Metatranscriptomics reveals the gene functions and metabolic properties of the major microbial community during Chinese Sichuan Paocai fermentation

Metatranscriptomics reveals microbial community function succession and characteristic flavor formation mechanisms during black rice wine fermentation

Black rice wine (BRW) is a traditional Chinese rice wine with unique flavors; however, the formation pathways of flavor compounds driven by microbiota remain unclear. This study employed HPLC and GC-MS to reveal that during BRW fermentation, free amino acids increased sevenfold, volatile compounds doubled, and 28 key characteristic flavor compounds were identified. Metatranscriptomic analysis indicated that during fermentation, driven by physicochemical factors and microbial interactions, Saccharomyces gradually became the dominant active microorganism (relative abundance 87.01%-97.70%). Other dominant microorganisms (relative abundance >0.1%), including Saccharomycopsis, Pediococcus, Wickerhamomyces, and Weissella, significantly decreased. Meanwhile, the microflora's signature functions underwent succession: transcription early, carbohydrate metabolism mid-stage, and autophagy late. These microbial and functional successions facilitated the accumulation of flavor compounds. Metabolic network reconstruction revealed that Saccharomyces was pivotal in substrate degradation and flavor formation, while other dominant microorganisms actively promoted these processes. This study provides insights into regulating BRW's flavor through microorganisms.

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.

Spontaneous fermentation mitigates the frequency of genes encoding antimicrobial resistance spreading from the phyllosphere reservoir to the diet

The phyllosphere microbiome of vegetable products constitutes an important reservoir for multidrug resistant bacteria and Antibiotic Resistance Genes (ARG). Vegetable products including fermented products such as Paocai therefore may serve as a shuttle for extrinsic microorganisms with ARGs into the gut of consumers. Here we study the effect of fermentation on Paocai ARG dissemination by metagenomic analysis. Microbial abundance and diversity of the Paocai microbiome were diminished during fermentation, which correlated with the reduction of abundance in ARGs. Specifically, as fermentation progressed, Enterobacterales overtook Pseudomonadales as the predominant ARG carriers, and Lactobacillales and Enterobacteriales became the determinants of Paocai resistome variation. Moreover, the dual effect of microbes and metal resistance genes (MRGs) was the major contributor driving Paocai resistome dynamics. We recovered several metagenome-assembled genomes (MAGs) carrying acquired ARGs in the phyllosphere microbiome. ARGs of potential clinical and epidemiological relevance such as tet M and emrB-qacA, were mainly hosted by non-dominant bacterial genera. Overall, our study provides evidence that changes in microbial community composition by fermentation aid in constraining ARG dispersal from raw ingredients to the human microbiome but does not eliminate them.

Integrated metatranscriptomics and metabolomics reveal microbial succession and flavor formation mechanisms during the spontaneous fermentation of Laotan Suancai

Laotan Suancai, a Chinese traditional fermented vegetable, possesses a unique flavor that depends on the fermentative microbiota. However, the drivers of microbial succession and the correlation between flavor and active microbiota remain unclear. A total of 21 characteristic flavor metabolites were identified in Laotan Suancai by metabolomics, including 8 sulfides, 6 terpenes, 3 organic acids, 2 isothiocyanates, 1 ester, and 1 pyrazine. Metatranscriptome analysis revealed variations in the active microbiota at different stages of fermentation, and further analysis indicated that organic acids were the primary drivers of microbial succession. Additionally, we reconstructed the metabolic network responsible for the formation of characteristic flavor compounds and identified Companilactobacillus alimentarius, Weissella cibaria, Lactiplantibacillus plantarum, and Loigolactobacillus coryniformis as the core functional microbes involved in flavor development. This study contributed to profoundly understanding the relationship between the active microbiota and flavor quality formation, as well as the targeted selection of starters with flavor regulation abilities.

Influences of Growth Stage and Ensiling Time on Fermentation Characteristics, Nitrite, and Bacterial Communities during Ensiling of Alfalfa

This study examined the impacts of growth stage and ensiling duration on the fermentation characteristics, nitrite content, and bacterial communities during the ensiling of alfalfa. Harvested alfalfa was divided into two groups: vegetative growth stage (VG) and late budding stage (LB). The fresh alfalfa underwent wilting until reaching approximately 65% moisture content, followed by natural fermentation. The experiment followed a completely randomized design, with samples collected after the wilting of alfalfa raw materials (MR) and on days 1, 3, 5, 7, 15, 30, and 60 of fermentation. The growth stage significantly influenced the chemical composition of alfalfa, with crude protein content being significantly higher in the vegetative growth stage alfalfa compared to that in the late budding stage (p < 0.05). Soluble carbohydrates, neutral detergent fiber, and acid detergent fiber content were significantly lower in the vegetative growth stage compared to the late budding stage (p < 0.05). Nitrite content, nitrate content, nitrite reductase activity, and nitrate reductase activity were all significantly higher in the vegetative growth stage compared to the late budding stage (p < 0.05). In terms of fermentation parameters, silage from the late budding stage exhibited superior characteristics compared to that from the vegetative growth stage. Compared to the alfalfa silage during the vegetative growth stage, the late budding stage group exhibited a higher lactate content and lower pH level. Notably, butyric acid was only detected in the silage from the vegetative growth stage group. Throughout the ensiling process, nitrite content, nitrate levels, nitrite reductase activity, and nitrate reductase activity decreased in both treatment groups. The dominant lactic acid bacteria differed between the two groups, with Enterococcus being predominant in vegetative growth stage alfalfa silage, and Weissella being predominant in late budding stage silage, transitioning to Lactiplantibacillus in the later stages of fermentation. On the 3rd day of silage fermentation, the vegetative growth stage group exhibited the highest abundance of Enterococcus, which subsequently decreased to its lowest level on the 15th day. Correlation analysis revealed that lactic acid bacteria, including Limosilactobacillus, Levilactobacillus, Loigolactobacillus, Pediococcus, Lactiplantibacillus, and Weissella, played a key role in nitrite and nitrate degradation in alfalfa silage. The presence of nitrite may be linked to Erwinia, unclassified_o__Enterobacterales, Pantoea, Exiguobacterium, Enterobacter, and Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium.

Metabolomics and metatranscriptomics reveal the influence mechanism of endogenous microbe (Staphylococcus succinus) inoculation on the flavor of fermented chili pepper

This study integrated metabolomic and metatranscriptomic techniques to examine how the endogenous microbe, Staphylococcus succinus, influenced the essential flavor of fermented chili peppers. The mechanisms governing spontaneous fermentation and S. succinus-inoculated fermentation were also elucidated. Esters (e.g., ethyl undecanoate, isoamyl acetate, and methyl salicylate), terpenes (e.g., terpinen-4-ol), and alcohols (e.g., α-terpineol, linalool, and 4-methyl-3-heptanol) were found to be the key aroma-active compounds, aspartic acid (Asp) and glutamic acid (Glu) were identified as primary flavoring free amino acids. Notably, during the early stages of S. succinus-inoculated fermentation, the production of these essential metabolites was abundant, while their gradual increase over time was observed in the case of spontaneous fermentation. Metatranscriptomic analysis revealed that S. succinus inoculation could up-regulate genes related to glycolysis, amino acid metabolism, and aroma compound synthesis. These changes sequentially boosted the production of sweet and umami free amino acids, enhanced organic acid levels, increased unique aroma compound generation, and further improved the flavor and quality of the fermented chili peppers. Therefore, S. succinus inoculation can augment the sensory quality of fermented chili peppers, making this strain a promising candidate for Sichuan pickle fermentation starters.

Meta-analysis of microbiomes reveals metagenomic features of fermented vegetables

An insightful exploration of the fermented vegetable microbiome is the key to improving food quality and sustainability. Based on 57 fermented vegetable samples from China, Ireland, the UK, and Germany retrieved from public genome databases, we conducted a high-resolution meta-analysis of the fermented vegetable microbiomes. There were significant differences in the microbiota composition and functional pathway diversity of the tested samples, as reflected by the differences in their geographical origins. Metagenomic analysis also revealed the metagenomic features of carbohydrate-active enzymes and antibiotic resistance genes in the fermented vegetable metagenomes. Five putative new species were detected by recovering 221 metagenome-assembled genomes belonging to the genera Rubrobacteraceae, Bifidobacteriaceae, and Ruminococcaceae. Our results provide new ecological insights into the implications of fermented vegetable microbiota composition and functional potential and highlight the importance of high-resolution metagenomic analysis to further investigate the fermented food microbiome.

Microbial Diversity of Anaerobic-Fermented Coffee and Potential for Inhibiting Ochratoxin-Produced Aspergillus niger

Coffee flavor considerably depends on the fermentation process, with contributing factors including fermentation temperature, oxygen concentration, and microbial diversity. Efficient controlling of the fermentation can improve the quality of coffee beverages. Therefore, several studies on coffee fermentation processes have been conducted in various regions. The objective of this study was to assess the microbial diversity of coffee beans undergoing anaerobic fermentation at various temperatures (4 °C or 37 °C) and fermentation durations (12 h or 36 h) using full-length 16S rRNA sequencing. This analysis aimed to evaluate the inhibitory effects of the fermented metabolites against ochratoxin-producing Aspergillus niger. From our results, Acetobacter was identified as the dominant microbial community at higher fermentation temperatures, whereas Leuconostoc and Gluconobacter were the dominant genera at lower temperatures. However, at lower temperatures, changes in microbial communities were relatively slow. This study expands our knowledge of the microbial diversity involved in the anaerobic fermentation of coffee beans in Taiwan. The findings of this study can be used in future research to cultivate microorganisms linked to the quality and improve the quality of coffee beverages through fermentation.

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.

Bacteria and filamentous fungi running a relay race in Daqu fermentation enable macromolecular degradation and flavor substance formation

As the saccharifying and fermentative agent, medium-temperature Daqu (MT-Daqu) plays an irreplaceable role in the production of strong-flavor Baijiu. Numerous studies have focused on the microbial community structure and potential functional microorganisms, however, little is known about the succession of active microbial community and the formation mechanism of community function during MT-Daqu fermentation. In this study, we presented an integrated analysis of metagenomics, metatranscriptomics, and metabonomics covering the whole fermentation process of MT-Daqu to reveal the active microorganisms and their participations in metabolic networks. The results showed that dynamic of metabolites were time-specific, and the metabolites and co-expressed active unigenes were further classified into four clusters according to their accumulation patterns, with members within each cluster displaying a uniform and clear pattern of abundance across fermentation. Based on KEGG enrichment analysis in co-expression clusters and succession of active microbial community, we revealed that Limosilactobacillus, Staphylococcus, Pichia, Rhizopus, and Lichtheimia were metabolically active members at the early stage, and their metabolic activities were conducive to releasing abundant energy to drive multiple basal metabolisms such as carbohydrates and amino acids. Thereafter, during the high temperature period and at the end of fermentation, multiple heat-resistant filamentous fungi were transcriptionally active populations, and they acted as both the saccharifying agents and flavor compound producers, especially aromatic compounds, suggesting their crucial contribution to enzymatic activity and aroma of mature MT-Daqu. Our findings revealed the succession and metabolic functions of the active microbial community, providing a deeper understanding of their contribution to MT-Daqu ecosystem.

Metatranscriptomics Reveals Sequential Expression of Genes Involved in the Production of Melanogenesis Inhibitors by the Defined Microbial Species in Fermented Unpolished Black Rice

Fermented products require metabolic enzymes from the microbial community for desired final products. Using a metatranscriptomic approach, the role of microorganisms in fermented products on producing compounds with a melanogenesis inhibition activity has not yet been reported. Previously, unpolished black rice (UBR) fermented with the E11 starter containing Saccharomyces cerevisiae, Saccharomycopsis fibuligera, Rhizopus oryzae, and Pediococcus pentosaceus (FUBR) showed potent melanogenesis inhibition activity. This study aimed to investigate the function of these defined microbial species in producing melanogenesis inhibitors in the FUBR using a metatranscriptomic approach. The melanogenesis inhibition activity increased in a fermentation time-dependent manner. Genes related to melanogenesis inhibitors synthesis such as carbohydrate metabolism, amino acids synthesis, fatty acids/unsaturated fatty acids synthesis, and carbohydrate transporters were analyzed. Most genes from R. oryzae and P. pentosaceus were upregulated in the early stage of the fermentation process, while those of S. cerevisiae and S. fibuligera were upregulated in the late stage. FUBR production using different combinations of the four microbial species shows that all species were required to produce the highest activity. The FUBR containing at least R. oryzae and/or P. pentosaceus exhibited a certain level of activity. These findings were in agreement with the metatranscriptomic results. Overall, the results suggested that all four species sequentially and/or coordinately synthesized metabolites during the fermentation that led to a FUBR with maximum melanogenesis inhibition activity. This study not only sheds light on crucial functions of certain microbial community on producing the melanogenesis inhibitors, but also paves the way to initiate quality improvement of melanogenesis inhibition activity in the FUBR. IMPORTANCE Fermentation of food is a metabolic process through the action of enzymes from certain microorganisms. Although roles of the microbial community in the fermented food were investigated using metatranscriptomic approach in terms of flavors, but no study has been reported so far on the function of the microorganisms on producing compounds with a melanogenesis inhibition activity. Therefore, this study explained the roles of the defined microorganisms from the selected starter in the fermented unpolished black rice (FUBR) that can produce melanogenesis inhibitor(s) using metatranscriptomic analysis. Genes from different species were upregulated at different fermentation time. All four microbial species in the FUBR sequentially and/or coordinately synthesized metabolites during fermentation that led to a FUBR with maximal melanogenesis inhibition activity. This finding contributes to a deeper understanding of the roles of certain microbial community during fermentation and led to the knowledge-based improvement for the fermented rice with potent melanogenesis inhibition activity.

Impact of Inoculating with Indigenous Bacillus marcorestinctum YC-1 on Quality and Microbial Communities of Yibin Yacai (Fermented Mustard) during the Fermentation Process

Bacillus species play an important role in improving the quality of some fermented foods and are also one of the dominant bacteria in Yibin Yacai (fermented mustard). However, little is known about their effects on the quality of Yibin Yacai. Here, the effect of Bacillus marcorestinctum YC-1 on the quality and microbial communities of Yibin Yacai during the fermentation process was investigated. Results indicated that the inoculation of Bacillus marcorestinctum YC-1 promoted the growth of Weissella spp. and Lactobacillus spp. and inhibited the growth of pathogens, accelerating the synthesis of free amino acids and organic acids and the degradation of nitrite. Furthermore, inoculating Yibin Yacai with YC-1 could effectively enhance the synthesis of alcohols and terpenoids in yeasts, thus producing more linalool, terpinen-4-ol, and α-muurolen in Yibin Yacai, and endowing it with pleasant floral, fruity, woody, and spicy aromas. These findings reveal that the inoculation of B. marcorestinctum YC-1 can improve the quality and safety of Yibin Yacai by changing microbial communities as fermentation proceeds.

Effects of post-fermentation on the flavor compounds formation in red sour soup

Red Sour Soup (RSS) is a traditional fermented food in China. After two rounds of fermentation, sour soup has a mellow flavor. However, the microbial composition and flavor formation processes in post-fermentation in RSS are unclear. This study investigates the bacteria composition of RSS during the post-fermentation stage (0–180 days) using high-throughput sequencing. The results show that lactic acid bacteria (LAB) are dominant during the post-fermentation process, and their abundance gradually increases with fermentation time. Additionally, gas chromatography-mass spectrometry was used to detect volatile flavor compounds in the post-fermentation process. Seventy-seven volatile flavor compounds were identified, including 24 esters, 14 terpenes, 9 aromatic hydrocarbons, 9 alkanes, 6 heterocyclic compounds, 3 alcohols, 3 acids, 3 ketones, 2 phenols, 2 aldehydes, 1 amine, and 1 other. Esters and aromatic hydrocarbons are the main volatile compounds in RSS during the post-fermentation process. Orthogonal partial least squares screening and correlation analysis derived several significant correlations, including 48 pairs of positive correlations and 19 pairs of negative correlations. Among them, Acetobacter spp., Clostridium spp. and Sporolactobacillus spp. have 15, 14, 20 significant correlation pairs, respectively, and are considered the most important bacterial genera post-fermentation. Volatile substances become abundant with increasing fermentation time. LAB are excessive after more than 120 days but cause a drastic reduction in volatile ester levels. Thus, the post-fermentation time should be restricted to 120 days, which retains the highest concentrations of volatile esters in RSS. Overall, these findings provide a theoretical basis to determine an optimal post-fermentation time duration, and identify essential bacteria for manufacturing high-quality starter material to shorten the RSS post-fermentation processing time.

Metatranscriptomic and metataxonomic insights into the ultra-small microbiome of the Korean fermented vegetable, kimchi

Presently, pertinent information on the ultra-small microbiome (USM) in fermented vegetables is still lacking. This study analyzed the metatranscriptome and metataxonome for the USM of kimchi. Tangential flow filtration was used to obtain a USM with a size of 0.2 μm or less from kimchi. The microbial diversity in the USM was compared with that of the normal microbiome (NM). Alpha diversity was higher in the USM than in NM, and the diversity of bacterial members of the NM was higher than that of the USM. At the phylum level, both USM and NM were dominated by Firmicutes. At the genus level, the USM and NM were dominated by Lactobacillus, Leuconostoc, and Weissella, belonging to lactic acid bacteria. However, as alpha diversity is higher in the USM than in the NM, the genus Akkermansia, belonging to the phylum Verrucomicrobia, was detected only in the USM. Compared to the NM, the USM showed a relatively higher ratio of transcripts related to “protein metabolism,” and the USM was suspected to be involved with the viable-but-nonculturable (VBNC) state. When comparing the sub-transcripts related to the “cell wall and capsule” of USM and NM, USM showed a proportion of transcripts suspected of being VBNC. In addition, the RNA virome was also identified, and both the USM and NM were confirmed to be dominated by pepper mild mottle virus (PMMoV). Additionally, the correlation between metataxonome and metatranscriptome identified USM and NM was estimated, however, only limited correlations between metataxonome and metatranscriptome were estimated. This study provided insights into the relationship between the potential metabolic activities of the USM of kimchi and the NM.

Microbial succession and exploration of higher alcohols-producing core bacteria in northern Huangjiu fermentation

Higher alcohols (HAs) are abundant compounds that provide important flavors in Huangjiu, but they also cause hangover. Previous studies have shown the production of HAs to be related to yeast, but the correlations between HAs and other microorganisms are rarely reported. In this study, we detected changes in levels of HAs and microbial dynamics during the Huangjiu fermentation process. Relationships were characterized using Pearson’s correlation coefficient. The functional core HA-producing bacteria were selected by bidirectional orthogonal partial least squares (O2PLS). The result showed that 2-methyl-1-propanol, phenethyl alcohol and 3-methyl-1-butanol were the principle HAs present at high levels. Lactococcus and Saccharomyces were predominant at the genus level of bacteria and fungi, respectively. A total of 684 correlations between HAs and microorganisms were established. Five genera were screened as functional core HA-producing bacteria. Our findings might provide some new inspiration for controlling the content of HAs, enhancing international prestige and market expansion of Huangjiu.

Transcriptome and protein networks to elucidate the mechanism underlying nitrite degradation by Lactiplantibacillus plantarum

Excessive nitrite residue is one of the bottlenecks in the production of many fermented foods. Lactiplantibacillus plantarum PK25 obtained from traditional Chinese pickles exhibited excellent nitrite degradation ability. Here, transcriptome, protein-protein interaction networks, and phenotype were performed to evaluate systematically the mechanism of nitrite degradation of L. plantarum PK25. The results demonstrated that genes expression varied considerably at key time points for nitrite degradation. 553 (upregulated: 366, downregulated: 187) and 767 (upregulated: 425, downregulated: 342) differentially expressed genes were identified at 6 h and 24 h, respectively. The hub genes were mainly enriched in carbohydrate metabolism, energy metabolism, and nucleotide synthesis. PK25 expanded its carbon source utilizing profile and improved glycolysis to produce more ATP to counteract environmental stress. The related enzymes including glycoside hydrolase, sugar ABC transporter protein, and PTS sugar transporter were 5.714, 5.885, and 3.578-fold upregulated at the transcriptional level. For strain to sustain energy levels and acid generation, pyruvate metabolism was critical, with the result that phosphoenolpyruvate synthase and pyruvate oxidase were up-regulated to accelerate the pyruvate transition. To repair DNA lesions induced by nitrite, both base excision repair mechanism and recombinational DNA repair pathway were exploited, such as endodeoxyribonuclease upregulated 5.314 and 19.687-fold at the two moments. The results provided a theoretical reference and practical possibility to reduce nitrite residue and improve safety during food fermented products.

Global genome and comparative transcriptomic analysis reveal the inulin consumption strategy of Lactiplantibacillus plantarum QS7T

Sichuan pickle is a natural combination of probiotics and dietary fibers, in which a strain Lactiplantibacillus plantarum QS7T was found to be capable of efficiently metabolizing inulin. However, the underlying molecular mechanism of inulin consumption by the strain QS7T is unclear. Therefore, this study firstly investigated the metabolic characteristics of inulin in the strain QS7T, and the results showed it could grow very well on the medium containing inulin as a carbon source (maximum OD_{600 nm}, 1.891 ± 0.028) and degrade both short-chain oligofructose and long-chain fructan components through thin layer chromatography analysis. Genomic sequencing and analysis revealed a high percentage of functional genes associated with carbohydrate transport and metabolism, particularly glycoside hydrolase (GH) genes responsible for hydrolysing carbohydrates, within the genome of the strain QS7T. Furthermore, comparative transcriptomic analysis of L. plantarum QS7T in response to inulin or glucose indicated that functional genes associated with inulin consumption including several genes encoding PTS sugar transporters and two predicted GH32 family genes encoding beta-fructofuranosidase and beta-fructosidase were significantly up-regulated by inulin compared to the gene expression on glucose. In conclusion, we obtained a mechanistic understanding of interplay between probiotic L. plantarum QS7T derived from Sichuan pickle and natural dietary fiber, inulin; totally two operons including a sacPTS1 operon responsible for metabolizing short-chain oligofructose primarily in the cytoplasm and a fos operon responsible for extracellularly degrading all moderate and long-chain fructan components linked to inulin consumption by L. plantarum QS7T.

Next-Generation Food Research: Use of Meta-Omic Approaches for Characterizing Microbial Communities Along the Food Chain

Microorganisms exist along the food chain and impact the quality and safety of foods in both positive and negative ways. Identifying and understanding the behavior of these microbial communities enable the implementation of preventative or corrective measures in public health and food industry settings. Current culture-dependent microbial analyses are time-consuming and target only specific subsets of microbes. However, the greater use of culture-independent meta-omic approaches has the potential to facilitate a thorough characterization of the microbial communities along the food chain. Indeed, these methods have shown potential in contributing to outbreak investigation, ensuring food authenticity, assessing the spread of antimicrobial resistance, tracking microbial dynamics during fermentation and processing, and uncovering the factors along the food chain that impact food quality and safety. This review examines the community-based approaches, and particularly the application of sequencing-based meta-omics strategies, for characterizing microbial communities along the food chain. Expected final online publication date for the Annual Review of Food Science and Technology, Volume 13 is March 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Antibiotic Resistance Characterization of Bacteria Isolated from Traditional Chinese Paocai

In this work, the antibiotic resistance of 218 isolates to 9 different antibiotics was analyzed with minimum inhibitory concentration method. All Lactobacillus pentosus strains were found to be resistant to streptomycin sulfate and ciprofloxacin hydrochloride. Lactococcus lactis strains were resistant to streptomycin sulfate. Specifically, 90% Klebsiella oxytoca and all Citrobacter freundii strains were resistant to ampicillin sodium. 30% K. oxytoca strains were resistant to ciprofloxacin hydrochloride. All Bacillus albus strains were resistant to erythromycin and 80% strains were resistant to ampicillin sodium. Results from PCR analysis revealed that 90 isolates carried the aadE gene. The tetM gene was detected in four L. pentosus isolates. And the streptomycin resistant gene aadA was detected in one L. pentosus isolate. Metagenome analysis revealed that 74.7% genes associated with antibiotic resistance were antibiotic resistance genes. The tetM and aadA genes, detected in PCR analysis, were also retrieved from the paocai metagenome. In brief, this study generated the antibiotic resistance profile of some paocai-originated bacteria strains. L. pentosus found in the final edible paocai were inherently resistant to antibiotics, such as streptomycin and ciprofloxacin. Results in this work reminds us to carefully choose the LAB strains for traditional Chinese paocai production to avoid potential spreading of antibiotic resistant genes.