Metagenomic analysis of bacterial community structure and functions during the fermentation of da-jiang, a Chinese traditional fermented food

Effect of bacteriocin RSQ01 on milk microbiota during pasteurized milk preservation

Milk has high risk for microbial contamination. RSQ01, a bacteriocin, previously has shown potentiality for pasteurized milk preservation. This study analyzed the effects of RSQ01 on milk microbiota by comparison of bacterial number and composition in 3 pasteurized milk groups: controls without RSQ01, treatment group with the addition of 2 × MIC (low concentration) and 4 × MIC RSQ01 (high concentration). Integrated 16S rDNA sequencing and metagenomics of these groups after 3 d of storage showed inhibition of RSQ01 on microbiota diversity. Pathogenic bacteria such as Salmonella showed a decrease in relative abundance after RSQ01 treatment, while probiotic bacteria such as Lactococcus showed an increase, indicating that RSQ01 contributed to milk preservation by maintaining a low abundance of pathogens and a relatively high abundance of probiotics. Further investigations revealed that milk preservation was primarily attributed to the ability of RSQ01 to decrease the relative abundance of genes related to metabolism of energy and nutrients (e.g., vitamins, lipids, and amino acids) of microbiota, with change of genetic, environmental, and cellular processes. Interestingly, RSQ01 generally reduced the relative abundance of virulence factors- and quorum-sensing-related genes in microbiota, likely reducing virulence and resistance. The findings provided insights into microbiomics mechanisms regarding pasteurized milk preservation of bacteriocins.

Differential mediation of biogeochemical processes through bioturbation by fiddler and sesarmid mangrove crabs

Macrobenthic bioturbation is vital to facilitate nutrient turnover in estuarine ecosystems and drives spatial heterogeneity in the sediment matrix. In this study, we compared the sediment physico-chemical properties, microbial community structure and functional genes in vertically-stratified sediment samples from bioturbated (burrows of Parasesarma bidens and Tubuca arcuata) and non-bioturbated area in mangrove ecosystems (the Hanjiang River Estuary, Southern China). The result indicated that bioturbation by P. bidens and T. arcuata had significantly different effects on sediment properties, with the action of P. bidens enhancing nutrient accumulation while T. arcuata promoted N2O emission. Burrow microhabitats harbored distinctive microbial communities although the dominant phylum and genera shared considerable similarity with the control sediment surface with Woeseia dominating in vertical profiles across different habitats. Co-occurrence network analysis revealed that crab bioturbation promoted formation of less complex but more functionally-specialized microbial communities. Crab bioturbation enhanced nutrient metabolism and separated clusters in dendrogram demonstrated the species-specific effect between P. bidens and T. arcuata. Our work verified the significance of bioturbators in regulating biogeochemical processes and highlighted the species-specific bioturbation effect between two dominant mangrove crabs (P. bidens vs. T. arcuata).

The quality characteristics and microbial communities of three components in traditional split-fermented red sour soup

Red sour soup is a Guizhou specialty condiment made by the natural fermentation of tomatoes and chili. In this study, three components (tomato acid, chili acid, and tomato and chili mixed acid) of split-fermented red sour soup were explored to compare the quality characteristics and microbial communities in the middle and late fermentation stages. The titratable acidity of mixed acids was lower than that of tomato acid and chili acid in the middle stage, but it was significantly increased in the late stage. The cell viability of lactic acid bacteria was mostly higher than that of yeasts during the whole fermentation. Also significantly increased in the late stage of fermentation were sensory scores and the signal intensity of sour substances. However, the signal intensity of both bitter and salty substances decreased, and the total amount of free amino acids was reduced. In addition, the antioxidant capacity of the samples and the dominant microorganisms were different between the two fermentation stages, Lactobacillus and Kazachstania were the key common genus of the different components of split-fermented red sour soup. It is anticipated that this study would provide us an insight into the quality characteristics and microbial communities of split-fermented red sour soup.

Impact of microorganisms on key processes of organic acid metabolism during the occurrence and disappearance of paocai pellicle

In vegetable fermentation, pellicle is a common quality deterioration phenomenon. This study investigates the characteristics of glucose, organic acids, amino acids, and biogenic amines during the pellicle occurrence and disappearance of paocai. The results revealed a slight increase in pH of the fermentation system after pellicle occurred, and glucose was the main carbohydrate that microbial activity primary relied on. The microorganisms responsible for pellicle formation consumed organic acids in brine, but the lactic acid in paocai gradually increased and exceeded 25 mg/g. The appearance of pellicle caused a decrease in total free amino acids from 200.390 mg/100 g to 172.079 when pellicle occurred, whereas its impact on biogenic amines was not apparent. Through Kyoto Encyclopedia of Genes and Genomes pathway enrichment of metagenomics sequencing data, screening, and sorting of the key enzymes involved in organic acid metabolism, it was observed that the composition and species of the key microorganisms capable of metabolizing organic acids were more abundant before the appearance of pellicle. When pellicle occurred, lactic acid may be metabolized by Lactobacillus plantarum; in contrast, Lactobacillus and Pichia were associated with citric acid metabolism, and Lactobacillus, Pichia, Saccharomycodes, and Kazachstania were linked to malic acid metabolism. Moreover, Prevotella, Kazachstania, Lactobacillus, Vibrio, and Siphonobacter were implicated in succinic acid metabolism. Additionally, the production of tartaric acid and oxalic acid in paocai and brine resulted from abiotic effects. This knowledge offers a theoretical basis for precise control of paocai fermentation process. PRACTICAL APPLICATION: Our study revealed the specific situation of the metabolites produced by the microorganisms during the pollution and recovery process of pellicle in paocai fermentation, especially the effect of pellicle on the key process of organic acid metabolism. These research results provided theoretical basis for precise control of paocai fermentation.

Effects of Salinity on Physicochemical Properties, Flavor Compounds, and Bacterial Communities in Broad Bean Paste-Meju Fermentation

Broad bean paste (BBP) is a traditional fermented soy food, and its high salt content not only prolongs the fermentation time but also threatens human health. In this study, three BBP-meju with different salt concentrations were prepared, and the effects of varying salinity on fermentation were comprehensively compared. The results showed that salt-reduced fermentation contributed to the accumulation of amino acid nitrogen, reducing sugars, free amino acids, and organic acids. Alcohols, esters, aldehydes, and acids were the main volatile flavor compounds in BBP-meju, and the highest total volatile flavor compounds were found in medium-salt meju. Bacillus, Staphylococcus, Aspergillus, and Mortierella were the dominant microbial communities during fermentation, and there were also three opportunistic pathogens, Enterobacter, Pantoea, and Brevundimonas, respectively. According to Spearman correlation analysis, Wickerhamomyces, Bacillus, Staphylococcus, and Mortierella all showed highly significant positive correlations with ≥3 key flavor compounds, which may be the core functional flora. Furthermore, the dominant microbial genera worked synergistically to promote the formation of high-quality flavor compounds and inhibit the production of off-flavors during salt-reduced fermentation. This study provides a theoretical reference for the quality and safety control of low-salt fermented soy foods.

Metagenomic analysis of core differential microbes between traditional starter and Round-Koji-mechanical starter of Chi-flavor Baijiu

Xiaoqu starter serves as the saccharifying and fermenting agent in the production of Cantonese soybean-flavor (Chi-flavor) Baijiu, and the complex microbial communities determine the flavor and quality of the product. Round-Koji-mechanical starter (produced by using an automated starter-making disk machine) is advantageous as it decreases operator influence, labor costs, and fermentation time, but the product quality is lower compared to traditional starter. Thus, two types of starters (traditional and Round-Koji-mechanical starter) from a Cantonese Baijiu factory were compared in a metagenomic analysis to investigate the differences in microbial community composition and core microbes. The results showed that several core microbes related to carbohydrate metabolism, amino acid metabolism and lipid metabolism, were differentially enriched in the traditional starter. Mucor lusitanicus and Rhizopus delemar were significantly positively correlated with the three key metabolic pathways. Saccharomyces cerevisiae, Cyberlindnera fabianii, Kluyveromyces marxianus, Lactobacillus fermentum, Mucor ambiguous, Rhizopus microspores, Rhizopus azygosporus, Mucor circinelloides, and Ascoidea rubescens were significantly positively correlated with two of the three key metabolic pathways. The results of this study provide a basis for understanding the differential core microbes in traditional and Round-Koji-mechanical starters of Chi-flavor Baijiu, and they also provide guidance for improving Round-Koji-mechanical starter.

Ultrasound-assisted fermentation for antioxidant peptides preparation from okara: Optimization, stability, and functional analyses

This study investigated the effects of ultrasound-assisted fermentation (UAF) on the preparation of antioxidant peptides (UAFP) from okara and examined their content, chemical structures, and antioxidant activity. After the optimal ultrasonic processing (time, 20 min; frequency, 45 KHz; power, 120 W/L), the peptide content yield reached the maximum of 12.36 ± 0.02 mg/mL, and their DPPH free radical scavenging rate was 65.15 ± 0.32 %. UAF increased the number of globular aggregates with deeper gullies, a looser structure, and higher porosity. The experiments conducted using the oxidative stress injury model of HepG2 cells showed that okara UAFP promoted cell growth and exerted a protective effect. Moreover, ultrasonic treatment remarkably improved the environmental stability (NaCl, glucose, sodium benzoate, temperature, pH, metal ions) and antioxidant activity of UAFP. Concisely, optimal ultrasonic processing can aid the fermentation of agroindustrial by-products to prepare antioxidant peptides, such as natural food antioxidant peptides from soybean waste.

Analysis of Pickled Cucumber Products, Based on Microbial Diversity and Flavor Substance Detection

Changes to the microbial community during pickled cucumber fermentation were studied using the 16S rDNA technique. The changes of volatile organic compounds (VOCs) during pickled cucumber fermentation were studied by gas chromatograph-ion mobility spectrometry. At the phylum level, Cyanophyta and Proteobacteria were the dominant flora in the natural fermentation group, and Firmicutes were the dominant flora in the added-bacteria fermentation group. At the generic level, the addition of Lactobacillus led to changes in the community of the bacteria in the added-bacterial fermentation group and decreased the species abundance of other bacteria. In total, 75 volatile organic compounds were identified from naturally fermented pickled cucumber, and 60 volatile organic compounds were identified from fermented pickled cucumber with bacterial addition. The main metabolites were esters, aldehydes, acids, alcohols, ketones, alkanes, nitriles, and alkenes. These metabolites will bring their unique aroma components to the pickled cucumber. Metabolomic analysis of the O2PLS model showed that Weissella and Lactobacillus were closely and positively correlated with nine alcohols, six esters, five aldehydes, four acids, three ketones, and one pyrazine. Pseudomonas and norank_f_Mitochondria show a close positive correlation with four kinds of alcohols, two kinds of esters, one kind of aldehyde, and one kind of nitrile.

Unraveling the carbohydrate metabolic characteristics of Leuconostoc mesenteroides J18 through metabolite and transcriptome analyses

The metabolic characteristics of Leuconostoc mesenteroides subsp. mesenteroides J18, which is mainly responsible for kimchi fermentation, on various carbon sources were investigated through carbon utilization, metabolite, and transcriptome analyses at different culture conditions (10 and 30 °C with/without 2.5% NaCl). The metabolic features of strain J18 were relatively similar across the four culture conditions. However, the metabolic characteristics of strain J18 showed significant variations depending on the carbon source. These distinct metabolic traits of strain J18 on various carbon sources were validated through transcriptomic analyses and the reconstruction of metabolic pathways. The transcriptional expression of the metabolic pathways in response to each carbon source consistently correlated with the production profiles of metabolites, including ethanol, acetoin, diacetyl, and riboflavin, in each carbon source. Our findings suggests that the abundance of Leu. mesenteroides during fermentation and the taste and flavor of fermented food products can be controlled by altering the carbon sources.

Exploring the microbial diversity of novel misos with metagenomics

Interest in fermented foods, especially plant-based ones, has increased considerably in the last decade. Miso-a Japanese paste traditionally fermented with soybeans, salt, and kōji (Aspergillus oryzae grown on grains or beans)-has gained attention among chefs for its rich flavour and versatility. Some chefs have even been experimenting with making novel misos with untraditional substrates to create new flavours. Such novel fermented foods also offer new scientific opportunities. To explore the microbial diversity of these new traditional foods, we sampled six misos made by the team at a leading restaurant called Noma in Copenhagen (Denmark), using yellow peas (including a nixtamalised treatment), lupin seeds, Swedish Vreta peas, grey peas, and Gotland lentils as substrates. All misos were made with the same recipe and fermented for 3 months at 28 °C. Samples were collected at the end of fermentation for subsequent shotgun metagenomic sequencing and a genome-resolved metagenomic analysis. The taxonomic profile of the samples revealed the presence of kōji mould (A. oryzae) and Bacillus amyloliquefaciens in all misos. Various species of the genera Latilactobacillus, Lactiplantibacillus, Pediococcus and Staphylococcus were also detected. The Metagenome-Assembled Genomes (MAGs) revealed genomic sequences belonging to 12 different species and functional analyses of these MAGs were performed. Notably, we detected the presence of Exiguobacterium-the first reported instance of the genus in miso-and Average Nucleotide Identity (ANI) analyses suggest a potentially new species. We hope these results will improve the scientific literature on misos and contribute to developing novel fermented plant-based foods.

Comparative pangenome analysis of Enterococcus faecium and Enterococcus lactis provides new insights into the adaptive evolution by horizontal gene acquisitions

BACKGROUND

Enterococcus faecium and E. lactis are phylogenetically closely related lactic acid bacteria that are ubiquitous in nature and are known to be beneficial or pathogenic. Despite their considerable industrial and clinical importance, comprehensive studies on their evolutionary relationships and genomic, metabolic, and pathogenic traits are still lacking. Therefore, we conducted comparative pangenome analyses using all available dereplicated genomes of these species.

RESULTS

E. faecium was divided into two subclades: subclade I, comprising strains derived from humans, animals, and food, and the more recent phylogenetic subclade II, consisting exclusively of human-derived strains. In contrast, E. lactis strains, isolated from diverse sources including foods, humans, animals, and the environment, did not display distinct clustering based on their isolation sources. Despite having similar metabolic features, noticeable genomic differences were observed between E. faecium subclades I and II, as well as E. lactis. Notably, E. faecium subclade II strains exhibited significantly larger genome sizes and higher gene counts compared to both E. faecium subclade I and E. lactis strains. Furthermore, they carried a higher abundance of antibiotic resistance, virulence, bacteriocin, and mobile element genes. Phylogenetic analysis of antibiotic resistance and virulence genes suggests that E. faecium subclade II strains likely acquired these genes through horizontal gene transfer, facilitating their effective adaptation in response to antibiotic use in humans.

CONCLUSIONS

Our study offers valuable insights into the adaptive evolution of E. faecium strains, enabling their survival as pathogens in the human environment through horizontal gene acquisitions.

Microbiome and metabolome in home-made fermented soybean foods of India revealed by metagenome-assembled genomes and metabolomics

Grep-chhurpi, peha, peron namsing and peruñyaan are lesser-known home-made fermented soybean foods prepared by the native people of Arunachal Pradesh in India. Present work aims to study the microbiome, their functional annotations, metabolites and recovery of metagenome-assembled genomes (MAGs) in these four fermented soybean foods. Metagenomes revealed the dominance of bacteria (97.80 %) with minor traces of viruses, eukaryotes and archaea. Bacillota is the most abundant phylum with Bacillus subtilis as the abundant species. Metagenome also revealed the abundance of lactic acid bacteria such as Enterococcus casseliflavus, Enterococcus faecium, Mammaliicoccus sciuri and Staphylococcus saprophyticus in all samples. B. subtilis was the major species found in all products. Predictive metabolic pathways showed the abundance of genes associated with metabolisms. Metabolomics analysis revealed both targeted and untargeted metabolites, which suggested their role in flavour development and therapeutic properties. High-quality MAGs, identified as B. subtilis, Enterococcus faecalis, Pediococcus acidilactici and B. velezensis, showed the presence of several biomarkers corresponding to various bio-functional properties. Gene clusters of secondary metabolites (antimicrobial peptides) and CRISPR-Cas systems were detected in all MAGs. This present work also provides key elements related to the cultivability of identified species of MAGs for future use as starter cultures in fermented soybean food product development. Additionally, comparison of microbiome and metabolites of grep-chhurpi, peron namsing and peruñyaan with that of other fermented soybean foods of Asia revealed a distinct difference.

Detection of the Microbial Composition of Some Commercial Fermented Liquid Products via Metagenomic Analysis

The fermented liquid sector is developing all over the world due to its contribution to health. Our study has contributed to the debate about whether industrially manufactured fermented liquids live up to their claims by analyzing pathogens and beneficial bacteria using a 16S rRNA sequencing technique called metagenomic analysis. Paenibacillus, Lentibacillus, Bacillus, Enterococcus, Levilactobacillus, and Oenococcus were the most abundant bacterial genera observed as potential probiotics. Pseudomonas stutzeri, Acinetobacter, and Collimonas, which have plant-growth-promoting traits, were also detected. The fact that we encounter biocontroller bacteria that promote plant growth demonstrates that these organisms are widely used in foods and emphasizes the necessity of evaluating them in terms of public health. Their potential applications in agriculture may pose a danger to food hygiene and human health in the long term, so our data suggest that this should be evaluated.

A systematic review on the flavor of soy-based fermented foods: Core fermentation microbiome, multisensory flavor substances, key enzymes, and metabolic pathways

The characteristic flavor of fermented foods has an important impact on the purchasing decisions of consumers, and its production mechanisms are a concern for scientists worldwide. The perception of food flavor is a complex process involving olfaction, taste, vision, and oral touch, with various senses contributing to specific properties of the flavor. Soy-based fermented products are popular because of their unique flavors, especially in Asian countries, where they occupy an important place in the dietary structure. Microorganisms, known as the souls of fermented foods, can influence the sensory properties of soy-based fermented foods through various metabolic pathways, and are closely related to the formation of multisensory properties. Therefore, this review systematically summarizes the core microbiome and its interactions that play an active role in representative soy-based fermented foods, such as fermented soymilk, soy sauce, soybean paste, sufu, and douchi. The mechanism of action of the core microbial community on multisensory flavor quality is revealed here. Revealing the fermentation core microbiome and related enzymes provides important guidance for the development of flavor-enhancement strategies and related genetically engineered bacteria.

Microbial diversity and functional genes of red vinasse acid based on metagenome analysis

Red vinasse acid has a distinct flavor and a vivid red color that are directly tied to the intricate metabolic activities of microorganisms that produce it. In this study, metagenomic technology was used to mine its functional genes and examine the microbial diversity of red vinasse acid. The findings revealed the identification of 2,609 species, 782 genera, and 63 phyla of microorganisms, and the dominant genus was Lactobacillus. Amino acid metabolism and carbohydrate metabolism were significant activities among the 16,093 and 49,652 genes that were annotated in the evolutionary genealogy of genes: Non-supervised Orthologous Groups (eggNOG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, respectively. In gluconeogenesis, red vinasse acid encodes 194 genes controlling the transporter protein systems of different sugars and has key enzyme genes that catalyze the conversion of intracellular sugars into glycolytic intermediates. In amino acid flavor formation, red vinasse acid contains 32 control genes for branched-chain aminotransferase (BCAT), 27 control genes for aromatic-amino-acid transaminase (ArAT), 60 control genes for keto acid invertase, 123 control genes for alcohol/aldehyde dehydrogenase, and 27 control genes for acetyl esterase, which have the basis for the formation of strong flavor substances from amino acids.

Recent developments in horizontal gene transfer with the adaptive innovation of fermented foods

Horizontal gene transfer (HGT) has contributed significantly to the adaptability of bacteria, yeast and mold in fermented foods, whose evidence has been found in several fermented foods. Although not every HGT has biological significance, it plays an important role in improving the quality of fermented foods. In this review, how HGT facilitated microbial domestication and adaptive evolution in fermented foods was discussed. HGT can assist in the industrial innovation of fermented foods, and this adaptive evolution strategy can improve the quality of fermented foods. Additionally, the mechanism underlying HGT in fermented foods were analyzed. Furthermore, the critical bottlenecks involved in optimizing HGT during the production of fermented foods and strategies for optimizing HGT were proposed. Finally, the prospect of HGT for promoting the industrial innovation of fermented foods was highlighted. The comprehensive report on HGT in fermented foods provides a new trend for domesticating preferable starters for food fermentation, thus optimizing the quality and improving the industrial production of fermented foods.

Metagenomics Reveals the Microbial Community Responsible for Producing Biogenic Amines During Mustard [Brassica juncea (L.)] Fermentation

Biogenic amines (BAs) are considered potential hazards produced during fermented food processing, and the production of BAs is closely related to microbial metabolism. In this work, the changes of BA content were analyzed during mustard fermentation, and microbes and gene abundance responsible for producing BAs were revealed by metagenomic analyses. The results showed that cadaverine, putrescine, tyramine, and histamine were generated during mustard fermentation, which mainly accumulate in the first 6 days of fermentation. According to the metagenome sequencing, the predominant genus was Bacillus (64.78%), followed by Lactobacillus (11.67%), Weissella (8.88%), and Leuconostoc (1.71%) in the initial fermentation stage (second day), while Lactobacillus (76.03%) became the most dominant genus in the late stage. In addition, the gene abundance of BA production enzymes was the highest in the second day and decreased continuously as fermentation progressed. By tracking the source of the enzyme in the KEGG database, both Bacillus and Delftia closely correlated to the generation of putrescine. Besides, Bacillus also correlated to the generation of tyramine and spermidine, and Delftia also correlated to the generation of cadaverine and spermine. In the processes of fermentation, the pH of fermented mustard showed slower decrease compared with other similar fermented vegetables, which may allow Bacillus to grow at high levels before the pH <4. This study reveals the change of BA content and microbes involved in BA formation during mustard fermentation.

Predictive Microbial Community and Functional Gene Expression Profiles in Pineapple Peel Fermentation Using 16S rRNA Gene Sequences

Pineapple peel (PP) is a by-product with the potential to be used as a raw material for functional beverages. Traditional PP fermentation has so far paid little attention to the microbial community and its role in the fermentation process. As a result, the current research looked into the microbial communities and their roles during PP fermentation. A metagenomic approach based on the 16S rRNA sequencing data was used to assess the microbial communities. Subsequent analysis was performed using PICRUSt (phylogenetic investigation of communities by reconstruction of unobserved states) to analyze the microbial functions in the fermentation system. The microecology of the fermentation process in three samples was predominated by Firmicutes. Furthermore, the well-known probiotic genera Weissella, Lactobacillus, and Lactococcus were found to be predominating in the gumer, promic, and control samples, respectively. It was obvious that microenvironmental differences have an effect on the microbial composition of PP fermentation. Moreover, functional prediction revealed that carbohydrate metabolism was the most prevalent metabolic pathway during the fermentation process. Additionally, it was discovered that all of the bacteria found in the samples played significant roles in carbohydrate, amino acid, vitamin, and co-factor metabolism, which can be inferred to result in the production of beneficial metabolites.

Shotgun sequence-based metataxonomic and predictive functional profiles of Pe poke, a naturally fermented soybean food of Myanmar

Pe poke is a naturally fermented sticky soybean food of Myanmar. The present study was aimed to profile the whole microbial community structure and their predictive gene functionality of pe poke samples prepared in different fermentation periods viz. 3 day (3ds), 4 days (4ds), 5 days (5ds) and sun-dried sample (Sds). The pH of samples was 7.6 to 8.7, microbial load was 2.1-3.9 x 108 cfu/g with dynamic viscosity of 4.0±1.0 to 8.0±1.0cP. Metataxonomic profile of pe poke samples showed different domains viz. bacteria (99.08%), viruses (0.65%), eukaryota (0.08%), archaea (0.03%) and unclassified sequences (0.16%). Firmicutes (63.78%) was the most abundant phylum followed by Proteobacteria (29.54%) and Bacteroidetes (5.44%). Bacillus thermoamylovorans was significantly abundant in 3ds and 4ds (p<0.05); Ignatzschineria larvae was significantly abundant in 5ds (p<0.05), whereas, Bacillus subtilis was significantly abundant in Sds (p <0.05). A total of 172 species of Bacillus was detected. In minor abundance, the existence of bacteriophages, archaea, and eukaryotes were also detected. Alpha diversity analysis showed the highest Simpson's diversity index in Sds comparable to other samples. Similarly, a non-parametric Shannon's diversity index was also highest in Sds. Good's coverage of 0.99 was observed in all samples. Beta diversity analysis using PCoA showed no significant clustering. Several species were shared between samples and many species were unique to each sample. In KEGG database, a total number of 33 super-pathways and 173 metabolic sub-pathways were annotated from the metagenomic Open Reading Frames. Predictive functional features of pe poke metagenome revealed the genes for the synthesis and metabolism of wide range of bioactive compounds including various essential amino acids, different vitamins, and enzymes. Spearman's correlation was inferred between the abundant species and functional features.

Metagenomic analysis reveals the linkages between bacteria and the functional enzymes responsible for potential ammonia and biogenic amine production in alfalfa silage

AIMS

To clarify the molecular mechanisms underlying ammonia (NH₃ ) and biogenic amines (BAEs) formation in alfalfa silage, whole metagenomic sequencing analysis was performed to identify the linkages between functional bacteria and their responsible enzymes in alfalfa silage prepared with and without sucrose addition.

METHODS AND RESULTS

Genes encoding nitrite reductase (nirB) resulting in NH₃ formation were the most abundant and were mostly assigned to Enterobacter cloacae and Klebsiella oxytoca. Putrescine-related genes, classified mainly to encode ornithine decarboxylase (odcA), were predominantly carried by Escherichia coli, Ent. cloacae and Citrobacter sp. Escherichia coli and Kl. oxytoca were the important species responsible for cadaverine and tyramine formation. Ent. cloacae, E. coli, and Kl. oxytoca dominated the bacterial community in naturally fermented alfalfa silage, whilst sucrose-treated silages greatly inhibited the growth of these species by promoting the dominance of Lactobacillus plantarum, thus decreasing the concentrations of NH₃ , cadaverine, putrescine and tyramine.

CONCLUSIONS

Enterobacteriaceae bacteria are mainly responsible for the NH₃ , putrescine, cadaverine and tyramine formations in alfalfa silage.

SIGNIFICANCE AND IMPACT OF THE STUDY

Whole metagenomic sequencing analysis served as a useful tool to identify the linkages between functional bacteria and associated enzymes responsible for NH₃ and BAEs formation.

Characterization of Structural and Physicochemical Properties of an Exopolysaccharide Produced by Enterococcus sp. F2 From Fermented Soya Beans

The present study sought to isolate a novel exopolysaccharide (EPS-F2) from Enterococcus sp. F2 through ethanol precipitation, anion-exchange, and gel-filtration chromatography and characterize the physicochemical properties by spectral techniques. EPS-F2 was identified as a neutral homo-exopolysaccharide composed of only glucose with a high molecular weight of 1.108 × 10⁸ g/mol. It contained →6)-α-D-Glcp-(1→ linkage in the main chain and →3, 6)-α-D-Glcp-(1→ branch chain). Moreover, EPS-F2 possessed excellent thermal stability (266.6°C), water holding capacity (882.5%), oil holding capacity (1867.76%), and emulsifying activity against various edible oils. The steady shear experiments exhibited stable pseudo plasticity under various conditions (concentrations, temperatures, and pHs). The dynamic oscillatory measurements revealed that EPS-F2 showed a liquid-like behavior at a low concentration (2.5%), while a solid-like behavior at high concentrations (3.0 and 3.5%). Overall, these results suggest that EPS-F2 could be a potential alternative source of functional additives and ingredients and be applied in food industries.

Characterization and correlation of microbial communities and metabolite and volatile compounds in doenjang fermentation

To investigate the general fermentation features of doenjang, a traditional Korean fermented soybean paste, eleven batches of doenjang were prepared. The bacterial and fungal communities and the metabolites such as free sugars, organic acids, amino acids, and volatile compounds were analyzed during fermentation. Tetragenococcus, Aspergillus, and Debaryomyces were the most common microbes; galactose, fructose, and glucose were the major sugars; and lactate and acetate were the major organic acids. Spearman correlation analyses showed that the quantity of meju was correlated with only Pediococcus and Halomonas abundance, while solar salt concentration was correlated with the relative abundance of many microbial taxa and the amount of glycerol and total volatile compounds. The abundance of heterolactic acid bacteria, such as Tetragenococcus, Pediococcus, Weissella, and Enterococcus, was positively correlated with the levels of lactate, acetate, and ethanol, suggesting that heterolactic acid fermentation may be a major metabolism pathway during the fermentation of doenjang. The abundance of Weissella, Hyphopichia, and Wickerhamomyces was positively correlated with ethyl acetate levels, whereas the abundance of Staphylococcus and Bacillus was positively correlated with the concentration of major volatile compounds, 3-methylbutanoic acid and tetramethylpyrazine, respectively, suggesting that they may play important roles in the production of flavor compounds during fermentation.

Microbial Communities and Physicochemical Characteristics of Traditional Dajiang and Sufu in North China Revealed by High-Throughput Sequencing of 16S rRNA

The process of soybean fermentation has been practiced for more than 3,000 years. Although Dajiang and Sufu are two popular fermented soybean products consumed in North China, limited information is available regarding their microbial composition. Hence, the current study sought to investigate, and compare, the physicochemical indicators and microbial communities of traditional Dajiang and Sufu. Results showed that the titratable acidity (TA), and salinity, as well as the lactic acid, and malic acid contents were significantly higher in Sufu samples compared to Dajiang. Furthermore, Sufu samples contain abundant sucrose and fructose, while the acetic acid content was lower in Sufu compared to Dajiang samples. Moreover, the predominant bacterial phyla in Dajiang and Sufu samples were Firmicutes and Proteobacteria, while the major genera comprise Bacillus, Lactobacillus, Tetragenococcus, and Weissella. Moreover, Dajiang samples also contained abundant Pseudomonas, and Brevundimonas spp., while Halomonas, Staphylococcus, Lysinibacillus, Enterobacter, Streptococcus, Acinetobacter, and Halanaerobium spp. were abundant in Sufu samples. At the species level, Bacillus velezensis, Tetragenococcus halophilus, Lactobacillus rennini, Weissella cibaria, Weissella viridescens, Pseudomonas brenneri, and Lactobacillus acidipiscis represented the major species in Dajiang, while Halomonas sp., Staphylococcus equorum, and Halanaerobium praevalens were the predominant species in Sufu. Acetic acid and sucrose were found to be the primary major physicochemical factor influencing the bacterial communities in Dajiang and Sufu, respectively. Furthermore, Bacillus subtilis is strongly correlated with lactic acid levels, L. acidipiscis is positively correlated with acetic acid levels, while Staphylococcus sciuri and S. equorum are strongly, and positively, correlated with malic acid. Following analysis of carbohydrate and amino acid metabolism in all samples, cysteine and methionine metabolism, as well as fatty acid biosynthesis-related genes are upregulated in Dajiang compared to Sufu samples. However, such as the Staphylococcus, W. viridescens, and P. brenneri, as potentially foodborne pathogens, existed in Dajang and Sufu samples. Cumulatively, these results suggested that Dajiang and Sufu have unique bacterial communities that influence their specific characteristics. Hence, the current study provides insights into the microbial community composition in Dajiang and Sufu samples, which may facilitate the isolation of functional bacterial species suitable for Dajiang and Sufu production, thus improving their production efficiency.

Deciphering Bacterial Community Structure, Functional Prediction and Food Safety Assessment in Fermented Fruits Using Next-Generation 16S rRNA Amplicon Sequencing

Fermented fruits and vegetables play an important role in safeguarding food security world-wide. Recently, robust sequencing-based microbial community analysis platforms have improved microbial safety assessment. This study aimed to examine the composition of bacteria and evaluate the bacterial safety of fermented fruit products using high-throughput 16S-rRNA metagenomic analysis. The operational taxonomic unit-based taxonomic classification of DNA sequences revealed 53 bacterial genera. However, the amplicon sequencing variant (ASV)-based clustering revealed 43 classifiable bacterial genera. Taxonomic classifications revealed that the abundance of Sphingomonas, which was the predominant genus in the majority of tested samples, was more than 85–90% among the total identified bacterial community in most samples. Among these identified genera, 13 low abundance genera were potential opportunistic pathogens, including Acinetobacter, Bacillus, Staphylococcus, Clostridium, Klebsiella, Mycobacterium, Ochrobactrum, Chryseobacterium, Stenotrophomonas, and Streptococcus. Of these 13 genera, 13 major opportunistic pathogenic species were validated using polymerase chain reaction. The pathogens were not detected in the samples of different stages and the final products of fermentation, except in one sample from the first stage of fermentation in which S. aureus was detected. This finding was consistent with that of ASV-based taxonomic classification according to which S. aureus was detected only in the sample from the first stage of fermentation. However, S. aureus was not significantly correlated with the human disease pathways. These results indicated that fermentation is a reliable and safe process as pathogenic bacteria were not detected in the fermentation products. The hybrid method reported in this study can be used simultaneously to evaluate the bacterial diversity, their functional predictions and safety assessment of novel fermentation products. Additionally, this hybrid method does not involve the random detection of pathogens, which can markedly decrease the time of detection and food safety verification. Furthermore, this hybrid method can be used for the quality control of products and the identification of external contamination.

The change of water content and role of microbe in the sludge drying process

In this study, the pure terephthalic acid sludge was treated by a drying process which was an economical and environmentally method. The water change and metabolic pathways for bacterial community function prediction were analyzed. The microbial community changes were studied by high-throughput sequencing to draw the dynamic succession model. Then multiple statistics was used to determine the key factors of the reduction. The results showed that the main stage of water loss in the PTA sludge drying process was the high temperature period where the water lost by evaporation accounted for more than 90% of the total removal. The main metabolic pathways for bacterial community function were amino acid (7.72%-8.71% of Kyoto encyclopedia of genes and genomes relative abundance and 8.26%-9.51% of Cluster of orthologous groups of proteins relative abundance) and carbohydrate metabolism. The model describing the dynamic succession of microbial communities showed that the dominant bacteria changed from Nitrospira, Novosphingobium and Azohydromonas to Pseudomonas, Paeniglutamicibac and Pelotomaculum. The key factors for water loss were Gemmatimonas, Novosphingobium and Azohydromonas with the correlation coefficients of 0.887, 0.772, 0.783, respectively; the key factors for dry matter loss were Pelotomaculum, total organic matter, dissovlved organic carbon and carbon/nitrogen ratio; the key factors for toxic substance loss were Brevundimonas, Novosphingobium and Gemmatimonas. These results provided theoretical support for the application and demonstration for hazardous waste sludge reduction.

Integrative Metagenomics-Metabolomics for Analyzing the Relationship Between Microorganisms and Non-volatile Profiles of Traditional Xiaoqu

Xiaoqu, one of three traditional jiuqu in China, is a saccharifying and fermenting agent used in Xiaoqu jiu brewing, with different ingredient compositions and preparation techniques used in various regions. The yield and quality of Xiaoqu jiu are significantly affected by the metabolites and microbiota of Xiaoqu; however, the associated relationship remains poorly understood. This study aimed to analyze this relationship in three typical traditional Xiaoqu from the Guizhou province in China. The non-volatile metabolites of Xiaoqu were detected using gas chromatography time-of-flight mass spectrometry, whereas the classification and metabolic potential of the microbiota were investigated using metagenomic sequencing. Results show that Firmicutes, Proteobacteria, and Actinobacteria represent the dominant bacterial phyla, with Lactobacillus, Bacillus, Acinetobacter, Leuconostoc, and Weissella found to be the dominant bacterial genera. Meanwhile, Ascomycota, Mucoromycota, and Basidiomycota are the dominant fungal phyla with Aspergillus, Saccharomyces, Pichia, Rhizopus, and Phycomyces being the predominant fungal genera. Functional annotation of the microbiota revealed a major association with metabolism of carbohydrates, cofactors, and vitamins, as well as amino acids. A total of 39 significantly different metabolites (SDMs) were identified that are involved in 47 metabolic pathways, primarily that of starch and sucrose; glycine, serine, and threonine; glyoxylate and dicarboxylate; pyruvate; as well as biosynthesis of pantothenate and CoA. Further, based on Spearman's correlation analysis, Aspergillus, Saccharomyces, Lactobacillus, Acetobacter, Weissella, Pantoea, Desmospora, and Bacillus are closely correlated with production of physicochemical indexes and SDMs. Moreover, the metabolic network generated for the breakdown of substrates and formation of SDMs in Xiaoqu was found to primarily center on the metabolism of carbohydrates and the tricarboxylic acid cycle. These results provide insights into the functional microorganisms and metabolic patterns present in traditional Guizhou Xiaoqu and might guide researchers in the production of stable and efficient Xiaoqu in the future.