PacBio sequencing combined with metagenomic shotgun sequencing provides insight into the microbial diversity of zha-chili

Effect of Sichuan Pepper (Zanthoxylum genus) Addition on Flavor Profile in Fermented Ciba Chili (Capsicum genus) Using GC-IMS Combined with E-Nose and E-Tongue

This study examined the flavor profiles of fermented Ciba chili, comparing samples with Sichuan pepper (HJ) to those without Sichuan pepper (CK), using three analytical techniques: E-tongue, E-nose, and gas chromatography-ion mobility spectrometry (GC-IMS). The results obtained from the E-tongue and E-nose exhibited a clear difference in taste and flavor between CK and HJ. In detail, CK mainly exhibited a sour flavor profile, whereas HJ displayed an intricate and rich flavor. The HS-GC-IMS results identified a total of 60 compounds in the samples, with terpenes, alcohols, and esters being the primary volatile flavor compounds. Additionally, Zanthoxylum was found to significantly enhance the concentration of these compounds in fermented Ciba chili. Through robust principal component analysis (rPCA), 17 distinct flavor compounds were selected. Correlation analysis revealed that most terpenes exhibited positive correlations with LY2/LG, LY2/gCT1, LY2/Gct, LY2/G, LY2/Gh, and terpenes were found in higher concentrations in HJ. This study contributes a theoretical basis and provides data support for optimizing the fermentation process and elucidating the underlying mechanism of characteristic aroma formation in Ciba chili after fermentation.

Bacterial diversity and its correlation with sensory quality of two types of zha-chili from Shennongjia region, China

In the Shennongjia region of China, two types of zha-chili with distinct flavors exist: the first type (P zha-chili) uses a significant amount of chili pepper but no potato, while the other (PP zha-chili) contains a smaller amount of chili pepper but a proportion of potato. In order to investigate the bacterial diversity and sensory properties of these two types of zha-chili, this study employed a combination of amplicon sequencing, culture-based methods, and sensory technology. The results of the study showed statistically significant differences (P < 0.05) in bacterial diversity and communities between the two types of zha-chili. In particular, four dominant lactic acid bacteria (LAB) genera - Lactiplantibacillus, Lactococcus, Leuconostoc, and Weissella - were significantly enriched in PP zha-chili. The findings suggest that the proportions of chili pepper and potato can influence the bacterial diversity and content of LAB, with a higher proportion of chili pepper potentially inhibiting the growth of harmful species within the Enterobacteriaceae family. The study also used culture-based methods to identify the most dominant bacteria in the zha-chili samples as Lactiplantibacillus plantarum group, Companilactobacillus alimentarius, and Lacticaseibacillus paracasei. Correlation analysis indicated that LAB likely plays a significant role in shaping the aroma profile of zha-chili, with Levilactobacillus, Leuconostoc, Lactiplantibacillus, and Lactococcus showing correlation with E-nose sensory indices. However, these LAB were not significantly correlated with the taste properties of zha-chili. The study provides new insights into the influence of chili pepper and potato on the microbial diversity and flavor properties of zha-chili, and also presents potential LAB isolates for future research on zha-chili.

Molecular Detection and Identification of Plant-Associated Lactiplantibacillus plantarum

Lactiplantibacillus plantarum is a lactic acid bacterium often isolated from a wide variety of niches. Its ubiquity can be explained by a large, flexible genome that helps it adapt to different habitats. The consequence of this is great strain diversity, which may make their identification difficult. Accordingly, this review provides an overview of molecular techniques, both culture-dependent, and culture-independent, currently used to detect and identify L. plantarum. Some of the techniques described can also be applied to the analysis of other lactic acid bacteria.

Unraveling the effect of the combination of modified atmosphere packaging and ε-polylysine on the physicochemical properties and bacterial community of greater amberjack (Seriola dumerili)

The combined effect of ε-polylysine (PL) and modified atmosphere packaging (MAP; 60% CO2/40% N2) on the bacterial community of greater amberjack filets and their physicochemical properties was evaluated at 4°C. The total viable counts (TVC), psychrotrophic bacterial count, sensory index, texture analysis, and total volatile basic nitrogen (TVB-N) revealed that PL, MAP, and MAP + PL treatment delayed the deterioration of greater amberjack filets. These treatment groups also showed decreased accumulation of biogenic amines. High-throughput 16S rRNA gene sequencing results indicated that these treatments suppressed the growth of Pseudomonas in greater amberjack filets. Furthermore, the MAP + PL treatment group was observed to be more effective than the PL and MAP groups, extending the shelf life of greater amberjack filets by 6 days. This investigation showed that the combination of PL and MAP has the potential to retain the quality and extend the shelf life of greater amberjack.

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.

Application progress of intelligent flavor sensing system in the production process of fermented foods based on the flavor properties

Fermented foods are sensitive to the production conditions because of microbial and enzymatic activities, which requires intelligent flavor sensing system (IFSS) to monitor and optimize the production process based on the flavor properties. As the simulation system of human olfaction and gustation, IFSS has been widely used in the field of food with the characteristics of nondestructive, pollution-free, and real-time detection. This paper reviews the application of IFSS in the control of fermentation, ripening, and shelf life, and the potential in the identification of quality differences and flavor-producing microbes in fermented foods. The survey found that electronic nose (tongue) is suitable to monitor fermentation process and identify food authenticity in real time based on the changes of flavor profile. Gas chromatography-ion mobility spectrometry and nuclear magnetic resonance technology can be used to analyze the flavor metabolism of fermented foods at various production stages and explore the correlation between flavor substances and microorganisms.

UPLC-MS-MS-based lipidomics for the evaluation of changes in lipids during dry-cured mutton ham processing

Six key stages in the processing of dry-cured muton ham were selected, and changes in the main lipid metabolites as well as the major pathways involved were identified using a lipidic metabolomics approach based on UPLC-MS-MS. In total, 581 lipid metabolites from 22 subclasses were identified, including 521 significantly differential lipids (p < 0.05, VIP > 1). Glycerolipids (GL) were the most abundant lipids, followed by glycerophospholipids (GP), fatty acyls (FA), and sphingolipids (SL). PCA and OPLS-DA of metabolites showed that the quality of mutton ham changed the most during the P3 fermenting stage, including TG(18:1/18:2/18:3), PE(20:5/18:1), and TG(16:1/18:1/18:4) that were significantly downregulated, and CE(20:3), FFA(24:6), LPC(20:3/0:0), and FFA(18:4) that were significantly upregulated. Moreover, glycerophospholipid metabolism and sphingolipid metabolism were the key metabolic pathways involved in the processing of dry-cured mutton ham. Our results provide a basis for quality control and product improvement of dry-cured mutton ham.

Insights into the Aroma Profile of Sauce-Flavor Baijiu by GC-IMS Combined with Multivariate Statistical Analysis

Aroma is among the principal quality indicators for evaluating Baijiu. The aroma profiles of sauce-flavor Baijiu produced by 10 different manufacturers were determined by GC-IMS. The results showed that GC-IMS could effectively separate the volatile compounds in Baijiu, and a total of 80 consensus volatile compounds were rapidly detected from all samples, among which 29 volatile compounds were identified, including 5 alcohols, 14 esters, 2 acids, 2 ketones, 5 aldehydes, and 1 furan. According to the differences in aroma profile found by multivariate statistical analysis, these sauce-flavor Baijiu produced by 10 different manufacturers can be further divided into three types. The relative odor activity value of the identified volatile compounds indicated that seven volatile compounds contributed most to the aroma of sauce-flavor Baijiu in order of aroma contribution rate, and they were ethyl hexanoate, ethyl pentanoate, ethyl 2-methylbutanoate, ethyl octanoate (also known as octanoic acid ethyl ester), ethyl 3-methylbutanoate, ethyl butanoate, and ethyl isobutyrate. Correspondingly, the main aromas of these sauce-flavor Baijiu produced by 10 different manufacturers were sweet, fruity, alcoholic, etheral, cognac, rummy, and winey. On the one hand, this study proved that GC-IMS is well adapted to the detection of characteristic volatile aroma compounds and trace compounds in Baijiu, which is of positive significance for improving the aroma fingerprint and database of sauce-flavor Baijiu. On the other hand, it also enriched our knowledge of Baijiu and provided references for the evaluation and regulation of the flavor quality of sauce-flavor Baijiu.

Bacterial Communities and Prediction of Microbial Metabolic Pathway in Rice Wine Koji From Different Regions in China

Rice wine koji, a traditional homemade starter culture in China, is nutritious and delicious. The final quality of rice wine koji is closely related to the structure of its microbial community. However, the diversity of natural microorganisms in rice wine koji from different regions has not been evaluated. In this study, the microbial population of 92 naturally fermented rice koji samples collected from Hubei, Guangxi, and Sichuan was systematically analyzed by high-throughput sequencing. From all the rice wine koji samples, 22 phyla and 479 bacterial genera were identified. Weissella, Pediococcus, Lactobacillus, Enterobacter, Lactococcus, Pantoea, Bacillus, Staphylococcus, and Leuconostoc were the dominant genera in rice wine koji. The bacterial community structure of rice wine koji samples from different regions was significantly different (p < 0.05). The bacterial community composition of the samples from Hubei and Guangxi was similar, but significantly different from that of SC samples (p < 0.05). These differences may be caused by variations in geography, environment, or manufacturing. In addition, the results of microbial phenotype prediction by BugBase and bacterial functional potential prediction by PICRUSt showed that eight of the nine predicted phenotypic functions of rice wine koji samples from different regions were significantly different (p < 0.05) and that vigorous bacterial metabolism occurred in rice wine koji samples.

The Depth-Depended Fungal Diversity and Non-depth-Depended Aroma Profiles of Pit Mud for Strong-Flavor Baijiu

Microorganisms in pit mud are the essential factor determining the style of strong flavor Baijiu. The spatial distribution characteristics of fungal communities and aroma in the pit mud for strong flavor Baijiu from Xinjiang, China, were investigated using Illumina MiSeq high-throughput sequencing and electronic nose technology. A total of 138 fungal genera affiliated with 10 fungal phyla were identified from 27 pit mud samples; of these, Saccharomycopsis, Aspergillus, and Apiotrichum were the core fungal communities, and Aspergillus and Apiotrichum were the hubs that maintain the structural stability of fungal communities in pit mud. The fungal richness and diversity, as well as aroma of pit mud, showed no significant spatial heterogeneity, but divergences in pit mud at different depths were mainly in pH, total acid, and high abundance fungi. Moisture, NH4 +, and lactate were the main physicochemical factors involved in the maintenance of fungal stability and quality in pit mud, whereas pH had only a weak effect on fungi in pit mud. In addition, the fungal communities of pit mud were not significantly associated with the aroma. The results of this study provide a foundation for exploring the functional microorganisms and dissecting the brewing mechanism of strong flavor Baijiu in Xinjiang, and also contributes to the improvement of pit mud quality by bioaugmentation and controlling environmental physicochemical factors.

Diversity of microbiota, microbial functions, and flavor in different types of low-temperature Daqu

Light-flavor Baijiu is made from grain materials using a combination of three types of low-temperature Daqu (Hongxin, Houhuo, and Qingcha). This study comprehensively examined the microbial structure, microbial functions, and flavor characteristics of the three types of low-temperature Daqu using high-throughput sequencing and electronic senses, and it further clarified the relationship between the microbiota and flavor in low-temperature Daqu. The results showed that Hongxin had the highest bacterial richness and diversity, while Houhuo had the lowest. Both fungal richness and diversity were significantly higher in Qingcha than in Hongxin and Houhuo. The differences in peak temperature during Daqu-making led to significant differences in the structure of microbial communities, microbial functions, and flavor quality in the three types of low-temperature Daqu, and could be leveraged for screening and enriching functional microorganisms for Baijiu-making. Co-exclusion patterns between lactic acid bacteria and Bacillus in low-temperature Daqu resulted in a negative correlation between amino acid transport metabolism and carbohydrate transport metabolism. The different types of low-temperature Daqu had distinct flavor profiles, and the differences in the taste profiles were more significant. Dominated by Thermoactinomyces and Lactobacillus, and together with Saccharopolyspora, Bacillus, Streptomyces, Saccharomycopsis, and Thermoascus, they formed the core microbiota that influencing the flavor of low-temperature Daqu. The bacteria mainly influenced the taste of low-temperature Daqu, whereas the fungi mainly influenced the aroma. Each type of low-temperature Daqu contributed to the flavor of light-flavor Baijiu: Hongxin could elevate the levels of aromatic compounds, Houhuo could regulate the bitterness and sourness, and Qingcha could inhibit the generation of sulfur organic compounds. The results of the present study enrich and refine our knowledge of low-temperature Daqu, promoting the further evolution of traditional brewing methods.

The Fungal Communities and Flavor Profiles in Different Types of High-Temperature Daqu as Revealed by High-Throughput Sequencing and Electronic Senses

Polymicrobial co-fermentation is among the distinct character of high-temperature Daqu. However, fungal communities in the three types of high-temperature Daqu, namely, white high-temperature Daqu, black high-temperature Daqu, and yellow high-temperature Daqu, are yet to be characterized. In this study, the fungal diversity, taste, and aroma profiles in the three types of high-temperature Daqu were investigated by Illumina MiSeq high-throughput sequencing, electronic tongue, and electronic nose, respectively. Ascomycota and Basidiomycota were detected as the absolute dominant fungal phylum in all types of high-temperature Daqu samples, whereas Thermomyces, Thermoascus, Aspergillus, Rasamsonia, Byssochlamys, and Trichomonascus were identified as the dominant fungal genera. The fungal communities of the three types of high-temperature Daqu differed significantly (p < 0.05), and Thermomyces, Thermoascus, and Monascus could serve as the biomarkers in white high-temperature Daqu, black high-temperature Daqu, and yellow high-temperature Daqu, respectively. The three types of high-temperature Daqu had an extremely significant difference (p < 0.01) in flavor: white high-temperature Daqu was characterized by sourness, bitterness, astringency, richness, methane, alcohols, ketones, nitrogen oxides, and sulfur organic compounds; black high-temperature Daqu was characterized by aftertaste-A, aftertaste-B, methane-aliph, hydrogen, and aromatic compounds; and yellow high-temperature Daqu was characterized by saltiness, umami, methane, alcohols, ketones, nitrogen oxides, and sulfur organic compounds. The fungal communities in the three types of high-temperature Daqu were significantly correlated with taste but not with aroma, and the aroma of high-temperature Daqu was mainly influenced by the dominant fungal genera including Trichomonascus, Aspergillus, Thermoascus, and Thermomyces. The result of the present study enriched and refined our knowledge of high-temperature Daqu, which had positive implications for the development of traditional brewing technique.

Rice varieties affect bacterial diversity, flavor, and metabolites of zha-chili

The structure and diversity of bacterial communities in spontaneously fermented zha-chili prepared using two different rice varieties (glutinous rice and indica rice) were investigated using high-throughput sequencing. Through metabolic pathway prediction, electronic senses and metabolite analysis, the relationships among the rice varieties used for preparation and the bacterial microbiota, flavor, and organic acid/amino acid metabolites in zha-chili were elucidated. We observed that the structure of bacterial communities in zha-chili samples differed significantly with the rice variety used during fermentation (p < 0.05), and that there was a greater abundance of bacterial species in zha-chili prepared using glutinous rice. Lactic acid bacteria were predominant in zha-chili, with an average relative abundance of 77.09%. The aroma of zha-chili was influenced by the raw material itself, while the characteristic tastes of zha-chili - including sourness, umami and richness - were significantly correlated with the bacterial microbiota. In addition, the abundance of lactic acid bacteria was positively correlated with the levels of organic acids and negatively correlated with the levels of amino acids. This also made the zha-chili prepared using glutinous rice sourer and imparted more umami taste to the zha-chili prepared using indica rice. Our observations provide a reference for the evaluation of zha-chili quality and could effectively guide the improvement of zha-chili products.