Sourdough bacterial dynamics revealed by metagenomic analysis in Brazil

Cellular variability as a driver for bioprocess innovation and optimization

Cellular heterogeneity plays a crucial role in biotechnological processes, significantly influencing metabolic activity, product yield, and process consistency. This review explores the different dimensions of cellular heterogeneity, focusing on its manifestation at both single-cell and population levels. The study examines how factors such as asymmetric cell division, age, and environmental conditions contribute to functional diversity within cell populations, with an emphasis on microorganisms like yeast. Age-related cellular heterogeneity, in particular, is highlighted for its impact on metabolic pathways, mitochondrial function, and secondary metabolite production, which directly affect bioprocess outcomes. Furthermore, the review discusses advanced techniques for detecting and managing heterogeneity, including surface marker-based approaches, which utilize proteins, polysaccharides, and lipids, and label-free methods that leverage cellular volume and physical properties for separation. Understanding and controlling cellular heterogeneity is essential for optimizing industrial bioprocesses, improving yield, and ensuring product quality. The review also underscores the potential of emerging biotechnological tools, such as real-time single-cell analysis and microfluidic devices, in enhancing separation techniques and managing cellular diversity for better process efficiency and robustness.

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.

Isolation, identification, and stability of sourdough microbiota from spontaneously fermented Norwegian legumes

Fermentation has recently been rediscovered as an attractive technique to process legumes, as it can improve the nutritional quality and value of the end product. This study investigated the dynamics and stability of the microbial communities in spontaneously fermented sourdoughs made from flours of two cultivars of faba beans and two cultivars of peas. Sourdoughs were established by the backslopping technique, and the microbial development at 22 °C and 30 °C was followed by culture dependent and culture independent methods. The utilization of substrates and formation of metabolites were also determined by high-performance liquid chromatography. A stable pH was reached in all the sourdoughs after 11-15 days of daily backslopping. Lactic acid bacteria and yeast from pH stable sourdoughs were isolated, characterized and identified. The fermentation temperature influenced the development of the microbial community and the substrate utilization during spontaneous fermentation. In the 30 °C fermentations, one species dominated (Lactiplantibacillus plantarum/pentosus), a lower pH was achieved, and the available substrates were more extensively converted. The 22 °C fermentation resulted in a more diverse microbial community (Lactiplantibacillus, Leuconostoc, Pediococcus), a higher pH, and more residual substrates were available after fermentation. Yeasts were only detected in one of the pea sourdoughs fermented at 30 °C, with Saccharomyces cerevisiae being the dominant species. Nearly all sourdoughs were depleted of maltose after 24 h fermentation cycles, and higher levels of lactic and acetic acid were detected in 30 °C fermen-tations. This research adds to our understanding of the autochthonous microbial community present in faba beans and peas as well as their natural capacity to establish themselves and ferment legume flours. These findings enhance the possibilities of utilizing and improving plant based protein sources.

16S-rRNA-Based Metagenomic Profiling of the Bacterial Communities in Traditional Bulgarian Sourdoughs

Sourdoughs (SDs) are spontaneously formed microbial ecosystems composed of various species of lactic acid bacteria (LAB) and acid-tolerant yeasts in food matrices of cereal flours mixed with water. To date, more than 90 LAB species have been isolated, significantly impacting the organoleptic characteristics, shelf life, and health properties of bakery products. To learn more about the unique bacterial communities involved in creating regional Bulgarian sourdoughs, we examined the metacommunities of five sourdoughs produced by spontaneous fermentation and maintained by backslopping in bakeries from three geographic locations. The 16S rRNA gene amplicon sequencing showed that the former genus Lactobacillus was predominant in the studied sourdoughs (51.0-78.9%). Weissella (0.9-42.8%), Herbaspirillum (1.6-3.8%), Serratia (0.1-11.7%), Pediococcus (0.2-7.5%), Bacteroides (0.1-1.3%), and Sphingomonas (0.1-0.5%) were also found in all 5 samples. Genera Leuconostoc, Enterococcus, Bacillus, and Asaia were sample-specific. It is interesting to note that the genus Weissella was more abundant in wholegrain samples. The greatest diversity at the species level was found in the former genus Lactobacillus, presented in the sourdough samples with 13 species. The UPGMA cluster analysis clearly demonstrated similarity in species' relative abundance between samples from the same location. In addition, we can conclude that the presence of two main clusters-one including samples from mountainous places (the cities of Smolyan and Bansko) and the other including samples from the city of Ruse (the banks of the Danube River)-may indicate the impact of climate and geographic location (e.g., terrain, elevation, land use, and nearby water bodies and their streams) on the abundance of microbiome taxa. As the bacterial population is crucial for bread standardization, we expect the local bakery sector to be interested in the relationship between process variables and their effect on bacterial dynamics described in this research study.

Effect of Alkali on the Microbial Community and Aroma Profile of Chinese Steamed Bread Prepared with Chinese Traditional Starter

Alkali is an indispensable additive in Chinese steamed bread (CSB) production. This work aimed to evaluate the key roles of alkali in the microbial community of dough fermented using Chinese traditional starter (CTS) and the aroma profiles of CSB. The dominant fungi in CTS and fermented dough were members of the phylum Ascomycota and the genus Saccharomyces. Pediococcus, Companilactobacillus, and Weissella were the dominant bacterial genera in CTS and fermented dough. Adding alkali could retain the types of dominant yeasts and LAB derived from CTS, decrease the relative abundance of Companilactobacillus crustorum and Weissella cibaria, and increase that of Pediococcus pentosaceus, in fermented dough. Principal component analysis (PCA) indicated that adding alkali decreased the content of sourness-related volatiles in CSB fermented by CTS. Correlation analysis showed that Pediococcus and Weissella in fermented dough were positively correlated with the lipid oxidation flavor-related compounds in CSB, and Lactobacillus was positively correlated with sourness-related aroma compounds. Synthetic microbial community experiments indicated that CSB fermented by the starter containing P. pentosaceus possessed a strong aroma, and adding alkali weakened the flavor intensity. Alkali addition could promote the formation of ethyl acetate and methyl acetate with a pleasant fruity aroma in W. cibaria-associated CSB.

Probiotics in the Sourdough Bread Fermentation: Current Status

Sourdough fermentation is an ancient technique to ferment cereal flour that improves bread quality, bringing nutritional and health benefits. The fermented dough has a complex microbiome composed mainly of lactic acid bacteria and yeasts. During fermentation, the production of metabolites and chemical reactions occur, giving the product unique characteristics and a high sensory quality. Mastery of fermentation allows adjustment of gluten levels, delaying starch digestibility, and increasing the bio-accessibility of vitamins and minerals. This review focuses on the main steps of sourdough fermentation, the microorganisms involved, and advances in bread production with functional properties. The impact of probiotics on human health, the metabolites produced, and the main microbial enzymes used in the bakery industry are also discussed.

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.

Taxonomic structure of bacterial communities in sourdoughs of spontaneous fermentation

The article is devoted to the study of the microbiome of spontaneously fermented sourdoughs. The aim of the work was to study the inf luence of the technological parameters of sourdough propagations on the taxonomic structure of the microbiome of spontaneously fermented sourdoughs. Two spontaneously fermented sourdoughs were studied: dense rye sourdough and liquid rye sourdough, both prepared using the same batch of peeled rye f lour. To study the taxonomic structure of the sourdough microbiome in dynamics, the method of high-throughput sequencing of 16S rRNA gene fragments of microorganisms was used. It was shown that the technological parameters of sourdough (humidity, temperature) do not affect the taxonomic composition of the microbiome of dense rye or liquid rye sourdough at the phylum/class/genus level. It was found that during the f irst three days of propagations, bacteria from the phyla Proteobacteria and Firmicutes dominated in the microbial community. In the phylum Proteobacteria, microorganisms from the order Enterobacterales took a large share, which persisted for three days of backslopping. The phylum Firmicutes was represented by lactic acid bacteria of the genera Weissella, Lactobacillus, Leuconostoc, Pediococcus, Lactococcus. It was established by classical microbiological methods that after a day of fermentation, the number of lactic acid bacteria cells was signif icantly higher in liquid rye sourdough compared to dense one. However, with further propagation of sourdoughs, the number of cells was comparable, while signif icant changes occurred at the level of genera and species. It was shown that as the relative number of lactic acid bacteria of the genus Lactobacillus increased, a gradual displacement of the coccal forms of Lactococcus, Leuconostoc, Weissella, Pediococcus happened. With further propagation of sourdough after 10 days, the position of the dominant groups of bacteria was occupied by representatives of the phylum Firmicutes, lactic acid bacteria of the genus Lactobacillus. The inf luence of the mode and parameters of the sourdough on the species composition of lactobacilli, which demonstrated a low bacterial diversity, is shown. In the f irst three days of propagations, lactobacilli L. curvatus, L. brevis, and Lactiplantibacil- lus sp. dominated in both sourdoughs. After a month of backslopping, Fructilactobacillus sanfranciscensis and Companilactobacillus sp. dominated in dense rye sourdough, and L. pontis dominated in liquid rye sourdough

Effect of Staphylococcus aureus Contamination on the Microbial Diversity and Metabolites in Wholewheat Sourdough

Wholewheat sourdough products are becoming increasingly more popular, and Staphylococcus aureus is a common opportunistic pathogen in dough products. The effects of S. aureus contamination (102 cfu/g) on metabolites as well as titratable acidity (TTA), pH, and microbial diversity of sourdough were investigated. S. aureus contamination significantly decreased the content of mannose while increasing the sorbitol in sourdough (p < 0.05). The S. aureus contamination significantly reduced the number of lactic acid bacteria (LAB), such as Lactobacillus curvatus, and the TTA values (p < 0.05). Furthermore, S. aureus contamination significantly reduced the content of most esters and acid flavor compounds while significantly increasing the content of 2,4-decadienal (p < 0.05), which is a compound that could have a negative impact on the flavor of sourdough. The PCA model developed based on volatile metabolites data could be used to distinguish contamination of S. aureus in sourdough cultured for 4 h. Sorbitol, 2,3-dimethylundecane, 1-pentanol, and 3-methylbutanoic acid were newly found to be the characteristic metabolites in S. aureus-contaminated sourdough.

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.

Isolation and Characterization of Lactic Acid Bacteria and Yeasts from Typical Bulgarian Sourdoughs

Traditional sourdoughs in Bulgaria were almost extinct during the centralized food production system. However, a rapidly developing trend of sourdough revival in the country is setting the demand for increased production and use of commercial starter cultures. The selection of strains for such cultures is based on geographical specificity and beneficial technological properties. In this connection, the aim of this study was to isolate, identify and characterize lactic acid bacteria (LAB) and yeasts from typical Bulgarian sourdoughs for the selection of strains for commercial sourdough starter cultures. Twelve samples of typical Bulgarian sourdoughs were collected from different geographical locations. All samples were analyzed for pH, total titratable acidity and dry matter content. Enumeration of LAB and yeast was also carried out. Molecular identification by 16S rDNA sequence analysis was performed for 167 LAB isolates, and 106 yeast strains were identified by ITS1-5.8S-ITS2 rRNA gene partial sequence analysis. The LAB strains were characterized according to their amylolytic and proteolytic activity and acidification capacity, and 11 strains were selected for further testing of their antimicrobial properties. The strains with the most pronounced antibacterial and antifungal activity are listed as recommended candidates for the development of starter cultures for sourdoughs or other food products.

Statistical Approach to Potentially Enhance the Postbiotication of Gluten-Free Sourdough

Fermented products are permanently under the attention of scientists and consumers, both due to nutritional importance and health promoting effects. The fermented functional foods contribute to a more balanced diet and increase the immune responses (among many other health effects) with positive implications for quality of life. In this sense, improving the sourdough’s fermentation to boost the biotic (postbiotic and paraprobiotic) properties of the sourdough-based products has positive impacts on the nutritional and functional properties of the final baked products. These enhanced sourdoughs can be obtained in controlled fermentation conditions and used as sourdough bread improvers or novel bioingredients. In this context, our work aimed to optimize, using statistical tools, a gluten-free sourdough based on chickpea, quinoa, and buckwheat fermentation with selected lactic acid bacteria (LAB) to enhance its postbiotic properties. The most important biotechnological parameters were selected by Plackett–Burman Design (PBD) and then Response Surface Methodology (RSM) was applied to evaluate the interactions between the selected factors to maximize the gluten-free sourdough’s properties. As a result, the optimized fermented sourdough had antimicrobial activity with inhibition ratios between 71 and 100% against the Aspergillus niger, Aspergillus flavus, Penicillium spp. molds and against the Bacillus spp endospore-forming Gram-positive rods. The optimized variant showed a total titratable acidity (TTA) of 40.2 mL NaOH 0.1N. Finally, the high-performance liquid chromatography (HPLC) analysis highlighted a heterofermentative profile for the organic acids from the optimized sourdough. Among flavonoids and polyphenols, the level of caffeic and vanillic acids increased after lactic acid fermentation. The comparison between the optimized sourdough and the control evidenced significant differences in the metabolite profiles, thus highlighting its potential postbiotication effect.

Overcoming bread quality decay concerns: main issues for bread shelf life as a function of biological leavening agents and different extra ingredients used in formulation. A review

As is widely accepted, the quality decay of freshly baked bread that affects product shelf life is the result of a complex multifactorial process that involves physical staling, together with microbiological, chemical and sensorial spoilage. In this context, this paper provides a critical review of the recent literature about the main factors affecting shelf life of bread during post-baking. An overview of the recent findings about the mechanism of bread staling is firstly provided. Afterwards, the effect on staling induced by baker's yeasts and sourdough as well as by the extra ingredients commonly utilized for bread fortification is also addressed and discussed. As inclusion/exclusion criteria, only papers dealing with wheat bread and not with long-life bread or gluten-free bakery products are taken into consideration. Despite recent developments in international scientific literature, the whole mechanism that induces bread staling is far from being completely understood and the best analytical methods to be adopted to measure and/or describe in depth this process appear still debated. In this topic, the effects induced on bread shelf life by the use of biological leavening agents (baker's yeasts and sourdough) as well as by some extra ingredients included in the bread recipe have been individuated as two key issues to be addressed and discussed in terms of their influence on the kinetics of bread staling. © 2020 Society of Chemical Industry.

Bacterial diversity and flavor profile of Zha-Chili, a traditional fermented food in China

Zha-chili is a traditional Chinese fermented food with special flavor, which is often used as an appetizer in condiments and an important energy source. The final quality of zha-chili is closely related to its microbial community structure. However, the differences of bacterial diversity in zha-chili from different regions and how bacterial species affect zha-chili fermentation process and flavor quality have not been reported. In this study, the bacterial diversity and flavor quality of zha-chili samples from different regions were analyzed using Illumina Miseq high-throughput sequencing, electronic nose and electronic tongue technology. Twenty-three bacterial phyla and 665 bacterial genera were identified in all zha-chili samples. Firmicutes, Proteobacteria and Actinobacteria were the dominant bacterial phyla in zha-chili samples, while Lactobacillus, Pseudomonas, Pediococcus, Weissella and Staphylococcus were the dominant bacterial genera. The bacterial community structure of zha-chili samples from different regions was significantly diverse (p < 0.05). The flavor of zha-chili samples also varied in different regions, and the discrepancy of taste was much greater than that of aroma. Moreover, there were significant correlations (p < 0.05) between 6 dominant bacterial genera and 8 flavor indicators (3 aroma indicators, 5 taste indicators). In addition, the results of microbiome phenotypes prediction by BugBase and bacterial functional potential prediction using PICRUSt showed that eight out of nine predicted phenotypic functions of zha-chili samples from different regions were significantly different (p < 0.05), bacterial metabolism was vigorous in the zha-chili samples, and Lactobacillus was the dominant bacterial genus involved in metabolism during fermentation.

Evaluation of Enzymatic Cleaning on Food Processing Installations and Food Products Bacterial Microflora

Biofilms are a permanent source of contamination in food industries and could harbor various types of microorganisms, such as spoiling bacteria. New strategies, such as enzymatic cleaning, have been proposed to eradicate them. The purpose of this study was to evaluate the impact of enzymatic cleaning on the microbial flora of installations in a processing food industry and of the final food product throughout its shelf life. A total of 189 samples were analyzed by classical microbiology and 16S rDNA metagenetics, including surface samples, cleaning-in-place (CIP) systems, and food products (at D₀, D_{end of the shelf life}, and D_{end of the shelf life +7 days}). Some surfaces were highly contaminated with spoiling bacteria during conventional cleaning while the concentration of the total flora decreased during enzymatic cleaning. Although the closed circuits were cleaned with conventional cleaning before enzymatic cleaning, there was a significant release of microorganisms from some parts of the installations during enzymatic treatment. A significant difference in the total flora in the food products at the beginning of the shelf life was observed during enzymatic cleaning compared to the conventional cleaning, with a reduction of up to 2 log CFU/g. Metagenetic analysis of the food samples at the end of their shelf life showed significant differences in bacterial flora between conventional and enzymatic cleaning, with a decrease of spoiling bacteria (Leuconostoc sp.). Enzymatic cleaning has improved the hygiene of the food processing instillations and the microbial quality of the food throughout the shelf life. Although enzymatic cleaning is not yet commonly used in the food industry, it should be considered in combination with conventional sanitizing methods to improve plant hygiene.

Effect of Oral Probiotic Lactobacillus rhamnosus GR-1 and Lactobacillus reuteri RC-14 on the Vaginal Microbiota, Cytokines and Chemokines in Pregnant Women

Spontaneous preterm birth is associated with vaginal microbial dysbiosis. As certain strains of lactobacilli help restore homeostasis in non-pregnant women, the goal was to determine the effect of Lactobacillus rhamnosus GR-1 and Lactobacillus reuteri RC-14 administered orally, twice daily for 12 weeks on the vaginal microbiota, cytokines and chemokines of low-risk pregnant women. A double-blind, placebo-controlled, randomized trial comparing probiotic lactobacilli to placebo daily was performed in 86 asymptomatic pregnant women who had an Intermediate or Bacterial Vaginosis Nugent score at 13 weeks. After drop outs, 32 women receiving probiotics and 34 receiving placebo completed the study. The Nugent score returned to normal in 30% of the women in both groups at 28 weeks and was maintained until 35 weeks. The majority of subjects had normal pregnancy outcomes. Ninety-three bacterial species were detected at 13 weeks, with Lactobacillus iners, Lactobacillus crispatus, Gardnerella vaginalis and Atopobium vaginae being the most abundant across pregnancy. There was no difference in the Shannon diversity index between the probiotic and placebo groups at 13, 28 or 35 weeks. Almost all subjects consumed fermented foods and many of the organisms in the vagina are also known to be present in fermented foods. Interleukin-4 in the placebo group and Interleukin-10 in both probiotic and placebo groups increased slightly at 28 weeks but were not different at 35 weeks when compared to 13 weeks. In conclusion, this study showed no adverse issues resulting from 12 week use of probiotic Lactobacillus strains GR-1 and RC-14 during pregnancy in women at low risk for premature birth. The vaginal microbiota demonstrated flux irrespective of this oral probiotic administration.