A Genomic View of Lactobacilli and Pediococci Demonstrates that Phylogeny Matches Ecology and Physiology

Starter Culture Development and Innovation for Novel Fermented Foods

Interest in fermented foods is increasing because fermented foods are promising solutions for more secure food systems with an increased proportion of minimally processed plant foods and a smaller environmental footprint. These developments also pertain to novel fermented food for which no traditional template exists, raising the question of how to develop starter cultures for such fermentations. This review establishes a framework that integrates traditional and scientific knowledge systems for the selection of suitable cultures. Safety considerations, the use of organisms in traditional food fermentations, and the link of phylogeny to metabolic properties provide criteria for culture selection. Such approaches can also select for microbial strains that have health benefits. A science-based approach to the development of novel fermented foods can substantially advance their value through more secure food systems, food products that provide health-promoting microbes, and the provision of foods that improve human health.

New insight into protective effect against oxidative stress and biosynthesis of exopolysaccharides produced by Lacticaseibacillus paracasei NC4 from fermented eggplant

Fermented eggplant is a traditional fermented food, however lactic acid bacteria capable of producing exopolysaccharide (EPS) have not yet been exploited. The present study focused on the production and protective effects against oxidative stress of an EPS produced by Lacticaseibacillus paracasei NC4 (NC4-EPS), in addition to deciphering its genomic features and EPS biosynthesis pathway. Among 54 isolates tested, strain NC4 showed the highest EPS yield and antioxidant activity. The maximum EPS production (2.04 ± 0.11 g/L) was achieved by culturing in MRS medium containing 60 g/L sucrose at 37 °C for 48 h. Under 2 mM H2O2 stress, the survival of a yeast model Saccharomyces cerevisiae treated with 0.4 mg/mL NC4-EPS was 2.4-fold better than non-treated cells, which was in agreement with the catalase and superoxide dismutase activities measured from cell lysates. The complete genome of NC4 composed of a circular chromosome of 2,888,896 bp and 3 circular plasmids. The NC4 genome comprises more genes with annotated function in nitrogen metabolism, phosphorus metabolism, cell division and cell cycle, and iron acquisition and metabolism as compared to other reported L. paracasei. Of note, the eps gene cluster is not conserved across L. paracasei. Pathways of sugar metabolism for EPS biosynthesis were proposed for the first time, in which gdp pathway only present in few plant-derived bacteria was identified. These findings shed new light on the cell-protective activity and biosynthesis of EPS produced by L. paracasei, paving the way for future efforts to enhance yield and tailor-made EPS production for food and pharmaceutical industries.

Gut microbiome changes in mouse, Mongolian gerbil, and hamster models following Clostridioides difficile challenge

Introduction

Clostridioides difficile infection (CDI), as well as its etiology and pathogenesis, have been extensively investigated. However, the absence of suitable CDI animal models that reflect CDI symptoms and the associated gut microbiome changes in humans has limited research progress in this field. Thus, we aimed to investigate whether Mongolian gerbils, which present a range of human pathological conditions, can been used in studies on CDI. Methods: In this study, we infected Mongolian gerbils and two existing CDI model animals, mice and hamsters, with the hypervirulent ribotype 027 C. difficile strain, and comparatively analyzed changes in their gut microbiome composition via 16S rRNA gene sequencing.

Methods

In this study, we infected Mongolian gerbils and two existing CDI model animals, mice and hamsters, with the hypervirulent ribotype 027 C. difficile strain, and comparatively analyzed changes in their gut microbiome composition via 16S rRNA gene sequencing.

Results

The results obtained showed that C. difficile colonized the gastrointestinal tracts of the three rodents, and after the C. difficile challenge, C57BL/6J mice did not manifest CDI symptoms and their intestines showed no significant pathological changes. However, the hamsters showed explosive intestinal bleeding and inflammation and the Mongolian gerbils presented diarrhea as well as increased infiltration of inflammatory cells, mucus secretion, and epithelial cell shedding in their intestinal tissue. Further, intestinal microbiome analysis revealed significant differences with respect to intestinal flora abundance and diversity. Specifically, after C. difficile challenge, the Firmicutes/Bacteroidetes ratio decreased for C57BL/6J mice, but increased significantly for Mongolian gerbils and hamsters. Furthermore, the abundance of Proteobacteria increased in all three models, especially in hamsters, while that of Verrucomicrobia only increased significantly in C57BL/6J mice and Mongolian gerbils. Our results also indicated that differences in the relative abundances of Lactobacillaceae and Akkermansia were primarily responsible for the observed differences in response to C. difficile challenge.

Conclusion

Based on the observed responses to C. difficile challenge, we concluded for the first time that the Mongolian gerbil could be used as an animal model for CDI. Additionally, the taxa identified in this study may be used as biomarkers for further studies on CDI and to improve understanding regarding changes in gut microbiome in CDI-related diseases.

Characterization of Genomic, Physiological, and Probiotic Features of Lactiplantibacillus plantarum JS21 Strain Isolated from Traditional Fermented Jiangshui

This study aimed to understand the genetic and metabolic traits of a Lactiplantibacillus plantarum JS21 strain and its probiotic abilities through laboratory tests and computer analysis. L. plantarum JS21 was isolated from a traditional fermented food known as "Jiangshui" in Hanzhong city. In this research, the complete genetic makeup of JS21 was determined using Illumina and PacBio technologies. The JS21 genome consisted of a 3.423 Mb circular chromosome and five plasmids. It was found to contain 3023 protein-coding genes, 16 tRNA genes, 64 rRNA operons, 40 non-coding RNA genes, 264 pseudogenes, and six CRISPR array regions. The GC content of the genome was 44.53%. Additionally, the genome harbored three complete prophages. The evolutionary relationship and the genome collinearity of JS21 were compared with other L. plantarum strains. The resistance genes identified in JS21 were inherent. Enzyme genes involved in the Embden-Meyerhof-Parnas (EMP) and phosphoketolase (PK) pathways were detected, indicating potential for facultative heterofermentative pathways. JS21 possessed bacteriocins plnE/plnF genes and genes for polyketide and terpenoid assembly, possibly contributing to its antibacterial properties against Escherichia coli (ATCC 25922), Escherichia coli (K88), Staphylococcus aureus (CMCC 26003), and Listeria monocytogenes (CICC 21635). Furthermore, JS21 carried genes for Na+/H+ antiporters, F0F1 ATPase, and other stress resistance genes, which may account for its ability to withstand simulated conditions of the human gastrointestinal tract in vitro. The high hydrophobicity of its cell surface suggested the potential for intestinal colonization. Overall, L. plantarum JS21 exhibited probiotic traits as evidenced by laboratory experiments and computational analysis, suggesting its suitability as a dietary supplement.

The effect of seed germination and Bacillus spp. on the ripening of plant cheese analogs

Consumer demand for plant cheeses is increasing, but challenges of improving both flavor and quality remain. This study investigated the microbiological and physicochemical impact of seed germination and fermentation with Bacillus velezensis and Bacillus amyloliquefaciens on the ripening of plant cheese analogs. Chlorine treatment or addition of Lactiplantibacillus plantarum and Lactococcus lactis controlled microbial growth during seed germination. Lp. plantarum and Lc. lactis also served as starter cultures for the acidification of soy and lupine milk and were subsequently present in the unripened plant cheese as dominant microbes. Acidification also inhibited the growth and metabolic activity of bacilli but Bacillus spores remained viable throughout ripening. During plant cheese ripening, Lc. lactis was inactivated before Lp. plantarum and the presence of bacilli during seed germination delayed Lc. lactis inactivation. Metagenomic sequencing of full-length 16S rRNA gene amplicons confirmed that the relative abundance of the inoculated strains in each ripened cheese sample exceeded 99%. Oligosaccharides including raffinose, stachyose, and verbascose were rapidly depleted in the initial stage of ripening. Both germination and the presence of bacilli during seed germination had impact on polysaccharide hydrolysis during ripening. Bacilli but not seed germination enhanced proteolysis of plant cheese during ripening. In conclusion, the use of germination with lactic acid bacteria in combination with Bacillus spp. exhibited the potential to improve the quality of ripened plant cheeses with a positive effect on the reduction of hygienic risks.

IMPORTANCE

The development of novel plant-based fermented food products for which no traditional templates exist requires the development of starter cultures. Although the principles of microbial flavor formation in plant-based analogs partially overlap with dairy fermentations, the composition of the raw materials and thus likely the selective pressure on the activity of starter cultures differs. Experiments that are described in this study explored the use of seed germination, the use of lactic acid bacteria, and the use of bacilli to reduce hygienic risks, to acidify plant milk, and to generate taste-active compounds through proteolysis and fermentative conversion of carbohydrates. The characterization of fermentation microbiota by culture-dependent and culture-independent methods also confirmed that the starter cultures used were able to control microbial communities throughout 90 d of ripening. Taken together, the results provide novel tools for the development of plant-based analogs of fermented dairy products.

Conversion of Phytochemicals by Lactobacilli: (Phospho)-β-glucosidases Are Specific for Glucosylated Phytochemicals Rather than Disaccharides

Food-fermenting lactobacilli convert glycosylated phytochemicals to glycosyl hydrolases and thereby alter their biological activity. This study aimed to investigate the microbial transformation of β-glucosides of phytochemicals in comparison with utilization of cellobiose. Four homofermentative and four heterofermentative lactobacilli were selected to represent the metabolic diversity of Lactobacillaceae. The genomes of Lactobacillus crispatus, Companilactobacillus paralimentarius, Lacticaseibacillus paracasei, and Lactiplantibacillus plantarum encoded for 8 to 22 enzymes, predominantly phospho-β-glucosidases, with predicted activity on β-glucosides. Levilactobacillus hammesii and Furfurilactobacillus milii encoded for 3 β-glucosidases, Furfurilactobacillus rossiae for one, and Fructilactobacillus sanfranciscensis for none. The hydrolysis of amygdalin, esculin, salicin, glucosides of quercetin and genistein, and ginsenosides demonstrated that several strains hydrolyzed β-glucosides of phytochemicals but not cellobiose. Taken together, several of the carbohydrate-active enzymes of food-fermenting lactobacilli are specific for glycosides of phytochemicals.

The quest for the perfect loaf of sourdough bread continues: Novel developments for selection of sourdough starter cultures

Sourdough fermentation, one of the oldest unit operations in food production, is currently experiencing a revival in bread production at the household, artisanal, and the industrial level. The expanding use of sourdough fermentation in bread production and the adaptation of fermentation to large scale industrial bread production also necessitate the development of novel starter cultures. Developments in the last years also have expanded the tools that are used to assess the metabolic potential of specific strains, species or genera of the Lactobacillaceae and have identified multiple ecological and metabolic traits as clade-specific. This review aims to provide an overview on the clade-specific metabolic potential of members of the Lactobacillaceae for use in sourdough baking, and the impact of these clade-specific traits on bread quality. Emphasis is placed on carbohydrate metabolism, including the conversion of sucrose and starch to soluble polysaccharides, conversion of amino acids, and the metabolism of organic acids. The current state of knowledge to compose multi-strain starter cultures (synthetic microbial communities) that are suitable for back-slopping will also be discussed. Taken together, the communication outlines the current tools for selection of microbes for use in sourdough baking.

Microbiology of fermented soy foods in Asia: Can we learn lessons for production of plant cheese analogues?

The food industry is facing the challenge of creating innovative, nutritious, and flavored plant-based products, due to consumer's increasing demand for the health and environmental sustainability. Fermentation as a unique and effective tool plays an important role in the innovation of food products. Traditional fermented soy foods are popular in many Asian and African countries as nutritious, digestible and flavorful daily staples or condiments. They are produced by specific microorganisms with the unique fermentation process in which microorganisms convert the ingredients of whole soybean or soybean curd to flavorful and functional molecules. This review provides an overview on traditional fermented food produced from soy, including douchi, natto, tempeh, and sufu as well as stinky tofu, including the background of these products, the manufacturing process, and the microbial diversity involved in fermentation procedures as well as flavor volatiles that were identified in the final products. The contribution of microbes to the quality of these five fermented soy foods is discussed, with the comparison to the role of cheese ripening microorganisms in cheese flavor formation. This communication aims to summarize the microbiology of fermented soy foods in Asia, evoking innovative ideas for the development of new plant-based fermented foods especially plant-based cheese analogues.

Lactiplantibacillus brownii sp. nov., a novel psychrotolerant species isolated from sauerkraut

A Gram-stain-positive, rod-shaped, facultatively anaerobic and homofermentative strain, named WILCCON 0030T, was isolated from sauerkraut (fermented cabbage) collected from a local market in the Moscow region of Russia. Comparative analyses based on 16S rRNA gene sequence similarity and whole genome relatedness indicated that strain WILCCON 0030T was most closely related to the type strains Lactiplantibacillus nangangensis NCIMB 15186T, Lactiplantibacillus daoliensis LMG 31171T and Lactiplantibacillus pingfangensis LMG 31176T. However, the average nucleotide identity and digital DNA-DNA hybridization prediction values with these closest relatives only ranged from 84.6 to 84.9 % and from 24.1 to 24.7 %, respectively, and were below the 95.0 and 70.0% thresholds for species delineation. Substantiated by further physiological and biochemical analyses, strain WILCCON 0030T represents a novel species within the genus Lactiplantibacillus for which we propose the name Lactiplantibacillus brownii sp. nov. (type strain WILCCON 0030T=DSM 116485T=LMG 33211T).

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.

Metagenomics and metagenome-assembled genomes mining of health benefits in jalebi batter, a naturally fermented cereal-based food of India

Jalebi is one of the oldest Indian traditional fermented wheat-based confectioneries. Since jalebi is prepared by natural fermentation, diverse microbial community is expected to play bio-functional activities. Due to limited studies, information on microbial community structure in jalebi is unknown. Hence, the present study is aimed to profile the microbial community in jalebi by shotgun metagenomics and also to predict putative probiotic and functional genes by metagenome-assembled genome (MAG). Bacteria were the most abundant domain (91.91%) under which Bacillota was the most abundant phylum (82%). The most abundant species was Lapidilactobacillus dextrinicus followed by several species of lactic acid bacteria, acetic acid bacteria including few yeasts. Lap. dextrinicus was also significantly abundant in jalebi when compared to similar fermented wheat-based sourdough. Additionally, Lap. bayanensis, Pediococcus stilesii, and yeast- Candida glabrata, Gluconobacter japonicus, Pichia kudriavzevii, Wickerhamomyces anomalus were only detected in jalebi, which are not detected in sourdough. Few viruses and archaea were detected with < 1 % abundance. In silico screening of genes from the abundant species was mined using both KEGG and EggNOG database for putative health beneficial attributes. Circular genomes of five high-quality MAGs, identified as Lapidilactobacillus dextrinicus, Enterococcus hirae, Pediococcus stilesii, Acetobacter indonesiensis and Acetobacter cibinongensis, were constructed separately and putative genes were mapped and annotated. The CRISPR/Cas gene clusters in the genomes of four MAGs except Acetobacter cibinongensis were detected. MAGs also showed several secondary metabolites. Since, the identified MAGs have different putative genes for bio-functional properties, this may pave the way to selectively culture the uncultivated putative microbes for jalebi production. We believe this is the first report on metagenomic and MAGs of jalebi.

Antibiotic Resistance and Probiotics: Knowledge Gaps, Market Overview and Preliminary Screening

Probiotics are among those products, the use of which is increasing, and they are available primarily as food/dietary supplements, as well as in the form of medicines. This study aims to assess the attitudes and practices of health professionals and students of health sciences, give a short overview of the probiotics currently on the market, and conduct a screening of five food supplements and one drug with respect to antibiotic resistance. Nearly half of the respondents in our survey state that probiotics have no side effects, while only 6.3% believe that the use of probiotics can lead to antibiotic resistance. In addition, more than 40% of the participants throw unused probiotics into municipal waste. The market analysis results indicate that probiotic products on the Serbian market have highly variable CFU counts, while the declared health claims cover numerous beneficial health effects, and they are sometimes even registered as medicines. Lactobacilli are frequently present in probiotic supplements, and are sold in pharmacies and online. The experimental results showed that antibiotic resistance is present in different types of lactobacilli in probiotic products. The risk of using probiotics, regardless of their beneficial health effects, should be taken into account in the future. An update to the regulations governing probiotics, including a stipulation for antimicrobial resistance (AMR) testing, should be established, and guidelines for their proper use and disposal put into place.

Does sourdough bread provide clinically relevant health benefits?

During the last decade, scientific interest in and consumer attention to sourdough fermentation in bread making has increased. On the one hand, this technology may favorably impact product quality, including flavor and shelf-life of bakery products; on the other hand, some cereal components, especially in wheat and rye, which are known to cause adverse reactions in a small subset of the population, can be partially modified or degraded. The latter potentially reduces their harmful effects, but depends strongly on the composition of sourdough microbiota, processing conditions and the resulting acidification. Tolerability, nutritional composition, potential health effects and consumer acceptance of sourdough bread are often suggested to be superior compared to yeast-leavened bread. However, the advantages of sourdough fermentation claimed in many publications rely mostly on data from chemical and in vitro analyzes, which raises questions about the actual impact on human nutrition. This review focuses on grain components, which may cause adverse effects in humans and the effect of sourdough microbiota on their structure, quantity and biological properties. Furthermore, presumed benefits of secondary metabolites and reduction of contaminants are discussed. The benefits claimed deriving from in vitro and in vivo experiments will be evaluated across a broader spectrum in terms of clinically relevant effects on human health. Accordingly, this critical review aims to contribute to a better understanding of the extent to which sourdough bread may result in measurable health benefits in humans.

Genome Analysis of Potential Probiotic Levilactobacillus brevis AcCh91 Isolated from Indian Home-Made Fermented Milk Product (Chhurpi)

Consumption of naturally fermented milk (NFM) products is the dietary culture in India. The mountainous people of Arunachal Pradesh in India prepare the assorted artisanal home-made NFM products from cow and yak milk. Previously, we isolated and identified 76 strains of lactic acid bacteria (LAB) from NFM products of Arunachal Pradesh, viz. mar, chhurpi and churkam. We hypothesized that some of these LAB strains may possess probiotic potentials; hence, we investigated the probiotic potentials of these strains. On the basis of in vitro and genetic screening for probiotic attributes including haemolytic ability, 20 LAB strains were selected out of 76 strains, for further analysis. Using in silico analysis, viz. multivariate heatmap and PCA (principal component analysis) biplot, Levilactobacillus brevis AcCh91 was selected as the most promising probiotic strain, which was further characterized by the whole-genome analysis. Lev. brevis AcCh91 showed the highest survival rate of 93.38% in low pH and 86.68 ± 2.69% in low bile and the highest hydrophobicity average of 86.34 ± 5.53%. This strain also showed auto-aggregation and co-aggregation with antimicrobial properties against the pathogens, showed ability to produce beta-galactosidase and cholesterol reduction property and, most importantly, produced GABA, an important psychobiotic element. Genomic analysis of Lev. brevis AcCh91 showed the presence of genes corresponding to GABA, vitamins, amino acids, cholesterol reduction, immunomodulation, bioactive peptides and antioxidant activity. The absence of antimicrobial-resistant genes and virulence factors was observed. Hence, genome analysis supports the probiotic potentials of Lev. brevis AcCh91, which may be further investigated to understand its health-promoting properties.

Limosilactobacillus kribbianus sp. nov., isolated from pig faeces

A rod-shaped, aerotolerant, Gram-stain-positive bacterium isolated from pig faeces was designated as strain YH-lim2214T. Analysis of the 16S rRNA gene sequence revealed that the isolate was most closely related to Limosilactobacillus pontis KCTC 25258T with 98.0 % similarity. The average nucleotide identity and average amino acid identity values between YH-lim2214T and the most closely related strain Lm. pontis KCTC 25258T were 81.4 and 81.3 %, respectively. The major fatty acids were C18 : 1  ω9c, summed feature 7 and C16 : 0. The cell-wall peptidoglycan type was A4α l-Lys-d-Asp. The genomic DNA G+C content was 51.1 mol%. The chemotaxonomic, phenotypic and phylogenetic properties of YH-lim2214T (=KCTC 25572T=JCM 35701T) suggest that it represents a novel taxon, for which the name Limosilactobacillus kribbianus sp. nov. is proposed.

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

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

Ligilactobacillus ubinensis sp. nov., a novel species isolated from the wild ferment of a durian fruit (Durio zibethinus)

A Gram-stain-positive, rod-shaped, non-spore-forming, catalase-negative, urease-negative, homofermentative and facultatively anaerobic strain, named WILCCON 0076^T, was isolated from a wild ferment of pieces of a 'Kampung' durian fruit collected on the island of Ubin (Pulau Ubin), Singapore. The durian had fallen to the ground from a durian tree (Durio zibethinus), on which a group of long-tailed macaques had been observed picking and eating the fruits. Comparative analyses of 16S rRNA gene sequences indicated that WILCCON 0076^T potentially represented a novel species within the genus Ligilactobacillus, with the most closely related type strain being Ligilactobacillus agilis DSM 20509^T (16S rRNA gene sequence similarity of 97.2 %). Average nucleotide identity and digital DNA-DNA hybridization prediction values were only 86.0% and 18.9 %, respectively. On the basis of the results of a polyphasic approach that included phylogenomic, chemotaxonomic and morphological analyses, we propose a novel species with the name Ligilactobacillus ubinensis sp. nov. (type strain WILCCON 0076^T=DSM 114293^T=LMG 32698^T).

Lactobacillus for the treatment and prevention of atopic dermatitis: Clinical and experimental evidence

Atopic dermatitis (AD) is a chronic inflammatory skin disease, accompanied by itching and swelling. The main pathological mechanism of AD is related to the imbalance between Type 2 helper cells (Th2 cells) and Type 1 helper cells (Th1 cells). Currently, no safe and effective means to treat and prevent AD are available; moreover, some treatments have side effects. Probiotics, such as some strains of Lactobacillus, can address these concerns via various pathways: i) facilitating high patient compliance; ii) regulating Th1/Th2 balance, increasing IL-10 secretion, and reducing inflammatory cytokines; iii) accelerating the maturation of the immune system, maintaining intestinal homeostasis, and improving gut microbiota; and iv) improving the symptoms of AD. This review describes the treatment and prevention of AD using 13 species of Lactobacillus. AD is commonly observed in children. Therefore, the review includes a higher proportion of studies on AD in children and fewer in adolescents and adults. However, there are also some strains that do not improve the symptoms of AD and even worsen allergies in children. In addition, a subset of the genus Lactobacillus that can prevent and relieve AD has been identified in vitro. Therefore, future studies should include more in vivo studies and randomized controlled clinical trials. Given the advantages and disadvantages mentioned above, further research in this area is urgently required.

Genetic and phenotypic assessment of the antimicrobial activity of three potential probiotic lactobacilli against human enteropathogenic bacteria

Introduction

Lactobacilli are avid producers of antimicrobial compounds responsible for their adaptation and survival in microbe-rich matrices. The bactericidal or bacteriostatic ability of lactic acid bacteria (LAB) can be exploited for the identification of novel antimicrobial compounds to be incorporated in functional foodstuffs or pharmaceutical supplements. In this study, the antimicrobial and antibiofilm properties of Lactiplantibacillus pentosus L33, Lactiplantibacillus plantarum L125 and Lacticaseibacillus paracasei SP5, previously isolated form fermented products, were examined, against clinical isolates of Staphylococcus aureus, Salmonella enterica subsp. enterica serovar Enteritidis and Escherichia coli.

Methods

The ability of viable cells to inhibit pathogen colonization on HT-29 cell monolayers, as well as their co-aggregation capacity, were examined utilizing the competitive exclusion assay. The antimicrobial activity of cell-free culture supernatants (CFCS) was determined against planktonic cells and biofilms, using microbiological assays, confocal microscopy, and gene expression analysis of biofilm formation-related genes. Furthermore, in vitro analysis was supplemented with in silico prediction of bacteriocin clusters and of other loci involved in antimicrobial activity.

Results

The three lactobacilli were able to limit the viability of planktonic cells of S. aureus and E. coli in suspension. Greater inhibition of biofilm formation was recorded after co-incubation of S. enterica with the CFCS of Lc. paracasei SP5. Predictions based on sequence revealed the ability of strains to produce single or two-peptide Class II bacteriocins, presenting sequence and structural conservation with functional bacteriocins.

Discussion

The efficiency of the potentially probiotic bacteria to elicit antimicrobial effects presented a strain- and pathogen-specific pattern. Future studies, utilizing multi-omic approaches, will focus on the structural and functional characterization of molecules involved in the recorded phenotypes.

Limosilactobacillus reuteri Regulating Intestinal Function: A Review

Probiotics have extensive use in daily life, due to the function of the changing intestinal metabolism and material conversion processes, wherein they remodel the intestinal microbiota, regulate the intestinal function and affect the organism’s health. Limosilactobacillus reuteri (L. reuteri), originally discovered in breast milk and currently reported to be present within the gut of almost all vertebrates and mammals, is an intestinal probiotic with prebiotic efficacy. Most L. reuteri have good intestinal colonization and bacteriocin secretion abilities, which can increase the expression of the mucin (mucoprotein) genes 2 MUC2 and MUC13, which in turn promote the development and maturation of intestinal organoids, and augment mucin secretion. In enteritis patients, L. reuteri downregulates α Tumor necrosis factor-α, (TNF-α), Interleukin-6 (IL-6), IL-8, and IL-12 expression to attenuate inflammation. It also induces the host’s production of immunoglobulin A (IGA), which manipulates the intestinal microbial community, inhibiting the growth of pathogens. L. reuteri has been widely used in daily life. with in-depth studies having been conducted on the prebiotic effects of L. reuteri. However, the complexity of its application in a clinical setting is still unclear because the pathogenesis of various diseases still requires a large amount of data and theoretical support.

Strain-specific effect of Limosilactobacillus fermentum with distinct genetic lineages on loperamide-induced constipation in mice: attributing effects to certain genes

In 2013, Limosilactobacillus fermentum was regarded as a "generally recognized as safe" organism by the US Food and Drug Administration, and emerging evidence showed that it can exert beneficial health effects on humans. In this study, five L. fermentum strains from different phylogroups of a phylogenetic tree containing 224 L. fermentum strains were chosen, and their protective effects against loperamide-induced constipation in mice were studied. Animal experiments showed that L. fermentum YN54 significantly alleviated weight loss, increased fecal moisture, accelerated intestinal peristalsis, and increased the small intestinal transit rate in mice with constipation by regulating gastrointestinal peptides and increasing the amount of intestinal short-chain fatty acids. However, the other four L. fermentum strains (XJ61, CECT5716, WX115, and GD121) did not relieve constipation in mice treated with loperamide. A comparative genomic analysis of these strains was conducted and "L. fermentum YN54 only" genes were functionally annotated and validated with the other three L. fermentum strains (FJ12, GX51, and ZH1010) that had different functional genes. Finally, the genes involved in the synthesis of fatty acid hydrase, polysaccharides, and cell membranes were identified to be associated with the probiotic effect of L. fermentum on mice with constipation through preliminary experiments in this study.

Lactic acid bacteria: prominent player in the fight against human pathogens

INTRODUCTION

The human microbiome is a unique repository of diverse bacteria. Over 1000 microbial species reside in the human gut, which predominantly influences the host's internal environment and plays a significant role in host health. Lactic acid bacteria have long been employed for multiple purposes, ranging from food to medicines. Lactobacilli, which are often used in commercial food fermentation, have improved to the point that they might be helpful in medical applications.

AREAS COVERED

This review summarises various clinical and experimental evidence on efficacy of lactobacilli in treating a wide range of infections. Both laboratory based and clinical studies have been discussed.

EXPERT OPINION

Lactobacilli are widely accepted as safe biological treatments and host immune modulators (GRAS- Generally regarded as safe) by the US Food and Drug Administration and Qualified Presumption of Safety. Understanding the molecular mechanisms of lactobacilli in the treatment and pathogenicity of bacterial infections can help with the prediction and development of innovative therapeutics aimed at pathogens which have gained resistance to antimicrobials. To formulate effective lactobacilli based therapy significant research on the effectiveness of different lactobacilli strains and its association with demographic distribution is required. Also, the side effects of such therapy needs to be evaluated.

The plasmid-encoded lactose operon plays a vital role in the acid production rate of Lacticaseibacillus casei during milk beverage fermentation

Lacticaseibacillus casei is used extensively in the fermented milk-beverage industry as a starter culture. Acid production capacity during fermentation is the main criterion for evaluating starters although it is strain-dependent. In this study, the acid production rates of 114 L. casei strains were determined and then classified into high acid (HC), medium acid (MC), and low acid (LC) groups. Comparative genomics analysis found that the lac operon genes encoding the phosphoenolpyruvate-lactose phosphotransferase system (PTS^Lac) were located on plasmids in the HC strains; however, it is notable that the corresponding operons were located on the chromosome in LC strains. Real-time PCR analysis showed that the copy numbers of lac operon genes in HC strains were between 3.1 and 9.3. To investigate the relationship between copy number and acid production rate, the lac operon cluster of the HC group was constitutively expressed in LC strains. The resulting copy numbers of lac operon genes were between 15.8 and 18.1; phospho-β-galactosidase activity increased by 1.68–1.99-fold; and the acid production rates increased by 1.24–1.40-fold, which enhanced the utilization rate of lactose from 17.5 to 42.6% in the recombinant strains. The markedly increased expression of lac operon genes increased lactose catabolism and thereby increased the acid production rate of L. casei.

Metabolic framework of spontaneous and synthetic sourdough metacommunities to reveal microbial players responsible for resilience and performance

BACKGROUND

In nature, microbial communities undergo changes in composition that threaten their resiliency. Here, we interrogated sourdough, a natural cereal-fermenting metacommunity, as a dynamic ecosystem in which players are subjected to continuous environmental and spatiotemporal stimuli.

RESULTS

The inspection of spontaneous sourdough metagenomes and transcriptomes revealed dominant, subdominant and satellite players that are engaged in different functional pathways. The highest microbial richness was associated with the highest number of gene copies per pathway. Based on meta-omics data collected from 8 spontaneous sourdoughs and their identified microbiota, we de novo reconstructed a synthetic microbial community SDG. We also reconstructed SMC-SD43 from scratch using the microbial composition of its spontaneous sourdough equivalent for comparison. The KEGG number of dominant players in the SDG was not affected by depletion of a single player, whereas the subdominant and satellite species fluctuated, revealing unique contributions. Compared to SMC-SD43, SDG exhibited broader transcriptome redundancy. The invariant volatilome profile of SDG after in situ long-term back slopping revealed its stability. In contrast, SMC-SD43 lost many taxon members. Dominant, subdominant and satellite players together ensured gene and transcript redundancy.

CONCLUSIONS

Our study demonstrates how, by starting from spontaneous sourdoughs and reconstructing these communities synthetically, it was possible to unravel the metabolic contributions of individual players. For resilience and good performance, the sourdough metacommunity must include dominant, subdominant and satellite players, which together ensure gene and transcript redundancy. Overall, our study changes the paradigm and introduces theoretical foundations for directing food fermentations. Video Abstract.

Heterofermentative lactic acid bacteria such as Limosilactobacillus as a strong inhibitor of aldehyde compounds in plant-based milk alternatives

Reduction of greenhouse gas emissions is important to limit climate change. Because ruminant animals emit greenhouse gases, the worldwide plant-based alternative market is an emerging trend for eating less meat and dairy products. To produce plant-based dairy products such as yogurt alternatives, certain lactic acid bacterial species, which are used for cow's milk fermentation, are often used. Substrate changes from cow's milk to plant-based milk caused nutritional changes, and unsaturated fatty acids are more enriched in plant-based milk alternatives than in cow's milk. Unsaturated fatty acids can lead to the formation of aldehydes, some of which are off-flavors; therefore, substrate changes have the potential to alter the suitable lactic acid bacterial species used for fermentation to control flavor formation, such as aldehyde compounds. However, differences in the effect of the fermentation processes on aldehyde compounds have not been evaluated among lactic acid bacterial species. In this study, we comprehensively evaluated the effect of lactic acid bacterial fermentation on aldehyde compounds in synthetic medium and plant-based milk alternatives using 20 species of lactic acid bacteria. Heterofermentative lactic acid bacteria such as strains belonging to Limosilactobacillus had a strong aldehyde-reducing ability, likely from differences in alcohol dehydrogenase function. Because the odor detection threshold of ethanol compounds was lower than that of their equivalent aldehyde compounds, our findings are valuable for the fermentation of plant-based milk alternatives with lactic acid bacteria with the goal of decreasing off-flavors derived from aldehyde compounds.

Calcium Determines Lactiplantibacillus plantarum Intraspecies Competitive Fitness

The importance of individual nutrients for microbial strain robustness and coexistence in habitats containing different members of the same species is not well understood. To address this for Lactiplantibacillus plantarum in food fermentations, we performed comparative genomics and examined the nutritive requirements and competitive fitness for L. plantarum strains B1.1 and B1.3 isolated from a single sample of teff injera fermentation batter. Compared to B1.1 and other L. plantarum strains, B1.3 has a smaller genome, limited biosynthetic capacities, and large mobilome. Despite these differences, B1.3 was equally competitive with B1.1 in a suspension of teff flour. In commercially sourced, nutrient-replete MRS (cMRS) medium, strain B1.3 reached 3-fold-higher numbers than B1.1 within 2 days of passage. Because B1.3 growth and competitive fitness were poor in mMRS medium (here called mMRS), a modified MRS medium lacking beef extract, we used mMRS to identify nutrients needed for robust B1.3 growth. No improvement was observed when mMRS was supplemented with nucleotides, amino acids, vitamins, or monovalent metals. Remarkably, the addition of divalent metal salts increased the growth rate and cell yields of B1.3 in mMRS. Metal requirements were confirmed by inductively coupled plasma mass spectrometry, showing that total B1.3 intracellular metal concentrations were significantly (up to 2.7-fold) reduced compared to B1.1. Supplemental CaCl₂ conferred the greatest effect, resulting in equal growth between B1.1 and B1.3 over five successive passages in mMRS. Moreover, calcium supplementation reversed a B1.3 strain-specific, stationary-phase, flocculation phenotype. These findings show how L. plantarum calcium requirements affect competitive fitness at the strain level.

IMPORTANCE Ecological theory states that the struggle for existence is stronger between closely related species. Contrary to this assertion, fermented foods frequently sustain conspecific individuals, in spite of their high levels of phylogenetic relatedness. Therefore, we investigated two isolates of Lactiplantibacillus plantarum, B1.1 and B1.3, randomly selected from a single batch of teff injera batter. These strains spanned the known genomic and phenotypic range of the L. plantarum species, and in laboratory culture medium used for strain screening, B1.3 exhibited poor growth and was outcompeted by the more robust strain B1.1. Nonetheless, B1.1 and B1.3 were equally competitive in teff flour. This result shows how L. plantarum has adapted for coexistence in that environment. The capacity for the single macronutrient calcium to restore B1.3 competitive fitness in laboratory culture medium suggests that L. plantarum intraspecies diversity found in food systems is fine-tuned to nutrient requirements at the strain level.

Research Update on the Impact of Lactic Acid Bacteria on the Substance Metabolism, Flavor, and Quality Characteristics of Fermented Meat Products

This paper reviews the effects of domestic and foreign influences on the substance metabolism pathways and the flavor and flora of LAB in fermented meat products to provide a new theoretical basis for developing new products for the industrial application of lactic acid bacteria (LAB) in fermented meat products. LAB are extensively used among commonly fermented ingredients, such as fermented meat products and yogurt. As fermenting agents, LAB metabolize proteins, lipids, and glycogen in meat products through their enzyme system, which affects the tricarboxylic acid cycle, fatty acid metabolism, amino acid decomposition, and other metabolic processes, and decompose biological macromolecules into small molecules, adding a special flavor with a certain functionality to the final product. Metabolites of LAB in the fermentation process also exert nitrite degradation, as well as antibacterial and antioxidant functions, which improve the physical and chemical qualities of fermented meat products. While fermenting meat products, LAB not only add unique flavor substances to the products, but also improve the safety profile of fermented foods.

Genomic Insight Into Lacticaseibacillus paracasei SP5, Reveals Genes and Gene Clusters of Probiotic Interest and Biotechnological Potential

The Lacticaseibacillus paracasei species is comprised by nomadic bacteria inhabiting a wide variety of ecological niches, from fermented foodstuffs to host-associated microenvironments. Lc. paracasei SP5 is a novel strain, originally isolated from kefir grains that presents desirable probiotic and biotechnological attributes. In this study, we applied genomic tools to further characterize the probiotic and biotechnological potential of the strain. Firstly, whole genome sequencing and assembly, were performed to construct the chromosome map of the strain and determine its genomic stability. Lc. paracasei SP5 carriers several insertion sequences, however, no plasmids or mobile elements were detected. Furthermore, phylogenomic and comparative genomic analyses were utilized to study the nomadic attributes of the strain, and more specifically, its metabolic capacity and ability to withstand environmental stresses imposed during food processing and passage through the gastrointestinal (GI) tract. More specifically, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Carbohydrate-active enzyme (CAZymes) analyses provided evidence for the ability of the stain to utilize an array of carbohydrates as growth substrates. Consequently, genes for heat, cold, osmotic shock, acidic pH, and bile salt tolerance were annotated. Importantly bioinformatic analysis showed that the novel strain does not harbor acquired antimicrobial resistance genes nor virulence factors, in agreement with previous experimental data. Putative bacteriocin biosynthesis clusters were identified using BAGEL4, suggesting its potential antimicrobial activity. Concerning microbe-host interactions, adhesins, moonlighting proteins, exopolysaccharide (EPS) biosynthesis genes and pilins mediating the adhesive phenotype were, also, pinpointed in the genome of Lc. paracasei SP5. Validation of this phenotype was performed by employing a microbiological method and confocal microscopy. Conclusively, Lc. paracasei SP5 harbors genes necessary for the manifestation of the probiotic character and application in the food industry. Upcoming studies will focus on the mechanisms of action of the novel strain at multiple levels.

Occurrence of phenotypic variation in Paenibacillus polymyxa E681 associated with sporulation and carbohydrate metabolism

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We report phenotypic variation in P. polymyxa E681 occurred when grown on media.

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F-type exhibited faster cell growth than B-type after utilization of carbon sources.

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2-DE identified proteins involved in various metabolic activities.

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The motility is mediated via the downregulation of sporulation and flagella production.

We report the phenotypic variation in Paenibacillus polymyxa E681 (E681), a plant growth-promoting rhizobacterium (PGPR) isolated from a winter barley root in Korea. Phenotypic variation (F-type) occurred when E681 (B-type) was grown in the media, and F-type was generated from B-type. B- and F-types were characterized by their morphological, Biolog, and GC-MIDI analyses. F-type cells altered the original biological capacity of B-type cells on endospore and flagella formation, changes in pH in culture, and carbon utilization. In growth curve analysis, B-type variants recovered bacterial growth as the variation occurred after the decline phase, but F-type variants did not. To determine this cause, we conducted comparative proteome analysis between B- and F-types using two-dimensional gel electrophoresis (2-DE). Of the identified proteins, 47% were involved in glycolysis and other metabolic pathways associated with carbohydrate metabolism. Therefore, our findings provide new knowledge on the mechanism of phenotypic variation and insights into agricultural biotechnology.

Acids produced by lactobacilli inhibit the growth of commensal Lachnospiraceae and S24-7 bacteria

The Lactobacillaceae are an intensively studied family of bacteria widely used in fermented food and probiotics, and many are native to the gut and vaginal microbiota of humans and other animals. Various studies have shown that specific Lactobacillaceae species produce metabolites that can inhibit the colonization of fungal and bacterial pathogens, but less is known about how Lactobacillaceae affect individual bacterial species in the endogenous animal microbiota. Here, we show that numerous Lactobacillaceae species inhibit the growth of the Lachnospiraceae family and the S24-7 group, two dominant clades of bacteria within the gut. We demonstrate that inhibitory activity is a property common to homofermentative Lactobacillaceae species, but not to species that use heterofermentative metabolism. We observe that homofermentative Lactobacillaceae species robustly acidify their environment, and that acidification alone is sufficient to inhibit growth of Lachnospiraceae and S24-7 growth, but not related species from the Clostridiales or Bacteroidales orders. This study represents one of the first in-depth explorations of the dynamic between Lactobacillaceae species and commensal intestinal bacteria, and contributes valuable insight toward deconvoluting their interactions within the gut microbial ecosystem.

After the storm-Perspectives on the taxonomy of Lactobacillaceae

In 2020, a taxonomic reorganization of the lactic acid bacteria reclassified over 300 species in 7 genera and 2 families into one family, the Lactobacillaceae, with 31 genera including 23 new genera to include organisms formerly classified as Lactobacillus species. This communication aims to provide a debrief on the taxonomic reorganization of lactobacilli to identify shortcomings in the proposed taxonomic framework, and to outline perspectives and opportunities provided by the current taxonomy of the Lactobacillaceae. The current taxonomy of lactobacilli not only necessitates becoming familiar with 23 new genus names but also provides substantial new opportunities in scientific discovery and regulatory approval of these organisms. First, description of new species in the Lactobacillaceae is facilitated and a solid framework for description of novel genera is provided. Second, the current taxonomy greatly enhances the resolution of genus-level sequencing approaches (e.g., 16S rRNA-based metagenomics) when identifying the composition and function of microbial communities. Third, the current taxonomy greatly facilitates the formulation of hypotheses linking phylogeny to metabolism and ecology of lactobacilli.

Lactobacillus in Food Animal Production—A Forerunner for Clean Label Prospects in Animal-Derived Products

Lactobacillus, the largest genus within the lactic acid bacteria group, has served diverse roles in improving the quality of foods for centuries. The heterogeneity within this genus has resulted in the industry's continued use of their well-known functions and exploration of novel applications. Moreover, the perceived health benefits in many applications have also made them fond favorites of consumers and researchers alike. Their familiarity lends to their utility in the growing “clean label” movement, of which consumers prefer fewer additions to the food label and opt for recognizable and naturally-derived substances. Our review primarily focuses on the historical use of lactobacilli for their antimicrobial functionality in improving preharvest safety, a critical step to validate their role as biocontrol agents and antibiotic alternatives in food animal production. We also explore their potential as candidates catering to the consumer-driven demand for more authentic, transparent, and socially responsible labeling of animal products.

The Impacts of Lactiplantibacillus plantarum on the Functional Properties of Fermented Foods: A Review of Current Knowledge

One of the most varied species of lactic acid bacteria is Lactiplantibacillus plantarum (Lb. plantarum), formerly known as Lactobacillus plantarum. It is one of the most common species of bacteria found in foods, probiotics, dairy products, and beverages. Studies related to genomic mapping and gene locations of Lb. plantarum have shown the novel findings of its new strains along with their non-pathogenic or non-antibiotic resistance genes. Safe strains obtained with new technologies are a pioneer in the development of new probiotics and starter cultures for the food industry. However, the safety of Lb. plantarum strains and their bacteriocins should also be confirmed with in vivo studies before being employed as food additives. Many of the Lb. plantarum strains and their bacteriocins are generally safe in terms of antibiotic resistance genes. Thus, they provide a great opportunity for improving the nutritional composition, shelf life, antioxidant activity, flavour properties and antimicrobial activities in the food industry. Moreover, since some Lb. plantarum strains have the ability to reduce undesirable compounds such as aflatoxins, they have potential use in maintaining food safety and preventing food spoilage. This review emphasizes the impacts of Lb. plantarum strains on fermented foods, along with novel approaches to their genomic mapping and safety aspects.

Evaluation of IR Biotyper for Lactiplantibacillus plantarum Typing and Its Application Potential in Probiotic Preliminary Screening

IR Biotyper (IRBT), which is a spectroscopic system for microorganism typing based on Fourier transform infrared (FTIR) technology, has been used to detect the spread of clones in clinical microbiology laboratories. However, the use of IRBT to detect probiotics has rarely been reported. Herein, we evaluated the discriminatory power of IRBT to type Lactiplantibacillus plantarum isolates at the strain level and explored its application potential in probiotic preliminary selection. Twenty Lactiplantibacillus isolates collected from pickled radishes during successive fermentation were used to test the robustness of IRBT at the strain level. IRBT was then compared with genotyping methods such as whole-genome sequencing (WGS), pulsed-field gel electrophoresis (PFGE), and multilocus sequence typing (MLST) to evaluate its discrimination power. IRBT distributed the 20 isolates into five clusters, with L. argentoratensis isolate C7-83 being the most distant from the other isolates, which belonged to L. plantarum. IRBT showed good reproducibility, although deviation in the discriminative power of IRBT was found at the strain level across laboratories, probably due to technical variance. All examined methods allowed bacterial identification at the strain level, but IRBT had higher discriminatory power than MLST and was comparable to the WGS and PFGE. In the phenotypic comparison study, we observed that the clustering results of probiotic physiological attributes (e.g., sensitivity to acid and bile salts, hydrophobicity of the cell surface, and resistance to antibiotics) were consistent with the typing results of IRBT. Our results indicated that IRBT is a robust tool for L. plantarum strain typing that could improve the efficiency of probiotic identification and preliminary screening, and can potentially be applied in probiotic traceability and quality control.

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.

Omics Approaches to Assess Flavor Development in Cheese

Cheese is characterized by a rich and complex microbiota that plays a vital role during both production and ripening, contributing significantly to the safety, quality, and sensory characteristics of the final product. In this context, it is vital to explore the microbiota composition and understand its dynamics and evolution during cheese manufacturing and ripening. Application of high-throughput DNA sequencing technologies have facilitated the more accurate identification of the cheese microbiome, detailed study of its potential functionality, and its contribution to the development of specific organoleptic properties. These technologies include amplicon sequencing, whole-metagenome shotgun sequencing, metatranscriptomics, and, most recently, metabolomics. In recent years, however, the application of multiple meta-omics approaches along with data integration analysis, which was enabled by advanced computational and bioinformatics tools, paved the way to better comprehension of the cheese ripening process, revealing significant associations between the cheese microbiota and metabolites, as well as their impact on cheese flavor and quality.

Optimization of a cultivation procedure to selectively isolate lactic acid bacteria from insects

AIMS

Natural niches and transmission routes of lactic acid bacteria (LAB) are highly versatile. Proposed routes of transmission to food fermentations are from plant material via insects or vice versa. This study aimed to establish a method for the selective isolation of LAB from insects.

METHODS AND RESULTS

Varied parameters that influence growth and selectivity are temperature, type of carbohydrate and atmosphere. Additionally, effects of antibiotics to suppress non-LAB species were evaluated. A model consortium consisting of 12 species representing different lifestyles was inoculated in growth medium to identify conditions for highest diversity and recovery rate. The method was applied to isolate LAB from Drosophila melanogaster, Sitotroga cerealella, Tribolium castaneum and Tenebrio molitor. Isolated species were Leuconostoc mesenteroides, Paucilactobacillus vaccinostercus and Lactiplantibacillus plantarum from D. melanogaster and L. mesenteroides, Pediococcus pentosaceus and Latilactobacillus curvatus from T. molitor. No LAB could be isolated from T. castaneum and S. cerealella. 16S rDNA amplicon sequencing of DNA obtained from insects corroborated part of our results.

CONCLUSION

A combination of different enrichment conditions ensures a high probability to isolate LAB species from insects and can be helpful above already known non-cultivation methods.

SIGNIFICANCE AND IMPACT OF THE STUDY

The novel method allows to selectively isolate LAB from insects and the strategy of the method is of interest to study other niches.

Common Inflammatory Mechanisms in COVID-19 and Parkinson's Diseases: The Role of Microbiome, Pharmabiotics and Postbiotics in Their Prevention

In the last decade, metagenomic studies have shown the key role of the gut microbiome in maintaining immune and neuroendocrine systems. Malfunction of the gut microbiome can induce inflammatory processes, oxidative stress, and cytokine storm. Dysfunction of the gut microbiome can be caused by short-term (virus infection and other infectious diseases) or long-term (environment, nutrition, and stress) factors. Here, we reviewed the inflammation and oxidative stress in neurodegenerative diseases and coronavirus infection (COVID-19). Here, we reviewed the renin-angiotensin-aldosterone system (RAAS) involved in the processes of formation of oxidative stress and inflammation in viral and neurodegenerative diseases. Moreover, the coronavirus uses ACE2 receptors of the RAAS to penetrate human cells. The coronavirus infection can be the trigger for neurodegenerative diseases by dysfunction of the RAAS. Pharmabiotics, postbiotics, and next-generation probiotics, are considered as a means to prevent oxidative stress, inflammatory processes, neurodegenerative and viral diseases through gut microbiome regulation.

Antimicrobial plant secondary metabolites, MDR transporters and antimicrobial resistance in cereal-associated lactobacilli: is there a connection?

Cereal-associated lactobacilli resist antimicrobial plant secondary metabolites. This study aimed to identify multi-drug-resistance (MDR) transporters in isolates from mahewu, a Zimbabwean fermented cereal beverage, and to determine whether these MDR-transporters relate to resistance against phenolic compounds and antibiotics. Comparative genomic analyses indicated that all seven mahewu isolates harbored multiple MATE and MFS MDR proteins. Strains of Lactiplantibacillus plantarum and Limosilactobacillus fermentum encoded for the same gene, termed mahewu phenolics resistance gene mprA, with more than 99% nucleotide identity, suggesting horizontal gene transfer. Strains of Lp. plantarum were more resistant than strains of Lm. fermentum to phenolic acids, other antimicrobials and antibiotics but the origins of strains were not related to resistance. The resistance of several strains exceeded EFSA thresholds for several antibiotics. Analysis of gene expression in one strain each of Lp. plantarum and Lm. fermentum revealed that at least one MDR gene in each strain was over-expressed during growth in wheat, sorghum and millet relative to growth in MRS5 broth. In addition, both strains over-expressed a phenolic acid reductase. The results suggest that diverse lactobacilli in mahewu share MDR transporters acquired by lateral gene transfer, and that these transporters mediate resistance to secondary plant metabolites and antibiotics.

Genomic and Phylogenetic Analysis of Lactiplantibacillus plantarum L125, and Evaluation of Its Anti-Proliferative and Cytotoxic Activity in Cancer Cells

Lactiplantibacillus plantarum is a diverse species that includes nomadic strains isolated from a variety of environmental niches. Several L. plantarum strains are being incorporated in fermented foodstuffs as starter cultures, while some of them have also been characterized as probiotics. In this study, we present the draft genome sequence of L. plantarum L125, a potential probiotic strain presenting biotechnological interest, originally isolated from a traditional fermented meat product. Phylogenetic and comparative genomic analysis with other potential probiotic L. plantarum strains were performed to determine its evolutionary relationships. Furthermore, we located genes involved in the probiotic phenotype by whole genome annotation. Indeed, genes coding for proteins mediating host–microbe interactions and bile salt, heat and cold stress tolerance were identified. Concerning the potential health-promoting attributes of the novel strain, we determined that L. plantarum L125 carries an incomplete plantaricin gene cluster, in agreement with previous in vitro findings, where no bacteriocin-like activity was detected. Moreover, we showed that cell-free culture supernatant (CFCS) of L. plantarum L125 exerts anti-proliferative, anti-clonogenic and anti-migration activity against the human colon adenocarcinoma cell line, HT-29. Conclusively, L. plantarum L125 presents desirable probiotic traits. Future studies will elucidate further its biological and health-related properties.

Whole-Genome Sequencing, Phylogenetic and Genomic Analysis of Lactiplantibacillus pentosus L33, a Potential Probiotic Strain Isolated From Fermented Sausages

Lactobacillus is a diverse genus that includes species of industrial and biomedical interest. Lactiplantibacillus pentosus, formerly known as Lactobacillus pentosus, is a recently reclassified species, that contains strains isolated from diverse environmental niches, ranging from fermented products to mammalian gut microbiota. Importantly, several L. pentosus strains present health-promoting properties, such as immunomodulatory and antiproliferative activities, and are regarded as potential probiotic strains. In this study, we present the draft genome sequence of the potential probiotic strain L. pentosus L33, originally isolated from fermented sausages. Comprehensive bioinformatic analysis and whole-genome annotation were performed to highlight the genetic loci involved in host-microbe interactions and the probiotic phenotype. Consequently, we found that this strain codes for bile salt hydrolases, adhesins and moonlighting proteins, and for Class IIb bacteriocin peptides lacking the GxxxG and GxxxG-like motifs, crucial for their inhibitory activity. Its adhesion ability was also validated in vitro, on human cancer cells. Furthermore, L. pentosus L33 contains an exopolysaccharide (EPS) biosynthesis cluster, and it does not carry transferable antibiotic resistance genes. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and CAZymes analyses showed that L. pentosus L33 possesses biosynthetic pathways for seven amino acids, while it can degrade a wide array of carbohydrates. In parallel, Clusters of Orthologous Groups (COGs) and KEGG profiles of L. pentosus L33 are similar to those of 26 L. pentosus strains, as well as of two well documented L. plantarum probiotic strains. Conclusively, L. pentosus L33 exhibits good probiotic potential, although further studies are needed to elucidate the extent of its biological properties.

LC-MS/MS quantitation of α-amylase/trypsin inhibitor CM3 and glutathione during wheat sourdough breadmaking

AIMS

This study aimed to quantify α-amylase/trypsin inhibitor (ATI) CM3 and glutathione (GSH) during wheat sourdough breadmaking.

METHODS AND RESULTS

Breads were made with two wheat cultivars and fermented with Fructilactobacillus sanfranciscensis, F. sanfranciscensis ΔgshR or Latilactobacillus sakei; chemically acidified and straight doughs served as controls. Samples were analysed after mixing, after proofing and after baking. GSH and CM3 were quantified by multi-reaction-monitoring-based methods on an LC-QTRAP mass spectrometer. Undigested ATI extracts were further examined by SDS-PAGE.

CONCLUSIONS

GSH abundance was similar after mixing and after proofing but increased after baking (p < 0.001), regardless of fermentation. In breads baked with cv. Brennan, the samples fermented with lactobacilli had higher GSH abundance (p < 0.001) than in the controls. CM3 relative abundance remained similar after mixing and after proofing but decreased after baking (p < 0.001) across all treatments. This trend was supported by the SDS-PAGE analysis in which ATI band intensities decreased after baking (p < 0.001) in all experimental conditions. The overall effect of baking exerted a greater effect on the abundances of GSH and CM3 than fermentation conditions.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first report to quantify ATI over the course of breadmaking by LC-MS/MS in sourdough and straight dough processes.

Bacteriocin production and inhibition of Bacillus subtilis by Lactobacillus paracasei HD1.7 in an indirect coculture system

A broad-spectrum antimicrobial peptide named Paracin 1.7 was produced by Lactobacillus paracasei HD1.7, which was isolated from Chinese sauerkraut juice. In this study, the influence of cocultivation on the communication mechanism of L. paracasei HD1.7 and Bacillus subtilis was investigated. The two bacterial strains were grown in monoculture and indirect coculture, and the growth of both bacteria and bacteriocin production as well as the transcriptional level of luxS in L. paracasei HD1.7 and spo0A in B. subtilis were monitored. Bacteriocin production and cell numbers were increased significantly when L. paracasei HD1.7 cells were indirectly cocultured with B. subtilis, and bacteriocin-producing L. paracasei HD1.7 can prevent the growth and sporulation of B. subtilis. After indirect coculture with B. subtilis, the expression of luxS in L. paracasei HD1.7 increased in the exponential growth phase and decreased in the stationary phase compared to monoculture. The expression of spo0A in B. subtilis dropped in the indirect coculture compared to the monoculture. It indicate that the upregulation of luxS is due to a response to a secreted compound produced by B. subtilis. The results show L. paracasei HD1.7 has an amensalism on B. subtilis, while B. subtilis has a commensalism on L. paracasei HD1.7.

Wildlife symbiotic bacteria are indicators of the health status of the host and its ecosystem

Lactic acid bacteria (LAB) are gut symbionts that can be used as a model to understand the host-microbiota crosstalk under unpredictable environmental conditions such as wildlife ecosystems. The aim of this study was to determine whether viable LAB can be informative of the health status of wild boar populations. We monitored the genotype and phenotype of LAB based on markers that included safety and phylogenetic origin, antibacterial activity and immunomodulatory properties. A LAB profile dominated by lactobacilli appears to stimulate protective immune responses and relates to strains widely used as probiotics, resulting in a potentially healthy wildlife population whereas microbiota overpopulated by enterococci was observed in a hostile environment. These enterococci were closely related to pathogenic strains that have developed mechanisms to evade innate immune system, posing a potential risk for the host health. Furthermore, our LAB isolates displayed antibacterial properties in a species-dependent manner. Nearly all of them were able to inhibit bacterial pathogens, raising the possibility of using them as a la carte antibiotic alternative in the unexplored field of wildlife disease mitigation. Our study highlights that microbiological characterization of LAB is a useful indicator of wildlife health status and the ecological origin from which they derive. Significance Statement The wildlife symbiotic microbiota is an important component to the greater for greater diversity and functionality of their bacterial populations, influencing the host health and adaptability to its ecosystem. Although many microbes are partly responsible for the development of multiple physiological processes, only certain bacterial groups such as lactic acid bacteria (LAB) have the capacity to overpopulate the gut, promoting health (or disease) when specific genetic and environmental conditions are present. LAB have been exploited in many ways due to their probiotic properties, in particular lactobacilli, however their relationship with wildlife gut-associated microbiota hosts remains to be elucidated. On the other hand, it is unclear whether LAB such as enterococci, which have been associated with detrimental health effects, could lead to disease. These important questions have not been properly addressed in the field of wildlife, and therefore, should be clearly attained.

Sourdough production: fermentation strategies, microbial ecology, and use of non-flour ingredients

Sourdough production is an ancient method to ferment flour from cereals for the manufacturing of baked goods. This review deals with the state-of-the-art of current fermentation strategies for sourdough production and the microbial ecology of mature sourdoughs, with a particular focus on the use of non-flour ingredients. Flour fermentation processes for sourdough production are typically carried out by heterogeneous communities of lactic acid bacteria and yeasts. Acetic acid bacteria may also occur, although their presence and role in sourdough production can be criticized. Based on the inoculum used, sourdough productions can be distinguished in fermentation processes using backslopping procedures, originating from a spontaneously fermented flour-water mixture (Type 1), starter culture-initiated fermentation processes (Type 2), and starter culture-initiated fermentation processes that are followed by backslopping (Type 3). In traditional recipes for the initiation and/or propagation of Type 1 sourdough productions, non-flour ingredients are often added to the flour-water mixture. These ingredients may be the source of an additional microbial inoculum and/or serve as (co-)substrates for fermentation. An example of the former is the addition of yoghurt; an example of the latter is the use of fruit juices. The survival of microorganisms transferred from the ingredients to the fermenting flour-water mixture depends on the competitiveness toward particular strains of the microbial species present under the harsh conditions of the sourdough ecosystem. Their survival and growth is also determined by the presence of the appropriate substrates, whether or not carried over by the ingredients added.

D- and l-amino acid concentrations in culture broth of Lactobacillus are highly dependent on the phylogenetic group of Lactobacillus

d-amino acids produced by Lactobacillus are thought to contribute to the taste quality and health functions; however, no studies have comprehensively evaluated the concentrations of the D- and L-forms of amino acids separately in individual Lactobacillus strains. To gain insight into amino acid concentrations in Lactobacillus, we evaluated amino acid concentrations in culture broth of Lactobacillus separately for the D- and L-forms. Lactobacillus strains were cultured in culture broth, and the amino acid concentrations in supernatant were assessed. The amino acid concentrations obtained by liquid chromatography-tandem mass spectrometry (LC-MS/MS) were subjected to cluster analysis based on Bray-Curtis distance with Ward's minimum variance method. In the analysis of amino acid concentrations under culture with different monosaccharides, the distances among strains cultured with the same monosaccharide were significantly greater than those among cultures of the same strain under different monosaccharides (p < 0.01). The cluster analysis of amino acid concentrations under culture with the same monosaccharide suggested that strains belonging to the same phylogenetic group of Lactobacillus exhibited similar concentrations of amino acids. Data analyses of 70 strains belonging to 17 Lactobacillus taxa indicated that the concentrations of amino acids were highly dependent on the phylogenetic group of Lactobacillus and that the group differences in amino acid concentration were strongly driven by differences in l-serine and d-alanine concentrations. Our results indicate that it is important to evaluate D- and l-amino acids separately when evaluating variations in amino acid concentrations. Because d-alanine has the potential to affect taste quality, the results of this study may provide insight into the taste quality of fermented food produced by Lactobacillus.