set of genes related to folate biosynthesis; both strains were able to adhere to Caco-2 cell lines with adhesion rates of 6·59% ± 3·73 and 0·84% ± 0·48. Laboratory prepared clover silage, inoculated with each bacteriocinogenic Pediococcus strain and contaminated with L. monocytogenes, proved the hypothesis for bioprotective effect of the tested strains, with the tested pathogen eliminated in the first 24 h of the experiment. These results indicate that evaluated strains can be potential beneficial candidates for application in silage production.

Physicochemical and microbiological evaluation of antioxidant-rich traditional black carrot beverage: Kanji

BACKGROUND

Daucus carota subsp. sativus (Black carrots) are underutilized in context to their nutritional properties. In this study, Kanji, a naturally fermented probiotic beverage, was prepared using Daucus carota subsp. sativus (var. Punjab Black Beauty). Analysis of the physicochemical and microbiological profile of the naturally fermented Kanji was investigated to boost its utilization for commercial purpose.

RESULTS

The physicochemical parameters observed in the fermented Kanji beverage were pH 3.47, total soluble solids 3°B, lactic acid 0.99%, total sugars 36.32 mg/mL, total reducing sugars 27.16 mg/mL, flavonoids 38.14 mg/mL, phenols 40.8 mg/mL, antioxidant activity 79.96% and ascorbic acid 110 mg/100 mL. The microbiological analysis revealed an exponential increase in lactic acid bacterial count from 3.96 to 8.33 log CFU/mL. Out of 11 bacterial strains isolated from Kanji, the bacterial strain with high growth potential was genotypically characterized as Pediococcus acidilactici with accession number MK028218.

CONCLUSION

The lactic acid bacterial Kanji beverage was characterized as a potential plant-based probiotic with high antioxidant activity. This functional autochthonous starter from the Kanji can be used for selective fermentation of black carrots for Kanji ascertaining its microbiological safety, unique flavor and aroma, and consumption as a commercial non-dairy-based probiotic beverage.

Antimicrobial properties of Pediococcus acidilactici and Pediococcus pentosaceus isolated from silage

AIMS

The objective of this study was to isolate multifunctional bacteriocin-producing strains; to characterize the expressed bacteriocin for the control of Listeria monocytogenes and vancomycin-resistant Enterococcus; to evaluate the safety of studied strains; and to explore their antifungal activity.

METHODS AND RESULTS

Two Pediococcus strains were isolated from silage samples obtained from an organic farm in Belogradchik, Bulgaria. The strains were identified by 16S rRNA sequencing analysis and characterized as bacteriocins producers. Strong antimicrobial activity was detected against more than 74 different strains of Listeria monocytogenes, 27 different vancomycin-resistant Enterococcus strains. In addition, studied strains were able to inhibit the growth of strains of Alternaria alternate, Aspergillus flavus, Aspergillus niger, Cladosporium sphaerospermum, Penicillium chrysogenum and Penicillium expansum. Some aspects of the antimicrobial mode of action were evaluated, including killing curves and aggregation properties. Both strains generated positive PCR results for the presence of pediocin PA-1, but not for other bacteriocins evaluated in this screening process. Metabolomic analysis of the cell-free supernatants from both strains was performed in order to explain the observed antifungal activity against different moulds. According to PCA and PLS-DA score plot, P. acidilactici ST3522BG and P. pentosaceus ST3633BG were clearly clustered from control (MRS). Increases in the production of benzoic acid, 2-hydroxyisocaproic acid, β-phenyl-lactic acid, α-hydroxybutyric acid and 1,3-butanediol were recorded, these metabolites were previously described as antifungal.

CONCLUSIONS

Pediococcus acidilactici ST3522BG and P. pentosaceus ST3633BG were evaluated as producing bacteriocin strains with high specificity against Listeria and vancomycin-resistant Enterococcus species. In addition, both investigated Pediococcus strains were evaluated as producer of effective antifungal metabolites with potential for the inhibition of mycotoxin-producing moulds.

SIGNIFICANCE AND IMPACT OF THE STUDY

To the best of our knowledge, this report is a pioneer in the evaluation of Pediococcus strains isolated from silage with highly specific bacteriocinogenic antimicrobial activity against Listeria spp. and vancomycin-resistant Enterococcus spp., and antifungal activity against mycotoxin-producing moulds.

Changes in the chemical and sensory profile of ripened Italian salami following the addition of different microbial starters

In this work, Italian salami were produced using microbial starters (Pediococcus pentosaceus, Lactobacillus sakei, and Staphylococcus xylosus) and compared to a control sample (without starter). Metabolomics in combination with microbiological and sensory analyses were used to investigate the overall quality. Samples were analyzed immediately after stuffing, following 7, 30, and 45 days of ripening. Each microbial starter imposed distinctive metabolomic signatures at the end of ripening. The accumulated discriminant compounds were mainly related to lipid oxidation (including hydroxy- and epoxy derivatives of fatty acids) following the inoculation with L. sakei. However, the inoculation with P. pentosaceus resulted in the accumulation of γ-glutamyl peptides, compounds driving a kokumi-related taste. Noteworthy, our findings supported the involvement of the chemical compounds profiled in the definition of final taste and aroma. This information paves the way towards the definition of more objective and tailored starters-related flavours enhancement approaches in the sector of cured meat.

Probiotic potential and anticancer properties of Pediococcus sp. isolated from traditional dairy products

Herein, 18 lactic acid bacteria isolated from 30 samples of traditional dairy products were identified, and their probiotic potential was evaluated. According to the results, almost all strains showed the probiotic properties sufficiently, though M1 had better characterise. 16S rRNA gene sequencing revealed that this strain belongs to the Pediococcus sp. (<95 % similarity). This strain had substantial antipathogenic activity and did not show any worrying antibiotic resistance. Also, the strain was resistant to high concentrations of bile salt (1 %), NaCl (6.5 %), and low pH (2). Furthermore, it was revealed that cell-free supernatant (CFS), heat-killed cells and live cells derived from M1 significantly decreased the viability of MCF-7 cells so that the CFS resulted in 85 % cell death. Flow cytometry and western blot analysis determined that this compound induced apoptosis in the cancerous cells through increasing the BAX protein expression and decreasing the Bcl-2 protein expression.

Novel insight into physicochemical and flavor formation in naturally fermented tilapia sausage based on microbial metabolic network

The quality and flavor formation in fermented fish sausages are based on the complex metabolism of microbial community. In this study, the dynamic changes of physicochemical characteristics, volatile compounds, and microbial communities in the naturally fermented tilapia sausage were studied during the fermentation process. The main physical indexes (gel strength, whiteness, and hardness), dominant flavor free amino acids (glycine, alanine, and glutamic acid) and characteristic volatile flavor compounds (hexanal, heptanal, octanal, benzaldehyde, (E)-2-octenal, 4-ethylbenzaldehyde, (E)-2-heptenal, (E,E)-2,4-decadienal, 1-octen-3-ol, 2-pentylfuran, and 2-ethyl-furan) were significantly enhanced after fermentation, and were positively correlated with Lactococcus, Pediococcus, Enterococcus, and Lactobacillus. The microbial metabolic network showed that Lactococcus, Pediococcus, and Enterococcus played a significant role in the formation of physicochemical and flavor characteristics, while the accumulation of biogenic amines might result from the metabolism of Enterococcus, Enterobacter, and Citrobacter. Isolation of lactic acid bacteria in Lactococcus and Pediococcus might be suitable to improve the fermented tilapia sausage. Microbial metabolic network has revealed the physicochemical and flavor formation of tilapia sausage and can provide guidance for future research on screening of starters.

Phylotype-Level Characterization of Complex Communities of Lactobacilli Using a High-Throughput, High-Resolution Phenylalanyl-tRNA Synthetase (pheS) Gene Amplicon Sequencing Approach

The lactobacilli identified to date encompass more than 270 closely related species that were recently reclassified into 26 genera. Because of their relevance to industry, there is a need to distinguish between closely related and yet metabolically and regulatory distinct species, e.g., during monitoring of biotechnological processes or screening of samples of unknown composition. Current available methods, such as shotgun metagenomics or rRNA gene-based amplicon sequencing, have significant limitations (high cost, low resolution, etc.). Here, we generated a phylogeny of lactobacilli based on phenylalanyl-tRNA synthetase (pheS) genes and, from it, developed a high-resolution taxonomic framework which allows for comprehensive and confident characterization of the community diversity and structure of lactobacilli at the species level. This framework is based on a total of 445 pheS gene sequences, including sequences of 276 validly described species and subspecies (of a total of 282, including the proposed L. timonensis species and the reproposed L. zeae species; coverage of 98%), and allows differentiation between 265 species-level clades of lactobacilli and the subspecies of L. sakei The methodology was validated through next-generation sequencing of mock communities. At a sequencing depth of ∼30,000 sequences, the minimum level of detection was approximately 0.02 pg per μl DNA (equaling approximately 10 genome copies per μl template DNA). The pheS approach, along with parallel sequencing of partial 16S rRNA genes, revealed considerable diversity of lactobacilli and distinct community structures across a broad range of samples from different environmental niches. This novel complementary approach may be applicable to industry and academia alike.IMPORTANCE Species formerly classified within the genera Lactobacillus and Pediococcus have been studied extensively at the genomic level. To accommodate their exceptional functional diversity, the over 270 species were recently reclassified into 26 distinct genera. Despite their relevance to both academia and industry, methods that allow detailed exploration of their ecology are still limited by low resolution, high cost, or copy number variations. The approach described here makes use of a single-copy marker gene which outperforms other markers with regard to species-level resolution and availability of reference sequences (98% coverage). The tool was validated against a mock community and used to address diversity of lactobacilli and community structure in various environmental matrices. Such analyses can now be performed at a broader scale to assess and monitor the assembly, structure, and function of communities of lactobacilli at the species level (and, in some cases, even at the subspecies level) across a wide range of academic and commercial applications.

Probiotic characterization of Pediococcus strains isolated from Iranian cereal-dairy fermented product: Interaction with pathogenic bacteria and the enteric cell line Caco-2

In present study, we investigated the probiotic potential of three Pediococcus spp. isolated from Iranian traditional fermented cereal-dairy product, Tarkhineh. These 3 strains were identified as Pediococcus acidilactici VKU2, P. acidilactici IAH-5 and P. pentosaceus DHR005 by 16S rRNA gene sequencing. All the strain were found tolerate to pH 3 and 0.3% oxall for 3 h as well as simulated gastric and intestinal juice. P. acidilactici IAH-5 showed the highest cholesterol removal (67.52%), hydroxyl radical scavenging activity (58.32%), hydrophobicity (40.3%) and auto-aggregation (48%). Pediococcus spp. inhibited the growth of tested pathogens (Escherichia coli ATCC 25922, Pseudomonas aeruginosa PTCC 1707, Salmonella typhimurium PTCC 1609, and Staphylococcus aureus ATCC 25923) which the most susceptible strain was S. aureus. In competition assay, P. acidilactici IAH-5 was able to inhibited adhesion of 67.3% of S. typhimurium and in inhibition assay 45.8% of the pathogenic adhesion to Caco-2 cells were decreased. P. acidilactici VKU2 and P. acidilactici IAH-5 showed 16.32 and 12.25% adhesion to simulated epithelial cell line which were also confirmed by scanning electron microscopy. Pediococcus spp. did not showed DNase production or hemolytic activity which confirm its safety aspects. Our findings suggested that the P. acidilactici IAH-5 has the best properties with probiotic features and cholesterol assimilation for its application as novel bio-therapeutic and bio-preservation agents.

A Review on Adventitious Lactic Acid Bacteria from Table Olives

Spontaneous fermentation constitutes the basis of the chief natural method of processing of table olives, where autochthonous strains of lactic acid bacteria (LAB) play a dominant role. A thorough literature search has unfolded 197 reports worldwide, published in the last two decades, that indicate an increasing interest in table olive-borne LAB, especially in Mediterranean countries. This review attempted to extract extra information from such a large body of work, namely, in terms of correlations between LAB strains isolated, manufacture processes, olive types, and geographical regions. Spain produces mostly green olives by Spanish-style treatment, whereas Italy and Greece produce mainly green and black olives, respectively, by both natural and Spanish-style. More than 40 species belonging to nine genera of LAB have been described; the genus most often cited is Lactobacillus, with L. plantarum and L. pentosus as most frequent species—irrespective of country, processing method, or olive type. Certain LAB species are typically associated with cultivar, e.g., Lactobacillus parafarraginis with Spanish Manzanilla, or L. paraplantarum with Greek Kalamata and Conservolea, Portuguese Galega, and Italian Tonda di Cagliari. Despite the potential of native LAB to serve as starter cultures, extensive research and development efforts are still needed before this becomes a commercial reality in table olive fermentation.

A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae

The genus Lactobacillus comprises 261 species (at March 2020) that are extremely diverse at phenotypic, ecological and genotypic levels. This study evaluated the taxonomy of Lactobacillaceae and Leuconostocaceae on the basis of whole genome sequences. Parameters that were evaluated included core genome phylogeny, (conserved) pairwise average amino acid identity, clade-specific signature genes, physiological criteria and the ecology of the organisms. Based on this polyphasic approach, we propose reclassification of the genus Lactobacillus into 25 genera including the emended genus Lactobacillus, which includes host-adapted organisms that have been referred to as the Lactobacillus delbrueckii group, Paralactobacillus and 23 novel genera for which the names Holzapfelia, Amylolactobacillus, Bombilactobacillus, Companilactobacillus, Lapidilactobacillus, Agrilactobacillus, Schleiferilactobacillus, Loigolactobacilus, Lacticaseibacillus, Latilactobacillus, Dellaglioa, Liquorilactobacillus, Ligilactobacillus, Lactiplantibacillus, Furfurilactobacillus, Paucilactobacillus, Limosilactobacillus, Fructilactobacillus, Acetilactobacillus, Apilactobacillus, Levilactobacillus, Secundilactobacillus and Lentilactobacillus are proposed. We also propose to emend the description of the family Lactobacillaceae to include all genera that were previously included in families Lactobacillaceae and Leuconostocaceae. The generic term 'lactobacilli' will remain useful to designate all organisms that were classified as Lactobacillaceae until 2020. This reclassification reflects the phylogenetic position of the micro-organisms, and groups lactobacilli into robust clades with shared ecological and metabolic properties, as exemplified for the emended genus Lactobacillus encompassing species adapted to vertebrates (such as Lactobacillus delbrueckii, Lactobacillus iners, Lactobacillus crispatus, Lactobacillus jensensii, Lactobacillus johnsonii and Lactobacillus acidophilus) or invertebrates (such as Lactobacillus apis and Lactobacillus bombicola).

Selection of non-Lactobacillus strains to be used as starters for sourdough fermentation

The suitability of forty-one non-Lactobacillus strains to be used as selected starters for sourdough fermentation was evaluated. According to the data collected, Pediococcus pentosaceus OA1 and S3N3 and Leuconostoc citreum PRO17 were selected based on the optimal acidification and growth performances and the intense proteolytic activity (increase of TFFA up to 80%) on whole wheat flour doughs. A relevant degradation of phytic acid (up to 58%) and the increase of phenols content and scavenging activity (4- and 2-folds, respectively) were also observed. The technological performances were compared to two representative Lactobacillus strains (Lactobacillus plantarum and Lactobacillus sanfranciscensis). The investigation of the robustness of the selected strains during the propagation (back-slopping procedure) showed their long-term dominance only when singly-inoculated; while Leuc. citreum PRO17 dominated the fermentation when the strains were co-inoculated. The sourdoughs obtained by the non-Lactobacillus selected strains (singly or pooled) were used for breadmaking. Selected sourdoughs allowed the production of breads characterized by in-vitro protein digestibility (IVPD) higher than that of breads obtained with Lactobacillus strains or baker's yeast. The aroma profile, estimated by GC/MS, was complex and characterized by high concentration of the typical compounds (hexanol, 3-methylbutanol and 2-pentylfuran) of sourdough bread.

Impact of pH on succession of sourdough lactic acid bacteria communities and their fermentation properties

Sourdough, a traditional fermented dough, is made via natural fermentation by lactic acid bacteria (LAB). Its pH changes from near neutral to acid during the subculture process. However, the product quality of subcultured sourdough depends on the unpredictable succession of LAB communities, the influential factors of which are still unclear. To elucidate one end of the LAB community succession mechanism, we evaluated the effect of pH by designing four subculture experiments using a model medium adjusted to pH 6.7, 5.5, and 4.5, as well as a natural sourdough subculture. All experiments began by inoculating a sourdough LAB mixture, and both bacterial successions and fermentative properties were monitored until ten subculture steps. In media subcultures, lactic acid production was higher in higher pH media. Three LAB genera, Weissella, Pediococcus, and Lactobacillus, each represented by one operational taxonomic unit (OTU), were successively detected in all subcultures. In later steps with lower pH media, an OTU closely related to Lactobacillus brevis dominated, replacing an OTU closely related to the Weissella cibaria-confusa group that was more dominant than the L. brevis OTU in the near-neutral pH medium. In the sourdough subculture, the three genera were also detected, while Lactobacillus was dominant in earlier steps due to the emergence of an OTU closely related to Lactobacillus sanfranciscensis. These results suggest that a lower pH is favorable for the sequence of sourdough bacterial community evolution finalizing with Lactobacillus domination. Further research is needed to elucidate additional factors other than pH that influence the pattern of LAB community shift.

Evaluation of Potential Probiotics Bacillus subtilis WB60, Pediococcus pentosaceus, and Lactococcus lactis on Growth Performance, Immune Response, Gut Histology and Immune-Related Genes in Whiteleg Shrimp, Litopenaeus vannamei

An eight-week feeding trial was conducted to evaluate the effects of different dietary probiotic supplements in juvenile whiteleg shrimp, Litopenaeus vannamei. A basal control diet without probiotics (CON), and five other diets by supplementing Bacillus subtilis at 10⁷ CFU/g diet (BS₇), B. subtilis (BS₈), Pediococcus pentosaceus (PP₈), and Lactococcus lactis (LL₈) at 10⁸ CFU/g diet, and oxytetracycline (OTC) at 4 g/kg diet were used. Whiteleg shrimp with initial body weights of 1.41 ± 0.05 g (mean ± SD) were fed with these diets. Growth of shrimp fed BS₈ and LL₈ diets was significantly higher than those of shrimp fed the CON diet (p < 0.05). Superoxide dismutase activity in shrimp fed PP₈ and LL₈ diets was significantly higher than that of shrimp fed the CON diet (p < 0.05). Lysozyme activity of shrimp fed probiotics and OTC diets significantly improved compared to those on the CON diet (p < 0.05). The intestinal histology showed healthier guts for shrimp fed the probiotic diets (p < 0.05). Immune-related gene expression in shrimp fed BS₈, PP₈ and LL₈ diets was recorded as significantly higher than that of shrimp fed CON and OTC diets (p < 0.05). Also, results of the challenge test for 7 days and the digestive enzyme activity of shrimp fed BS₈, PP₈, and LL₈ were significantly improved compared to those on the CON diet (p < 0.05). Therefore, these results indicated that L. lactis at 10⁸ CFU/g could be an ideal probiotic for whiteleg shrimp, and also B. subtilis WB60 and P. pentosaceus at 10⁸ CFU/g could improve the growth, immunity, histology, gene expression, digestive enzyme activity, and disease resistance, while replacing antibiotics.

A Pediococcus strain to rescue honeybees by decreasing Nosema ceranae- and pesticide-induced adverse effects

Honeybees ensure a key ecosystemic service by pollinating many agricultural crops and wild plants. However, since few decades, managed bee colonies have declined worldwide. This phenomenon is considered to be multifactorial, with a strong emphasis on both parasites and pesticides. Infection by the parasite Nosema ceranae and exposure to pesticides can contribute to adverse effects, resulting in a perturbation of the honeybee physiology. We thus hypothesized that probiotic treatment could be promising to treat or prevent these disturbances. The aim of this study was to evaluate the effects of probiotics on N. ceranae-infected and intoxicated honeybees (by the insecticide thiamethoxam and the fungicide boscalid). For this purpose, experiments were conducted with five probiotics. Among them, Pediococcus acidilactici (PA) showed the best protective effect against the parasite and pesticides. PA significantly improved the infected honeybee lifespan as prophylactic and curative treatments (respectively 2.3 fold and 1.7 fold). Furthermore, the exposure to pesticides induced an increase of honeybee mortality compared with the control group (p < .001) that was restored by the PA treatment. Despite its beneficial effect on honeybee lifespan, the PA administration did not induce changes in the gut bacterial communities (neither in abundance or diversity). N. ceranae and the pesticides were shown to deregulate genes involved in honeybee development (vitellogenin), immunity (serine protease 40, defensin) and detoxification system (glutathione peroxidase-like 2, catalase), and these effects were corrected by the PA treatment. This study highlights the promising use of PA to protect honeybees from both pathogens and pesticides.

In vitro characterization and analysis of probiotic species in the chicken intestine by real-time polymerase chain reaction

Two experiments, 1 in vitro and 1 in vivo study, were conducted to analyze probiotic species characteristics and survival in the intestine of broiler birds. The in vitro study characterized the effect of bile salt supplementation and pH on the proliferation of Lactobacillus reuteri, Pediococcus acidilactici, Bifidobacterium animalis, and Enterococcus faecium. L. reuteri and P. acidilactici growth was maximal when the media was supplemented with 1.0% bile salt, whereas B. animalis and E. faecium growth was maximal when the media was supplemented with 0.5% bile salt. Altering the pH between 2.5 and 5.8 did not significantly (P > 0.05) alter the proliferation of L. reuteri and B. animalis. Decreasing the pH from 5.8 to 2.0 decreased P. acidilactici growth, whereas it increased the E. faecium proliferation. The in vivo study quantified the concentration of L. reuteri, P. acidilactici, B. animalis, E. faecium, and L. salivarius in different intestinal sections from birds supplemented with and without synbiotic containing the above 5 bacteria species. Birds were supplemented with and without synbiotic for 18 d, after which all birds were fed the same basal diet with no synbiotic. At 72 h of feeding, the basal diet with no synbiotics, when the probiotic species in the feed is expected not to confound the recovery of probiotic species from the intestine, intestinal contents were collected. L. reuteri, P. acidilactici, E. faecium, and L. salivarius were below detectable amount in the control group. L. reuteri concentration expressed as copy numbers/g and as percentage of total bacteria was highest in the jejunum and ileum, respectively. E. faecium concentration was highest in the ileum. The copy number of P. acidilactici increased at the duodenum and plateaued after duodenum. L. salivarius concentration was highest in the jejunum. It can be concluded that real-time PCR can be applied to quantify the concentrations of probiotic species in the intestine and probiotic species differ in their ability to colonize different sections of the intestine.

Changes of bioactive compounds in barley industry by-products during submerged and solid state fermentation with antimicrobial Pediococcus acidilactici strain LUHS29

In this study, changes of bioactive compounds (crude protein (CP), crude fat (CF), dietary fiber (DF), fatty acids (FAs), free amino acids (FAAs), phenolic compounds (PCs), biogenic amines (BAs), lignans, and alkylresorcinols) in barley industry by-products (BB) during submerged and solid state fermentation (SSF) with Pediococcus acidilactici were analyzed. It was established that both fermentation conditions reduce the CP and CF content in BB (by 25.8% and 35.9%, respectively) and increase DF content (on average by 25.0%). Fermentation increases the oleic, arachidic, eicosadienoic, behenic, and lignoceric FA in BB samples. The highest total BA content was found in untreated samples (290.6 mg/kg). Solid state fermentation increased the content of the alkylresorcinol C19:0. Finally, collecting data about the changes of these compounds during technological processes is very important, because according to the specific compounds formed during fermentation, further recommendations for by-product valorization and uses in food, pharmaceutical, or feed industries can be suggested.

Lactic Acid Bacteria Isolation from Spontaneous Sourdough and Their Characterization Including Antimicrobial and Antifungal Properties Evaluation

This research effort aimed at isolating and phenotypically characterizing lactic acid bacteria (LAB) isolates from a spontaneous rye sourdough manufactured following traditional protocols, as well as at evaluating their antimicrobial and antifungal properties as key features for future industrial applications. Thirteen LAB strains of potential industrial interest were isolated and identified to species-level via PCR. Most of the sourdough isolates showed versatile carbohydrate metabolisms. The Leuconostoc mesenteroides No. 242 and Lactobacillus brevis No. 173 demonstrated to be gas producers; thus, revealing their heterofermenter or facultative homofermenter features. Viable counts higher than 7.0 log10 (CFU/mL) were observed for Lactobacillus paracasei No. 244, Lactobacillus casei No. 210, L. brevis No. 173, Lactobacillus farraginis No. 206, Pediococcus pentosaceus No. 183, Lactobacillus uvarum No. 245 and Lactobacillus plantarum No. 135 strains, after exposure at pH 2.5 for 2 h. Moreover, L. plantarum No. 122, L. casei No. 210, Lactobacillus curvatus No. 51, L. paracasei No. 244, and L. coryniformins No. 71 showed growth inhibition properties against all the tested fifteen pathogenic strains. Finally, all LAB isolates showed antifungal activities against Aspergillus nidulans, Penicillium funiculosum, and Fusarium poae. These results unveiled the exceptionality of spontaneous sourdough as a source of LAB with effective potential to be considered in the design of novel commercial microbial single/mixed starter cultures, intended for application in a wide range of agri-food industries, where the antimicrobial and antifungal properties are often sought and necessary. In addition, metabolites therefrom may also be considered as important functional and bioactive compounds with high potential to be employed in food and feed, as well as cosmetic and pharmaceutical applications.

Comparative studies of versatile extracellular proteolytic activities of lactic acid bacteria and their potential for extracellular amino acid productions as feed supplements

BACKGROUND

Increasing understanding on the functions of amino acids (AA) has led to new commercial applications and expansion of the worldwide markets. However, the current technologies rely heavily on non-food grade microorganism and chemical synthesis for the production of AA. Several studies reported that lactic acid bacteria (LAB) have the capability of producing AA owing to their well-established proteolytic system and amino acid biosynthesis genes. Hence, the objectives of this study were to explore the extracellular proteolytic activity of LAB isolated from various Malaysian fermented foods and their potential to produce AA extracellularly as feed supplements.

RESULTS

All the studied LAB isolates were versatile extracellular protease producers, whereby extracellular protease activities were detected from acidic to alkaline pH (pH 5, pH 6.5, pH 8) using qualitative and quantitative proteolytic assays. The highest proteolytic activity at pH 5 (15.76 U/mg) and pH 8 (19.42 U/mg) was achieved by Lactobacillus plantarum RG14, while Lactobacillus plantarum RS5 exhibited the highest proteolytic activity of 17.22 U/mg at pH 6.5. As for the results of AA production conducted in de Man, Rogosa and Sharpe medium and analysed by high pressure liquid chromatography system, all LAB isolates were capable of producing an array of AA. Generally, Pediococcus sp. showed greater ability for AA production as compared to Lactobacillus sp. Moreover, the studied LAB were able to produce a few major feed supplement AA such as methionine, lysine, threonine and tryptophan. P. pentosaceus TL-3 recorded the highest methionine and threonine productivity of 3.72 mg/L/h and 5.58 mg/L/h respectively. However, L. plantarum I-UL4 demonstrated a lysine productivity of 1.24 mg/L/h, while P. acidilactici TP-6 achieved up to 1.73 mg/L/h of tryptophan productivity.

CONCLUSION

All the 17 studied LAB isolates possessed versatile extracellular proteolytic system and have vast capability of producing various amino acids including a few major feed supplement AA such as methionine, lysine, threonine and tryptophan. Despite AA production was strain dependent, the studied LAB isolates possessed vast potential and can be exploited further as a bio-agent or an alternative amino acids and bioactive peptide producers.

PCR Analysis Methods for Detection and Identification of Beer-Spoilage Lactic Acid Bacteria

Polymerase chain reaction (PCR) analysis enables rapid and accurate detection of beer-spoilage lactic acid bacteria (LAB). Hop resistance genes, horA and horC, are utilized as genetic markers to determine the spoilage ability of LAB strains. PCR analysis of horA and horC, combined with multiplex PCR methods of 12 beer-spoilage species, enables simultaneous and comprehensive detection easily and inexpensively.

Antibiotic susceptibility profile of Pediococcus spp. from diverse sources

The aim of the present study was to assess the antibiotic susceptibility profile of Pediococcus strains from diverse sources. From a total of 115 dairy and non-dairy samples, 40 Pediococcus strains were isolated. Their biochemical and molecular characterization confirmed them as P. pentosaceus and P. acidilactici. All the 40 identified isolates were evaluated for antibiotic susceptibility using disc diffusion assay against a total of 20 antibiotics. The isolates exhibited varied range of responses towards the antibiotics depending on the strain type, source and location of isolation. All the isolates were either sensitive or intermediate resistant to amoxycillin, erythromycin, ceftriaxone, cloxacillin, cefoperazone, penicillin, netillin, gentamycin and chloramphenicol. Resistance towards vancomycin and nalidixic acid was exhibited by most of the isolates. A total of 16 strains belonging to dosa batter (n = 4; n = number of isolates), fermented vegetables (n = 4), fermented grape juice (n = 4), idly batter (n = 3) and the only isolate from butter milk exhibited sensitivity/intermediate towards 80-90% of the studied antibiotics. No considerable difference in susceptibility pattern was observed between the two Pediococcus species, i.e., P. pentosaceus and P. acidilactici. Overall, the maximum resistance was exhibited by isolates belonging to silage (Sil-2; 50%) followed by cow milk (PD-41), dosa batter (8-PD) and human isolate (PD-45) which showed resistance towards 40% of studied antibiotics. The susceptibility profiling of Pediococcus strains will be helpful in their safer selection for future food and feed applications.

Fermented Soybean Meal Increases Lactic Acid Bacteria in Gut Microbiota of Atlantic Salmon (Salmo salar)

The main goal of the present study was to address the effect of feeding fermented soybean meal-based diet to Atlantic salmon on gut microbiota. Further, expression of genes of interest, including cathelicidin antimicrobial peptide (cath), mucin 2 (muc2), aquaporin (aqp8ab), and proliferating cell nuclear antigen (pcna), in proximal intestine of fish fed either experimental diet was analyzed. Three experimental diets, including a control fishmeal (30% FM), soybean meal (30% SBM), or fermented soybean meal diet (30% FSBM) were randomly assigned to triplicate tanks during a 50-day trial. The PCR-TTGE showed microbiota composition was influenced by experimental diets. Bands corresponding to genus Lactobacillus and Pediococcus were characteristic in fish fed the FSBM-based diet. On the other hand, bands corresponding to Isoptericola, Cellulomonas, and Clostridium sensu stricto were only observed in fish FM-based diet, while Acinetobacter and Altererythrobacter were detected in fish fed SBM-based diet. The expression of muc2 and aqp8ab were significantly greater in fish fed the FSBM-based diet compared with the control group. Our results suggest feeding FSBM to Atlantic salmon may (1) boost health and growth physiology in fish by promoting intestinal lactic acid bacteria growth, having a prebiotic-like effect, (2) promote proximal intestine health by increasing mucin production, and (3) boost intestinal trans-cellular uptake of water. Further research to better understands the effects of bioactive compounds derived from the fermentation process of plant feedstuff on gut microbiota and the effects on health and growth in fish is required.

DFAST and DAGA: web-based integrated genome annotation tools and resources

Quality assurance and correct taxonomic affiliation of data submitted to public sequence databases have been an everlasting problem. The DDBJ Fast Annotation and Submission Tool (DFAST) is a newly developed genome annotation pipeline with quality and taxonomy assessment tools. To enable annotation of ready-to-submit quality, we also constructed curated reference protein databases tailored for lactic acid bacteria. DFAST was developed so that all the procedures required for DDBJ submission could be done seamlessly online. The online workspace would be especially useful for users not familiar with bioinformatics skills. In addition, we have developed a genome repository, DFAST Archive of Genome Annotation (DAGA), which currently includes 1,421 genomes covering 179 species and 18 subspecies of two genera, Lactobacillus and Pediococcus, obtained from both DDBJ/ENA/GenBank and Sequence Read Archive (SRA). All the genomes deposited in DAGA were annotated consistently and assessed using DFAST. To assess the taxonomic position based on genomic sequence information, we used the average nucleotide identity (ANI), which showed high discriminative power to determine whether two given genomes belong to the same species. We corrected mislabeled or misidentified genomes in the public database and deposited the curated information in DAGA. The repository will improve the accessibility and reusability of genome resources for lactic acid bacteria. By exploiting the data deposited in DAGA, we found intraspecific subgroups in Lactobacillus gasseri and Lactobacillus jensenii, whose variation between subgroups is larger than the well-accepted ANI threshold of 95% to differentiate species. DFAST and DAGA are freely accessible at https://dfast.nig.ac.jp.

Preliminary probiotic and technological characterization of Pediococcus pentosaceus strain KID7 and in vivo assessment of its cholesterol-lowering activity

The study was aimed to characterize the probiotic properties of a Pediococcus pentosaceus strain, KID7, by in vitro and in vivo studies. The strain possessed tolerance to oro-gastrointestinal transit, adherence to the Caco-2 cell line, and antimicrobial activity. KID7 exhibited bile salt hydrolase activity and cholesterol-lowering activity, in vitro. In vivo cholesterol-lowering activity of KID7 was studied using atherogenic diet-fed hypercholesterolemic mice. The experimental animals (C57BL/6J mice) were divided into 4 groups viz., normal diet-fed group (NCD), atherogenic diet-fed group (HCD), atherogenic diet- and KID7-fed group (HCD-KID7), and atherogenic diet- and Lactobacillus acidophilus ATCC 43121-fed group (HCD-L.ac) as positive control. Serum total cholesterol (T-CHO) level was significantly decreased by 19.8% in the HCD-KID7 group (P < 0.05), but not in the HCD-L.ac group compared with the HCD group. LDL cholesterol levels in both HCD-KID7 and HCD-L.ac groups were decreased by 35.5 and 38.7%, respectively, compared with HCD group (both, P < 0.05). Glutamyl pyruvic transaminase (GPT) level was significantly lower in the HCD-KID7 and HCD-L.ac groups compared to HCD group and was equivalent to that of the NCD group. Liver T-CHO levels in the HCD-KID7 group were reduced significantly compared with the HCD group (P < 0.05) but not in the HCD-L.ac group. Analysis of expression of genes associated with lipid metabolism in liver showed that low-density lipoprotein receptor (LDLR), cholesterol-7α-hydroxylase (CYP7A1) and apolipoprotein E (APOE) mRNA expression was significantly increase in the HCD-KID7 group compared to the HCD group. Furthermore, KID7 exhibited desired viability under freeze-drying and subsequent storage conditions with a combination of skim milk and galactomannan. P. pentosaceus KID7 could be a potential probiotic strain, which can be used to develop cholesterol-lowering functional food after appropriate human clinical trials.

Identification of thermo tolerant lactic acid bacteria isolated from silage prepared in the hot and humid climate of Southwestern Japan

To develop high-quality silage starters adapted to hot and humid weather, 12 LAB isolates from silage produced in Kyushu and Okinawa, Japan were characterized based on their morphological features, growth curves and sugar utilization. In addition, the nucleotide sequences of the V2-V3 region of their 16S rRNA genes and the 16S-23S rRNA intergenic spacer (ITS) regions were determined. The isolates were also subjected to RAPD-PCR analysis, DNA-DNA hybridization, G+C content analysis and immuno-identification using species-specific monoclonal antibodies and SDS-PAGE profiling. Nearly all of the isolates exhibited high thermotolerance and rapid growth. Combining ITS sequence analysis, RAPD-PCR and immuno-identification enabled rapid and accurate identification of closely related LAB strains that other methods failed to appropriately differentiate; for example, L. plantarum was distinguished from L. pentosus, and L. casei was distinguished from L. rhamonsus. Using the aforementioned techniques, the isolated strains were identified as L. plantarum, L. rhamonsus, L. rapi, Pediococcus pentosaceus and P. lolii. Our findings also showed that there is greater diversity among thermophilic LABs in silage prepared in a hot and humid environment.