Identification of Lactobacillus brevis using a species-specific AFLP-derived marker

Recent and Advanced DNA-Based Technologies for the Authentication of Probiotic, Protected Designation of Origin (PDO) and Protected Geographical Indication (PGI) Fermented Foods and Beverages

The authenticity of probiotic products and fermented foods and beverages that have the status of protected designation of origin (PDO) or geographical indication (PGI) can be assessed via numerous methods. DNA-based technologies have emerged in recent decades as valuable tools to achieve food authentication, and advanced DNA-based methods and platforms are being developed. The present review focuses on the recent and advanced DNA-based techniques for the authentication of probiotic, PDO and PGI fermented foods and beverages. Moreover, the most promising DNA-based detection tools are presented. Strain- and species-specific DNA-based markers of microorganisms used as starter cultures or (probiotic) adjuncts for the production of probiotic and fermented food and beverages have been exploited for valuable authentication in several detection methods. Among the available technologies, propidium monoazide (PMA) real-time polymerase chain reaction (PCR)-based technologies allow for the on-time quantitative detection of viable microbes. DNA-based lab-on-a-chips are promising devices that can be used for the on-site and on-time quantitative detection of microorganisms. PCR-DGGE and metagenomics, even combined with the use of PMA, are valuable tools allowing for the fingerprinting of the microbial communities, which characterize PDO and PGI fermented foods and beverages, and they are necessary for authentication besides permitting the detection of extra or mislabeled species in probiotic products. These methods, in relation to the authentication of probiotic foods and beverages, need to be used in combination with PMA, culturomics or flow cytometry to allow for the enumeration of viable microorganisms.

Advances in characterization of probiotics and challenges in industrial application

An unbalanced diet and poor lifestyle are common reasons for numerous health complications in humans. Probiotics are known to provide substantial benefits to human health by producing several bioactive compounds, vitamins, short-chain fatty acids and short peptides. Diets that contain probiotics are limited to curd, yoghurt, kefir, kimchi, etc. However, exploring the identification of more potential probiotics and enhancing their commercial application to improve the nutritional quality would be a significant step to utilizing the maximum benefits. The complex evolution patterns among the probiotics are the hurdles in their characterization and adequate application in the industries and dairy products. This article has mainly discussed the molecular methods of characterization that are based on the analysis of ribosomal RNA, whole genome, and protein markers and profiles. It also has critically emphasized the emerging challenges in industrial applications of probiotics.

Metabolomic evaluation of different starter culture effects on water-soluble and volatile compound profiles in nozawana pickle fermentation

Metabolomic characterization of a lactic-fermented pickle of nozawana (Brassica rapa L. var. hakabura) was conducted to evaluate the effects of different starter culture strains on the chemical profiles. We compared the profiles of water-soluble and volatile compounds obtained by non-targeted nuclear magnetic resonance and solid-phase microextraction gas chromatography/mass spectrometry analyses. Principal component analyses indicated that the fermented samples differed significantly in terms of the levels of various compounds, including taste- and aroma-active components, such as water-soluble residual sugars, organic acids, mannitol, ethanol, dihydroxyacetone, ornithine, γ-aminobutyric acid, choline, volatile isothiocyanates, 3,4-epithiobutyl cyanide, 2,3-butanedione, acetoin, ethyl acetate, dimethyl trisulfide, and S-methyl thioacetate. Fermentation with a Latilactobacillus curvatus culture was associated with a unique metabolite profile characterized by higher levels of isothiocyanates and hexanoic acid and lower levels of lactic acid, acetic acid, acetoin, and 2,3-butanedione. These variations in the chemical profile might be associated with different qualities in fermented nozawana pickle products.

Lactobacillus plantarum Shinshu N-07 isolated from fermented Brassica rapa L. attenuates visceral fat accumulation induced by high-fat diet in mice

Lactobacillus plantarum Shinshu N-07 (N07) and Lactobacillus curvatus #4G2 (#4G2) were isolated from fermented Brassica rapa L. and selected as promising probiotics with anti-adiposity activities based on in vitro assays. The anti-adiposity effects of these two strains were investigated using a diet-induced obesity animal model. Epididymal adipose tissue weight and adipocyte area were significantly lower and serum triglycerides and glucose tended to be lower in mice fed the high-fat diet supplemented with N07 compared with those fed the unsupplemented high-fat diet. Strain N07 suppressed hepatic steatosis, with accompanying downregulation of lipogenic genes in the liver. Expression of inflammatory cytokines and macrophage infiltration markers tended to be suppressed by N07 supplementation. Upregulation of uncoupling protein-1 in epididymal adipose tissue by N07 suggested that the transformation of white adipose tissue to brown might have been induced. Intestinal microbiota analysis revealed that a decrease in abundance of family S24-7 (phylum Bacteroidetes) following ingestion of the high-fat diet was partly recovered by supplementation with N07. Changes in those parameters were not observed in mice fed the high-fat diet supplemented with strain #4G2, suggesting strain specificities. Thus, N07 is a potential probiotic strain that could be used to develop functional foods that attenuate visceral fat accumulation after an appropriate human intervention trial.

Multi fragment melting analysis system (MFMAS) for one-step identification of lactobacilli

The accurate identification of lactobacilli is essential for the effective management of industrial practices associated with lactobacilli strains, such as the production of fermented foods or probiotic supplements. For this reason, in this study, we proposed the Multi Fragment Melting Analysis System (MFMAS)-lactobacilli based on high resolution melting (HRM) analysis of multiple DNA regions that have high interspecies heterogeneity for fast and reliable identification and characterization of lactobacilli. The MFMAS-lactobacilli is a new and customized version of the MFMAS, which was developed by our research group. MFMAS-lactobacilli is a combined system that consists of i) a ready-to-use plate, which is designed for multiple HRM analysis, and ii) a data analysis software, which is used to characterize lactobacilli species via incorporating machine learning techniques. Simultaneous HRM analysis of multiple DNA fragments yields a fingerprint for each tested strain and the identification is performed by comparing the fingerprints of unknown strains with those of known lactobacilli species registered in the MFMAS. In this study, a total of 254 isolates, which were recovered from fermented foods and probiotic supplements, were subjected to MFMAS analysis, and the results were confirmed by a combination of different molecular techniques. All of the analyzed isolates were exactly differentiated and accurately identified by applying the single-step procedure of MFMAS, and it was determined that all of the tested isolates belonged to 18 different lactobacilli species. The individual analysis of each target DNA region provided identification with an accuracy range from 59% to 90% for all tested isolates. However, when each target DNA region was analyzed simultaneously, perfect discrimination and 100% accurate identification were obtained even in closely related species. As a result, it was concluded that MFMAS-lactobacilli is a multi-purpose method that can be used to differentiate, classify, and identify lactobacilli species. Hence, our proposed system could be a potential alternative to overcome the inconsistencies and difficulties of the current methods.

Molecular typing tools for identifying and characterizing lactic acid bacteria: a review

Identification and classification of beneficial microbes is of the highest significance in food science and related industries. Conventional phenotypic approaches pose many challenges, and they may misidentify a target, limiting their use. Genotyping tools show comparatively better prospects, and they are widely used for distinguishing microorganisms. The techniques already employed in genotyping of lactic acid bacteria (LAB) are slightly different from one another, and each tool has its own advantages and disadvantages. This review paper compiles the comprehensive details of several fingerprinting tools that have been used for identifying and characterizing LAB at the species, sub-species, and strain levels. Notably, most of these approaches are based on restriction digestion, amplification using polymerase chain reaction, and sequencing. Nowadays, DNA sequencing technologies have made considerable progress in terms of cost, throughput, and methodology. A research journey to develop improved versions of generally applicable and economically viable tools for fingerprinting analysis is ongoing globally.

Tracking of deliberately inoculated Leuconostoc mesenteroides and Lactobacillus brevis in kimchi

The objective of this study was to track intentionally inoculated Leuconostoc mesenteroides (11251) and Lactobacillus brevis (B151) strains in kimchi using random amplified polymorphic DNA (RAPD), repetitive element palindromic PCR (rep-PCR), and comparative housekeeping gene sequences analysis. The 16S rRNA gene provided species-level information for 30 colonies randomly picked from kimchi inoculated with strains 11251 and B151. Out of 30 colonies, one colony was matched to strain 11251, and two colonies were found identical to strain B151 reference strain in inoculated kimchi. Notably, among the three tools, strain 11251 was best tracked by comparative gene sequence analysis, while strain B151 tracked by all three tools. Our results suggest that the gene sequence analysis is a more reliable tool for tracking of desired strains than RAPD and rep-PCR. Based on the findings, it is recommended that gene sequence analysis could be used to avoid misuse of industrially useful strains within the growing food industry.

Novel insights into the enterotoxigenic potential and genomic background of Staphylococcus aureus isolated from raw milk

In this study, 53 Staphylococcus (S.) aureus strains were typed by 16S-23S rDNA intergenic spacer region (ISR) typing and staphylococcal enterotoxin gene (SEg) typing for all the staphylococcal enterotoxin (se) and staphylococcal enterotoxin-like toxin (sel) genes known to date, revealing a higher discriminatory power than that of multi locus sequence typing. Six strains, one of each ISR- and SEg-type, were genome sequenced and the ability to produce some classical and new SEs when growing in milk was investigated. The manual analysis of the six genomes allowed us to confirm, correct and expand the results of common available genomic data pipelines such as VirulenceFinder. Moreover, it enabled us to (i) investigate the actual location of se and sel genes, even for genes such as selY, whose location (in the core genome) was so far unknown, (ii) find novel allelic variants of se and sel genes and pseudogenes, (iii) correctly annotate se and sel genes and pseudogenes, and (iv) discover a novel type of enterotoxin gene cluster (egc), i.e. the egc type 5 in strains 356P and 364P, while S. argenteus MSHR1132 harbored the egc type 6. Four of the six S. aureus strains produced sufficient amounts of SEA, SEC, SED and SEH in milk to cause staphylococcal food poisoning (SFP), with S. aureus 372 P being the highest producer of SED in milk found to date, producing as much as ca. 47,300 ng/mL and 49,200 ng/mL of SED, after 24 and 48 h of incubation in milk at 37 °C, respectively. S. aureus 372 P released a low amount of SER in milk, most likely because the seR gene was present as a pseudogene, putatively encoding only 51 amino acids. These findings confirm that not only the classical SEs, but also the new ones can represent a potential hazard for the consumers' health if produced in foods in sufficient amounts. Therefore, the detection of SEs in foods, especially if involved in SFP cases, should focus not only on classical, but also on all the new SEs and SEls known to date. Where reference methods are unavailable, the presence of the relevant genes, by using the conventional and real time PCR protocols we exhaustively provided herein, and their nucleotide sequences, should be investigated.

Tracking of Intentionally Inoculated Lactic Acid Bacteria Strains in Yogurt and Probiotic Powder

The present work aimed at tracking intentionally inoculated lactic acid bacteria (LAB) strains in yogurt and probiotic powder. Leuconostoc (Leu.) mesenteroides (11251), Lactobacillus (L.) brevis (B151), and Lactobacillus plantarum (LB41^K) strains were tracked in yogurt, and L. plantarum (LB41^P) was tracked in a commercial probiotic powder. The yogurt was intentionally inoculated with the selected bacterial strains. Two types of yogurt with known and unknown bacterial pools were utilized. The standard 16S rRNA gene sequencing was used to evaluate the initial screening. The molecular typing tools, random amplified polymorphic DNA (RAPD), repetitive element palindromic PCR (rep-PCR), and comparative gene sequence analysis of selected housekeeping loci were used to track the inoculated dubious strains. Out of 30 random selections for each inoculation, the developed method identified seven (11251), nine (B151), and five (LB41^K) colonies in the yogurt. The validation was performed by identifying 7 colonies (LB41^P) out of 30 in the probiotic powder. The DNA banding profiles and the gene sequence alignments led to the identification of the correct inoculated strains. Overall, the study summarizes the use of molecular tools to identify the deliberately inoculated LAB strains. In conclusion, the proposed polyphasic approach effectively tracked the intentionally inoculated strains: Leu. mesenteroides, L. brevis, and L. plantarum (LB41^K) in yogurt and L. plantarum (LB41^P) in probiotic powder. The study demonstrates how to track industrially relevant misused LAB strains in marketable food products.

Characterization of Microbiota that Influence Immunomodulatory Effects of Fermented Brassica rapa L

Lactic acid bacteria (LAB) exert beneficial health effects by regulating immune responses. Brassica rapa L., known as Nozawana, is commonly consumed as a lactic acid-fermented food called nozawana-zuke. Few studies have investigated changes in the bacterial community and cytokine production activities during the fermentation of B. rapa L. In order to obtain more detail information, we herein conducted a study on fresh B. rapa L. fermented for 28 d. An amplicon analysis of the 16S rRNA gene revealed that Lactobacillales predominated during fermentation, and the microbiota became less diverse on day 7 or later. Fermented B. rapa L. promoted the production of interferon (IFN)-γ and interleukin (IL)-10 by mouse spleen cells more than non-fermented vegetables. Lactobacillus curvatus was the predominant species during fermentation, followed by L. plantarum and L. brevis. L. sakei was occasionally detected. A correlation analysis showed that IFN-γ concentrations positively correlated with the numbers of L. curvatus and L. plantarum, while those of IL-10 correlated with the numbers of L. sakei in addition to these 2 species. Significantly higher levels of IFN-γ and IL-10 were induced by fermented B. rapa L. when isolated Lactobacillus strains were added as starter cultures. These results suggest that the Lactobacillus species present in fermented B. rapa L. are beneficial for manufacturing vegetables with immunomodulatory effects.

Molecular typing of Lactobacillus brevis isolates from Korean food using repetitive element-polymerase chain reaction

Lactobacillus brevis is a part of a large family of lactic acid bacteria that are present in cheese, sauerkraut, sourdough, silage, cow manure, feces, and the intestinal tract of humans and rats. It finds its use in food fermentation, and so is considered a "generally regarded as safe" organism. L. brevis strains are extensively used as probiotics and hence, there is a need for identifying and characterizing these strains. For identification and discrimination of the bacterial species at the subspecific level, repetitive element-polymerase chain reaction method is a reliable genomic fingerprinting tool. The objective of the present study was to characterize 13 strains of L. brevis isolated from various fermented foods using repetitive element-polymerase chain reaction. Repetitive element-polymerase chain reaction was performed using three primer sets, REP, Enterobacterial Repetitive Intergenic Consensus (ERIC), and (GTG)₅, which produced different fingerprinting patterns that enable us to distinguish between the closely related strains. Fingerprinting patterns generated band range in between 150 and 5000 bp with REP, 200-7500 bp with ERIC, and 250-2000 bp with (GTG)₅ primers, respectively. The Jaccard's dissimilarity matrices were used to obtain dendrograms by the unweighted neighbor-joining method using genetic dissimilarities based on repetitive element-polymerase chain reaction fingerprinting data. Repetitive element-polymerase chain reaction proved to be a rapid and easy method that can produce reliable results in L. brevis species.