Bacterial diversity and community structure in Chongqing radish paocai brines revealed using PacBio single-molecule real-time sequencing technology

Microbial network and fermentation modulation of Napier grass and sugarcane top silage in southern Africa

IMPORTANCE

Feed shortage in the tropics is a major constraint to the production of livestock products such as milk and meat. In order to effectively utilize of local feed resources, the selected lactic acid bacteria (LAB) strain was used to prepare Napier grass and sugarcane top silage. The results showed that the two silages inoculated with LAB formed a co-occurrence microbial network dominated by Lactiplantibacillus during the fermentation process, regulated the microbial community structure and metabolic pathways, and improved the silage fermentation quality. This is of great significance for alleviating feed shortage and promoting sustainable production of livestock.

Determination of the Bacterial Community of Mustard Pickle Products and Their Microbial and Chemical Qualities

We assessed the microbial and chemical qualities and microbiomes of 14 mustard pickle products coded sequentially from A to N and sold in traditional Taiwanese markets. The results showed that the aerobic plate count and lactic acid bacteria count of commercially available mustard pickle products were 2.18-4.01 and <1.0-3.77 log CFU/g, respectively. Moreover, no coliform bacteria, Escherichia coli, Staphylococcus aureus, Salmonella spp., or Listeria monocytogenes were detected in any of the samples. Analysis of the chemical quality showed that the sulfite content of all samples exceeded 30 ppm, which is the food additive limit in Taiwan. Furthermore, the mean contents of eight biogenic amines in the mustard pickle product samples were below 48.0 mg/kg. The results of high-throughput sequencing showed that the dominant bacterial genera in sample A were Proteus spp. (25%), Vibrio (25%), and Psychrobacter (10%), in sample C they were Weissella (62%) and Lactobacillus (15%), in sample E it was Lactobacillus (97%), and in sample J it was Companilactobacillus (57%). Mustard pickle product samples from different sources contained different microbiomes. The dominant bacterial family was Lactobacillaceae in all samples except for sample A. In contrast, the microbiome of sample A mainly consisted of Morganellaceae and Vibrionaceae, which may have resulted from environmental contamination during storage and sales. The result of this work suggests it may be necessary to monitor sulfite levels and potential sources of bacterial contamination in mustard pickle products, and to take appropriate measures to rule out any public health risks.

Replacing the Addition of Sulfite in Mustard Pickle Products by High-Hydrostatic-Pressure Processing to Delay Quality Deterioration during Storage

This study aimed to assess the use of the high-hydrostatic-pressure (HHP) method (200-600 MPa, 5 min) for bleaching mustard pickle products as an alternative to the conventional method of sulfite addition. The aerobic plate count (APC) and lactic acid bacteria count (LAB) of the samples decreased with the increase in pressure, and the yeast count decreased to no detectable levels. Next, compared with the control group (no high-pressure treatment) the L* (lightness), W (whiteness), ΔE (color difference), and texture (hardness and chewiness) of the HHP-processed samples, which increased significantly with increasing pressure, while the a* (redness) and b* (yellowness) values decreased slightly. This indicates that HHP processing gave the mustard pickle a harder texture and a brighter white color and appearance. Furthermore, when the mustard pickle was treated with HHP 400 and 600 MPa for 5 min and stored at 25 °C for 60 days, it was found that the APC and LAB counts in the HHP-processed group recovered rapidly and did not differ from those in the control group (the non-HHP treated group) but significantly delayed the growth of yeast, the increase in pH value, and total volatile basic nitrogen (TVBN). The high-throughput sequencing (HTS) analysis revealed that the predominant bacterial genera in the non-HHP-treated mustard pickle were Lactiplantibacillus (74%), Lactilactobacillus (12%), and Levilactobacillus (6%); after 60 days of storage, Companilactobacillus (80%) became dominant. However, after 60 days of storage, Lactiplantibacillus (92%) became dominant in the samples processed at 400 MPa, while Levilactobacillus (52%), Pediococcus (17%), and Lactiplantibacillus (17%) became dominant in the samples processed at 600 MPa. This indicated that the HHP treatment changed the lactic acid bacterial flora of the mustard pickle during the storage period. Overall, it is recommended to treat the mustard pickle with HHP above 400 MPa for 5 min to improve its texture and color and delay the deterioration of quality during storage. Therefore, HHP technology has the potential to be developed as a treatment technique to replace the addition of sulfite.

Effects of Brines and Containers on Flavor Production of Chinese Pickled Chili Pepper (Capsicum frutescens L.) during Natural Fermentation

The effects of (fresh/aged) brine and (pool/jar) containers on the flavor characteristics of pickled chili peppers were investigated based on a multivariate analysis integrated with kinetics modeling. The results showed that the effect of brine on organic acid, sugar, and aroma was more dominant than that of containers, while free amino acids production was more affected by containers than brines. Chili pepper fermented using aged brine exhibited higher acidity (3.71−3.92) and sugar (7.92−8.51 mg/g) than that using fresh brine (respective 3.79−3.96; 6.50−9.25 mg/g). Besides, chili peppers fermented using pool containers showed higher free amino acids content (424.74−478.82 mg/100 g) than using a jar (128.77−242.90 mg/100 g), particularly with aged brine. As for aroma, the number of volatiles in aged brine was higher (88−96) than that in fresh brine (76−80). The contents of the esters, alcohols, and ketones were significantly higher in the aged brine samples than those in fresh brine (p < 0.05), while terpenes in chili pepper fermented using the pool were higher than those using the jar. In general, jar fermentation with aged brine contributed more flavor to pickled chili peppers than other procedures.

The Application of Metagenomics to Study Microbial Communities and Develop Desirable Traits in Fermented Foods

The microbial communities present within fermented foods are diverse and dynamic, producing a variety of metabolites responsible for the fermentation processes, imparting characteristic organoleptic qualities and health-promoting traits, and maintaining microbiological safety of fermented foods. In this context, it is crucial to study these microbial communities to characterise fermented foods and the production processes involved. High Throughput Sequencing (HTS)-based methods such as metagenomics enable microbial community studies through amplicon and shotgun sequencing approaches. As the field constantly develops, sequencing technologies are becoming more accessible, affordable and accurate with a further shift from short read to long read sequencing being observed. Metagenomics is enjoying wide-spread application in fermented food studies and in recent years is also being employed in concert with synthetic biology techniques to help tackle problems with the large amounts of waste generated in the food sector. This review presents an introduction to current sequencing technologies and the benefits of their application in fermented foods.

Nutritional Content Dynamics and Correlation of Bacterial Communities and Metabolites in Fermented Pickled Radishes Supplemented With Wheat Bran

Wheat bran supplementation in cereal food processing improves the nutritional value and quality of the final products. However, whether wheat bran has the potential as a biofortifier to enhance nutritional and flavor of fermented vegetables remains unknown. The study aimed to evaluate the potential of wheat bran supplementation for nutrition and flavor fortification during radish fermentation, and to explore the role of microorganisms in nutritional and flavor development. Using high-throughput sequencing coupled with high-performance liquid chromatography and headspace solid-phase microextraction-gas chromatography-mass spectrometry, the microbial community profiles and nutritional and flavor changes of wheat bran-treated samples were analyzed and compared with control samples. Correlation analysis between bacteria taxa with metabolites were also performed. The results showed that wheat bran treatment increased the content of most free amino acids (FAAs), α-linolenate, thiamine, and riboflavin in the samples (p < 0.05). In addition, the increased consumption of reducing sugar and glutamate in the wheat bran-treated samples was due to the production of secondary metabolites such as lactic acid, ethanol, acetic acid, and GABA (p < 0.05). Moreover, compared with control samples, the flavor of the wheat bran-treated pickled radish was preferable. Wheat bran increased the amount of alcohol, ester, acid, and ketones compounds but reduced the number of sulfides, which increased the aroma but decreased the pungent flavor. Additionally, the correlation analysis suggested that Lactobacillus, the most dominant genus, was boosted by wheat bran and was positively associated with most of FAAs, GABA, and lactate, while negatively associated with most sulfides. Therefore, compared with the control, wheat bran treatment could improve the nutritional values and sensorial properties of radish pickles. New areas of research should explore the co-fermentation of other vegetables with wheat bran, and the potential of this processing technique to provide consumers with products of high nutritional quality.

Microbial composition and correlation between microbiota and quality-related physiochemical characteristics in chongqing radish paocai

Chongqing radish paocai (paocai) is produced by fermentation of fresh vegetables. It gained attention for its non-negligible contribution in Sichuan cuisine and potential health benefits. This study explored microbial structures in six home-made paocai using high through-put sequencing. Key microbial communities were identified based on significant correlations with quality-related physiochemical attributes. Results suggest bacterial diversity level significantly decreased during fermentation, while fungal diversity level were inconsistent across different alpha-diversity indexes. Firmicutes and Proteobacteria were the predominant bacterial phylum in all samples. Lactic acid bacteria, namely Lactobacillus and L. plantarum were the predominant bacteria at genus and species levels. Fungi had overall weak correlations with physiochemical attributes, several bacterial species significantly correlated with physiochemical attributes, including Lactobacillus plantarum, Lactobacillus acetotolerans, and Weissella cibaria. Overall, this study identified key microbial communities and discussed their functional roles that could contribute to consistent production of high-quality Chongqing radish paocai.

Metagenomic Study on Chinese Homemade Paocai: The Effects of Raw Materials and Fermentation Periods on the Microbial Ecology and Volatile Components

“Chinese paocai” is typically made by fermenting red radish or cabbage with aged brine (6–8 w/w). This study aimed to reveal the effects of paocai raw materials on fermentation microorganisms by metagenomics sequencing technology, and on volatile organic compounds (VOCs) by gas chromatography–mass spectroscopy, using red radish or cabbage fermented for six rounds with aged brine. The results showed that in the same fermentation period, the microbial diversity in cabbage was higher than that in red radish. Secundilactobacillus paracollinoides and Furfurilactobacillus siliginis were the characteristic bacteria in red radish paocai, whereas 15 species of characteristic microbes were found in cabbage. Thirteen kinds of VOCs were different between the two raw materials and the correlation between the microorganisms and VOCs showed that cabbage paocai had stronger correlations than radish paocai for the most significant relationship between 4-isopropylbenzyl alcohol, α-cadinol, terpinolene and isobutyl phenylacetate. The results of this study provide a theoretical basis for understanding the microbiota and their relation to the characteristic flavors of the fermented paocai.

Microbial Communities and Physiochemical Properties of Four Distinctive Traditionally Fermented Vegetables from North China and Their Influence on Quality and Safety

The bacterial communities and physicochemical characteristics of four types of extremely distinctive traditionally fermented vegetables (pickled pepper (PP), pickled Brassica napobrassica (PBN), salted flowers of wild chives (SFWC), and pickled cucumber (PC)) were identified and compared from north China. Lactobacillus was the main bacterial genus in PP and PBN samples, with Oceanobacillus only being observed in PBN. The predominant genus in SFWC was Weissella, while in PC they were were Carnimonas and Salinivibrio. At the species level, Companilactobacillus ginsenosidimutans, Fructilactobacillus fructivorans, and Arcobacter marinus were abundant in PP and PBN. Levilactobacillus brevis and Companilactobacillus alimentarius were enriched in PP, and L. acetotolerans, Ligilactobacillus acidipiscis and Pediococcus parvulus were observed in PBN. Weissella cibaria and Kosakonia cowanii were abundant in SFWC. Moreover, tartaric acid was the most physicochemical factor influencing microbial composition, followed by malic acid, titratable acidity (TA), and lactic acid. Furthermore, functional analysis demonstrated that the most genes of the bacterial profiles correlated with carbohydrate metabolism. However, some foodborne pathogens were existed, such as Staphylococcus and Arcobacter marinus. The results of this study provide detailed insight into the relationship between the bacterial communities and physicochemical indices of fermented vegetables, and may improve the quality and safety of traditional Chinese fermented vegetables.

Effects of salt concentration on the quality of paocai, a fermented vegetable product from China

BACKGROUND

Paocai is a traditional Chinese fermented vegetable food. As the most important ingredient, salt has crucial effects on the bacterial community and volatile compounds of paocai. To demonstrate the effects of salt on the fermentation of paocai, the bacterial composition and volatile compounds were investigated using high-throughput sequencing and gas chromatography-mass spectrometry (GC-MS).

RESULTS

The salt had no significant effects on the bacterial community at the phylum level. Proteobacteria and Bacteroidetes gradually decreased during the fermentation, and Firmicutes gradually increased as the dominant bacteria in the late stage of fermentation. At the genus level, Lactobacillus and Lactococcus gradually increased in relative abundance during the fermentation and became the dominant bacteria in paocai. High salt levels can contribute to the growth of Lactobacillus, which became the dominant genus in paocai. The salt concentration affected the profiles of volatile compounds in paocai after fermentation. A total of 42 volatile components were detected by GC-MS, among which phenols, aldehydes, and nitriles were the main ones. A high salt concentration will increase the volatile compound content, mainly aldehydes and alcohols, and improve the flavor of paocai. At the same time, the electronic tongue analysis also showed that a high salt concentration made a major contribution to the flavor of paocai.

CONCLUSIONS

These data are helpful to elucidate the effects of salt on the quality of paocai and contribute to improving the quality and reducing the use of salt. © 2021 Society of Chemical Industry.

Improving the quality of Suancai by inoculating with Lactobacillus plantarum and Pediococcus pentosaceus

The quality characteristics of Suancai fermented with Lactobacillus plantarum CGMCC No.20193 (Lb. plantarum) and Pediococcus pentosaceus CGMCC No. 20192 (P. pentosaceus) were investigated. Their inoculation affected the bacterial communities revealed by Pacbio Sequel platform. After fermentation, the dominant phylum and genus in inoculation and spontaneous fermented Suancai were Firmicutes and Lactobacillus. Compared with single inoculation, the co-inoculation of Lb. plantarum and P. pentosaceus had a higher bacterial diversity. The Suancai co-inoculated with Lb. plantarum and P. pentosaceus had a more similar VCs profile with spontaneous fermented Suancai. The inoculation of Lb. plantarum and P. pentosaceus increased the content of organic acids, such as lactate, acetate, citrate, succinate, malate and tartrate. The most amino acids content in Suancai fermented with Lb. plantarum and P. pentosaceus were higher than that in spontaneous fermented Suancai. Compared single inoculation, the Suancai co-inoculated with Lb. plantarum and P. pentosaceus had a higher similarity of organoleptic tastes with spontaneous fermented Suancai. These results may facilitate the understanding of the starters' effects on the Suancai fermentation and the selection of applicable starters to manipulate the flavor.

A new Leuconostoc citreum strain discovered in the traditional sweet potato sour liquid fermentation as a novel bioflocculant for highly efficient starch production

Sour liquid fermentation is commonly used in the sedimentation process of traditional starch production, where bacteria play a critical role in starch flocculation. In this study, the dynamic changes of bacterial compositions during sweet potato sour liquid (SPSL) fermentation were profiled using the single-molecule real-time (SMRT) sequencing, unveiling that Leuconostoc citreum, Leuconostoc pseudomesenteroides, Lactococcus lactis, and Lactobacillus plantarum were the dominant microorganisms in the process, and Leuconostoc citreum exhibited a strong positive correlation with starch flocculation rate (FR). In total, 75 lactic acid bacterial (LAB) strains were isolated from the SPSL, but only 7 of them caused starch flocculation. For the first time, Leuconostoc citreum strains were reported with excellent starch-flocculating abilities (up to 55.56% FR in 20 min), which might be attributed to their ability to connect starch granules through the cell surface to form large aggregation. This study provides a comprehensive understanding of the bacterial dynamics in SPSL fermentation at the species level. A starch flocculation yield of 93.63% was achieved within 1 h by using the newly discovered Leuconostoc citreum SJ-57. The time required for total starch sedimentation was reduced from 10 h to 4 h, compared with the traditional process. These results suggest that this novel bioflocculant is more suitable for modernizing the traditional SPSL fermentation process and achieving rapid and highly efficient starch sedimentation.

Metagenomic analysis of microbial community succession during the pickling process of Zhacai (preserved mustard tuber) and its correlation with Zhacai biochemical indices

BACKGROUND

Industrial Fuling Zhacai is pickled by a method summarized as 'three times pickled and pressed', in which raw mustard tubers are subjected to three stages of pickling in different salt concentrations, with a pressing operation at the end of each stage to remove brine. This study used Illumina MiSeq technology and multivariate statistical analyses to investigate microbial community succession during the pickling process and its correlation with Zhacai biochemical indices.

RESULTS

A total of 19 phyla, 208 genera, and 295 species of bacteria were identified. Lactobacillus was the dominant genus of bacteria in all three stages and Lactobacillus sakei was the dominant species in the first and second stages. A total of six phyla, 200 genera and 301 species of fungi were also identified. According to a PICRUSt2 prediction, the main functions of the bacterial and fungal communities were carbohydrate and protein metabolism, while alcohol metabolism was also a function of fungi. Nine bacterial genera closely correlated with Zhacai biochemical indices: Acinetobacter, Pseudomonas, Pedobacter, Erwinia, Lactobacillus, Chryseobacterium, Flavobacterium, Duganella, and Paenarthrobacter. Six genera of fungi correlated closely: Penicillium, Cystobasidium, Cladosporium, Plenodomus, Aspergillus, and Simplicillium. All these genera probably originated from the surface microorganisms of raw mustard tuber.

CONCLUSION

This study reveals the succession patterns of microbial community structures during the pickling process of industrial Zhacai and infers the core functional flora, providing reference data for Zhacai pickling process control. © 2020 Society of Chemical Industry.

Differences in the bacterial profiles and physicochemical between natural and inoculated fermentation of vegetables from Shanxi Province

Purpose

Fermented vegetables can be divided into two types, natural fermented and artificially inoculated fermented. By detecting and identifying the changes of bacterial diversity using physical and chemical indicators during natural and inoculation fermentation, we analyzed and determined the dominant bacteria in the fermentation process and revealed the relationship between bacteria and volatile substances.

Methods

We used the Illumina Miseq to sequence the bacteria in fermented vegetable samples at different fermentation periods, and calculated the total number of mesophilic microorganisms and lactic acid bacteria. We used the pH and nitrite to monitor the acidification process. GC-MS was used to determine volatile flavor compounds. Finally, we analyzed the correlation between volatile flavor compounds and bacteria.

Results

Total mesophilic microorganisms and the number of lactic acid bacteria in the inoculated fermentation were higher than the natural fermentation. The bacterial diversity Shannon and Simpson indexes of the natural fermentation, higher than those of inoculated fermentation in 0~7 days, were between 55~71% and 36~45%, respectively. On the 7th day, the proportion ofLactobacillusin the natural fermentation and inoculated fermentation were 53.4% and 90.2%, respectively, which were significantly different.Lactobacilluswas the dominant genus in the fermented vegetables and an important genus to promote the formation of volatile flavors.Lactobacilluswas negatively correlated with two volatile substances (4-[2,2,6-trimethyl-7-oxabicyclo [4.1.0] hept-1-yl]-3-Buten-2-one (K4) and a-Phellandrene (X1)) and played a leading role in the fermentation process.

Conclusions

Results demonstrated that the total number of mesophilic microorganisms and lactic acid bacteria in inoculated fermentation were more than those in natural fermentation. Inoculated fermentation can shorten the fermentation cycle and reduce the content of nitrite. Lactic acid bacteria were the dominant bacteria in fermented vegetables.

Evaluation and comparison of the microbial communities and volatile profiles in homemade suansun from Guangdong and Yunnan provinces in China

BACKGROUND

Suansun is a traditional salt-free fermented bamboo shoot product that has been widely consumed as a cooking ingredient in south China for centuries. The aim of this study was to evaluate and compare the microbial and metabolic diversity in samples of two kinds of suansun, namely Guangdong suansun (GD) and Yunnan suansun (YN), using high-throughput sequencing (HTS) and headspace solid-phase microextraction-gas chromatograph-mass spectrometry (HS-SPME/GC-MS), respectively, and then to assess the influence of environmental factors on the microbial communities.

RESULTS

The results showed that Lactobacillus and Serratia were the most abundant bacterial genera in both the GD and YN groups. For the fungi, Pichia, Candida, and Debaryomyces were the major genera in the GD group, whereas Pichia and Zygosaccharomyces were the dominant genera in the YN group. The canonical correlation analysis (CCA) results demonstrated that three environmental factors - temperature, longitude, and altitude - play a more important role in affecting the microbial community composition of suansun than physical and chemical factors. The fugal community composition was more influenced by environmental factors than the bacterial community. The volatile profile of the GD group differed from that of the YN group, and the difference was mainly reflected in the relative alcohol, aldehyde, ester, and aromatic compound content.

CONCLUSIONS

This study provided insights into the microbial and metabolic profiles of suansun products. The findings might be useful for the improvement and standardization of suansun production. © 2020 Society of Chemical Industry.

Microbiota Succession and Chemical Composition Involved in the Radish Fermentation Process in Different Containers

Traditional Chinese fermented vegetables are a type of brine-salted fermented vegetable product. During the spontaneous fermentation, various compounds are produced, degraded, and converted, influencing the quality of the fermented pickle. To ascertain the effect of different containers on the fermentation process of the pickles, this study investigated the bacterial diversity and the chemical composition characteristics of the pickle (radish) fermented in commonly used containers including glass jars (GL), porcelain jars (PO), and plastic jars (PL). The correlation between chemical compounds and microbial community was further analyzed. The changes in pH values suggested that PL may facilitate the quickest fermentation of the pickles, while the process in PO progressed at the lowest rate. The PL brine samples contained higher levels of lactic acid and threonine, while more abundant volatile chemical compounds were evident in PO. The container materials had no significant influence on the microbial structure, wherein Lactobacillus was the absolute dominant genus in all containers. But container material did have an effect on the abundance of specific genus, such as Lactococcus and Pediococcus. The correlation between these major genera was also analyzed and gene function prediction indicated that the top three pathways were: carbohydrate metabolism, amino acid metabolism, and energy metabolism. Lactobacillus negatively correlated with methionine, tyrosine, lysine, and arginine, but positively correlated with ammonia, and lactic acid and acetic acid both just correlated with Pediococcus. This study provides new insights into the microbiota succession and chemical compounds involved in the vegetable fermentation.

Characterization of a probiotic starter culture with anti-Candida activity for Chinese pickle fermentation

A probiotic starter can be used for Chinese pickle fermentation and the resulting product may be a promising anti-Candida probiotic.

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.