Investigation of Microbial Communities of Chinese Sourdoughs Using Culture-Dependent and DGGE Approaches

Postbiotic characterization of a potential probiotic yeast isolate, and its microencapsulation in alginate beads coated layer-by-layer with chitosan

Considering biosafety concerns and survivability limitations of probiotics (PRO) under different stresses, application of postbiotics and encapsulated PRO has received considerable attentions. Accordingly, the objective of the present study was to investigate the postbiotic capabilities of a potential PRO yeast isolate and the effect of encapsulation with alginate (Alg) and chitosan (Ch) on its survival under SGI conditions. Sequencing results of the PCR products led to the identification of Saccharomyces cerevisiae as the selected potential PRO yeast isolated from wheat germ sourdough. High survival of the isolate under simulated gastrointestinal (SGI) conditions (95.74%), its proper adhesion abilities, as well as its potent inhibitory activity against Listeria monocytogenes (75.84%) and Aspergillus niger (77.35%) were approved. Interestingly, the yeast cell-free supernatant (CFS) showed the highest antioxidant (84.35%) and phytate-degrading (56.19%) activities compared to the viable and heat-dead cells of the isolate. According to the results of the HPLC-based assay, anti-ochratoxin A (OTA) capability of the dead cells was also significantly (P < 0.05) higher than that of the viable cell. Meanwhile, the yeast CFS had no anti-OTA and antimicrobial activities against the foodborne bacteria and fungi tested. Further, microencapsulation of the yeast isolate in Alg beads coated layer-by-layer with Ch (with 77.02% encapsulation efficacy and diameter of 1059 μm based on the field emission scanning electron microscopy analysis) significantly enhanced its survivability under SGI conditions in comparison with the free cells. In addition, electrostatic cross-linking between negatively charged carboxylic groups of Alg and positively charged amino groups of Ch was verified in accordance with Fourier transform infrared and zeta potential data. Human and/or industrial food trials in future are needed for practical applications of these emerging ingredients.

Effects of Co-Fermentation of Lactiplantibacillus plantarum and Saccharomyces cerevisiae on Digestive and Quality Properties of Steamed Bread

The leavening of wheat-based steamed bread is carried out either with a pure yeast culture or with traditional starter cultures containing both lactic acid bacteria and yeast/mold. The use of variable starter cultures significantly affects steamed bread's quality attributes, including nutritional profile. In this paper, differences in physicochemical properties, the type of digested starch, the production of free amino acids, and the specific volume of steamed bread under three fermentation methods (blank, yeast, and LP-GM4-yeast) were compared. The digestion characteristics (protein and starch hydrolysis) of steamed bread produced by using either yeast alone or a combination of Lactiplantibacillus plantrum and yeast (LP-GM4-yeast) were analyzed by an in vitro simulated digestion technique. It was found that the specific volume of steamed bread fermented by LP-GM4-yeast co-culture was increased by about 32%, the proportion of resistant starch was significantly increased (more than double), and soluble protein with molecular weight of 30-40 kDa was significantly increased. The results of this study showed that steamed bread produced by LP-GM4-yeast co-culture is more beneficial to human health than that by single culture.

Relationship between Microbial Composition of Sourdough and Texture, Volatile Compounds of Chinese Steamed Bread

The objective of this work was to explore the relationship between the microbial communities of sourdoughs collected from the Xinjiang and Gansu areas of China and the quality of steamed bread. Compared to yeast-based steamed bread, sourdough-based steamed bread is superior in terms of its hardness, adhesiveness, flexibility, and chewiness. It is rich in flavor compounds, but a significant difference in volatile flavor substances was observed between the two sourdoughs. A total of 19 strains of lactic acid bacteria (LAB) were isolated from the Gansu sourdough sample, in which Lactiplantibacillus plantarum and Pediococcus pentosaceus were the dominant species, accounting for 42.11% and 36.84%, respectively. A total of 16 strains of LAB were isolated from the Xinjiang sourdough sample, in which Lactiplantibacillus plantarum was the dominant species, accounting for 75%. High-throughput sequencing further confirmed these results. Clearly, the species diversity of Gansu sourdough was higher. The volatile profiles of the sourdoughs were similar, but differences in the individual volatile compounds were detected between the sourdoughs of the Gansu and Xinjiang regions. These results point out that the differences in the microbiota and the dominant strains lead to differences in the quality of sourdoughs from region to region. This investigation offers promising guidance on improving the quality of traditional steamed bread by adjusting the microorganisms in sourdough.

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.

Screening of Sourdough Starter Strains and Improvements in the Quality of Whole Wheat Steamed Bread

In this study, yeast, lactic acid bacteria, and acetic acid bacteria were isolated from traditional Chinese sourdough to enhance the organoleptic quality of whole wheat steamed bread. The Saccharomyces cerevisiae, Lactobacillus johnsonii, and Acetobacter pasteurianum showed superior fermentability and acid production capacity when compared with other strains from sourdough, which were mixed to produce the compound starter. It was found that the volume of whole wheat steamed bread leavened with compound starter increased by 12.8% when compared with that of the whole wheat steamed bread made by commercial dry yeast (DY-WB). A total of 38 volatile flavors were detected in the whole wheat steamed bread fermented by the compound starter (CS-WB), and the type of volatile flavors increased by 14 species when compared to the bread fermented by the dry yeast. In addition, some unique volatile flavor substances were detected in CS-WB, such as acetoin, 3-hydroxy-butanal, butyraldehyde, cuparene, etc. Moreover, the hardness and the chewiness of CS-WB decreased by 31.1 and 33.7% when compared with DY-WB, respectively, while the springiness increased by 10.8%. Overall, the formulated compound starter showed a desirable improvement in the whole wheat steamed bread and could be exploited as a new ingredient for steamed bread.

Phenotypic and genotypic characterisation of Lactobacillus and yeast isolates from a traditional New Zealand Māori potato starter culture

Parāroa Rēwena is a traditional Māori sourdough produced by fermentation using a potato starter culture. The microbial composition of the starter culture is not well characterised, despite the long history of this product. The morphological, physiological, biochemical and genetic tests were conducted to characterise 26 lactic acid bacteria (LAB) and 15 yeast isolates from a Parāroa Rēwena potato starter culture. The results of sugar fermentation tests, API 50 CHL tests, and API ID 32 C tests suggest the presence of four different LAB phenotypes and five different yeast phenotypes. 16S rRNA and 26S rRNA sequencing identified the LAB as Lacticaseibacillus paracasei and the yeast isolates as Saccharomyces cerevisiae, respectively. Multilocus sequence typing (MLST) of the L. paracasei isolates indicated that they had identical genotypes at the MLST loci, to L. paracasei subsp. paracasei IBB 3423 or L. paracasei subsp. paracasei F19. This study provides new insights into the microbial composition of the traditional sourdough Parāroa Rēwena starter culture.

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16S sequencing, Multilocus sequencing typing for LAB in the potato starter culture.

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26S sequencing for yeast in the starter culture.

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Lacticaseibacillus paracasei subsp. paracasei IBB3423.

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Lacticaseibacillus paracasei subsp. paracasei F19.

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Saccharomycescerevisiae.

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

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

Microbial community diversity of traditional dough starter (Jiaozi) from two provinces in northwest China

Purpose

Microbial community composition is crucial for the flavor and quality of fermented foods. However, the microbiota of Chinese traditional dough starter (Jiaozi) from different origins has scarcely been studied. The aim of this study was to determine the composition of bacterial and fungal communities in six Jiaozi collected from two provinces in northwest China.

Methods

Our study determined the composition of bacterial and fungal communities in six Jiaozi through Illumina MiSeq sequencing of the 16S rRNA gene and the ITS regions.

Result

A total of 234 operational taxonomic units (OTUs) for bacteria and 490 OTUs for fungi were identified. Furthermore, Lactobacillus, Weissella, Acetobacter, Sphingomonas, and Serratia were identified as the predominant bacterial genera in Jiaozi samples, while Saccharomyces, Candida, Alternaria, unclassified Filobasidiales, and Mycosphaerella were the most abundant fungal genera. The results revealed that the six samples could be grouped into two groups based on their province of origin. In the results of PCA and HCA analysis, the first three principal components which were chosen could explain 99.93% and 90.99% of the total bacterial and fungal communities, respectively.

Conclusion

The results indicated high levels of bacteria and fungi in traditional Jiaozi and highlighted the possible influence of geographic areas on microbial diversity.

Diversity of bacterial communities in traditional sourdough derived from three terrain conditions (mountain, plain and basin) in Henan Province, China

To elucidate the bacterial community composition of sourdoughs from different terrain conditions, thirty-two Chinese traditional sourdough samples were collected from three terrain conditions (mountain, plain and basin) in Henan Province. High-throughput sequencing and culture-dependent approaches were employed to identify the bacterial diversity of the sourdough samples. A total of two hundred and six isolates were characterized via 16S rRNA gene sequencing. Pediococcus pentosaceus was isolated from every sample and was the predominant species in the sourdough samples, accounting for 58% of the relative abundance. High-throughput sequencing revealed that the predominant genera (mainly Pediococcus) in the basin group were significantly different from those in the mountain and plain groups. The genus Lactobacillus was predominant in the plain and mountain sourdough samples. Pediococcus pentosaceus was the absolute dominant strain in the basin sourdough samples. Acetobacter, which was widely distributed only in mountain samples, was recognized as the representative genus of the mountain samples. Moreover, we first reported Gluconobacter oxydans in sourdough. This study provided insight into the bacterial diversity of sourdough from three terrain conditions (mountain, plain and basin) in Henan Province and could serve as a reference for the isolation of desired bacterial strains.

Fungal Species Diversity in French Bread Sourdoughs Made of Organic Wheat Flour

Microbial communities are essential for the maintenance and functioning of ecosystems, including fermented food ecosystems. The analysis of food microbial communities is mainly focused on lactic acid bacteria (LAB), while yeast diversity is less understood. Here, we describe the fungal diversity of a typical food fermented product, sourdough bread. The species diversity of 14 sourdoughs collected from bakeries located all over France was analyzed. Bakeries were chosen to represent diverse bakery practices and included bakers and farmer-bakers. Both non-culture-based (pyrosequencing of Internal Transcribed Spacer 1 amplicons) and culture-based methods were used. While both identification methods were in agreement regarding the dominant yeast species of each sourdough, the ITS1 metabarcoding analysis identified an increased number of fungal species in sourdough communities. Two third of the identified sequences obtained from sourdoughs were Saccharomycetales, mostly in the Kazachstania genus. No Saccharomycetales species was shared by all the sourdoughs, whereas five other fungal species, mainly known plant pathogens, were found in all sourdoughs. Interestingly, Saccharomyces cerevisiae, known as “baker’s yeast,” was identified as the dominant species in only one sourdough. By contrast, five Kazachstania species were identified as the dominant sourdough species, including one recently described Kazachstania species, Kazachstania saulgeensis and an undescribed Kazachstania sp. Sourdoughs from farmer-bakers harbored Kazachstania bulderi, Kazachstania unispora and two newly described Kazachstania species, while sourdough from bakers mostly carried Kazachstania humilis as the dominant species. Such yeast diversity has not been found in sourdoughs before, highlighting the need to maintain different traditional food practices to conserve microbial diversity.

Dynamic and Functional Characteristics of Predominant Species in Industrial Paocai as Revealed by Combined DGGE and Metagenomic Sequencing

The microbial community during the fermentation of industrial paocai, a lactic acid fermented vegetable food, was investigated via combined denaturing gradient gel electrophoresis (DGGE) and metagenomic sequencing. Firmicutes and Proteobacteria were identified as the dominant phyla during the fermentation. DGGE results of the bacterial community analysis showed that many genera were observed during the fermentation of industrial paocai, but the same predominant genus and species were observed: Lactobacillus and Lactobacillus (L.) alimentarius/L. paralimentarius. The abundance of L. alimentarius/L. paralimentarius increased fast during the initial stage of fermentation and approximately remained constant during the later stage. Metagenomic sequencing was used to finally identify the predominant species and their genetic functions. Metabolism was the primary functions of the microbial community in industrial paocai fermentation, including carbohydrate metabolism (CM), overview (OV), amino acid metabolism (AAM), nucleotide metabolism (NM), energy metabolism (EM), etc. The predominant species L. alimentarius and L. paralimentarius were involved in plenty of pathways in metabolism and played different roles in the metabolism of carbohydrate, amino acid, lipid to form flavor compounds during industrial paocai fermentation. This study provided valuable information about the predominant species in industrial paocai and its functional properties, which could enable us to advance our understanding of the fermentation mechanism during fermentation of industrial paocai. Our results will advance the understanding of the microbial roles in the industrial paocai fermentation and provide a theoretical basis for improving the quality of industrial paocai products.

Impact of process conditions on the microbial community dynamics and metabolite production kinetics of teff sourdough fermentations under bakery and laboratory conditions

Teff and teff sourdoughs are promising ingredients for bread production. Therefore, this study aimed at the characterization of spontaneous and flour-native starter culture-initiated teff sourdough productions under bakery and laboratory conditions. Backslopped laboratory and bakery teff sourdough productions were characterized by different lactic acid bacteria (LAB) and yeast species, but were both characterized by a pH below 4.0 after five backslopping steps. The sourdough-associated Lactobacillus sanfranciscensis was isolated for the first time from backslopped spontaneous teff sourdoughs. The autochthonous strain L. sanfranciscensis IMDO 150101 was tested as starter culture during laboratory teff sourdough fermentations. Its prevalence could be related to the process conditions applied, in particular the ambient temperature (below 30°C). Breads made with 20% teff sourdough (on flour basis) displayed interesting features compared with all-wheat-based reference breads. Teff sourdoughs were characterized as to their pH evolution, microbial community dynamics, and microbial species composition. Representative strains of the LAB species isolated from these sourdoughs, in particular L. sanfranciscensis, may be selected as starter cultures for the production of stable teff sourdoughs and flavorful breads, provided they are adapted to the environmental conditions applied.

Predominant yeasts in Chinese traditional sourdough and their influence on aroma formation in Chinese steamed bread

A total of 105 yeast isolates was obtained from 15 sourdough samples collected from different regions in China and subjected to random amplified polymorphic DNA (RAPD) analysis. Six species were identified including Pichia membranifaciens, which has not previously been reported in Chinese sourdoughs. Different species of yeast were used in single-culture fermentation to make Chinese steamed bread (CSB). The volatiles of the CSB were captured by solid-phase microextraction method, separated and identified by gas chromatography-mass spectrometry. In total, 41 volatile compounds were found in all the steamed breads. All CSBs showed a similar volatile profile; however, significant differences in the quantity of some volatile compounds were seen among the CSB fermented by different yeast species. A partial least squares discriminant analysis showed that the CSBs could be separated by their characteristic volatile profiles. The study suggested that the aromatic properties of CSB are determined by the yeast used.

Insights into the microbial diversity and community dynamics of Chinese traditional fermented foods from using high-throughput sequencing approaches

Chinese traditional fermented foods have a very long history dating back thousands of years and have become an indispensable part of Chinese dietary culture. A plethora of research has been conducted to unravel the composition and dynamics of microbial consortia associated with Chinese traditional fermented foods using culture-dependent as well as culture-independent methods, like different high-throughput sequencing (HTS) techniques. These HTS techniques enable us to understand the relationship between a food product and its microbes to a greater extent than ever before. Considering the importance of Chinese traditional fermented products, the objective of this paper is to review the diversity and dynamics of microbiota in Chinese traditional fermented foods revealed by HTS approaches.

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.

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.

A study revealing the key aroma compounds of steamed bread made by Chinese traditional sourdough

Aroma of Chinese steamed bread (CSB) is one of the important parameters that determines the overall quality attributes and consumer acceptance. However, the aroma profile of CSB still remains poorly understood, mainly because of relying on only a single method for aroma extraction in previous studies. Therefore, the objective of this study was to determine the volatile aroma compounds of five different samples of CSB using three different aroma extraction methods, namely solid-phase microextraction (SPME), simultaneous distillation-extraction (SDE), and purge and trap (P&T). All samples showed a unique aroma profile, which could be attributed to their unique microbial consortia. (E)-2-Nonenal and (E,E)-2,4-decadienal were the most prevalent aromatic compounds revealed by SDE, which have not been reported previously, while ethanol and acetic acid proved to be the most dominant compounds by both SPME and P&T. Our approach of combining three different aroma extraction methods provided better insights into the aroma profile of CSB, which had remained largely unknown in previous studies.