Comparison of bacterial diversity profiles and microbial safety assessment of salami, Chinese dry-cured sausage and Chinese smoked-cured sausage by high-throughput sequencing

The metabolic regulation mechanism of gallic acid on biogenic amines and nitrosamines in reduced-nitrite Chinese fermented sausages: A perspective of metabolomics and metagenomics

Reducing nitrites tends to increase the accumulation of hazardous biogenic amines (BAs) in Chinese fermented sausages (CFSs). Gallic acid (GA) has emerged as a potential alternative to reduce nitrite usage and control BAs. This study explored how GA inhibits BAs and nitrosamines accumulation in reduced-nitrite CFSs. Results demonstrated that combining 0.05% (w/w) GA with reduced nitrite effectively curbed BAs and N-nitrosodimethylamine, decreasing total BA from 271.48 to 125.46 mg/kg. Fifty-one metabolites associated with the metabolism of BAs and N-nitrosodimethylamine were identified. GA boosted Lactococcus while reducing spoilage bacteria and Macrococcus. This dual regulation suppressed BAs and dimethylamine accumulation by regulating amino acids and trimethylamine pathways. Consequently, GA achieved an 89.86% reduction in N-nitrosodimethylamine by decreasing the key precursors like putrescine, dimethylamine, and nitrite. These findings offer new insights into utilizing GA and similar plant polyphenols to manage BAs and nitrosamines in meat products with reduced nitrite usage.

Microbial dynamics and quality characteristics of spontaneously fermented salamis produced by replacing pork fat with avocado pulp

The aim of this study was to develop a novel and healthier fermented meat product by replacing pork fat with avocado pulp (AVP) during salami production. Experimental salamis were produced under laboratory conditions by substituting pork fat with AVP partially (10-AVP) and totally (20-AVP), while control salamis (CTR) remained AVP-free. The microbial composition of control and experimental salamis was assessed using a combined culture-dependent and -independent approach. Over a 20-days ripening period, lactic acid bacteria, coagulase-negative staphylococci, and yeasts dominated the microbial community, with approximate levels of 9.0, 7.0 and 6.0 log CFU/g, respectively. Illumina technology identified 26 taxonomic groups, with leuconostocs being the predominant group across all trials [constituting 31.26-59.12 % of relative abundance (RA)]. Gas Chromatography-Mass Spectrometry (GC-MS) analysis revealed changes in fatty acid composition and volatile organic compounds due to the substitution of pork fat with AVP. Specifically, monounsaturated fatty acids and terpene compounds increased, while saturated fatty acids and lipid oxidation products decreased. Although AVP influenced the sensory characteristics of the salamis, the highest overall satisfaction ratings were observed for the 10-AVP salamis. Consequently, substituting pork fat with AVP emerges as a viable strategy for producing healthier salamis and diversifying the meat product portfolio.

The changes of fungal community and flavor substances in Yunnan-style sausages: A comparative analysis of different drying methods

This study aimed to investigate alterations in the fungal community and flavor substances in Yunnan-style sausages subjected to natural air-dried fermentation (NF), variable-temperature drying (VT), and constant-temperature drying (CT) and analyze the potential relationship between fungal community and flavor substances. The findings revealed that the NF group and VT group were more conducive to enhancing the accumulation of dominant fungi and characteristic flavor substances in Yunnan-style sausages. Glu, Ala, His, and Lys were identified as key taste substances based on their taste activity values (TAV ≥ 1). A total of 272 volatile compounds(VOCS) were detected in the sausage samples, while 28 key aroma compounds were screened based on the odor activity value (OAV ≥ 1). Multivariate statistical analysis showed that 12 key aroma compounds (VIP > 1) could be considered discriminative compounds, including (E,E)-2,4-nonadienal, nonanal, heptanal, benzaldehyde, Dodecanal, cyclohexanol, and hexyl-Benzene, etc. Furthermore, Wickerhamoomyces and Debaryomyces were positively correlated with most of the key flavor substances and physicochemical indices (|r| > 0.6, P < 0.05), which were potential flavor-contributing fungi in Yunnan-style sausages.

The Potential Correlation between Bacterial Diversity and the Characteristic Volatile Flavor Compounds of Sichuan Sauce-Flavored Sausage

The distinctive taste of Sichuan sauce-flavored sausage comes from an intricate microbial metabolism. The correlation between microbial composition and distinct flavor components has not been researched. The study used headspace solid-phase microextraction action with gas chromatography mass spectrometry to find flavor components and high-throughput sequencing of 16S rRNA to look at the diversity and succession of microbial communities. The correlation network model forecasted the connection between essential bacteria and the development of flavors. The study revealed that the primary flavor compounds in Sichuan sauce-flavored sausages were alcohols, aldehydes, and esters. The closely related microbes were Leuconostoc, Pseudomonas, Psychrobacter, Flavobacterium, and Algoriella. The microbes aided in the production of various flavor compounds, such as 1-octen-3-ol, benzeneacetaldehyde, hexanal, (R,R)-2,3-butanediol, and ethyl caprylate. This work has enhanced our comprehension of the diverse functions that bacteria serve in flavor development during the fermentation of Sichuan sauce-flavored sausage.

Characterization the microbial diversity and metabolites of four varieties of Dry-Cured ham in western Yunnan of China

In this study, high-throughput sequencing and metabolomics analysis were conducted to analyze the microbial and metabolites of dry-cured Sanchuan ham, Laowo ham, Nuodeng ham, and Heqing ham that have fermented for two years produced from western Yunnan China. Results showed that at the genus level, the dominant bacteria in the four types of ham were Halomonas and Staphylococcus, while the dominant fungi were Aspergillus and Yamadazyma. A total 422 different metabolites were identified in four types of ham, mainly amino acids, peptides, fatty acids, and their structural analogs, which were involved in pantothenate and coenzyme A biosynthesis, caffeine, and tyrosine metabolism. The dominant microorganisms of the four types of ham were mainly related to the metabolism of fatty acids and amino acids. This research enhances the identification degree of these four types of dry-cured ham and provides a theoretical basis for developing innovative and distinctive ham products.

The Contribution of Microorganisms to the Quality and Flavor Formation of Chinese Traditional Fermented Meat and Fish Products

Guizhou sour meat and sour fish, Chaoshan fish sauce, Sichuan sausage and bacon, Cantonese sausage, Jinhua ham, and Xinjiang air-dried beef are eight representatives of Chinese traditional fermented meat and fish products (FMFPs), which are favored by Chinese consumers due to their high nutritional value and quality. The quality of the spontaneously fermented Chinese traditional FMFP is closely correlated with microorganisms. Moreover, the dominant microorganisms are significantly different due to regional differences. The effects of microorganisms on the texture, color, flavor, nutrition, functional properties, and safety of Chinese traditional FMFPs have not been not fully described. Additionally, metabolic pathways for flavor formation of Chinese traditional FMFPs have not well been summarized. This article describes the seven characteristic Chinese traditional FMFPs and correlated dominant microorganisms in different regions of China. The effects of microorganisms on the texture, color, and flavor of Chinese traditional FMFPs are discussed. Furthermore, the metabolic pathways of microbial regulation of flavor formation in Chinese traditional FMFPs are proposed. This work provides a theoretical basis for improvement of Chinese traditional FMFPs by inoculating functional microorganisms isolated from Chinese traditional fermented foods.

Structures and diversities of bacterial communities in oil-contaminated soil at shale gas well site assessed by high-throughput sequencing

Currently, there is limited understanding of the structures and variabilities of bacterial communities in oil-contaminated soil within shale gas development. The Changning shale gas well site in Sichuan province was focused, and high-throughput sequencing was used to investigate the structures of bacterial communities and functions of bacteria in soil with different degrees of oil pollution. Furthermore, the influences of the environmental factors including pH, moisture content, organic matter, total nitrogen, total phosphorus, oil, and the biological toxicity of the soil on the structures of bacterial communities were analyzed. The results revealed that Proteobacteria and Firmicutes predominated in the oil-contaminated soil. α-Proteobacteria and γ-Proteobacteria were the main classes under the Proteobacteria phylum. Bacilli was the main class in the Firmicutes phylum. Notably, more bacteria were only found in CN-5 which was the soil near the storage pond for abandoned drilling mud, including Marinobacter, Balneola, Novispirillum, Castellaniella, and Alishewanella. These bacteria exhibited resilience to higher toxicity and demonstrated proficiency in oil degradation. The functions including carbohydrate transport and metabolism, energy metabolism, replication, recombination and repair replication, signal transduction mechanisms, and amino acid transport and metabolism responded differently to varying concentrations of oil. The disparities in bacterial genus composition across samples stemmed from a complex play of pH, moisture content, organic matter, total nitrogen, total phosphorus, oil concentration, and biological toxicity. Notably, bacterial richness correlated positively with moisture content, while bacterial diversity showed a significant positive correlation with pH. Acidobacteria exhibited a significant positive correlation with moisture content. Litorivivens and Luteimonas displayed a significant negative correlation with pH, while Rhizobium exhibited a significant negative correlation with moisture content. Pseudomonas, Proteiniphilum, and Halomonas exhibited positive correlations not only with organic matter but also with oil concentration. Total nitrogen exhibited a significant positive correlation with Taonella and Sideroxydans. On the other hand, total phosphorus showed a significant negative correlation with Sphingomonas. Furthermore, Sphingomonas, Gp6, and Ramlibacter displayed significant negative correlations with biological toxicity. The differential functions exhibited no significant correlation with environmental factors but displayed a significant positive correlation with the Proteobacteria phylum. Aridibacter demonstrated a significant positive correlation with cell motility and cellular processes and signaling. Conversely, Pseudomonas, Proteiniphilum, and Halomonas were negatively correlated with differential functions, particularly in amino acid metabolism, carbohydrate metabolism, and membrane transport. Compared with previous research, more factors were considered in this research when studying structural changes in bacterial communities, such as physicochemical properties and biological toxicity of soil. In addition, the correlations of differential functions of communities with environmental factors, bacterial phyla, and genera were investigated.

The Effect of Lactiplantibacillus plantarum x3-2b Bacterial Powder on the Physicochemical Quality and Biogenic Amines of Fermented Lamb Jerky

In this study, a protective agent was added to prepare a high-activity Lactiplantibacillus plantarum x3-2b bacterial powder as a fermentation agent and explore its effect on the physicochemical quality, biogenic amines, and flavor of fermented lamb jerky. A composite protective agent, composed of 15% skim milk powder and 10% trehalose, was used, and bacterial mud was mixed with the protective agent at a 1:1.2 mass ratio. The resulting freeze-dried bacterial powder achieved a viable count of 5.1 lg CFU/g with a lyophilization survival rate of 87.58%. Scanning electron microscopy revealed enhanced cell coverage by the composite protective agent, maintaining the cell membrane's integrity. Inoculation with x3-2b bacterial powder increased the pH and the reduction in aw, enhanced the appearance and texture of fermented lamb jerky, increased the variety and quantity of flavor compounds, and reduced the accumulation of biogenic amines (phenethylamine, histamine, and putrescine). This research provides a theoretical basis for improving and regulating the quality of lamb jerky and establishes a foundation for the development of bacterial powder for the commercial fermentation of meat products.

Bacterial microbiota in different types of processed meat products: diversity, adaptation, and co-occurrence

As a double-edged sword, some bacterial microbes can improve the quality and shelf life of meat products, but others mainly responsible for deterioration of the safety and quality of meat products. This review aims to present a landscape of the bacterial microbiota in different types of processed meat products. After demonstrating a panoramic view of the bacterial genera in meat products, the diversity of bacterial microbiota was evaluated in two dimensions, namely different types of processed meat products and different meats. Then, the influence of environmental factors on bacterial communities was evaluated according to the storage temperature, packaging conditions, and sterilization methods. Furthermore, microbes are not independent. To explore interactions among those genera, co-occurrence patterns were examined. In these respects, this review highlighted the recent advances in fundamental principles that underlie the environmental adaption tricks and why some species tend to occur together frequently, such as metabolic cross-feeding, co-aggregate at microscale, and the intercellular signaling system. Further investigations are required to unveil the underlying molecular mechanisms that govern microbial community systems, ultimately contributing to developing new strategies to harness beneficial microorganisms and control harmful microorganisms.

The Volatile Flavor Substances, Microbial Diversity, and Their Potential Correlations of Inner and Surface Areas within Chinese Qingcheng Mountain Traditional Bacon

The objective of this study was to explore the microbial diversity, volatile flavor substances, and their potential correlations in inner and surface Chinese Qingcheng Mountain traditional bacon (CQTB). The results showed that there were 39 volatile flavor substances in inner and surface CQTB detected by headspace solid-phase microextraction and gas chromatography-mass spectrometry (HS-SPME-GC-MS). Moreover, significant differences in volatile flavor substances between the inner and surface CQTB were observed. Sixteen key volatile flavor substances were screened (OAV > 1), including guaiacol, nonanal, ethyl isovalerate, and others. High-throughput sequencing (HTS) result indicated that Firmicutes, Proteobacteria, and Actinobacteria were the predominant bacterial phyla, and Ascomycota and Mucoromycota were the predominant fungal phyla. Staphylococcus, Psychrobacter, and Brochothrix were the predominant bacteria, and Debaryomyces, Penicillium, and Mucor were the predominant fungal genera. Spearman correlation coefficient analysis suggested that Apiotrichum and Lactobacillus were closely and positively correlated with the formation of key phenol compounds. The present work demonstrates the microbial diversity and related volatile flavor substances and their potential correlations in CQTB and provides a theoretical basis for the development of microbial starter culture and green processing of CQTB.

Chitosan coating with grape peel extract: A promising coating to enhance the freeze-thaw stability of beef

This study investigated the effect of chitosan coating with grape peel extracts (CH + GPE) on the physiochemical properties, protein and lipid oxidation, microstructure, and bacterial community diversity of beef during freeze-thaw (F-T) cycles. The results indicated that the CH + GPE groups had lower pH values, total aerobic count, total volatile base nitrogen, and thiobarbituric acid reactive substance values and better protection against color, water holding capacity, and sensory quality after five F-T cycles. The CH + GPE coating effectively inhibited beef microstructure destruction during the F-T cycles. High-throughput sequencing analysis revealed that the CH + GPE coating contributed to a decline in the bacterial diversity of beef and inhibited the growth of pathogenic bacteria. Interestingly, the CH + GPE coating affected the correlation between quality parameters and bacteria in beef. Consequently, the CH + GPE coating can be used as a novel packaging for preventing the loss of frozen meat quality due to temperature fluctuations.

Microbial succession and its correlation with the dynamics of flavor compounds involved in the fermentation of Longxi bacon

Introduction

Longxi bacon is a traditional fermented meat from Gansu province, China. The ripening process of the bacon is crucial for quality and flavor. The aim of this study was to gain deeper knowledges on the bacterial and fungal community diversity and the changes of chemical components including fatty acids and volatile compounds at different time points during the ripening of the bacon and to understand the relationship between microbial profiles and the chemical components related the bacon flavor.

Methods

Bacon samples were collected from days 0, 15, 30, 60 and 90. The bacterial and fungal compositions were analyzed with next generation sequencing targeting the 16S rDNA loci for bacteria and ITS loci for fungi. The fatty acids and the volatile components were analyzed by headspace solid phase micro extraction followed by gas chromatography/mass spectrometry (HS-SPME-GC/MS).

Results

We found that the abundance of bacteria in bacon was higher than that of fungi, and Psychrobacter, Brochothrix, Phoma and Trichoderma was the dominant bacon's population. The largest contributors of volatiles were aldehydes, ketones and esters, and the main fatty acids were palmitic, oleic and linoleic acids. Pearson correlation analysis between microbial succession and key flavor substances showed that the production of Longxi bacon flavor is the result of a combination of bacteria and fungi. Ten bacteria genera and six fungi genera were determined as functional core microbiota for the flavor production based their dominance and functionality in microbial community. In addition, bacteria and fungi are involved in the oxidation and hydrolysis of fatty acids during the ripening of bacon, which also contributes to the formation of bacon flavor.

Discussion

This study provides a comprehensive analysis of the key microbiota involved in shaping bacon's distinctive flavor. Here, the results presented should provide insight into the influence of the microenvironment on the microbial community in bacon and lay a foundation for further investigations into the food ecology of bacon.

Cold Plasma Controls Nitrite Hazards by Modulating Microbial Communities in Pickled Radish

The hazard of nitrite caused by microorganisms is the main food safety problem in the pickle production. To seek a method to control the nitrite hazards of pickles by regulating microbial community without additional substances, we focused on cold plasma because Gram-negative and Gram-positive bacteria have different degrees of sensitivity to the sterilization of cold plasma. Using radish pickles as the experimental object, based on colony counting, dynamic monitoring of pH and nitrite, qPCR and high-throughput sequencing, it was found that when the raw material was treated with dielectric barrier discharge (DBD) cold plasma at 40 kV for 60 s, Gram-negative bacteria with the potential to produce nitrite were preferentially sterilized. Meanwhile, Gram-positive bacteria dominated by the lactic acid bacteria were retained to accelerate the acid production rate, initiate the self-degradation of nitrite in advance and significantly reduce the peak value and accumulation of nitrite during the fermentation process of pickled radish. This study preliminarily verified that DBD cold plasma can inhibit the nitrite generation and accelerate the self-degradation of nitrite by regulating the structure and abundance of microbial community in radish pickles, which provides an important reference for the control of nitrite hazards in the fermentation process of pickles without additives.

A comparative study of tea polyphenols and its palmitic acid-modified derivatives: their effects on the microbial ecosystem and biogenic amines in Chinese sausage

Control of biogenic amines (BAs) is important to guarantee the safety of sausage-like fermented meat products. This study investigated the influences of tea polyphenols (TP) and its lipophilic palmitic acid-modified derivatives, palmitoyl-TP (pTP) and palmitoyl-epigallocatechin gallate (pEGCG), on BAs and microbial ecosystem in Chinese sausages. TP, epigallocatechin gallate (EGCG), pTP, and pEGCG all reduced the formation of BAs and N-nitrosodimethylamine at 0.05% (g/g); yet, compared with TP and EGCG, the modified derivatives exhibited stronger action on BAs decreasing (P < 0.05), and pEGCG showed the highest effect (a reduction of total BAs from 376.22 to 168.98 mg/kg compared to control). The improved inhibitory effect of pTP and pEGCG should be attributed to their stronger dual-directional regulation of the bacterial and fungal communities during the natural fermentation of sausage. The modified pTP and pEGCG highly suppressed the growth of Staphylococcus, Candida, and Kurtzmaniella, all of which were positively correlated with BAs formation (all P < 0.05). However, pTP and pEGCG worked more effectively than the unmodified ones to promote Lactobacillus, Lactococcus, and Debaryomyces (all P < 0.05). The results above are significant for the application of palmitoyl-TP and similar TP derivatives in meat products in consideration of food safety.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13197-023-05717-z.

Application and Effect of Pediococcus pentosaceus and Lactiplantibacillus plantarum as Starter Cultures on Bacterial Communities and Volatile Flavor Compounds of Zhayu, a Chinese Traditional Fermented Fish Product

Zhayu is a type of traditional fermented fish product in China that is made through the fermentation of salted fish with a mixture of cereals and spices. Inoculation fermentation was performed using Pediococcus pentosaceus P1, Lactiplantibacillus plantarum L1, and a mixture of two strains, which were isolated from cured fish in Hunan Province. Compared with the natural fermentation, inoculation with lactic acid bacteria (LAB) accelerated the degradation of myosin and actin in Zhayu, increased the trichloroacetic acid (TCA)-soluble peptide content by about 1.3-fold, reduced the colony counts of Enterobacteriaceae and Staphylococcus aureus by about 40%, and inhibited their lipid oxidation. In the texture profile analysis performed, higher levels of hardness and chewiness were observed in the inoculation groups. In this study, the bacterial community and volatile flavor compounds were detected through 16S high-throughput sequencing and headspace solid-phase microextraction-gas chromatography-mass spectrometry (HS-SPME-GC-MS). Inoculation with L. plantarum L1 reduced around 75% abundance of Klebsiella compared with the natural fermentation group, which was positively correlated with 2,3-Butanediol, resulting in a less pungent alcohol odor in Zhayu products. The abundances of 2-pentylfuran and 2-butyl-3-methylpyrazine were increased over threefold in the L1 group, which may give Zhayu its unique flavor and aroma.

Bacteriobiota and Chemical Changes during the Ripening of Traditional Fermented "Pirot 'Ironed' Sausage"

"Pirot 'ironed' sausage" (Pis) is a traditional, fermented sausage, made from different types of meat (beef and chevon), without additives or starter cultures. The physical-chemical properties (pH, water activity, fats, moisture, and protein contents) were examined in the initial meat batter stuffing and during ripening. Total bacterial diversity was examined at different time points using both culturable (traditional) and non-culturable (NGS sequencing) approaches. During the ripening, a decrease in pH value, a_w, and moisture content was observed, as well as an increase in protein and fat content. At least a two-fold significant decrease was noted for colorimetric values during the ripening period. The dominance of Proteobacteria and Firmicutes was observed in the non-culturable approach in all studied samples. During the ripening process, an increase in Firmicutes (from 33.5% to 63.5%) with a decrease in Proteobacteria (from 65.4% to 22.3%) was observed. The bacterial genera that were dominant throughout the ripening process were Lactobacillus, Photobacterium, Leuconostoc, Weissella, and Lactococcus, while Carnobacterium, Brochothrix, and Acinetobacter were found also, but in negligible abundance. Among the culturable bacteria, Latilactobacillus sakei (Lactobacillus sakei) and Leuconostoc mesenteoides were present in all stages of ripening.

Quality relationship between smoked and air-dried bacon of Sichuan-Chongqing in China: Free amino acids, volatile compounds, and microbial diversity

The quality formation of Chinese bacon is closely related to flavor compounds and microbial composition; however, the contribution of microbial to flavor has not been fully explored. Previous studies have focused on the differences in microorganisms and flavor substances in smoked bacon. Thus, this study aims to investigate the relationship among microorganisms, free amino acids (FAAs), and volatile compounds (VOCs) in bacon produced by different drying processes. We analyzed the microbial composition by sequencing the V3-V4 region of the 16S rDNA gene and the fungal ITS2 region and flavor substances using an amino acid analyzer and chromatography-mass spectrometry (GC-MS). Results of taste activity values (TVA) and partial least squares discriminant analysis (PLS-DA) revealed that the flavor components of the two types of bacon had general and specific characteristics, with the key FAAs (glutamic acid, lysine, and alanine) being comparable and the key VOCs being dissimilar. Based on non-metric multidimensional scaling (NMDS) and linear discriminant analysis effect size (LefSe), bacteria had more biomarkers than fungi. Correlation analysis demonstrated that microorganisms, particularly bacteria (Staphylococcus and Salinivibrio), are crucial in regulating and shaping the flavor of bacon. Some sub-abundance of bacteria such as Kocuria enrich the flavor of bacon. These findings indicate that the simultaneous fermentation of multiple microorganisms is conducive to the recreation of the artisan flavor of Chinese bacon.

Effects of Fermentation on the Physicochemical Properties and Aroma of Lamb Liver Paste

The probiotic fermentation of lamb liver paste is a new method with which to utilize sheep by-products and address the issue of waste. In this study, a pH meter, chromaticity meter, texture analyzer, and gas chromatograph–mass spectrometer (GC–MS) were used to determine various indicators. The objective was to investigate the effect of fermentation on the physical properties and aroma of lamb liver paste. The results showed that the L* (brightness), a* (redness), and b* (yellowness) of the samples were significantly higher in the starter fermentation group than in the other two groups after storage for 0, 1, 7, 14, 21, and 28 days (p < 0.05). In addition, cohesiveness, adhesion, and chewiness were lower in the starter fermentation group after 7 days (p < 0.05). TVB-N and fat were lower in the starter fermentation group compared to the sterilization group at 28 days. pH was significantly lower in the starter fermentation group at the beginning of storage, and lactic acid bacteria numbers were significantly higher than in the sterilization groups (p < 0.05). Important aroma compounds, such as 2-undecenal, 1-octen-3-ol, and anethole, were significantly higher in the starter fermentation group than in the sterilization group (p < 0.05). Fermented lamb liver paste is a new by-product that exhibits a high degree of freshness and a low degree of fat oxidation during storage. This study provides a theoretical basis for future industrial production.

Challenges and perspectives of quantitative microbiome profiling in food fermentations

Spontaneously fermented foods are consumed and appreciated for thousands of years although they are usually produced with fluctuated productivity and quality, potentially threatening both food safety and food security. To guarantee consistent fermentation productivity and quality, it is essential to control the complex microbiota, the most crucial factor in food fermentations. The prerequisite for the control is to comprehensively understand the structure and function of the microbiota. How to quantify the actual microbiota is of paramount importance. Among various microbial quantitative methods evolved, quantitative microbiome profiling, namely to quantify all microbial taxa by absolute abundance, is the best method to understand the complex microbiota, although it is still at its pioneering stage for food fermentations. Here, we provide an overview of microbial quantitative methods, including the development from conventional methods to the advanced quantitative microbiome profiling, and the application examples of these methods. Moreover, we address potential challenges and perspectives of quantitative microbiome profiling methods, as well as future research needs for the ultimate goal of rational and optimal control of microbiota in spontaneous food fermentations. Our review can serve as reference for the traditional food fermentation sector for stable fermentation productivity, quality and safety.

Dynamic change of bacterial diversity, metabolic pathways, and flavor during ripening of the Chinese fermented sausage

Chinese fermented sausage is a famous fermented meat product with a complex microbiota that has a potential impact on flavor and quality. In this study, Lactobacillus plantarum MSZ2 and Staphylococcus xylosus YCC3 were used as starter cultures to investigate the change in bacterial diversity, metabolic pathways, and flavor compounds during the ripening process of fermented sausages. High-throughput sequencing technology and headspace solid-phase microextraction-gas chromatography–mass spectrometry (HS-SPME-GC/MS) were applied for characterizing the profiles of bacterial diversity, metabolic pathways, and flavor compounds in sausage samples on days 0, 6, and 12 during ripening. Results showed that Lactobacillus, Staphylococcus, Lactococcus, Leuconostoc, and Weissella were the most abundant bacterial genera found in the sausage samples during all stages of fermentation. Functional prediction reveals the abundance of 12 different metabolic pathways, the most important pathways are carbohydrate metabolism, nucleotide metabolism, lipid metabolism, and amino acid metabolism. A total of 63 volatile compounds were successfully identified in fermented sausage samples. Correlational analysis demonstrated that Staphylococcus and Leuconostoc were closely related to the formation of flavor compounds. Therefore, the present study may provide guidance for future use of microbiota to improve flavor, quality, and preservation of fermented sausages.

Physicochemical property, bacterial diversity, and volatile profile during ripening of naturally fermented dry mutton sausage produced from Jianzhou big-eared goat

Physicochemical properties, bacterial communities, and volatile compounds of mutton sausage produced from Jianzhou Big-Eared goat meat during natural ripening were investigated. Firmicutes and Bacteroidetes accounted for over 66% of all operational taxonomic units (OTUs) throughout the whole process, with Lachnospiraceae_NK4A136_group and Staphylococcus as the predominant genus during the early and later ripening periods, respectively. The evolution of microbial composition became less rich and diverse. The uncultured bacterium, the Lachnospiraceae_NK4A136_group, and Staphylococcus were marker bacteria on days 0, 7, and 26, respectively, with none on day 16. The bacteria distribution seemed to influence the volatile profile of mutton sausage throughout processing, with the bacterial composition on day 0 and day 7 clustered separately from day 16 and day 26, and the same pattern for the volatile profile. Meanwhile, the concentration of total volatile fraction significantly increased, and the majority of the volatile compounds were generated during late ripening. Non-anal, hexanal, decanal, heptanal, dodecyl aldehyde, benzaldehyde, 3-methylbutanal, γ-dodecalactone, 2-pentylfuran, and 1-octen-3-ol were key volatile compounds, contributing to the overall mutton sausage flavors. Based on Spearman’s correlation analysis, Staphylococcus as well as Psychrobacter were positively correlated with the production of the key volatile compounds, and other bacteria such as Lachnospiraceae_NK4A136_group, Bacteroides, Lactobacillus, Prevotella_1, Odoribacter, and so on were associated with the production of most alcohols and esters.

Effects of Microbial Communities on Volatile Profiles and Biogenic Amines in Beef Jerky from Inner Mongolian Districts

Beef jerky is a traditional fermented meat product from Inner Mongolia, handcrafted by artisans. We investigated the bacteria of the microbial community, volatile flavor components, and biogenic amines of Inner Mongolia beef jerky via high-throughput sequencing, solid-phase microextraction with gas chromatography−mass spectrometry, and high-performance liquid chromatography, respectively. Thirty-three bacteria were identified, predominantly from the genera Pseudomonas (45.4%), Ralstonia (13.4%), and Acinetobacter (7.3%). Fifty-nine volatile flavor compounds and eight biogenic amines were detected. Based on Spearman’s correlation coefficient, 20 bacterial genera were significantly associated with the dominant volatile compounds in the beef jerky samples (p < 0.05). The results demonstrated that beef jerky may be toxic due to cadaverine, putrescine, and histamine; moreover, the amounts of putrescine and cadaverine were positively correlated with the abundance of unclassified_f_Enterobacteriaceae (p < 0.05). These findings shed light on the formation of the microbial community, flavor components, and biogenic amines of beef jerky, thereby providing a basis for improving its quality.

Bacterial community diversity and its potential contributions to the flavor components of traditional smoked horsemeat sausage in Xinjiang, China

Smoked horsemeat sausage is a famous fermented traditional food in Xinjiang, China. However, the microbial diversity and its potential contributions to the flavor components of smoked horsemeat sausage are unclear. In this study, the microbial community and flavor components of smoked horsemeat sausage from six regions of Xinjiang were measured by using amplicon sequencing and headspace solid-phase microextraction combined with gas chromatography–mass spectrometry (HS-SPME-GC–MS) technology, respectively. Relations among microbial communities, flavor components and environmental factors were subsequently predicted based on redundancy analysis (RDA) and Monte Carlo permutation tests. Although smoked horsemeat sausage samples from different regions possessed distinct microbial communities, lactic acid bacteria (LAB) were identified as the dominant consortium in smoked horsemeat sausage. Lactobacillus, Vagococcus, Lactococcus, and Carnobacterium were detected at high abundance in different sausages. The moisture content, nitrite content, and pH of the sausage might be important factors influencing the dominant bacterial community, according to the RDA. Among the dominant consortia, the eight core bacterial genera showed considerable correlations with the formation of sixteen volatile compounds in smoked horsemeat sausage based on multivariate statistical analysis. For example, the levels of Leuconostoc and Lactobacillus were positively correlated with those of 1-hexadecanol, hexyl acetate, 2-methyl-phenol, 1-pentanol, d-limonene, and 2-heptanone, and the levels of Leuconostoc, Lactobacillus, and Weissella were negatively correlated with those of 1-octanol, acetic acid, octanal, heptanal, and 1-hexanol. This study will provide a theoretical basis for understanding the microbial metabolic modes of Xinjiang smoked horsemeat sausages.

Characterization of Quality Properties in Spoiled Mianning Ham

Deep spoilage is a cyclical and costly problem for the meat industry. Mianning ham is a famous dry-cured meat product in Sichuan, China. The aim of this work was to investigate the physicochemical characteristics, sources of odor, and associated microorganisms that cause spoilage of Mianning ham. High-throughput sequencing and solid-phase microextraction–gas-chromatography (SPME-GC-MS) techniques were used to characterize the physicochemical properties, microbial community structure, and volatile compounds of spoiled Mianning ham and to compare it with normal Mianning ham. The results showed that spoiled ham typically had higher moisture content, water activity (a_w), and pH, and lower salt content. The dominant bacterial phylum detected in deeply spoiled ham was Firmicutes (95.4%). The dominant bacterial genus was Clostridium_sensu_stricto_2 (92.01%), the dominant fungal phylum was Ascomycota (98.48%), and the dominant fungal genus was Aspergillus (84.27%). A total of 57 volatile flavor substances were detected in deeply spoiled ham, including 11 aldehydes, 2 ketones, 6 alcohols, 10 esters, 20 hydrocarbons, 6 acids, and 2 other compounds. Hexanal (279.607 ± 127.265 μg/kg) was the most abundant in deeply spoiled ham, followed by Butanoic acid (266.885 ± 55.439 μg/kg) and Nonanal (165.079 ± 63.923 μg/kg). Clostridium_sensu_stricto_2 promoted the formation of five main flavor compounds, Heptanal, (E)-2-Octenal, 2-Nonanone, Hexanal, and Nonanal, in deeply spoiled ham by correlation analysis of microbial and volatile flavor substances.

Improving the Flavor of Fermented Sausage by Increasing Its Bacterial Quality via Inoculation with Lactobacillus plantarum MSZ2 and Staphylococcus xylosus YCC3

This research aims to investigate the effects of Staphylococcus xylosus YCC3 (Sx YCC3) and Lactobacillus plantarum MSZ2 (Lp MSZ2) on lipid hydrolysis and oxidation, the bacterial community’s composition, and the volatile flavor compounds in fermented sausage. The bacterial community was examined by plate counting and high-throughput sequencing. Differential flavor compounds in non-inoculated and inoculated sausages were identified by principal component analysis (PCA) and orthogonal partial least squares discrimination analysis (OPLS-DA). The results showed that the free fatty acid (FFA) content was increased after inoculating with Sx YCC3 or Lp MSZ2. The pH, peroxide value (POV), thiobarbituric acid reactive substances (TBARS) value, lipoxygenase activity, and the counts of Enterobacteriaceae were lower in the inoculated sausage than in the non-inoculated sausage. The bacterial inoculation enhanced the competitiveness of Staphylococcus and Lactobacillus and restricted the growth of unwanted bacteria. The OPLS-DA revealed that (Z)-hept-2-enal, (E)-2-octenal, 1-nonanal, octanal, and 1-octen-3-ol were common differential flavor compounds that were found in the inoculated sausages but were not found in the non-inoculated sausages. A positive correlation was observed between the differential flavor compounds and the relative abundance of Staphylococcus or Lactobacillus, or the FFA content. Our results indicated that inoculation with Sx YCC3 or Lp MSZ2 can improve fermented sausages’ flavor by enhancing their bacterial quality and increasing their FFA content.

Study on taste characteristics and microbial communities in Pingwu Fuzhuan brick tea and the correlation between microbiota composition and chemical metabolites

Pingwu Fuzhuan brick tea (PWT) is considered the "Sichuan western road" border-selling tea. The taste and quality of Fuzhuan brick tea (FBT) is greatly influenced by microorganisms. Considering the dearth of studies on the taste and microbial community of PWT, this study aimed to investigate the taste characteristics using electronic tongue system and microbial community structures using high-throughput sequencing, followed by comparison with FBT from other regions and determining the correlation between microbial communities and chemical compositions. The taste strengths of sweetness, bitterness, umami and astringency in PWT were all at lower level compared to other regions FBT. Regarding microbial diversity, the fungal communities in PWT were distinct from those of other regions FBT in terms of taxonomic composition and abundance. Unclassified_k_Fungi and Aspergillus were the most dominant fungal genera in PWT. Candidatus_Microthrix, norank_f_Saprospiraceae, and norank_c_C10-SB1A were dominant bacterial genera in PWT, only distinct from those in Hunan FBT (HNT). Principal component analysis results showed that fungal or bacterial community structures of PWT and other regions FBT were distinctly different. Correlation analysis revealed important links between the top 50 microbial populations and metabolites.

SUPPLEMENTARY INFORMATION

The online version of this article contains supplementary material available at (10.1007/s13197-021-04976-y).

Influence of Tissue Type on the Bacterial Diversity and Community in Pork Bacon

In current study, bacterial diversity and community in different tissues of pork bacon were determined using high-throughput sequencing. In total, six phyla and 111 bacterial genera were identified. Among them, three dominant genera (Staphylococcus, Acinetobacter, and Macrococcus) were shared by all bacon samples. The linear discriminant analysis showed that 24 bacterial taxa significantly differentiated between the tissues. Results of non-metric Multidimensional Scaling and redundancy analysis showed that physicochemical characteristics of the tissue prominently structured the bacterial communities. Network analysis also illustrated that tissue type was an important factor impacting the bacterial interactions in different types of tissue. The results of current study can add valuable insights to the traditional homemade pork bacon.

Effects of Lactobacillus plantarum C7 and Staphylococcus warneri S6 on flavor quality and bacterial diversity of fermented meat rice, a traditional Chinese food

Fermented meat rice (FMR) is a traditional Chinese fermented food with special flavor and abundant microorganisms. Lactobacillus and Staphylococcus species have been found to be excellent strains in FMR during fermentation. However, their roles in FMR flavor formation remain yet to be elucidated. Here, we investigated the correlation between physicochemical properties and volatile flavor components, as well as the microbial community during FMR fermentation. First, we determined pH, total titratable acids (TTA), proteins, total lipids, organic acids, free amino acids (FAAs), and volatile flavor compounds (VFCs). With increasing fermentation time, inoculation with Lactobacillus plantarum C7+ Staphylococcus warneri S6 (LP + SW) accelerated the decrease in pH, increased TTA, and reduced protein and total lipid content of FMR. In addition, LP + SW inoculation resulted in significantly (P < 0.05) higher contents of β-eudesmol, nerolidol, ethyl caproate, citronellal, lactic acid, and most FAAs (aspartic acid, glutamic acid, alanine, and lysine) in FMR compared to natural fermentation. Second, inoculated fermentation promoted the growth of Lactobacillus plantarum and/or Staphylococcus warneri and inhibited the growth of some potentially pathogenic microorganisms such as Acinetobacter and Enhydrobacter. Lactobacillus and Staphylococcus were found to be highly correlated with the physicochemical properties and VFCs (P < 0.05) of FMR as indicated by redundancy analysis (RDA) and partial least squares (PLS, VIP > 1.0) analysis. Finally, Spearman's correlation (| r | ≥ 0.7, P < 0.05) analysis of SPSS was visualized by the Cytoscape software. The findings suggest that inoculation with L. plantarum C7 and/or S. warneri S6 can significantly improve the flavor quality of FMR.

Combined application of high-throughput sequencing and UHPLC-Q/TOF-MS-based metabolomics in the evaluation of microorganisms and metabolites of dry-cured ham of different origins

Ham fermentation relies on environmental and indigenous microorganisms forming a rich microbiome, which is pivotal to taste and flavor formation. Previous studies have focused on the appearance of differences of microorganisms and metabolites, this study aims to establish the relationship between microorganisms and metabolites over a period of two years in the fermentation of hams from Jinghua (JH2), Xuanwei (XW2), Rugao (RG2), Iberian (IB2) and Parma (PA2). We profiled bacterial communities by sequencing the V3-V4 region of the 16S rRNA genes and metabolites were analyzed using LC-Q-TOF-MS. LefSe analysis showed that different biomarkers in five ham groups. OPLS analysis showed that most differential metabolites are amino acids and were associated with four metabolic pathways. Correlation analysis implies a firm positive relationship between microorganisms and metabolites. This study provides novel insights into the taste and flavor quality of dry-cured hams of different origins due to fermentation.

Distinct bacterial community of a solid-state fermented Chinese traditional food huase sufu revealed by high-throughput sequencing

Sufu is a common solid-state traditional fermented food made from soybean. Huase sufu is a typical type found in several provinces of China, especially in Hubei. However, little is known about the bacterial community. High-throughput sequencing technology revealed that the dominant taxa at phylum level were: Firmicutes, Proteobacteria and Bacteroides, and at the genus level were: Pseudomonas, Lactococcus, Acinetobacter, etc. Additionally, LEfSe revealed that compared with the bacterial community of red sufu and white sufu, the biomarker genera for both huase sufu were Enterococcus, and Myroides. Moreover, there were twenty-eight hubs for the huase sufu samples, and four of them were dominant genera: Citrobacter, Myroides, Vagococcus, and Enterococcus. These results provide a new insight into our understanding of the bacterial diversity of huase sufu, and will facilitate the isolation, screening, and development potential bacterial strains for production of huase sufu.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10068-021-00963-3.