Metagenomic and metatranscriptomic analysis of the microbial community structure and metabolic potential of fermented soybean in Yunnan Province

Metatranscriptomics for Understanding the Microbiome in Food and Nutrition Science

Microbiome science has greatly expanded our understanding of the diverse composition and function of gut microorganisms over the past decades. With its rich microbial composition, the microbiome hosts numerous functionalities essential for metabolizing food ingredients and nutrients, resulting in the production of active metabolites that affect food fermentation or gut health. Most of these processes are mediated by microbial enzymes such as carbohydrate-active enzymes and amino acid metabolism enzymes. Metatranscriptomics enables the capture of active transcripts within the microbiome, providing invaluable functional insights into metabolic activities. Given the inter-kingdom complexity of the microbiome, metatranscriptomics could further elucidate the activities of fungi, archaea, and bacteriophages in the microbial ecosystem. Despite its potential, the application of metatranscriptomics in food and nutrition sciences remains limited but is growing. This review highlights the latest advances in food science (e.g., flavour formation and food enzymology) and nutrition science (e.g., dietary fibres, proteins, minerals, and probiotics), emphasizing the integration of metatranscriptomics with other technologies to address key research questions. Ultimately, metatranscriptomics represents a powerful tool for uncovering the microbiome activity, particularly in relation to active metabolic processes.

Analysis on microbial communities and characteristic flavor metabolic of PXDB-meju by partially substituting wheat flour with soybean flour and gluten flour

Pixian Douban (PXDB) is one of the most popular condiments in China due to its unique flavor. Wheat flour that contains abundant nutrients is an important raw material in producing flavors during PXDB fermentation. In this study, wheat flour was substituted with soybean flour and gluten flour that have higher proteins in portions of 10.4% and 4.2% (F1), 8.9% and 7.2% (F2), 9.6% and 5.8% (F3). The results indicated that the substitutions increased the amino acid nitrogen content and improved flavor quality compared with traditional group (CT). Especially, the key amino acids including spartate, glutamic, arginine and lysine, and the phenylacetaldehyde as one of the most important volatile compounds exhibited preferable higher contents in F2 group than those in CT group. Metagenomic analysis showed that the abundances of predominant bacteria, including Kosakonia_cowanii, unclassified_f__Enterobacteriaceae and unclassified_g__Enterobacter, were higher in the F2 compared to the CT. Lupinus_albus and Plutella_xylostella were the top two fungi in relative abundance, with higher growth rates in F2 than in CT. Furthermore, metabolism pathway analysis revealed higher relative abundance of enzymes producing key amino acids and phenethylaldehyde in the F2 compared to the CT. Meanwhile, these enzymes were exclusively annotated to the Kosakonia_cowanii, Bacillus_velezensis and Escherichia_coli in F2. This study provided a theoretical foundation for improving PXDB flavor quality in industry production.

Fermentative metabolic features of doenjang-meju as revealed by genome-centered metatranscriptomics

Fermentative features of doenjang-meju, a traditional Korean soybean brick, were investigated over 45 days via genome-centered metatranscriptomics. The pH value rapidly decreased within 10 days and successively increased after 20 days, along with an initial bacterial growth, including lactic acid bacteria, and subsequent fungal growth, suggesting their association. Polysaccharides and lipids underwent degradation, and amino acids, free sugars, and organic acids increased during the early stage. Metagenome analysis identified Aspergillus, Bacillus, Enterococcus, Staphylococcus, and Leuconostoc as major microbes, which were isolated and genome-sequenced. Metatranscriptomic analysis revealed the major roles of Bacillus and Enterococcus during the early period, shifting to Aspergillus dominance after 10 days. Metabolic pathway reconstruction and transcriptional analysis reveal that Aspergillus primarily decomposed polysaccharides to free sugars; Aspergillus and Bacillus metabolized lipids, free sugars, and organic acids generated by Enterococcus; and Aspergillus and Bacillus were instrumental in amino acid metabolism: their contributions varied by compounds and pathways.

The Rising Role of Omics and Meta-Omics in Table Olive Research

Table olives are often the result of fermentation, a process where microorganisms transform raw materials into the final product. The microbial community can significantly impact the organoleptic characteristics and safety of table olives, and it is influenced by various factors, including the processing methods. Traditional culture-dependent techniques capture only a fraction of table olives' intricate microbiota, prompting a shift toward culture-independent methods to address this knowledge gap. This review explores recent advances in table olive research through omics and meta-omics approaches. Genomic analysis of microorganisms isolated from table olives has revealed multiple genes linked to technological and probiotic attributes. An increasing number of studies concern metagenomics and metabolomics analyses of table olives. The former offers comprehensive insights into microbial diversity and function, while the latter identifies aroma and flavor determinants. Although proteomics and transcriptomics studies remain limited in the field, they have the potential to reveal deeper layers of table olives' microbiome composition and functionality. Despite the challenges associated with implementing multi-omics approaches, such as the reliance on advanced bioinformatics tools and computational resources, they hold the promise of groundbreaking advances in table olive processing technology.

Applications of multi-omics techniques to unravel the fermentation process and the flavor formation mechanism in fermented foods

Fermented foods are important components of the human diet. There is increasing awareness of abundant nutritional and functional properties present in fermented foods that arise from the transformation of substrates by microbial communities. Thus, it is significant to unravel the microbial communities and mechanisms of characteristic flavor formation occurring during fermentation. There has been rapid development of high-throughput and other omics technologies, such as metaproteomics and metabolomics, and as a result, there is growing recognition of the importance of integrating these approaches. The successful applications of multi-omics approaches and bioinformatics analyses have provided a solid foundation for exploring the fermentation process. Compared with single-omics, multi-omics analyses more accurately delineate microbial and molecular features, thus they are more apt to reveal the mechanisms of fermentation. This review introduces fermented foods and an overview of single-omics technologies - including metagenomics, metatranscriptomics, metaproteomics, and metabolomics. We also discuss integrated multi-omics and bioinformatic analyses and their role in recent research progress related to fermented foods, as well as summarize the main potential pathways involved in certain fermented foods. In the future, multilayered analyses of multi-omics data should be conducted to enable better understanding of flavor formation mechanisms in fermented foods.

In silico metatranscriptomic approach for tracking biofilm-related effectors in dairies and its importance for improving food safety

Sessile microorganisms are usually recalcitrant to antimicrobial treatments, and it is possible that finding biofilm-related effectors in metatranscriptomics datasets helps to understand mechanisms for bacterial persistence in diverse environments, by revealing protein-encoding genes that are expressed in situ. For this research, selected dairy-associated metatranscriptomics bioprojects were downloaded from the public databases JGI GOLD and NCBI (eight milk and 45 cheese samples), to screen for sequences encoding biofilm-related effectors. Based on the literature, the selected genetic determinants were related to adhesins, BAP, flagellum-related, intraspecific QS (AHL, HK, and RR), interspecific QS (LuxS), and QQ (AHL-acylases, AHL-lactonases). To search for the mRNA sequences encoding for those effector proteins, a custom database was built from UniprotKB, yielding 1,154,446 de-replicated sequences that were indexed in DIAMOND for alignment. The results revealed that in all the dairy-associated metatranscriptomic datasets obtained, there were reads assigned to genes involved with flagella, adhesion, and QS/QQ, but BAP-reads were found only for milk. Significant Pearson correlations (p < 0.05) were observed for transcripts encoding for flagella, RR, histidine kinases, adhesins, and LuxS, although no other significant correlations were found. In conclusion, the rationale used in this study was useful to demonstrate the presence of biofilm-associated effectors in metatranscriptomics datasets, pointing out to possible regulatory mechanisms in action in dairy-related biofilms, which could be targeted in the future to improve food safety.

Assessing the geographical distribution of 76 Dendrobium species and impacts of climate change on their potential suitable distribution area in China

The geographical distribution of plant resources is of great significance for studying the origin, distribution, and evolution of species. Climate and geographical factors help shape the distribution of plant species. Dendrobium is a commonly used traditional medicine and a precious economic crop in China. Owing to the over-exploitation and increasing medicinal demand of Dendrobium species plants, systematic investigation of the geographical distribution of the plants and analysis of their potential distribution under climate change are important for protecting Dendrobium plants. We adopted DIVA-GIS to analyze the georeferenced records of 76 species of the Dendrobium species collected from 2166 herbarium records. We analyzed the eco-geographical distribution and species richness of the genus Dendrobium to simulate the distribution of current and future scenarios using MaxEnt. The results revealed the distribution of Dendrobium in 30 provinces of China, with species abundance in Yunnan, Guangxi, Guangdong, and Hainan. Our model identified the following bioclimatic variables: precipitation in the driest months and the warmest seasons, isothermality, and range of annual temperature. Among them, annual precipitation is the most crucial bioclimatic variable affecting the distribution of 16 selected Dendrobium species. The change of climate in the future will lead to an increase in habitat suitability for some Dendrobium species as follows: D. officinal 2.12%, D. hancockii by 6.00%, D. hercoglossum by 8.25%, D. devonianum by 7.71%, D. henryi by 9.40%, and D. hainanense by 13.70%. By contrast, habitat suitability will dramatically decrease for other Dendrobium species: D. chrysotoxum by 0.89%, D. chrysanthum by 12.68%, D. fimbriatum by 5.07%, D. aduncum by 11.44%, D. densiflorum by 18.47%, D. aphyllum by 8.05%, D. loddigesii by 16.45%, D. nobile by 5.41%, D. falconeri by 8.73%, and D. moniliforme by 10.61%. The reduction of these species will be detrimental to the medicinal and economic value of the genus Dendrobium. Therefore, targeted development and reasonable management strategies should be adopted to conserve these valuable resources.

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.

Metabolic Features of Ganjang (a Korean Traditional Soy Sauce) Fermentation Revealed by Genome-Centered Metatranscriptomics

The taste and quality of soy sauce, a fermented liquid condiment popular worldwide, is greatly influenced by microbial metabolism during fermentation. To investigate the fermentative features of ganjang (a Korean traditional soy sauce), ganjang batches using meju (fermented soybean) bricks and solar salts were prepared, and organic compounds, microbial communities, metagenomes, and metatranscriptomes of ganjang were quantitively analyzed during fermentation. Polymeric compound analysis in the ganjang treated with/without microbial inhibitors revealed that indigenous enzymes of meju bricks might be primarily responsible for degrading polymeric compounds. Through metagenome binning and microbe sequencing, 17 high-quality genome sequences representing all major ganjang microbiota were obtained, and their transcriptional expressions were quantitatively analyzed by mapping metatranscriptome reads normalized by spike-in RNA sequencing to the 17 genomes, which revealed that microbial metabolism might primarily occur while meju bricks are in the ganjang solution and decrease significantly after the removal of meju bricks. Metabolic pathways for carbohydrates, proteins, and lipids of the major ganjang microbiota were reconstructed, and their metabolic genes were transcriptionally analyzed, revealing that facultative lactic acid fermentation by Tetragenococcus was the major fermentation process active in the ganjang fermentation and that aerobic respiration by facultatively aerobic bacteria such as Chromohalobacter, Halomonas, and Marinobacter was also an important metabolic process during fermentation. Although the abundances of Fungi and the corresponding transcriptional expression levels were generally much lower than those of Bacteria, our analysis suggests that yeasts such as Debaryomyces and Wickerhamomyces might be in large part responsible for producing biogenic amines and flavors.

IMPORTANCE The taste and quality of soy sauce, a popular fermented liquid condiment worldwide, is greatly influenced by microbial metabolism during fermentation. Spontaneous fermentation of ganjang (a Korean traditional soy sauce) in a nonsterile environment leads to the growth of diverse bacteria and fungi during fermentation, making it difficult to understand the mechanism of ganjang fermentation. Genome-centered metatranscriptomic analysis, combined with organic compound analysis, quantitative metagenome and metatranscriptome analyses, and metabolic pathway reconstruction and expressional analysis of the major ganjang microbiota during fermentation, would provide comprehensive insights into the metabolic features of ganjang fermentation.

Traditional uses, chemical constituents, pharmacological activities, and toxicological effects of Dendrobium leaves: A review

ETHNOPHARMACOLOGICAL RELEVANCE

In China, shi hu (stems of Dendrobium chrysotoxum Lindl, D. fimbriatum Hook. D. huoshanense Z.Z. Tang & S.J. Cheng, or D. nobile Lindl) and tie pi shi hu (stems of D. officinale Kimura et Migo) are famous traditional medicines and are listed in the Chinese Pharmacopoeia. However, the leaves of these Dendrobium plants are largely discarded.

AIM OF THE STUDY

To better utilize Dendrobium leaves, we summarize their traditional uses, chemical constituents, pharmacological activities, and toxicological effects.

MATERIALS AND METHODS

"Orchidaceae", "Dendrobium", "leaf", "traditional use", and "ethnobotany" were used as search terms to screen the literature. Cited references were collected between 1960 and 2020 from the Web of Science, China National Knowledge Internet (CNKI), SciFinder, and Google Scholar, primarily in English and Chinese.

RESULTS

Traditional uses of leaves from 16 Dendrobium species were identified in the literature. The major uses of Dendrobium leaves include treatments for dermatologic disorders, metabolic syndromes, nervous system disorders, and musculoskeletal system disorders. More than 50 chemical compounds have been identified in the leaves of 10 Dendrobium species, which primarily include flavonoids, bibenzyls, coumarins, N-containing compounds, and polysaccharides. Antihyperlipidemia, antihypertensive, antihyperuricemia, anti-inflammatory, antimicrobial, antioxidant, cytotoxic and antitumor, hepatoprotective, immunomodulatory, lipase-inhibitory, and/or tyrosinase-inhibitory activities have been reported for the leaves of six Dendrobium species. D. officinale leaves have been shown to exhibit no reproductive toxicity against male rats, while D. speciosum Sm. leaves have been observed to exhibit slight genotoxicity in an in vitro study. Among Dendrobium species, D. officinale leaves are the most widely studied.

CONCLUSIONS

D. officinale leaves represent a good example of the utilization of leaf resources of the Dendrobium genus. In the future, more extensive research for the development of Dendrobium leaves is needed.

Viruses in fermented foods: are they good or bad? Two sides of the same coin

The emergence of Coronavirus disease 2019 as a global pandemic has increased popular concerns about diseases caused by viruses. Fermented foods containing high loads of viable fungi and bacteria are potential sources for virus contamination. The most common include viruses that infect bacteria (bacteriophage) and yeasts reported in fermented milks, sausages, vegetables, wine, sourdough, and cocoa beans. Recent molecular studies have also associated fermented foods as vehicles for pathogenic human viruses. Human noroviruses, rotavirus, and hepatitis virus have been identified in different fermented foods through multiple routes. No severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) virus or close members were found in fermented foods to date. However, the occurrence/persistence of other pathogenic viruses reveals a potential vulnerability of fermented foods to SARS-CoV-2 contamination. On the other side of the coin, some bacteriophages are being suggested for improving the fermentation process and food safety, as well as owing potential probiotic properties in modern fermented foods. This review will address the diversity and characteristics of viruses associated with fermented foods and what has been changed after a short introduction to the most common next-generation sequencing platforms. Also, the risk of SARS-CoV-2 transmission via fermented foods and preventive measures will be discussed.

Bacterial and fungal communities and their predictive functional profiles in kinema, a naturally fermented soybean food of India, Nepal and Bhutan

Bacterial and fungal communities in kinema, a naturally fermented soybean food of the Eastern Himalayan regions of India, Nepal and Bhutan were profiled by high-throughout sequence analysis. Firmicutes (78.4%) was the most abundant phylum in kinema, followed by Proteobacteria (14.76%) and other phyla. Twenty seven species of Bacillus were detected, among which Bacillus subtilis (28.70%) was the most abundant bacterium, followed by B. licheniformis, B. thermoamylovorans, B. cereus, Ignatzschineria larvae, Corynebacterium casei, B. sonorensis, Proteus vulgaris, Brevibacillus borstelensis, Thermoactinomyces vulgaris, Lactobacillus fermentum and Ignatzschineria indica. Ascomycota was the most abundant fungal phylum in kinema. Wallemia canadensis, Penicillium spp., Aspergillus spp., Exobasidium spp., Arthrocladium spp., Aspergillus penicillioides, Mortierella spp., Rhizopus arrhizus and Mucor circinelloides, were major moulds, and Pichia sporocuriosa, Trichosporon spp., Saccharomycopsis malanga and Rhodotorula cycloclastica were abundant yeasts in kinema. We detected 277 species of bacteria among which, 99.09% were culturable and 0.91% were unculturable; and 80 fungal species among which, 33.72% were culturable and 66.28% were unculturable. Several unique bacterial genera to each country were observed, whereas no unique fungal genus was observed in kinema. Maximum coverage of sequencing depth was observed in all samples. Based on PCA plot, close relation was observed between samples of India and Nepal, whereas samples of Bhutan was clearly distinctive. Predictive functional features of bacterial and fungi related to metabolisms were inferred by the KEGG Orthology and MetaCyc databases, respectively.