Molecular and functional characterization of Lactobacillus sanfranciscensis strains isolated from sourdoughs

Functional Characterization of Different Fructilactobacillus sanfranciscensis Strains Isolated from Chinese Traditional Sourdoughs

Fructilactobacillus sanfranciscensis, the dominant species of lactic acid bacteria in sourdoughs, impacts the microstructure and flavor of steamed bread through exopolysaccharide production, acidification, proteolysis, and volatile compound generation. The aim of this study is to investigate the phenotypic diversity and technological traits of 28 F. sanfranciscensis strains of different genotypes isolated from Chinese traditional sourdoughs. The results showed that F. sanfranciscensis strains exhibited substantial variation in proteinase and peptidase activities and the amount of acidification and volatiles in fermented sourdoughs. However, we observed no significant differences in exopolysaccharide production among the strains. The strains Sx14 and Ts1 were further chosen for transcriptomics to gain a deep insight into their intraspecies diversity in sourdough fermentation. Significant transcriptome differentiations between these two strains after 12 h fermentation in sourdoughs were revealed. According to the results, the strain Sx14 possessed higher dipeptidase and aminopeptidase activities, galactose utilization, and lactic and acetic acid production abilities, whereas Ts1 showed higher transmembrane transport of substrates and fructose utilization.

Comparative Genomics Reveals Genetic Diversity and Variation in Metabolic Traits in Fructilactobacillus sanfranciscensis Strains

Fructilactobacillus sanfranciscensis is a significant and dominant bacterial species of sourdough microbiota from ecological and functional perspectives. Despite the remarkable prevalence of different strains of this species in sourdoughs worldwide, the drivers behind the genetic diversity of this species needed to be clarified. In this research, 14 F. sanfranciscensis strains were isolated from sourdough samples to evaluate the genetic diversity and variation in metabolic traits. These 14 and 31 other strains (obtained from the NCBI database) genomes were compared. The values for genome size and GC content, on average, turned out to 1.31 Mbp and 34.25%, respectively. In 45 F. sanfranciscensis strains, there were 162 core genes and 0 to 51 unique genes present in each strain. The primary functions of core genes were related to nucleotide, lipid transport, and amino acid, as well as carbohydrate metabolism. The size of core genes accounted for 41.18% of the pan-genome size in 14 F. sanfranciscensis strains, i.e., 0.70 Mbp of 1.70 Mbp. There were genetic variations among the 14 strains involved in carbohydrate utilization and antibiotic resistance. Moreover, exopolysaccharides biosynthesis-related genes were annotated, including epsABD, wxz, wzy. The Type IIA & IE CRISPR-Cas systems, pediocin PA-1 and Lacticin_3147_A1 bacteriocins operons were also discovered in F. sanfranciscensis. These findings can help to select desirable F. sanfranciscensis strains to develop standardized starter culture for sourdough fermentation, and expect to provide traditional fermented pasta with a higher quality and nutritional value for the consumers.

Sourdough starter culture microbiomes influence physical and chemical properties of wheat bread

Sourdough fermentation is an ancient leavening method that uses wild yeasts to produce carbon dioxide, contributing to bread rise, and bacteria which produce organic acids. Sourdough starter cultures are known to be diverse in terms of the microorganisms they comprise and while specific genera and species of microorganisms have been identified from starters and associated with specific attributes, overarching relationships between sourdough starter culture microbiomes and bread quality are not well understood. The objective of this study was to characterize differences in the physical and chemical properties of breads produced with sourdough starter cultures with unique microbiomes. Sourdough starter cultures (n = 20) of known microbial populations were used to produce wheat-based dough and bread, which were analyzed for chemical and physical properties then compared to their microbial populations in order to identify relationships between microbial profiles and dough/bread qualities. All samples were also compared to bread produced only with Saccharomyces cerevisiae (baker's yeast). Significant differences among pH, titratable acidity, loaf volume, crumb firmness, crust color, free amino acids, and organic acids were observed when comparing sourdough breads to the yeast-only control (p ≤ 0.05). Furthermore, bacterial diversity of sourdough starter cultures was correlated with lactic acid and free amino acid in the dough and loaf volume and crumb firmness of baked breads. No significant correlations were found between fungal diversity and measured outcomes. These data demonstrate the importance of considering sourdough starter microbiomes as an ingredient in baked goods and they contribute to quality and safety outcomes in bread production. PRACTICAL APPLICATION: Sourdough starter cultures have diverse and dynamic populations of bacteria and yeasts, which contribute to the production of bread products. These populations can influence the physical and chemical properties of sourdough fermentation and final breads. Understanding of the relationship between sourdough starter microbiomes and bread quality parameters can lead to targeted development of sourdough bread products with specific physical and chemical properties.

Characterization of Two Zymomonas mobilis Wild Strains and Analysis of Populations Dynamics during Their Leavening of Bread-like Doughs

Two Zymomonas mobilis wild strains (UMB478 and 479) isolated from water kefir were characterized for their biomass production levels and leavening performance when used as the inoculum of a real bread-like dough formulation. The obtained baked product would be consumable by people with adverse responses to Saccharomyces cerevisiae. In liquid cultures, the two strains reached similar biomass concentration (0.7 g CDW/L). UMB479 showed an interesting resistance to NaCl (MBC 30 g/L), that may be useful in the bakery sector. When inoculated in doughs, UMB479 produced the maximum dough volume (650 mL) after 5 h, glucose was almost consumed and 1 g/100 g of ethanol produced, +200% respective to UMB478. Using S. cerevisiae for comparison purposes, the dough doubled its volume fast, in only 2 h, but reached a final level of 575 mL, lower than that achieved by Z. mobilis. The analysis of bacterial and fungal population dynamics during dough leavening was performed through the Automated Ribosomal Intergenic Spacer Analysis (ARISA); doughs leavened by UMB479 showed an interesting decrease in fungal richness after leavening. S. cerevisiae, instead, created a more complex fungal community, similar before and after leavening. Results will pave the way for the use of Z. mobilis UMB479 in commercial yeast-free leavened products.

Bread Sourdough Lactic Acid Bacteria—Technological, Antimicrobial, Toxin-Degrading, Immune System-, and Faecal Microbiota-Modelling Biological Agents for the Preparation of Food, Nutraceuticals and Feed

This review intends to highlight the fact that bread sourdough is a very promising source of technological, antimicrobial, toxin-degrading, immune system-, and faecal microbiota-modelling biological agents for the preparation of food, nutraceuticals, and feed, which has great potential at industrial biotechnology scale. There are many applications of sourdough lactic acid bacteria (LAB), which are the main microorganisms in spontaneous sourdough. In addition to their application as pure technological strains in the food and feed industries, taking into consideration the specific properties of these microorganisms (antimicrobial, antifungal, immuno-, and microbiota-modulating, etc.), they are used as valuable ingredients in higher-value food as well as nutraceutical formulations. Additionally, a very promising application of LAB is their use in combination with plant- and/or animal-based ingredients to increase the functional properties of the whole combination due to different mechanisms of action, as well as desirable symbiotic activity. In addition to traditional foods prepared using sourdough microorganisms (bread, biscuits, meat products, dairy, beverages, etc.), they could find application in the preparation of added-value ingredients for the food, nutraceutical, and feed industries. Finally, this mini-review gives a brief introduction to the possible applications of sourdough LAB in the food, feed, and nutraceutical industries.

Functional, Nutritional, and Sensory Quality of Mixed Flours-Based Breads as Compared to Durum Wheat Semolina-Based Breads

Increasing preference of consumers and bakers towards bread manufactured with mixed flours and/or sourdough drove us to investigate about influence of flours and sourdough on crumb grain, chemical, sensory, and in vitro glycaemic index (GI) and antioxidant activity of bread. To this aim, we produced and compared six experimental breads: three were based on a mixture of flours (soft wheat, durum wheat semolina, barley, oat, rye, and buckwheat); three were semolina-based breads. Two different sourdoughs (wheat or mixed flours) were assessed. Compared to semolina breads, those containing a mixture of flours showed higher specific volume. The use of sourdough led to increased concentrations of total free amino acids (FAA). Mixed flours bread with addition of mixed flours sourdough was rich in some essential FAA and amino acid derivative bioactive gamma-aminobutyric acid. Type of flours had higher influence than sourdough addition on volatile organic compounds. All the mixed flours breads, although showing profiles of volatile organic compounds differing from those of semolina breads, resulted acceptable. In addition, they had lower GI and higher antioxidant activity than semolina breads. Type of flours had much higher impact on GI and antioxidant activity than sourdough.

Diversity and dynamics of sourdough lactic acid bacteriota created by a slow food fermentation system

Sourdough is a naturally fermented dough that is used worldwide to produce a variety of baked foods. Various lactic acid bacteria (LAB), which can determine the quality of sourdough baked foods by producing metabolites, have been found in the sourdough ecosystem. However, spontaneous fermentation of sourdough leads to unpredictable growth of various micro-organisms, which result in unstable product quality. From an ecological perspective, many researchers have recently studied sourdough LAB diversity, particularly the elucidation of LAB community interactions and the dynamic mechanisms during the fermentation process, in response to requests for the control and design of a desired sourdough microbial community. This article reviews recent advances in the study of sourdough LAB diversity and its dynamics in association with unique characteristics of the fermentation system; it also discusses future perspectives for better understanding of the complex sourdough microbial ecosystem, which can be attained efficiently by both in vitro and in situ experimental approaches.

Intraspecies diversity and genome-phenotype-associations in Fructilactobacillus sanfranciscensis

In this study the intraspecies diversity of Fructilactobacillus (F.) sanfranciscensis (formerly Lactobacillus sanfranciscensis) was characterized by comparative genomics supported by physiological data. Twenty-four strains of F. sanfranciscensis were analyzed and sorted into six different genomic clusters. The core genome comprised only 43,14 % of the pan genome, i.e. 0.87 Mbp of 2.04 Mbp. The main annotated genomic differences reside in maltose, fructose and sucrose as well as nucleotide metabolism, use of electron acceptors, and exopolysacchride formation. Furthermore, all strains are well equipped to cope with oxidative stress via NADH oxidase and a distinct thiol metabolism. Only ten of 24 genomes contain two maltose phosphorylase genes (mapA and mapB). In F. sanfranciscensis TMW 1.897 only mapA was found. All strains except those from genomic cluster 2 contained the mannitol dehydrogenase and should therefore be able to use fructose as external electron acceptor. Moreover, six strains were able to grow on fructose as sole carbon source, as they contained a functional fructokinase gene. No growth was observed on pentoses, i.e. xylose, arabinose or ribose, as sole carbon source. This can be referred to the absence of ribose pyranase rbsD in all genomes, and absence of or mutations in numerous other genes, which are essential for arabinose and xylose metabolism. Seven strains were able to produce exopolysaccharides (EPS) from sucrose. In addition, the strains containing levS were able to grow on sucrose as sole carbon source. Strains of one cluster exhibit auxotrophies for purine nucleotides. The physiological and genomic analyses suggest that the biodiversity of F. sanfranciscensis is larger than anticipated. Consequently, "original" habitats and lifestyles of F. sanfranciscensis may vary but can generally be referred to an adaptation to sugary (maltose/sucrose/fructose-rich) and aerobic environments as found in plants and insects. It can dominate sourdoughs as a result of reductive evolution and cooperation with fructose-delivering, acetate-tolerant yeasts.

Screening of Lactic Acid Bacteria and Yeasts from Sourdough as Starter Cultures for Reduced Allergenicity Wheat Products

Previous researchers have shown the potential of sourdough or related lactic acid bacteria in reducing wheat allergens. However, there are no mixed or single cultures for producing reduced allergenicity wheat products. In this study, twelve strains of lactic acid bacteria and yeast isolated from sourdough were evaluated for their ability to hydrolyze proteins and ferment dough. Strain Pediococcus acidilacticiXZ31 showed higher proteolytic activity on both casein and wheat protein substrates, and had strong ability to reduce wheat protein allergenicity. The tested Saccharomyces and non-Saccharomyces showed limited proteolysis. Strains Torulaspora delbrueckii JM1 and Saccharomyces cerevisiae JM4 demonstrated a higher capacity to ferment dough compared to other yeasts. These strains may be applied as starters for the preparation of reduced allergenicity wheat products.

A Probiotic Preparation Hydrolyzes Gliadin and Protects Intestinal Cells from the Toxicity of Pro-Inflammatory Peptides

Celiac disease (CD) is an autoimmune enteropathy caused by an intolerance to gluten proteins. It has been hypothesized that probiotic bacteria may exert beneficial effects by modulating inflammatory processes and by sustaining peptide hydrolysis at the intestinal level. This study aims at evaluating the capacity of a probiotic mixture (two different strains of lactobacilli and three of bifidobacteria) to hydrolyze gluten peptides following simulated gastrointestinal digestion of gliadin (PT-gliadin). The capacity of bacterial hydrolysates to counteract the toxic effects of gliadin-derived peptides in Caco-2 cells was also assessed. The protein and peptide mixtures, untreated or proteolyzed with the probiotic preparation, were analyzed before and after each proteolytic step with different techniques (SDS-PAGE, reverse phase HPLC, filtration on different molecular cut-off membranes). These experiments demonstrated that PT-gliadin can be further digested by bacteria into lower molecular weight peptides. PT-gliadin, untreated or digested with the probiotics, was then used to evaluate oxidative stress, IL-6 cytokine production and expression of tight junctions’ proteins—such as occludin and zonulin—in Caco-2 cells. PT-gliadin induced IL-6 production and modulation and redistribution of zonulin and occludin, while digestion with the probiotic strains reversed these effects. Our data indicate that this probiotic mixture may exert a protective role in CD.

Monitoring of Lactobacillus sanfranciscensis strains during wheat and rye sourdough fermentations by CRISPR locus length polymorphism PCR

Lactobacillus (L.) sanfranciscensis is a competitive key species in sourdough fermentations. However, the principles involved in establishing the commonly observed phenomenon of strain dominance are unresolved. This has been studied little because the methods for fast and reliable differentiation of strains and their monitoring during fermentation are tedious and cannot be done with large numbers of isolates. In this contribution, we present a strain-specific, PCR-based typing method that uses length heterogeneities of the clustered regularly interspaced short palindromic repeats (CRISPR) loci as they occur in the genomes of different strains. In silico analysis of 21 genomes revealed 14 different CRISPR genotypes. We then designed a primer set to simultaneously detect different strains in a multiplex PCR assay designated CRISPR locus length polymorphism PCR (CLLP-PCR). The usefulness of this method was evaluated in lab-scale sourdough fermentations conducted with rye and wheat flours. First, the flour was mixed with water to a dough yield of 200. Then each dough was inoculated with four different L. sanfranciscensis strains (TMW 1.1150, TMW 1.392, TMW 1.2142, and TMW 1.2138) at levels of 10⁹ cfu/g each. Sourdoughs were propagated at 28 °C for 5 days by back slopping 5% to the flour mass every 24 h. Samples were collected each day; DNA was isolated, and the presence of strains was detected qualitatively in the sourdoughs with PCR. L. sanfranciscensis TMW 1.392 became dominant as early as 2 days into the fermentation and remained the only detectable strain for the rest of the sampling period. CLLP-PCR proved to be useful in investigating the assertiveness of different strains of L. sanfranciscensis in sourdoughs. Therefore, CLLP-PCR may be used as a tool to investigate assertiveness of microorganisms in food fermentations at the strain level.

Lactic Acid Bacterium Population Dynamics in Artisan Sourdoughs Over One Year of Daily Propagations Is Mainly Driven by Flour Microbiota and Nutrients

This study aimed to: (i) assess at what extent traditional, daily propagated, sourdough can be considered a stable microbial ecosystem; (ii) ascertain the drivers of stability/variability. For this purpose, samples of sourdough, flour and environment were collected over 1 year from three different bakeries located in Altamura, Castellana Grotte, and Matera. Culture-dependent and –independent analyses were carried out on all the samples. In addition, sourdough and flour were subjected to biochemical characterization. In all the sourdoughs sampled at the same bakery, cell density of lactic acid bacteria fluctuated of one-two log cycles. However, 16S metagenetic analysis showed that sourdough bacterial microbiota was remarkably stable, in terms of species. Yet, some differences were found during time at intra-specific level. Indeed, bacterial strains succeeded in a 1-year lapse of time or even in 6-months, such as in the case of strains isolated from Altamura sourdough samples. Residual carbohydrates, lactic acid, ethanol and free amino acids varied in the same sourdough collected at different sampling times. These variations could be attributed to combination of various factors, such as fermentation temperature and strain succession. In addition, concentration of flour nutrients varied over 1 year and, in some cases, in a shorter time lapse. This may have favored certain strains over others. For this reason and also because of its inherent contamination by lactic acid bacteria, we found flour as the major driver of strains succession.

Wholemeal wheat flours drive the microbiome and functional features of wheat sourdoughs

This study aimed to evaluate the effect of soft (Triticum aestivum) and durum (Triticum durum) wheat flours at different extraction rate (type 00, 0, 1 and 2) and wholemeal flours on the microbial composition and functionality of type I sourdough. Enterobacteriaceae constituted the main component of the microbiome of refined soft and durum wheat flours. On the contrary, wholemeal durum wheat flour harboured mainly Xanthomonadaceae. Differences were also found between the soft and durum wheat flours. After 8 h of fermentation (1 day), a different behaviour of the microbiome components was observed. All the mature sourdoughs harboured a core microbiome constituted by 4 species (Pediococcus pentosaceus, Lactobacillus brantae, Pediococcus argentinicus and Weissella cibaria). Based on the type of flour, the relative abundance of each core species differed among sourdoughs. In addition, other dominant lactic acid bacteria species were variously detected in sourdoughs. Mature sourdoughs showed marked variations for the concentrations of glucose, fructose, maltose, lactic and acetic acids, ethanol and free amino acids (FAA). Specific correlations (r > 0.7; FDR < 0.05) were found between the microbiome and total phenols, fibres and metabolome of mature sourdoughs. Breads made by using wholemeal soft wheat or durum wheat doughs started by wholemeal wheat flour-based sourdoughs were characterized by the highest total amount of free cations (Ca²⁺, Zn²⁺, Fe²⁺, Mg²⁺), antioxidant activity and improved sensory traits.

A Metagenomic and in Silico Functional Prediction of Gut Microbiota Profiles May Concur in Discovering New Cystic Fibrosis Patient-Targeted Probiotics

Cystic fibrosis (CF) is a life-limiting hereditary disorder that results in aberrant mucosa in the lungs and digestive tract, chronic respiratory infections, chronic inflammation, and the need for repeated antibiotic treatments. Probiotics have been demonstrated to improve the quality of life of CF patients. We investigated the distribution of gut microbiota (GM) bacteria to identify new potential probiotics for CF patients on the basis of GM patterns. Fecal samples of 28 CF patients and 31 healthy controls (HC) were collected and analyzed by 16S rRNA-based pyrosequencing analysis of GM, to produce CF-HC paired maps of the distribution of operational taxonomic units (OTUs), and by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) for Kyoto Encyclopedia of Genes and Genomes (KEGG) biomarker prediction. The maps were scanned to highlight the distribution of bacteria commonly claimed as probiotics, such as bifidobacteria and lactobacilli, and of butyrate-producing colon bacteria, such as Eubacterium spp. and Faecalibacterium prausnitzii. The analyses highlighted 24 OTUs eligible as putative probiotics. Eleven and nine species were prevalently associated with the GM of CF and HC subjects, respectively. Their KEGG prediction provided differential CF and HC pathways, indeed associated with health-promoting biochemical activities in the latter case. GM profiling and KEGG biomarkers concurred in the evaluation of nine bacterial species as novel putative probiotics that could be investigated for the nutritional management of CF patients.

Genotyping of Lactobacillus sanfranciscensis isolates from Chinese traditional sourdoughs by multilocus sequence typing and multiplex RAPD-PCR

Lactobacillus sanfranciscensis is the predominant lactic acid bacteria (LAB) species in Chinese traditional sourdoughs and conduces to the flavor and rheology properties of Chinese steamed bread, a staple food originated in China over 1500years ago. The aim of this study is to describe the intraspecific diversity of 98 L. sanfranciscensis isolates from 11 Chinese traditional sourdoughs in different regions by multilocus sequence typing (MLST) and multiplex random amplified polymorphic DNA-polymerase chain reaction (multiplex RAPD-PCR). MLST scheme was reduced from six gene fragments (gdh, gyrA, mapA, nox, pgmA and pta) to five (gdh, gyrA, mapA, nox and pta) since the fragment of pgmA displayed only one allele. 10 different sequence types (STs) were revealed by MLST and 6 of them containing 79.8% of the isolates were classified into one clonal complex, demonstrating a close relationship among them. The multiplex-RAPD analysis was performed by employing the combined primers OPL-05+RD1 and divided the 98 L. sanfranciscensis isolates into 6 types with the similarity level of 70%. According to the result, it seems that the genotypic variations of L. sanfranciscensis strains showed by MLST have no relations to geographical origin. MLST seems to have a higher discriminatory power compared with multiplex-RAPD since it produced more groups, but multiplex-RAPD could help to distinguish some strains in the same ST. Hence, an optimal genotypic characterization of L. sanfranciscensis was obtained under the combination of MLST and multiplex-RAPD analysis, targeting different genetic variations.

Selected Probiotic Lactobacilli Have the Capacity To Hydrolyze Gluten Peptides during Simulated Gastrointestinal Digestion

The aim of this study was to demonstrate the capacity of probiotic lactobacilli to hydrolyze immunogenic gluten peptides. Eighteen commercial strains of probiotic lactobacilli with highly variable peptidase activity (i.e., aminopeptidase N, iminopeptidase, prolyl endopeptidyl peptidase, tripeptidase, prolidase, prolinase, and dipeptidase), including toward Pro-rich peptides, were tested in this study. Ten probiotic strains were selected on the basis of their specific enzyme activity. When pooled, these 10 strains provided the peptidase portfolio that is required to completely degrade the immunogenic gluten peptides involved in celiac disease (CD). The selected probiotic mixture was able to completely hydrolyze well-known immunogenic epitopes, including the gliadin 33-mer peptide, the peptide spanning residues 57 to 68 of the α9-gliadin (α9-gliadin peptide 57-68), A-gliadin peptide 62-75, and γ-gliadin peptide 62-75. During digestion under simulated gastrointestinal conditions, the pool of 10 selected probiotic lactobacilli strongly hydrolyzed the wheat bread gluten (ca. 18,000 ppm) to less than 10 ppm after 360 min of treatment. As determined by multidimensional chromatography (MDLC) coupled to nanoelectrospray ionization (nano-ESI)-tandem mass spectrometry (MS/MS), no known immunogenic peptides were detected in wheat bread that was digested in the presence of the probiotics. Accordingly, the level of cytokines (interleukin 2 [IL-2], IL-10, and interferon gamma [IFN-γ]) produced by duodenal biopsy specimens from CD patients who consumed wheat bread digested by probiotics was similar to the baseline value (negative control). Probiotics that specifically hydrolyze gluten polypeptides could also be used to hydrolyze immunogenic peptides that contaminate gluten-free products. This could provide a new and safe adjunctive therapy alternative to the gluten-free diet (GFD).IMPORTANCE This study confirmed that probiotic Lactobacillus strains have different enzymatic abilities for hydrolyzing polypeptides, including the Pro-rich epitopes involved in the pathology of CD. Ten lactobacilli with complementary peptidase activities that hydrolyze gluten peptides during simulated gastrointestinal digestion were selected and tested. The results collected showed the potential of probiotic formulas as novel dietary treatments for CD patients.

Microbial cell-free extracts affect the biochemical characteristics and sensorial quality of sourdough bread

This study aimed to improve the sensorial quality of sourdough wheat bread by the addition of cell-free enzyme extracts (CFEs) from Lactobacillus sanfranciscensis (SF), Hafnia alvei (HF) and Debaryomyces hansenii (DH). CFEs were suitable sources of peptidases, glutamate dehydrogenase and cystathionine γ-lyase. The concentration of free amino acids (FAA) in the sourdoughs containing CFEs was higher than the control sourdough, produced without addition of CFEs. The community-level catabolic profiles showed that the highest number of carbohydrates, polymers and carboxylic acids were consumed in the SF sourdough. Breads produced with CFEs were characterized by higher specific volume than the control. The use of CFEs impacted on the profile of volatile organic compounds. Overall, positive correlations were found between some key-aroma compounds and enzyme activities/precursor FAA. The SF bread, characterized by highest level of alcohols, received the highest score for aroma and sweetness in the sensory analysis.

Microbial Ecology and Process Technology of Sourdough Fermentation

From a microbiological perspective, sourdough is to be considered as a specific and stressful ecosystem, harboring yeasts and lactic acid bacteria (LAB), that is used for the production of baked goods. With respect to the metabolic impact of the sourdough microbiota, acidification (LAB), flavor formation (LAB and yeasts), and leavening (yeasts and heterofermentative LAB species) are most noticeable. Three distinct types of sourdough fermentation processes can be discerned based on the inocula applied, namely backslopped ones (type 1), those initiated with starter cultures (type 2), and those initiated with a starter culture followed by backslopping (type 3). A sourdough-characteristic LAB species is Lactobacillus sanfranciscensis. A sourdough-characteristic yeast species is Candida humilis. Although it has been suggested that the microbiota of a specific sourdough may be influenced by its geographical origin, region specificity often seems to be an artefact resulting from interpretation of the research data, as those are dependent on sampling, isolation, and identification procedures. It is however clear that sourdough-adapted microorganisms are able to withstand stress conditions encountered during their growth. Based on the technological setup, type 0 (predoughs), type I (artisan bakery firm sourdoughs), type II (industrial liquid sourdoughs), and type III sourdoughs (industrial dried sourdoughs) can be distinguished. The production of all sourdoughs, independent of their classification, depends on several intrinsic and extrinsic factors. Both the flour (type, quality status, etc.) and the process parameters (fermentation temperature, pH and pH evolution, dough yield, water activity, oxygen tension, backslopping procedure and fermentation duration, etc.) determine the dynamics and outcome of (backslopped) sourdough fermentation processes.

Different Flour Microbial Communities Drive to Sourdoughs Characterized by Diverse Bacterial Strains and Free Amino Acid Profiles

This work aimed to investigate whether different microbial assemblies in flour may influence the microbiological and biochemical characteristics of traditional sourdough. To reach this purpose, members of lactic acid bacteria, enterobacteria, and yeasts were isolated from durum wheat flour. Secondly, the isolated microorganisms (Pediococcus pentosaceus, Saccharomyces cerevisiae, Pantoea agglomerans, and Escherichia hermannii) were inoculated in doughs prepared with irradiated flour (gamma rays at 10 kGy), so that eight different microbial assemblies were obtained. Two non-inoculated controls were prepared, one of which (C-IF) using irradiated flour and the other (C) using non-irradiated flour. As shown by plate counts, irradiation of flour caused total inactivation of yeasts and a decrease of all the other microbial populations. However, acidification occurred also in the dough C-IF, due to metabolic activity of P. pentosaceus that had survived irradiation. After six fermentations, P. pentosaceus was the dominant lactic acid bacterium species in all the sourdoughs produced with irradiated flour (IF). Yet, IF-based sourdoughs broadly differed from each other in terms of strains of P. pentosaceus, probably due to the different microorganisms initially inoculated. Quantitative and qualitative differences of free amino acids concentration were found among the sourdoughs, possibly because of different microbial communities. In addition, as shown by culture-independent analysis (16S metagenetics), irradiation of flour lowered and modified microbial diversity of sourdough ecosystem.

Improving the antioxidant properties of quinoa flour through fermentation with selected autochthonous lactic acid bacteria

Lactic acid bacteria strains, previously isolated from the same matrix, were used to ferment quinoa flour aiming at exploiting the antioxidant potential. As in vitro determined on DPPH and ABTS radicals, the scavenging activity of water/salt-soluble extracts (WSE) from fermented doughs was significantly (P<0.05) higher than that of non-inoculated doughs. The highest inhibition of linoleic acid autoxidation was found for the quinoa dough fermented with Lactobacillus plantarum T0A10. The corresponding WSE was subjected to Reverse Phase Fast Protein Liquid Chromatography, and 32 fractions were collected and subjected to in vitro assays. The most active fraction was resistant to further hydrolysis by digestive enzymes. Five peptides, having sizes from 5 to 9 amino acid residues, were identified by nano-Liquid Chromatography-Electrospray Ionisation-Mass Spectra/Mass Spectra. The sequences shared compositional features which are typical of antioxidant peptides. As shown by determining cell viability and radical scavenging activity (MTT and DCFH-DA assays, respectively), the purified fraction showed antioxidant activity on human keratinocytes NCTC 2544 artificially subjected to oxidative stress. This study demonstrated the capacity of autochthonous lactic acid bacteria to release peptides with antioxidant activity through proteolysis of native quinoa proteins. Fermentation of the quinoa flour with a selected starter might be considered suitable for novel applications as functional food ingredient, dietary supplement or pharmaceutical preparations.

Sourdough-Based Biotechnologies for the Production of Gluten-Free Foods

Sourdough fermentation, a traditional biotechnology for making leavened baked goods, was almost completely replaced by the use of baker's yeast and chemical leavening agents in the last century. Recently, it has been rediscovered by the scientific community, consumers, and producers, thanks to several effects on organoleptic, technological, nutritional, and functional features of cereal-based products. Acidification, proteolysis, and activation of endogenous enzymes cause several changes during sourdough fermentation, carried out by lactic acid bacteria and yeasts, which positively affect the overall quality of the baked goods. In particular, the hydrolysis of native proteins of the cereal flours may improve the functional features of baked goods. The wheat flour processed with fungal proteases and selected lactic acid bacteria was demonstrated to be safe for coeliac patients. This review article focuses on the biotechnologies that use selected sourdough lactic acid bacteria to potentially counteract the adverse reactions to gluten, and the risk of gluten contamination.

Comparative proteomic analysis of biofilm and planktonic cells of Lactobacillus plantarum DB200

This study investigated the relative abundance of extracellular and cell wall associated proteins (exoproteome), cytoplasmic proteins (proteome), and related phenotypic traits of Lactobacillus plantarum grown under planktonic and biofilm conditions. Lactobacillus plantarum DB200 was preliminarily selected due to its ability to form biofilms and to adhere to Caco2 cells. As shown by fluorescence microscope analysis, biofilm cells became longer and autoaggregated at higher levels than planktonic cells. The molar ratio between glucose consumed and lactate synthesised was markedly decreased under biofilm compared to planktonic conditions. DIGE analysis showed a differential exoproteome (115 protein spots) and proteome (44) between planktonic and biofilm L. plantarum DB200 cells. Proteins up- or downregulated by at least twofold (p < 0.05) were found to belong mainly to the following functional categories: cell wall and catabolic process, cell cycle and adhesion, transport, glycolysis and carbohydrate metabolism, exopolysaccharide metabolism, amino acid and protein metabolisms, fatty acid and lipid biosynthesis, purine and nucleotide metabolism, stress response, oxidation/reduction process, and energy metabolism. Many of the above proteins showed moonlighting behavior. In accordance with the high expression levels of stress proteins (e.g., DnaK, GroEL, ClpP, GroES, and catalase), biofilm cells demonstrated enhanced survival under conditions of environmental stress.

Development of species-specific PCR primers and polyphasic characterization of Lactobacillus sanfranciscensis isolated from Korean sourdough

Lactobacillus sanfranciscensis is a bacterium used in sourdough that provides desirable properties such as better flavor and texture to the sourdough bread. Here, the intra-species diversity of L. sanfranciscensis strains isolated from Korean sourdough was studied using genotypic (multiplex-RAPD-PCR: multiplex-Randomly Amplified Polymorphic DNA-polymerase chain reaction) and phenotypic (VITEK2 Compact system) analyses. For this, a novel species-specific set of PCR primers was developed to identify L. sanfranciscensis using the recently published genome database. The primers were able to detect L. sanfranciscensis isolated from Korean sourdough with 100% accuracy. Genotyping and phenotyping analyses at the strain level demonstrated that Korean sourdough possesses various biotypes of L. sanfranciscensis strains. These strains were clustered into 5 subtypes (genotyping) or 7 subtypes (phenotyping). In summary, this strategy to construct novel primers reduced the chance of cross amplification and was able to identify the desired strain. The various strains isolated in this study can be used to develop a sourdough starter after the analysis of their fermentation characteristics.

Lactobacillus rossiae, a vitamin B12 producer, represents a metabolically versatile species within the Genus Lactobacillus

Lactobacillus rossiae is an obligately hetero-fermentative lactic acid bacterium, which can be isolated from a broad range of environments including sourdoughs, vegetables, fermented meat and flour, as well as the gastrointestinal tract of both humans and animals. In order to unravel distinctive genomic features of this particular species and investigate the phylogenetic positioning within the genus Lactobacillus, comparative genomics and phylogenomic approaches, followed by functional analyses were performed on L. rossiae DSM 15814^T, showing how this type strain not only occupies an independent phylogenetic branch, but also possesses genomic features underscoring its biotechnological potential. This strain in fact represents one of a small number of bacteria known to encode a complete de novo biosynthetic pathway of vitamin B₁₂ (in addition to other B vitamins such as folate and riboflavin). In addition, it possesses the capacity to utilize an extensive set of carbon sources, a characteristic that may contribute to environmental adaptation, perhaps enabling the strain's ability to populate different niches.

Use of sourdough fermentation and mixture of wheat, chickpea, lentil and bean flours for enhancing the nutritional, texture and sensory characteristics of white bread

This study aimed at investigating the addition of legume (chickpea, lentil and bean) flours to wheat flour bread. Type I sourdough containing legumes or wheat-legume flours were prepared and propagated (back slopped) in laboratory, according to traditional protocols that are routinely used for making typical Italian breads. Based on kinetic of acidification and culture-dependent data, the wheat-legume sourdough was further characterized and selected for bread making. As determined by RAPD-PCR and partial sequencing of 16S rDNA gene analyses, lactic acid bacteria in wheat-legume sourdough included Lactobacillus plantarum, Lactobacillus sanfranciscensis, Leuconostoc mesenteroides, Lactobacillus fermentum, Weissella cibaria, Lactobacillus pentosus, Lactobacillus coryneformis, Lactobacillus rossiae, Lactobacillus brevis, Lactobacillus parabuchneri and Lactobacillus paraplantarum. Two breads containing 15% (w/w) of legume (chickpea, lentil and bean) flours were produced using selected wheat-legume sourdough (WLSB) and traditional wheat sourdough (WSB). Compared to wheat yeasted bread (WYB), the level of total free amino acids (FAA) was higher in WSB and WLSB. Phytase and antioxidant activities were the highest in WLSB. Compared to bread WYB, the addition of legume flours decreased the in vitro protein digestibility (IVPD) (WYB versus WSB). However, the dough fermentation with WSLB favored an increase of IVPD. According to the levels of carbohydrates, dietary fibers and resistant starch, WSB and WLSB showed lower values of hydrolysis index (HI) compared to WYB. As showed by texture and image analyses and sensory evaluation of breads, a good acceptability was found for WSB and, especially, WLSB breads.

Diversity of the lactic acid bacterium and yeast microbiota in the switch from firm- to liquid-sourdough fermentation

Four traditional type I sourdoughs were comparatively propagated (28 days) under firm (dough yield, 160) and liquid (dough yield, 280) conditions to mimic the alternative technology options frequently used for making baked goods. After 28 days of propagation, liquid sourdoughs had the lowest pH and total titratable acidity (TTA), the lowest concentrations of lactic and acetic acids and free amino acids, and the most stable density of presumptive lactic acid bacteria. The cell density of yeasts was the highest in liquid sourdoughs. Liquid sourdoughs showed simplified microbial diversity and harbored a low number of strains, which were persistent. Lactobacillus plantarum dominated firm sourdoughs over time. Leuconostoc lactis and Lactobacillus brevis dominated only some firm sourdoughs, and Lactobacillus sanfranciscensis persisted for some time only in some firm sourdoughs. Leuconostoc citreum persisted in all firm and liquid sourdoughs, and it was the only species detected in liquid sourdoughs at all times; it was flanked by Leuconostoc mesenteroides in some sourdoughs. Saccharomyces cerevisiae, Candida humilis, Saccharomyces servazzii, Saccharomyces bayanus-Kazachstania sp., and Torulaspora delbrueckii were variously identified in firm and liquid sourdoughs. A total of 197 volatile components were identified through purge and trap-/solid-phase microextraction-gas chromatography-mass spectrometry (PT-/SPME-GC-MS). Aldehydes, several alcohols, and some esters were at the highest levels in liquid sourdoughs. Firm sourdoughs mainly contained ethyl acetate, acetic acid, some sulfur compounds, and terpenes. The use of liquid fermentation would change the main microbial and biochemical features of traditional baked goods, which have been manufactured under firm conditions for a long time.

Fermentation and proteome profiles of Lactobacillus plantarum strains during growth under food-like conditions

This study aimed at investigating the proteomic adaptation of Lactobacillus plantarum strains. Cultivation of L. plantarum strains under food-like conditions (wheat flour hydrolyzed, whey milk, tomato juice) affected some metabolic traits (e.g., consumption of carbohydrates and synthesis of organic acids) compared to de Man, Rogosa and Sharpe (MRS) broth. The analysis of the fermentation profile showed that the highest number of carbon sources metabolized by L. plantarum strains was found using cells cultivated in media containing low concentration of glucose or no glucose at all. The proteomic maps of the strains were comparatively determined after growth on MRS broth and under food-like conditions. The amount of proteins depended on strain and, especially, on culture conditions. Proteins showing decreased or increased amounts under food-like conditions were identified using MALDI-TOF-MS/MS or LC-nano-ESI-MS/MS. Changes of the proteome concerned proteins that are involved in carbohydrate transport and metabolism, energy metabolism, Sec-dependent secretion system, stress response, nucleotide metabolism, regulation of nitrogen metabolism, and protein biosynthesis. A catabolic repression by glucose on carbohydrate transport and metabolism was also found. The characterization of the proteomes in response to changing environmental conditions could be useful to get L. plantarum strains adapted for specific applications.

BIOLOGICAL SIGNIFICANCE

Microbial cell performance during food biotechnological processes has become one of the greatest concerns all over the world. L. plantarum is a lactic acid bacterium with a large industrial application for fermented foods or functional foods (e.g., probiotics). The present study compared the fermentation and proteomic profiling of L. plantarum strains during growth under food-like conditions and under optimal laboratory conditions (MRS broth). This study provides specific mechanisms of proteomic adaptation involved in the microbial performances (carbohydrates utilization, energy metabolism, stress resistance, etc.) affecting the main biotechnological tracts of L. plantarum strains. The finding of this study provides evidences that may be exploited to get strains adapted for specific applications in food biotechnology.

Timely approaches to identify probiotic species of the genus Lactobacillus

Over the past decades the use of probiotics in food has increased largely due to the manufacturer’s interest in placing “healthy” food on the market based on the consumer’s ambitions to live healthy. Due to this trend, health benefits of products containing probiotic strains such as lactobacilli are promoted and probiotic strains have been established in many different products with their numbers increasing steadily. Probiotics are used as starter cultures in dairy products such as cheese or yoghurts and in addition they are also utilized in non-dairy products such as fermented vegetables, fermented meat and pharmaceuticals, thereby, covering a large variety of products.

To assure quality management, several pheno-, physico- and genotyping methods have been established to unambiguously identify probiotic lactobacilli. These methods are often specific enough to identify the probiotic strains at genus and species levels. However, the probiotic ability is often strain dependent and it is impossible to distinguish strains by basic microbiological methods.

Therefore, this review aims to critically summarize and evaluate conventional identification methods for the genus Lactobacillus, complemented by techniques that are currently being developed.

Nutritional quality of fermented defatted soya and flaxseed flours and their effect on texture and sensory characteristics of wheat sourdough bread

The use of soya and flaxseed flours fermented with Pediococcus acidilactici for wheat sourdough bread production was investigated. The protein digestibility, biogenic amine contents of soya and flaxseed sourdoughs, texture and sensory features of bread were studied. The fermentation with P. acidilactici significantly improved soya and flaxseed protein extraction and increased protein digestibility on an average by 13.5%. The concentrations of histamine (3.8 ± 2.3 and 4.0 ± 0.2 mg/kg), tyramine (4.6 ± 0.7 and 19.3 ± 1.8 mg/kg) and putrescine (66.4 ± 1.3 and 11.3 ± 3.0 mg/kg) do not present a health risk for consumers due to their relatively low levels in fermented plant products. The flaxseed sourdoughs influenced a 17.5% higher specific volume and a 4.6% lower crumb hardness of bread than those of soya sourdoughs, and did not disimprove sensory properties of bread. However, the fermented soya additives decreased acceptability of bread because of intensive taste and odour.

Influence of artisan bakery- or laboratory-propagated sourdoughs on the diversity of lactic acid bacterium and yeast microbiotas

Seven mature type I sourdoughs were comparatively back-slopped (80 days) at artisan bakery and laboratory levels under constant technology parameters. The cell density of presumptive lactic acid bacteria and related biochemical features were not affected by the environment of propagation. On the contrary, the number of yeasts markedly decreased from artisan bakery to laboratory propagation. During late laboratory propagation, denaturing gradient gel electrophoresis (DGGE) showed that the DNA band corresponding to Saccharomyces cerevisiae was no longer detectable in several sourdoughs. Twelve species of lactic acid bacteria were variously identified through a culture-dependent approach. All sourdoughs harbored a certain number of species and strains, which were dominant throughout time and, in several cases, varied depending on the environment of propagation. As shown by statistical permutation analysis, the lactic acid bacterium populations differed among sourdoughs propagated at artisan bakery and laboratory levels. Lactobacillus plantarum, Lactobacillus sakei, and Weissella cibaria dominated in only some sourdoughs back-slopped at artisan bakeries, and Leuconostoc citreum seemed to be more persistent under laboratory conditions. Strains of Lactobacillus sanfranciscensis were indifferently found in some sourdoughs. Together with the other stable species and strains, other lactic acid bacteria temporarily contaminated the sourdoughs and largely differed between artisan bakery and laboratory levels. The environment of propagation has an undoubted influence on the composition of sourdough yeast and lactic acid bacterium microbiotas.

Glutathione improves the cold resistance of Lactobacillus sanfranciscensis by physiological regulation

The microenvironmental manipulation of glutathione (GSH) on improving cold resistance of Lactobacillus sanfranciscensis DSM 20451(T) was investigated in this study. It was proved that GSH relieves the metabolic disorder of cells under cold stress, and prevents the decreased activities of related key enzymes such as pyruvate kinase (PK), glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and lactate dehydrogenase (LDH) upon cold challenges. Higher intracellular ATP level was also found in cells with GSH under cold stress. Moreover, cells with imported GSH had significantly higher intracellular than the control during cold treatment. In addition, proteomics analysis showed more exciting findings that the protective function of GSH under cold stress was related to metabolic regulation and the multi-control against induced cross-stresses. These results broaden the knowledge about the physiological function of GSH, and suggest a practicable approach to improve the cold resistance of L. sanfranciscensis, a starter culture for sourdough, by the addition of GSH.