Sourdough authentication: quantitative PCR to detect the lactic acid bacterial microbiota in breads

Wheat Sourdough Breadmaking: A Scoping Review

Using sourdough in breadmaking can enhance bread's shelf-life and flavor compared to exclusive baker's yeast use and is believed to increase its nutritional quality and healthiness. Previous research established insight into the microbial ecology of sourdough, but the link between leavening agent use, processing, and bread quality remains elusive. However, such knowledge is key for standardization, research on the health benefits, and the definition of sourdough bread. In this systematic scoping review, we analyzed 253 studies and identified large variations in the type and amount of leavening agent, fermentation conditions, and bread quality (specific loaf volume and acidification). The interrelation between these elements and their effect on the extent of fermentation is discussed, together with issues preventing proper comparison of breadmaking procedures. With this review, we want to contribute to the dialogue concerning the definition of sourdough-type bread products and the research into the health benefits attributed to them.

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.

Challenges and perspectives of quantitative microbiome profiling in food fermentations

Spontaneously fermented foods are consumed and appreciated for thousands of years although they are usually produced with fluctuated productivity and quality, potentially threatening both food safety and food security. To guarantee consistent fermentation productivity and quality, it is essential to control the complex microbiota, the most crucial factor in food fermentations. The prerequisite for the control is to comprehensively understand the structure and function of the microbiota. How to quantify the actual microbiota is of paramount importance. Among various microbial quantitative methods evolved, quantitative microbiome profiling, namely to quantify all microbial taxa by absolute abundance, is the best method to understand the complex microbiota, although it is still at its pioneering stage for food fermentations. Here, we provide an overview of microbial quantitative methods, including the development from conventional methods to the advanced quantitative microbiome profiling, and the application examples of these methods. Moreover, we address potential challenges and perspectives of quantitative microbiome profiling methods, as well as future research needs for the ultimate goal of rational and optimal control of microbiota in spontaneous food fermentations. Our review can serve as reference for the traditional food fermentation sector for stable fermentation productivity, quality and safety.

Rapid sourdough yeast identification using panfungal PCR combined with high resolution melting analysis

The microbial composition of the sourdough starter affects the sourdough bread properties. Therefore, it is crucial to find a tool for rapid, time-saving, and economical identification of the sourdough microbiota. We focused on the rapid identification of sourdough yeasts. We designed a panfungal real time-PCR targeting the ITS2 region (ITS-amplicon) and a fragment of D1/D2 region of 26S rRNA gene (U-amplicon) and used high resolution melting analysis (HRM) for subsequent species identification. The sensitivity and specificity of our method were tested on the reference yeast cultures. We obtained divergent melting peaks (Tm). The further analysis of melt curves suggests the possibility to discriminate yeasts on the genus- and some on species-specific level in the mixed sample. The applicability of this method in routine practice was evaluated on nine sourdough samples. Revealed melt curves of U-amplicons were predominantly characteristic of the sourdough. The evaluation of the Tm and the shape of the melt curve was used to assess the sourdough yeasts. Additionally, using the HRM-PCR method the contamination with the ergot fungus DNA was revealed. Our data showed HRM-PCR is a simple, rapid, and inexpensive tool useful in identifying sourdough yeasts.

Microbiological quality of tempeh with different wraps: banana leaf versus plastic

Tempeh is a traditional Indonesian fermented food widely consumed and became staple food in some Indonesian diet. Commercially, tempeh is available in banana leaf or plastic wraps. The wraps are not only important for fermentation and giving final form of tempeh,  but also potential source of food microbiome. This study aimed to investigate the effect of different packaging materials on the lactic acid bacteria (LAB) quantity and community composition of tempeh from three manufacturers with different production environments. Each tempeh wrapped with banana leaf or plastic during the fermentation process and then LAB from every tempeh sample were quantified using qPCR and plate count method. Terminal Restriction Fragment Length Polymorphism analysis was carried out to assign bacterial community composition from these samples. The LAB population quantity of fresh tempeh from three manufacturers were essentially similar around 10 log CFU/g. However, there is a difference in the proportion of cultured and uncultured bacteria. Principal Coordinate Analyses based on Bray-Curtis similarity matrices showed an apparent clustering pattern for tempeh samples according to tempeh manufacturers. Meanwhile, packaging materials did not significantly influence changes in  bacterial community composition. The result of this work could be used for determination, authentication, and improvement of tempeh quality.

A Novel qPCR Method for the Detection of Lactic Acid Bacteria in Fermented Milk

The number of live lactic acid bacteria (LAB) is an important quality indicator for yogurt, the quantitative testing of LAB has become an important task in the evaluation of product quality and function. By analyzing and comparing the performance of 16S rRNA gene and tuf gene used in absolute quantification, the tuf gene with copy number 1 was selected as the target gene of six LAB. By drawing a standard curve to achieve qualitative and quantitative detection of six strains of LAB, the detection range was found to be 1 × 103-1 × 108 copies/µL. The traditional plate colony count and Flow Cytometry (FCM) were compared with the method of qPCR, which was used in this experiment. Meanwhile, the confocal laser microscope combined with STYO 9 and propidium iodide dyes was used to determine that the content of viable bacteria in the yogurt was more than 90%, which proved that the detection result using qPCR method was closer to the true level of LAB in yogurt. Compared with the existing methods, the method in this study allowed the qualitative and quantitative detection of the six kinds of LAB in yogurt, and the distribution of live and dead bacteria in yogurt could be calculated.

Proteomic Analysis Explores Interactions between Lactiplantibacillus plantarum and Saccharomyces cerevisiae during Sourdough Fermentation

Sourdough is a fermentation culture which is formed following metabolic activities of a multiple bacterial and fungal species on raw dough. However, little is known about the mechanism of interaction among different species involved in fermentation. In this study, Lactiplantibacillus plantarum Sx3 and Saccharomyces cerevisiae Sq7 were selected. Protein changes in sourdough, fermented with single culture (either Sx3 or Sq7) and mixed culture (both Sx3 and Sq7), were evaluated by proteomics. The results show that carbohydrate metabolism in mixed-culture-based sourdough is the most important metabolic pathway. A greater abundance of L-lactate dehydrogenase and UDP-glucose 4-epimerase that contribute to the quality of sourdough were observed in mixed-culture-based sourdough than those produced by a single culture. Calreticulin, enolase, seryl-tRNA synthetase, ribosomal protein L23, ribosomal protein L16, and ribosomal protein L5 that are needed for the stability of proteins were increased in mixed-culture-based sourdough. The abundance of some compounds which play an important role in enhancing the nutritional characteristics and flavour of sourdough (citrate synthase, aldehyde dehydrogenase, pyruvate decarboxylase, pyruvate dehydrogenase E1 and acetyl-CoA) was decreased. In summary, this approach provided new insights into the interaction between L. plantarum and S. cerevisiae in sourdough, which may serve as a base for further research into the detailed mechanism.

Commercial Organic Versus Conventional Whole Rye and Wheat Flours for Making Sourdough Bread: Safety, Nutritional, and Sensory Implications

Organic farming is gaining a broad recognition as sustainable system, and consumer demand for organic products has increased dramatically in the recent past. Whether organic agriculture delivers overall advantages over conventional agriculture is, however, contentious. Here, the safety, nutritional, and sensory implications of using commercial organic rye, soft, and durum wheat flours rather than conventional-made sourdough bread have been investigated. Culture-dependent and culture-independent approaches were used to explore the microbial architecture of flours and to study their dynamics during sourdough propagation. Besides biochemical features, the main nutritional (amino acid content, asparagine level, and antioxidant activity) characteristics of sourdoughs were investigated, and their effect on the structural, nutritional, and sensory profiles of breads assessed. Overall, the organic farming system led to flours characterized by lower content of asparagine and cell density of Enterobacteriaceae while showing higher concentration of total free amino acids. Differences of the flours mirrored those of sourdoughs and breads. The use of sourdough fermentation guaranteed a further improvement of the flour characteristics; however, a microbial and sensory profile simplification as well as a slight decrease of the biochemical parameters was observed between breads with sourdough after one-cycle fermentation and 10 days of propagation.

A study revealing volatile aroma produced by Pediococcus pentosaceus in dough fermentation

Pediococcus pentosaceus is important probiotics in Chinese Laomian. Its role in meat and fermented vegetable has been largely demonstrated, but few studies have investigated the role of P. pentosaceus in Chinese Laomian. For this purpose, we simulated Laomian fermentation using Saccharomyces cerevisiae and P. pentosaceus. Volatile aroma was detected by headspace solid-phase microextraction gas-chromatography-mass spectrometry. Real-time fluorescent quantitative polymerase chain reaction was used to determine dynamic growth of S. cerevisiae and P. pentosaceus in fermentation. Extracellular proteins were analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Folin-Ciocalteu method was used to detect extracellular protease activity in different pH values. Owing to addition of P. pentosaceus, the types and contents of esters increase, the relative contents of acetic acid hexyl ester, formic acid octyl ester, and heptanoic acid ethyl ester rise obliviously; especially, the relative content of hexanoic acid ethyl ester was highly correlated with P. pentosaceus by increasing 20.61%. As the gel electrophoresis results display, due to mixed fermentation of S. cerevisiae and P. pentosaceus, the 25k Da and 51k Da proteins expression quantity of P. pentosaceus clearly increased. Under neutral and alkaline culture conditions, the extracellular protease activity of P. pentosaceus is higher. This research benefits to gain insight into the fermentation actions of P. pentosaceus in Chinese Laomian.

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.

Storage stability and sourdough acidification kinetic of freeze-dried Lactobacillus curvatus N19 under optimized cryoprotectant formulation

In this study, the response surface methodology was used to optimize the cryoprotective agent (skimmed milk powder, lactose and sucrose) formulation for enhancing the viability of Lactobacillus curvatus N19 during freeze-drying and storage stability of cells freeze-dried by using optimum formulation was evaluated. Our results showed that the most significant cryoprotective agent influencing the viability of L. curvatus N19 to freezing and freeze-drying was sucrose and skim milk, respectively. The optimal formulation of cryoprotective agents was 20 g/100 mL skim milk, 3.57 g/100 mL lactose and 10 g/100 mL sucrose. Using the optimum formulation during freeze-drying, the cell survival was found more than 98%. Under the optimal conditions, although only storage of the cells at 4 °C for 6 month retained the maximum stability (8.85 log cfu/g), the employed protectant matrix showed promising results at 25 °C (7.89 log cfu/g). The storage stability of cells under optimized conditions was predicted by accelerated storage test, which was demonstrated that the inactivation rate constant of the freeze-dried L. curvatus N19 powder was 9.74 × 10^-6 1/d for 4 °C and 2.08 × 10^-3 1/d for 25 °C. The loss of specific acidification activity after the storage at 4 and 25 °C was determined.

Sourdough Fermented Breads are More Digestible than Those Started with Baker's Yeast Alone: An In Vivo Challenge Dissecting Distinct Gastrointestinal Responses

As a staple food, bread digestibility deserves a marked nutritional interest. Combining wide-spectrum characterization of breads, in vitro nutritional indices, and in vivo postprandial markers of gastrointestinal function, we aimed at comparing the digestibility of sourdough and baker's yeast breads. Microbiological and biochemical data showed the representativeness of the baker´s yeast bread (BYB) and the two sourdough breads (SB and t-SB, mainly differing for the time of fermentation) manufactured at semi-industrial level. All in vitro nutritional indices had the highest scores for sourdough breads. Thirty-six healthy volunteers underwent an in vivo challenge in response to bread ingestion, while monitoring gallbladder, stomach, and oro-cecal motility. SB, made with moderate sourdough acidification, stimulated more appetite and induced lower satiety. t-SB, having the most intense acidic taste, induced the highest fullness perception in the shortest time. Gallbladder response did not differ among breads, while gastric emptying was faster with sourdough breads. Oro-cecal transit was prolonged for BYB and faster for sourdough breads, especially when made with traditional and long-time fermentation (t-SB), whose transit lasted ca. 20 min less than BYB. Differences in carbohydrate digestibility and absorption determined different post-prandial glycaemia responses. Sourdough breads had the lowest values. After ingesting sourdough breads, which had a concentration of total free amino acids markedly higher than that of BYB, the levels in blood plasma were maintained at constantly high levels for extended time.

Influence of fermentation by different microflora consortia on pulque and pulque bread properties

BACKGROUND

Pulque bread is a traditional Mexican product obtained by fermentation using microflora present only in pulque. In this study, the possibility of creating a pulque microbial consortium under laboratory conditions and its applications were evaluated. A laboratory-made consortium was compared with a consortium originating in Mexico in bread and pulque production. They were tested in various growth medium systems: pulque made from agave sap and malt extract, Mexican wheat and rye pulque bread, and European wheat and rye bread.

RESULTS

Depending on the growth medium, consortiums showed differing influence on many factors, such as specific volume, weight loss after baking, soluble proteins, and crust and crumb color. Indigenous starters increased sensorial acceptance of pulque and Mexican rye bread, decreased pH, and increased titratable acidity of the breads at the highest level whereas laboratory consortia improved sensory acceptance of wheat breads. The laboratory-prepared starter in some cases improved antiradical activity. All pulques received similar consumer evaluations. However, malt pulque was the least appreciated beverage.

CONCLUSION

The results show the possibility of creating a pulque microbial consortium under laboratory conditions. Depending on the flour type and the breadmaking technique, the use of a particular microbial consortium allowed modification of certain physicochemical parameters. In conclusion, it is feasible to modify bread parameters to obtain features corresponding to consumer demands by using an appropriate microflora, pulque, or flour type. Moreover, this research describes, for the first time, the use of rye malt for pulque and rye flour for pulque bread preparation as raw materials. © 2019 Society of Chemical Industry.

Fermented Foods: Definitions and Characteristics, Impact on the Gut Microbiota and Effects on Gastrointestinal Health and Disease

Fermented foods are defined as foods or beverages produced through controlled microbial growth, and the conversion of food components through enzymatic action. In recent years, fermented foods have undergone a surge in popularity, mainly due to their proposed health benefits. The aim of this review is to define and characterise common fermented foods (kefir, kombucha, sauerkraut, tempeh, natto, miso, kimchi, sourdough bread), their mechanisms of action (including impact on the microbiota), and the evidence for effects on gastrointestinal health and disease in humans. Putative mechanisms for the impact of fermented foods on health include the potential probiotic effect of their constituent microorganisms, the fermentation-derived production of bioactive peptides, biogenic amines, and conversion of phenolic compounds to biologically active compounds, as well as the reduction of anti-nutrients. Fermented foods that have been tested in at least one randomised controlled trial (RCT) for their gastrointestinal effects were kefir, sauerkraut, natto, and sourdough bread. Despite extensive in vitro studies, there are no RCTs investigating the impact of kombucha, miso, kimchi or tempeh in gastrointestinal health. The most widely investigated fermented food is kefir, with evidence from at least one RCT suggesting beneficial effects in both lactose malabsorption and Helicobacter pylori eradication. In summary, there is very limited clinical evidence for the effectiveness of most fermented foods in gastrointestinal health and disease. Given the convincing in vitro findings, clinical high-quality trials investigating the health benefits of fermented foods are warranted.

Effect of a novel Lactobacillus paracasei starter on sourdough bread quality

The novel Lactobacillus paracasei K5 strain, recently isolated from Greek cheese, was evaluated as potential sourdough bread starter. Breads were made using different amounts of L. paracasei sourdoughs as well as traditional sourdough for comparison. Quality characteristics of the breads (acidity and rising) were examined, as well as rope spoilage through macroscopic observations and molecular analysis (PCR-DGGE). The highest acidity levels (3.15 g lactic acid and 1.13 g acetic acid per kg of bread) and better resistance to rope spoilage were observed when bread contained 30% w/w L. paracasei K5 sourdough. Spoilage in the L. paracasei K5 breads was observed at 15-16 days, 5 days later than the control breads. In addition, L. paracasei K5 sourdough improved the bread sensory properties, as reflected by consumer preference and GC/MS analysis of aroma volatiles. Therefore, L. paracasei K5 can be successfully used for sourdough bread making with good quality and extended shelf-life.