Microbial composition of Kombucha determined using amplicon sequencing and shotgun metagenomics

Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome

Complex microbiomes are part of the food we eat and influence our own microbiome, but their diversity remains largely unexplored. Here, we generated the open access curatedFoodMetagenomicData (cFMD) resource by integrating 1,950 newly sequenced and 583 public food metagenomes. We produced 10,899 metagenome-assembled genomes spanning 1,036 prokaryotic and 108 eukaryotic species-level genome bins (SGBs), including 320 previously undescribed taxa. Food SGBs displayed significant microbial diversity within and between food categories. Extension to >20,000 human metagenomes revealed that food SGBs accounted on average for 3% of the adult gut microbiome. Strain-level analysis highlighted potential instances of food-to-gut transmission and intestinal colonization (e.g., Lacticaseibacillus paracasei) as well as SGBs with divergent genomic structures in food and humans (e.g., Streptococcus gallolyticus and Limosilactobabillus mucosae). The cFMD expands our knowledge on food microbiomes, their role in shaping the human microbiome, and supports future uses of metagenomics for food quality, safety, and authentication.

Hi-C metagenomics facilitate comparative genome analysis of bacteria and yeast from spontaneous beer and cider

Sequence-based analysis of fermented foods and beverages' microbiomes offers insights into their impact on taste and consumer health. High-throughput metagenomics provide detailed taxonomic and functional community profiling, but bacterial and yeast genome reconstruction and mobile genetic elements tracking are to be improved. We established a pipeline for exploring fermented foods microbiomes using metagenomics coupled with chromosome conformation capture (Hi-C metagenomics). The approach was applied to analyze a collection of spontaneously fermented beers and ciders (n = 12). The Hi-C reads were used to reconstruct the metagenome-assembled genomes (MAGs) of bacteria and yeasts facilitating subsequent comparative genomic analysis, assembly scaffolding and exploration of "plasmid-bacteria" links. For a subset of beverages, yeasts were isolated and characterized phenotypically. The reconstructed Hi-C MAGs primarily belonged to the Lactobacillaceae family in beers, along with Acetobacteraceae and Enterobacteriaceae in ciders, exhibiting improved quality compared to conventional metagenomic MAGs. Comparative genomic analysis of Lactobacillaceae Hi-C MAGs revealed clustering by niche and suggested genetic determinants of survival and probiotic potential. For Pediococcus damnosus, Hi-C-based networks of contigs enabled linking bacteria with plasmids. Analyzing phylogeny and accessory genes in the context of known reference genomes offered insights into the niche specialization of beer lactobacilli. The subspecies-level diversity of cider Tatumella spp. was disentangled using a Hi-C-based graph. We obtained highly complete yeast Hi-C MAGs primarily represented by Brettanomyces and Saccharomyces, with Hi-C-facilitated chromosome-level genome assembly for the former. Utilizing Hi-C metagenomics to unravel the genomic content of individual species can provide a deeper understanding of the ecological interactions within the food microbiome, aid in bioprospecting beneficial microorganisms, improving quality control and improving innovative fermented products.

Microbiological characterization of kombucha and biocellulose film produced with black tea and cocoa bean shell infusion

The food industry is increasingly striving to produce probiotics-based food and beverages using sustainable processes. Therefore, the use of by-products in product development has been investigated by several authors. The aim of this work was to investigate the effects of cocoa bean shell infusion in the production of kombucha through microbiological and genetic characterization. Three beverage formulations were prepared, one based on black tea (KBT), one based on cocoa bean shell infusion (KCS) and one containing 50 % black tea and 50 % cocoa shell infusion (KBL). The infusions were prepared with water, filtered, and sucrose was added. They were then homogenized and a portion of finished kombucha and SCOBY (symbiotic culture of bacteria and yeast) were added. Fermentation took place for 13 days and aliquots were collected every three days for physicochemical and microbial count analyses. Samples from the last day of fermentation were sent for DNA sequencing, extraction and quantification. The results were subjected to analysis of variance and compared by using Tukey's test (p < 0.05). The results show that there was a significant decrease in pH over time in all samples, while the titratable acidity increased, indicating an acidification of the beverage due to the production of organic acids. There was an increase in lactic acid bacterial colonies in all the formulations, which have a probiotic nature and are not always found in this type of beverage. Regarding the taxonomic classification of the samples, microorganisms of the kingdoms Fungi and Bacteria, of the families Saccharomycetaceae and Acetobacteraceae, were found in KBT, KCS and KBL, but with different microbiological compositions, with different amounts of yeasts and bacteria. Therefore, the use of by-products such as cocoa bean shell in the production of kombucha can contribute to the reduction of waste in the food industry and, at the same time, accelerate fermentation increasing the presence of lactic acid bacteria when compared to black tea.

Evaluation of microbiota-induced changes in biochemical, sensory properties and volatile profile of kombucha produced by reformed microbial community

Kombucha is a traditional beverage produced by a living culture known as SCOBY or "symbiotic culture of bacteria and yeast". Culture-dependent production is essential for stable kombucha fermentation. The aim of this study was to design a microbial community and to determine the effect of that community on the flavor and chemical properties of kombucha. The fermentations were carried out using combinations of selected species including Pichia kudriavzevii, Brettanomyces bruxellensis, Dekkera bruxellensis, Komagataeibacter saccharivorans, Komagataeibacter xylinus, and Acetobacter papayae, which were previously isolated from kombucha. The effects of monocultures and cocultures on fermentation were investigated. The highest acetic acid producer was A. papayae, which has strong antioxidant properties. In the monoculture and coculture fermentations, aldehydes, acids, and esters were generally observed at the end of fermentation. This study confirms that microbiota reconstruction is a viable approach for achieving the production of kombucha with increased bioactive constituents and consumer acceptance.

Spatially structured microbial consortia and their role in food fermentations

Microbial consortia are important for the fermentation of foods. They bring combined functionalities to the fermented product, but stability and product consistency of fermentations with complex consortia can be hard to control. Some of these consortia, such as water- and milk-kefir and kombucha, grow as multispecies aggregates or biofilms, in which micro-organisms taking part in a fermentation cascade are spatially organized. The spatial organization of micro-organisms in these aggregates can impact what metabolic interactions are realized in the consortia, ultimately affecting the growth dynamics and evolution of microbes. A better understanding of such spatially structured communities is of interest from the perspective of microbial ecology and biotechnology, as multispecies aggregates can be used to valorize energy-rich substrates, such as plant-based substrates or side streams from the food industry.

Viability and Diversity of the Microbial Cultures Available in Retail Kombucha Beverages in the USA

Kombucha is a two-stage fermented sweetened tea beverage that uses yeast and lactic acid bacteria (LAB) to convert sugars into ethanol and lactate and acetic acid bacteria (AAB) to oxidize ethanol to acetate. Its popularity as a beverage grew from claims of health benefits derived from this vibrant microbial bioconversion. While recent studies have shed light on the diversity of cultures in Kombucha fermentation, there is limited information on the diversity, and especially viability, of cultures in retail beverages that advertise the presence of Kombucha and probiotic cultures. In this study, 12 Kombucha beverages produced by different manufacturers throughout the US were purchased and microbially characterized. Eight of the beverages contained viable Kombucha cultures, while 3 of the remaining 4 had viable Bacillus cultures as added probiotics. Amplicon profiling revealed that all contained Kombucha yeast and bacteria cells. The dominant yeasts detected were Lachancea cidri (10/12), Brettanomyces (9/12), Malassezia (6/12), and Saccharomyces (5/12). Dominant LAB included Liquorilactobacillus and Oenococcus oeni, and AAB were Komagataeibacter, Gluconobacter, and Acetobacter. One beverage had a significant amount of Zymomonas mobilis, an ethanol-producing bacterium from Agave cactus. While Kombucha beverages differ in the types and viability of cultures, all except one beverage contained detectable viable cells.

Customized 16S-23S rDNA ITS Amplicon Metagenomics for Acetic Acid Bacteria Species Identification in Vinegars and Kombuchas

Acetic acid bacteria (AAB) are involved in food and beverage production bioprocesses, like those in vinegar and kombucha. They oxidize sugars and alcohols into various metabolites, resulting in the final products' pleasant taste and aroma. The 16S rDNA amplicon metagenomics using Illumina technology is usually used to follow the microbiological development of these processes. However, the 16S rRNA gene sequences among different species of AAB are very similar, thus not enabling a reliable identification down to the species level but only to the genus. In this study, we have constructed primers for amplifying half of the 16S-23S rRNA gene internal transcribed spacer (ITS) for library construction and further sequencing using Illumina technology. This approach was successfully used to estimate the relative abundance of AAB species in defined consortia. Further application of this method for the analysis of different vinegar and kombucha samples proves it suitable for assessing the relative abundance of AAB species when these bacteria represent a predominant part of a microbial community.

Evaluation of the probiotic potential of yeast isolated from kombucha in New Zealand

The current study investigated the in vitro probiotic potential of yeast isolated from kombucha, a tea beverage fermented with a symbiotic culture of acetic acid bacteria and yeast. A total of 62 yeast strains were previously isolated from four different commercial kombucha samples sold in New Zealand. Fifteen representative isolates belonging to eight different species were evaluated for their growth under different conditions (temperature, low pH, concentrations of bile salts, and NaCl). Cell surface characteristics, functional and enzymatic activities of the selected strains were also studied in triplicate experiments. Results showed that six strains (Dekkera bruxellensis LBY1, Sachizosaccharomyces pombe LBY5, Hanseniaspora valbyensis DOY1, Brettanomyces anomalus DOY8, Pichia kudraivzevii GBY1, and Saccharomyces cerevisiae GBY2) were able to grow under low-acid conditions (at pH 2 and pH 3) and in the presence of bile salts. This suggests their potential to survive passage through the human gut. All 15 strains exhibited negative enzymatic activity reactions (haemolytic, gelatinase, phospholipase, and protease activities), and thus, they can be considered safe to consume. Notably, two of the fifteen strains (Pichia kudraivzevii GBY1 and Saccharomyces cerevisiae GBY2) exhibited desirable cell surface hydrophobicity (64.60-83.87%), auto-aggregation (>98%), co-aggregation, resistance to eight tested antibiotics (ampicillin, chloramphenicol, colistin sulphate, kanamycin, nalidixic acid, nitrofurantoin, streptomycin, and tetracycline), and high levels of antioxidant activities (>90%). Together, our data reveal the probiotic activities of two yeast strains GBY1 and GBY2 and their potential application in functional food production.

Elevated abundance of Komagataeibacter results in a lower pH in kombucha production; insights from microbiomic and chemical analyses

Kombucha consumption has grown rapidly worldwide in the last decade, with production at both small- and large scales. The complex fermentation process involves both bacterial and yeast species, but little is known regarding the progression of microbial development during production. We explored the microbial diversity of multiple batches across two kombucha types, i. e commercial scale versus laboratory-made (hereafter "home") kombucha brew using metabarcoding to characterize both fungal and bacterial communities. We found the microbial community of the commercial kombucha brew to be more complex than that of the home brew. Furthermore, PERMANOVA uncovered significant compositional differences between the bacterial (F = 2.68, R2 = 0.23, p = 00.001) and fungal (F = 3.18, R2 = 0.26, p = 00.006) communities between batches. For the home brew, both alpha and beta diversity analyses revealed no significant differences between all batches and replicates. When the microbial diversity of the home and commercial kombucha types were directly compared, the former had higher proportions of Ammoniphilus and Komagataeibacter. The commercial kombucha on the other hand were high in Anoxybacillus, Methylobacterium and Sphingomonas. For the fungal communities, the most dominant fungal genera detected in both kombucha types were similar. Linear model revealed significant correlations between some microorganisms and the sugars and organic acids assayed in this study. For example, rising glucose levels correlated with an increase in the relative abundance of Komagataeibacter (F = 7.115, Adj. R2 = 0.44, p = 00.0003). We believe these results contribute towards achieving a better control of the kombucha fermentation process and may assist in targeted product diversification.

Volatilome, Microbial, and Sensory Profiles of Coffee Leaf and Coffee Leaf-Toasted Maté Kombuchas

Kombucha is a fermented beverage traditionally made from the leaves of Camelia sinensis. The market has drastically expanded recently, and the beverage has become more elaborated with new, healthy food materials and flavors. Pruning and harvesting during coffee production may generate tons of coffee leaves that are discarded although they contain substantial amounts of bioactive compounds, including those found in maté tea and coffee seeds. This study characterized the changes in volatilome, microbial, and sensory profiles of pure and blended arabica coffee leaf tea kombuchas between 3-9 days of fermentation. Acceptance was also evaluated by consumers from Rio de Janeiro (n = 103). Kombuchas (K) were prepared using black tea kombucha starter (BTKS) (10%), sucrose (10%), a symbiotic culture of Bacteria and Yeasts (SCOBY) (2.5%), and a pure coffee leaf infusion (CL) or a 50:50 blend with toasted maté infusion (CL-TM) at 2.5%. The RATA test was chosen for sensory profile characterization. One hundred volatile organic compounds were identified when all infusions and kombucha samples were considered. The potential impact compounds identified in CL K and CL-TM K were: methyl salicylate, benzaldehyde, hexanal, nonanal, pentadecanal, phenylethyl-alcohol, cedrol, 3,5-octadien-2-one, β-damascenone, α-ionone, β-ionone, acetic acid, caproic acid, octanoic acid, nonanoic acid, decanoic acid, isovaleric acid, linalool, (S)-dihydroactinidiolide, isoamyl alcohol, ethyl hexanoate, and geranyl acetone. Aroma and flavor descriptors with higher intensities in CL K included fruity, peach, sweet, and herbal, while CL-TM K included additional toasted mate notes. The highest mean acceptance score was given to CL-TM K and CL K on day 3 (6.6 and 6.4, respectively, on a nine-point scale). Arabica coffee leaf can be a co-product with similar fingerprinting to maté and black tea, which can be explored for the elaboration of potentially healthy fermented beverages in food industries.

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.

Sucrose Concentration and Fermentation Temperature Impact the Sensory Characteristics and Liking of Kombucha

Kombucha is a fermented tea beverage consumed for its probiotics and functional properties. It has a unique sensory profile driven by the properties of tea polyphenols and fermentation products, including organic acids. Fermentation temperature and sucrose content affect the fermentation process and the production of organic acids; yet less is known about their impacts on the sensory profile and consumer acceptance. Thus, we aimed to examine the impact of sucrose concentration and fermentation temperature on sensory attributes and liking. For this study, kombucha tea was fermented at three different concentrations of sucrose and fermented at two temperatures for 11 days. Fermentation was monitored by pH, brix, and titratable acidity, and consumers (n = 111) evaluated the kombucha for sensory attributes and overall liking. The fermentation temperature resulted in significant differences in titratable acidity, with higher temperatures producing more organic acids, resulting in higher astringency, and suppressed sweetness. The lower fermentation was reported as significantly more liked, with no difference in liking between the 7.5% and 10% sucrose kombucha samples. Fermentation temperature had the greatest impact on the sensory profile rather than sucrose concentration, which had a greater effect on the fermentation rate and production organic acids.

Volatile, Microbial, and Sensory Profiles and Consumer Acceptance of Coffee Cascara Kombuchas

Given the substantial world coffee production, tons of coffee fruit cascara rich in bioactive compounds are discarded annually. Using this by-product to produce potentially healthy and acceptable foods is a sustainable practice that aggregates value to coffee production and may help improve people's lives. This study aimed to elaborate kombuchas from coffee cascara tea, evaluate their microbial profile, and monitor the changes in the volatile profile during fermentation, together with sensory attributes and acceptance by consumers from Rio de Janeiro (n = 113). Arabica coffee cascaras from Brazil and Nicaragua were used to make infusions, to which black tea kombucha, a Symbiotic Culture of Bacteria and Yeasts (SCOBY), and sucrose were added. Fermentation of plain black tea kombucha was also monitored for comparison. The volatile profile was analyzed after 0, 3, 6, and 9 days of fermentation via headspace solid phase microextraction GC-MS. A total of 81 compounds were identified considering all beverages, 59 in coffee cascara kombuchas and 59 in the black tea kombucha, with 37 common compounds for both. An increase mainly in acids and esters occurred during fermentation. Despite the similarity to black tea kombucha, some aldehydes, esters, alcohols, and ketones in coffee cascara kombucha were not identified in black tea kombucha. Potential impact compounds in CC were linalool, decanal, nonanal, octanal, dodecanal, ethanol, 2-ethylhexanol, ethyl acetate, ethyl butyrate, ethyl acetate, β-damascenone, γ-nonalactone, linalool oxide, phenylethyl alcohol, geranyl acetone, phenylacetaldehyde, isoamyl alcohol, acetic acid, octanoic acid, isovaleric acid, ethyl isobutyrate, ethyl hexanoate, and limonene. The mean acceptance scores for cascara kombuchas varied between 5.7 ± 0.53 and 7.4 ± 0.53 on a nine-point hedonic scale, with coffee cascara from three-day Nicaragua kombucha showing the highest score, associated with sweetness and berry, honey, woody, and herbal aromas and flavors. The present results indicate that coffee cascara is a promising by-product for elaboration of fermented beverages, exhibiting exotic and singular fingerprinting that can be explored for applications in the food industry.

Revealing the influence of microbiota on the flavor of kombucha during natural fermentation process by metagenomic and GC-MS analysis

In this work, raw Pu-erh tea (RAPT) was employed for kombucha preparation, and the microbial composition and volatile flavor compounds of the fermented tea had been investigated during natural fermentation process. The head space-solid phase microextraction-gas chromatograph mass spectrometry (HS-SPME-GC-MS) was performed for volatiles analysis of unfermented tea and kombucha fermented for 3 days (KF-3) and 6 days (KF-6). Meanwhile, the microbial community of KF-3 and KF-6 were evaluated by metagenomic analysis. A total of 72 volatile compounds were identified and obvious changes in volatiles were observed during the fermentation process based on the results of GC-MS and principal component analysis (PCA). Metagenomic sequencing analysis demonstrated that bacterium Komagataeibacter saccharivorans and unclassified-g-komagataeibacter and yeast Saccharomyces cerevisiae and Brettanomyces bruxellensis were the most common microbes contained in the sampled kombucha communities. Furthermore, the relevance among microbial community and volatile compounds was evaluated through correlation heatmap analysis. The results suggested that the main flavor volatiles of kombucha (i.e., acids, esters and terpenes) were closely related to species of genus Komagataeibacter, Gluconacetobacter, Saccharomyces, Brettanomyces, Acetobacter, Novacetimonas and Pichia microorganisms. The obtained results would help to better understand microbial communities and volatile compounds of kombucha, which could provide useful information for enhancing the flavor quality of kombucha products.

Innovative beverage creation through symbiotic microbial communities inspired by traditional fermented beverages: current status, challenges and future directions

Fermented beverages (FBs) are facing challenges in functional performance and flavor complexity, necessitating the development of new multi-functional options. Traditional fermented beverages (TFBs), both alcoholic and nonalcoholic, have gained increased attention for their health-promoting effects during the COVID-19 pandemic. This review summarized the primary commercially available probiotics of FBs, along with the limitations of single and mixed probiotic FBs. It also examined the recent research progress on TFBs, emphasizing the typical microbial communities (MC) of TFBs, and TFBs made from crops (grains, vegetables, fruits, etc.) worldwide and their associated functions and health benefits. Furthermore, the construction, technical bottlenecks of the synthetic MC involved in developing innovative FBs were presented, and the promising perspective of FBs was described. Drawing inspiration from the MC of TFBs, developing of stable and multifunctional FBs using synthetic MC holds great promise for beverage industry. However, synthetic MC suffers from structural instability and poorly acknowledged interaction mechanisms, resulting in disappointing results in FBs. Future researches should prioritize creating synthetic MC fermentation that closely resemble natural fermentation, tailored to meet the needs of different consumers. Creating personalized FBs with high-tech intelligence is vital in attracting potential consumers and developing novel beverages for the future.

Exopolysaccharides Producing Bacteria: A Review

Bacterial exopolysaccharides (EPS) are essential natural biopolymers used in different areas including biomedicine, food, cosmetic, petroleum, and pharmaceuticals and also in environmental remediation. The interest in them is primarily due to their unique structure and properties such as biocompatibility, biodegradability, higher purity, hydrophilic nature, anti-inflammatory, antioxidant, anti-cancer, antibacterial, and immune-modulating and prebiotic activities. The present review summarizes the current research progress on bacterial EPSs including their properties, biological functions, and promising applications in the various fields of science, industry, medicine, and technology, as well as characteristics and the isolation sources of EPSs-producing bacterial strains. This review provides an overview of the latest advances in the study of such important industrial exopolysaccharides as xanthan, bacterial cellulose, and levan. Finally, current study limitations and future directions are discussed.

Microbiome composition of kombucha tea from Türkiye using high-throughput sequencing

Kombucha is a fermented tea with a combination of yeast and bacteria. Kombucha teas may have a variable microbiota based on geographic origin and cultural conditions. The microbial flora of kombucha has been studied with culture-dependent methods. But, the improvement of the metataxonomic approach has broadened our perspective on fermented foods. In this study, a kombucha mother was procured from an artisanal supplier in Türkiye. High-throughput new-generation sequencing (16S rRNA and Internal Transcribed Spacer (ITS)) was carried out to investigate the microbial communities of kombucha after 7 days of fermentation in both liquid tea (L) and pellicle (P). Microbial counts, pH (4.42 ± 0.01 and 3.50 ± 0.02), and TA% (0.26 ± 0.02 and 0.60 ± 0.04) were also detected on the first and 7th days of fermentation. According to metataxonomic results, the dominant bacteria were Komagataeibacter obediens (%21.13), an acetic acid-producing bacteria, and the dominant fungal genus was Pichia kudriavzevii (64.35%) in L while Romboutsia sp. CE17 was the dominant bacteria (7%) and Pichia kudriavzevii was also the dominant yeast in P. This study also revealed different species which were not common in kombucha including propionic acid and butyric acid-producing bacteria such as Anaerotignum propionicum and Butyrivibrio fibrisolvens, a butyrivibriocin producing bacteria. Accordingly, different yeast species were detected such as Tetrapisispora phaffii and Ogataea polimorpha.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13197-023-05725-z.

Intracellular Antioxidant and Anti-Inflammatory Effects and Bioactive Profiles of Coffee Cascara and Black Tea Kombucha Beverages

Kombucha is a functional beverage obtained through fermentation of sweetened Camellia sinensis infusion by a symbiotic culture of bacteria and yeasts that exerts many beneficial biological effects, mostly related to its antioxidant and anti-inflammatory effects. Alternative raw materials have been used to create new kombucha or kombucha-like products. Coffee is the most important food commodity worldwide and generates large amounts of by-products during harvest and post-harvest processing. The main coffee by-product is the dried fruit skin and pulp, popularly known as cascara. To date, no studies have evaluated the potential bioactivity of coffee cascara kombucha. In this study, we aimed to measure and compare the effects of infusions and kombuchas made with arabica coffee cascaras (n = 2) and black tea leaves (n = 1), fermented for 0, 3, 6, and 9 days on the intracellular production of Reactive Oxygen Species (ROS) and Nitric Oxide (NO) in model cells. Oxidative stress was induced in HK-2 cells with indoxyl sulfate (IS) and high glucose (G). Inflammation was induced with lipopolysaccharide (LPS) in RAW 264.7 macrophage. The contents of phenolic compounds, caffeine, and other physicochemical parameters were evaluated. To the best of our knowledge, this is the first study providing information on the bioactive profile and on the potential biological effects of coffee cascara kombucha. Fermentation caused the release of bound phenolic compounds from the infusions, especially total chlorogenic acids, with an average increase from 5.4 to 10.7 mg/100 mL (98%) and 2.6-3.4 mg/100 mL (30%) in coffee cascara and black tea kombucha, respectively, up to day 9. All evaluated beverages reduced (p < 0.0001) similarly the intracellular ROS (41% reduction, on average) and uric acid (10-55%) concentrations in HK-2 model cells, reversing the induced oxidative stress. All beverages also reduced (p < 0.0001, 81-90%) NO formation in LPS-induced macrophages, exhibiting an anti-inflammatory effect. These potential health benefits may be mostly attributed to polyphenols and caffeine, whose contents were comparable in all beverages. Coffee cascara showed similar potential to C. sinensis to produce healthy beverages and support sustainable coffee production.

Integrated molecular approaches for fermented food microbiome research

Molecular technologies, including high-throughput sequencing, have expanded our perception of the microbial world. Unprecedented insights into the composition and function of microbial communities have generated large interest, with numerous landmark studies published in recent years relating the important roles of microbiomes and the environment-especially diet and nutrition-in human, animal, and global health. As such, food microbiomes represent an important cross-over between the environment and host. This is especially true of fermented food microbiomes, which actively introduce microbial metabolites and, to a lesser extent, live microbes into the human gut. Here, we discuss the history of fermented foods, and examine how molecular approaches have advanced research of these fermented foods over the past decade. We highlight how various molecular approaches have helped us to understand the ways in which microbes shape the qualities of these products, and we summarize the impacts of consuming fermented foods on the gut. Finally, we explore how advances in bioinformatics could be leveraged to enhance our understanding of fermented foods. This review highlights how integrated molecular approaches are changing our understanding of the microbial communities associated with food fermentation, the creation of unique food products, and their influences on the human microbiome and health.

Current understanding of the intratumoral microbiome in various tumors

It is estimated that in the future, the number of new cancer cases worldwide will exceed the 19.3 million recorded in 2020, and the number of deaths will exceed 10 million. Cancer remains the leading cause of human mortality and lagging socioeconomic development. Intratumoral microbes have been revealed to exist in many cancer types, including pancreatic, colorectal, liver, esophageal, breast, and lung cancers. Intratumoral microorganisms affect not only the host immune system, but also the effectiveness of tumor chemotherapy. This review concentrates on the characteristics and roles of intratumoral microbes in various tumors. In addition, the potential of therapies targeting intratumoral microbes, as well as the main challenges currently delaying these therapies, are explored. Furthermore, we briefly summarize existing technical methods used to characterize intratumoral microbes. We hope to provide ideas for exploring intratumoral microbes as potential biomarkers and targets for tumor diagnosis, treatment, and prognostication.

Biosynthesis of bacterial cellulose nanofibrils in black tea media by a symbiotic culture of bacteria and yeast isolated from commercial kombucha beverage

Bacterial cellulose has drawn the attention for its unique properties and applications including; medicine, pharmacy, food, agricultural, textile and electronics. The present study focused on the production of bacterial cellulose nanofibrils (BCNF) from black tea as cost effective alternative medium in addition to study the effect of gamma radiation on BCNF properties. A symbiotic culture of bacteria and yeast (SCOBY) were isolated from commercial Kombucha beverage and were identified as Acinetobacter lowffii and Candida krusei, respectively. The symbiotic culture was used for production of BCNF on Hestrin-Schramm (HS), black tea (BT) and modified BT media. BCNF was purified (0.5 N NaOH) and quantified by dry weight, yield and productivity determination. Characterization and effect of gamma radiation (5-25 kGy) on BCNF were studied using Scanning Electron Microscope (SEM), Fourier transform infrared (FTIR) and X-Ray Diffraction (XRD). The highest BCNF production was achieved using BT medium with 0.2% tea and 6.0% commercial sugar (with dry weight 4.77-4.61 g/l and productivity 68.14% and 65.85%, respectively). Supplementation of BT medium with 1% ethanol, 0.27% Na₂HPO₄ and 0.5% yeast extract individually, enhanced the BCNF production (7.85, 6.84 and 5.73 g/l), respectively. FTIR spectrum of BCNF from sugared water (SW), HS and BT showed similar structure with high purity. As a conclusion, gamma irradiation has no effect on the BCNF structure while showed different effects on its crystallinity index and size with the different doses. The changes in CrI were ranged between (17 and 23.5%), while the crystallinity size (Cs) was affected by gamma irradiation in a positive relationship where the crystalline size was decreased (33%) by exposure to 5 kGy then increased by increasing the dose of radiation reaching 25.7% at 25 kGy. SEM graphs showed the morphology of microbial culture and its symbiotic relationship in addition to the ultrafine structure of non-irradiated and irradiated BCNF.

Kombuchas from Green and Black Tea Modulate the Gut Microbiota and Improve the Intestinal Health of Wistar Rats Fed a High-Fat High-Fructose Diet

The Western diet can negatively affect the gut microbiota and is associated with metabolic disorders. Kombucha, a tea fermented by a symbiotic culture of bacteria and yeast (SCOBY), is known for its bioactive properties and has become popular in the last years. In this study, we evaluated the effects of regular kombucha consumption on the gut microbiota and on outcomes related to the intestinal health of Wistar rats fed a high-fat high-fructose diet. After eight weeks receiving a standard diet (AIN-93M) (n = 10) or a high-fat and high-fructose diet (HFHF) (n = 30) to induce metabolic disorders, the animals were subdivided into four groups: AIN-93M (n = 10); HFHF (n = 10); GTK (HFHF + green tea kombucha (n = 10); and BTK (HFHF + black tea kombucha; n = 10) for 10 weeks. Although body composition did not differ among the groups, the HFHF diet was associated with metabolic alterations, and stimulated the growth of gram-negative bacteria such as Proteobacteria and Bacteroides. Kombucha ingestion could somewhat modulate the gut microbiota, attenuating the effects of a Western diet by increasing propionate production and favoring the growth of beneficial bacteria, such as Adlercreutzia in the GTK group. Our results suggest that regular kombucha consumption may be beneficial to intestinal health, which can be mostly attributed to its high content and diversity of phenolic compounds.

Kombucha: Production and Microbiological Research

Kombucha is a sparkling sugared tea commonly prepared using a sugared tea infusion and fermented at ambient temperature for several days using a cellulose pellicle also called tea fungus that is comprised of acetic acid bacteria and yeast. Consumption of Kombucha has been reported as early as 220 B.C. with various reported potential health benefits and appealing sensory properties. During Kombucha fermentation, sucrose is hydrolysed by yeast cells into fructose and glucose, which are then metabolised to ethanol. The ethanol is then oxidised by acetic acid bacteria (AAB) to produce acetic acid which is responsible for the reduction of the pH and also contributes to the sour taste of Kombucha. Characterisation of the AAB and yeast in the Kombucha starter culture can provide a better understanding of the fermentation process. This knowledge can potentially aid in the production of higher quality products as these microorganisms affect the production of metabolites such as organic acids which are associated with potential health benefits, as well as sensory properties. This review presents recent advances in the isolation, enumeration, biochemical characteristics, conventional phenotypic identification system, and modern genetic identification techniques of AAB and yeast present in Kombucha to gain a better understanding of the microbial diversity of the beverage.

The Application of Metagenomics to Study Microbial Communities and Develop Desirable Traits in Fermented Foods

The microbial communities present within fermented foods are diverse and dynamic, producing a variety of metabolites responsible for the fermentation processes, imparting characteristic organoleptic qualities and health-promoting traits, and maintaining microbiological safety of fermented foods. In this context, it is crucial to study these microbial communities to characterise fermented foods and the production processes involved. High Throughput Sequencing (HTS)-based methods such as metagenomics enable microbial community studies through amplicon and shotgun sequencing approaches. As the field constantly develops, sequencing technologies are becoming more accessible, affordable and accurate with a further shift from short read to long read sequencing being observed. Metagenomics is enjoying wide-spread application in fermented food studies and in recent years is also being employed in concert with synthetic biology techniques to help tackle problems with the large amounts of waste generated in the food sector. This review presents an introduction to current sequencing technologies and the benefits of their application in fermented foods.

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.

Reconstruction of Simplified Microbial Consortia to Modulate Sensory Quality of Kombucha Tea

Kombucha is a fermented tea with a long history of production and consumption. It has been gaining popularity thanks to its refreshing taste and assumed beneficial properties. The microbial community responsible for tea fermentation—acetic acid bacteria (AAB), yeasts, and lactic acid bacteria (LAB)—is mainly found embedded in an extracellular cellulosic matrix located at the liquid–air interphase. To optimize the production process and investigate the contribution of individual strains, a collection of 26 unique strains was established from an artisanal-scale kombucha production; it included 13 AAB, 12 yeasts, and one LAB. Among these, distinctive strains, namely Novacetimonas hansenii T7SS-4G1, Brettanomyces bruxellensis T7SB-5W6, and Zygosaccharomyces parabailii T7SS-4W1, were used in mono- and co-culture fermentations. The monocultures highlighted important species-specific differences in the metabolism of sugars and organic acids, while binary co-cultures demonstrated the roles played by bacteria and yeasts in the production of cellulose and typical volatile acidity. Aroma complexity and sensory perception were comparable between reconstructed (with the three strains) and native microbial consortia. This study provided a broad picture of the strains’ metabolic signatures, facilitating the standardization of kombucha production in order to obtain a product with desired characteristics by modulating strains presence or abundance.

Microbes of traditional fermentation processes as synthetic biology chassis to tackle future food challenges

Microbial diversity is magnificent and essential to almost all life on Earth. Microbes are an essential part of every human, allowing us to utilize otherwise inaccessible resources. It is no surprise that humans started, initially unconsciously, domesticating microbes for food production: one may call this microbial domestication 1.0. Sourdough bread is just one of the miracles performed by microbial fermentation, allowing extraction of more nutrients from flour and at the same time creating a fluffy and delicious loaf. There are a broad range of products the production of which requires fermentation such as chocolate, cheese, coffee and vinegar. Eventually, with the rise of microscopy, humans became aware of microbial life. Today our knowledge and technological advances allow us to genetically engineer microbes - one may call this microbial domestication 2.0. Synthetic biology and microbial chassis adaptation allow us to tackle current and future food challenges. One of the most apparent challenges is the limited space on Earth available for agriculture and its major tolls on the environment through use of pesticides and the replacement of ecosystems with monocultures. Further challenges include transport and packaging, exacerbated by the 24/7 on-demand mentality of many customers. Synthetic biology already tackles multiple food challenges and will be able to tackle many future food challenges. In this perspective article, we highlight recent microbial synthetic biology research to address future food challenges. We further give a perspective on how synthetic biology tools may teach old microbes new tricks, and what standardized microbial domestication could look like.

Storage time and temperature affect microbial dynamics of yeasts and acetic acid bacteria in a kombucha beverage

Kombucha is a mildly sweet, slightly acidic fermented beverage, commercially available worldwide, that has attracted increasing consumers' interest due to its potential health benefits. Kombucha is commonly prepared using sugared black or green tea, but also other plant substrates are frequently utilised. Kombucha is obtained by fermentation using a symbiotic culture of bacteria and yeasts, whose composition varies depending on inoculum origin, plant substrates and environmental conditions. After fermentation, kombucha drinks are usually refrigerated at 4 °C, in order to maintain their biological and functional properties. There are no reports on the fate of microbial communities of kombucha in relation to long-term storage time and temperature. Here, for the first time, we monitored the diversity and dynamics of the microbial communities of a kombucha beverage fermented with different herbs during storage at 4 °C and at room temperature, for a period of 90 days, utilising culture-dependent and independent approaches. Moreover, cultivable yeasts and acetic acid bacteria (AAB) were isolated from the beverage, inoculated in pure culture, identified by molecular methods, and yeasts assessed for their functional properties. Total yeast counts were not affected by storage temperature and time, although their community composition changed, as Saccharomyces species significantly decreased after 45 days of storage at room temperature, completely disappearing after 90 days. On the other hand, Dekkera anomala (Brettanomyces anomalus), representing 52 % of the yeast isolates, remained viable up to 90 days at both storage temperatures, and was able to produce high levels of organic acids and exopolysaccharides. Data from DGGE (Denaturing Gradient Gel Electrophoresis) band sequencing confirmed that it was the dominant yeast species in all samples across storage. Other yeast isolates were represented by Saccharomyces and Zygosaccharomyces species. Among AAB, Gluconobacter oxydans, Novacetimonas hansenii and Komagataeibacter saccharivorans represented 46, 36 and 18 % of the isolates, whose occurrence remained unchanged across storage at 4 °C and did not vary up to 20 days of storage at room temperature. This work showed that the combination of culture-dependent and independent approaches is important for obtaining a complete picture of the distinctive core microbial community in kombucha beverages during storage, elucidating its diversity and composition, and preliminary characterizing yeast strains with putative functional activities.

Metagenome-Assembled Genomes of Komagataeibacter from Kombucha Exposed to Mars-Like Conditions Reveal the Secrets in Tolerating Extraterrestrial Stresses

Kombucha mutualistic community (KMC) is composed by acetic acid bacteria and yeasts, producing fermented tea with health benefits. As part of the BIOlogy and Mars EXperiment (BIOMEX) project, the effect of Mars-like conditions on the KMC was analyzed. Here, we analyzed metagenome-assembled genomes (MAGs) of the Komagataeibacter, which is a predominant genus in KMC, to understand their roles in the KMC after exposure to Mars-like conditions (outside the International Space Station) based on functional genetic elements. We constructed three MAGs: K. hansenii, K. rhaeticus, and K. oboediens. Our results showed that (i) K. oboediens MAG functionally more complex than K. hansenii, (ii) K. hansenii is a keystone in KMCs with specific functional features to tolerate extreme stress, and (iii) genes related to the PPDK, betaine biosynthesis, polyamines biosynthesis, sulfate-sulfur assimilation pathway as well as type II toxin-antitoxin (TA) system, quorum sensing (QS) system, and cellulose production could play important roles in the resilience of KMC after exposure to Mars-like stress. Our findings show the potential mechanisms through which Komagataeibacter tolerates the extraterrestrial stress and will help to understand minimal microbial composition of KMC for space travelers.

MicNet toolbox: Visualizing and unraveling a microbial network

Applications of network theory to microbial ecology are an emerging and promising approach to understanding both global and local patterns in the structure and interplay of these microbial communities. In this paper, we present an open-source python toolbox which consists of two modules: on one hand, we introduce a visualization module that incorporates the use of UMAP, a dimensionality reduction technique that focuses on local patterns, and HDBSCAN, a clustering technique based on density; on the other hand, we have included a module that runs an enhanced version of the SparCC code, sustaining larger datasets than before, and we couple the resulting networks with network theory analyses to describe the resulting co-occurrence networks, including several novel analyses, such as structural balance metrics and a proposal to discover the underlying topology of a co-occurrence network. We validated the proposed toolbox on 1) a simple and well described biological network of kombucha, consisting of 48 ASVs, and 2) we validate the improvements of our new version of SparCC. Finally, we showcase the use of the MicNet toolbox on a large dataset from Archean Domes, consisting of more than 2,000 ASVs. Our toolbox is freely available as a github repository (https://github.com/Labevo/MicNetToolbox), and it is accompanied by a web dashboard (http://micnetapplb-1212130533.us-east-1.elb.amazonaws.com) that can be used in a simple and straightforward manner with relative abundance data. This easy-to-use implementation is aimed to microbial ecologists with little to no experience in programming, while the most experienced bioinformatics will also be able to manipulate the source code's functions with ease.

Recent advances in Kombucha tea: Microbial consortium, chemical parameters, health implications and biocellulose production

In the present review the latest research studies on Kombucha tea are summarized. Special attention has been paid on microbial population, chemical parameters, biocellulose production, and mainly, on the latest evidences of the biological activities of Kombucha tea. Kombucha tea is a fermented sweetened black or green tea which is obtained from a fermentative process driven by a symbiotic culture of yeast, acetic acid bacteria and lactic acid bacteria. In the last years, its consumption has increasingly grown due to its multiple and potential benefits on human health. This fact has motivated a significant increase in the number of research studies that are focused on the biological activities of this beverage. In this context, this review gathers the main studies that have analyzed the different properties of Kombucha tea (as antioxidant, antimicrobial, antidiabetic, antitumoral, anti-inflammatory, antihypertensive, hepatoprotective, hypocholesterolemic, and probiotic activities). It is highlighted that nowadays few human-based evidences are available to prove the beneficial effect of Kombucha tea on humans' health. In conclusion, further work on Kombucha tea is needed since nowadays few information is available on both clinical studies and the characterization of bioactive compounds and their properties.

Microbial Diversity and Interaction Specificity in Kombucha Tea Fermentations

Despite the popularity of kombucha tea, the distribution of different microbes across kombucha ferments and how those microbes interact within communities are not well characterized. Using metagenomics, comparative genomics, synthetic community experiments, and metabolomics, we determined the taxonomic, ecological, and functional diversity of 23 distinct kombuchas from across the United States. Shotgun metagenomic sequencing demonstrated that the bacterium Komagataeibacter rhaeticus and the yeast Brettanomyces bruxellensis were the most common microbes in the sampled kombucha communities. To determine the specificity of bacterium-yeast interactions, we experimentally quantified microbial interactions within kombucha biofilms by measuring densities of interacting species and biofilm production. In pairwise combinations of bacteria and yeast, B. bruxellensis and individual strains of Komagataeibacter spp. were sufficient to form kombucha fermentations with robust biofilms, but Zygosaccharomyces bisporus, another yeast found in kombucha, did not stimulate bacteria to produce biofilms. Profiling the spent media of both yeast species using nuclear magnetic resonance spectroscopy suggested that the enhanced ability of B. bruxellensis to ferment and produce key metabolites in sucrose-sweetened tea may explain why it stimulates biofilm formation. Comparative genomics demonstrated that Komagataeibacter spp. with >99% genomic similarity can still have dramatic differences in biofilm production, with strong producers yielding five times more biofilm than the weakest producers.

IMPORTANCE Through an integration of metagenomic and experimental approaches, our work reveals the diversity and nature of interactions among key taxa in kombucha microbiomes through the construction of synthetic microbial pairs. Manipulation of these microbes in kombucha has the potential to shape both the fermentation qualities of kombucha and the production of biofilms and is valuable for kombucha beverage producers, biofilm engineers, and synthetic ecologists.

Global Regulatory Frameworks for Fermented Foods: A Review

In recent years, there has been a global resurgence of public interest in fermented foods. In parallel, there have been several new studies that associate the consumption of fermented foods with a variety of beneficial impacts. These combined developments have led to a renewed focus in research and innovation vis-à-vis fermented foods, particularly traditional fermented foods, with an aim to harness this information to develop novel fermented foodstuffs and ingredients and make them available in the market. Consequently, an ever greater and more diverse array of fermented foods, including functional fermented foods with health benefits, are becoming available for public consumption in global markets, with the number expected to grow substantially in the coming decade. This rapidly expanding portfolio of commercially available fermented foods has in turn required an evolution in the corresponding global regulatory frameworks. Due to the innovative and emerging nature of these foods, combined with historical differences in regulator approaches, significant disharmony exists across these frameworks, with individual nations and organizations often adopting unique approaches relating to the establishment of standards and specifications. In this review, we provide an overview of the current regulatory frameworks for a diversity of fermented foods across multiple jurisdictions, with special emphasis on differences in legislative structures and approaches, regulatory harmonization, and current legislative limitations. Overall, the review provides important perspective and context in relation to current global fermented food regulatory practices with possible directions and recommendations for future legislative efforts.

Interaction and Application of Molds and Yeasts in Chinese Fermented Foods

Fermentation is an ancient food preservation and processing technology with a long history of thousands of years, that is still practiced all over the world. Fermented foods are usually defined as foods or beverages made by controlling the growth of microorganisms and the transformation of raw and auxiliary food components, which provide the human body with many beneficial nutrients or health factors. As fungus widely used in traditional Chinese fermented foods, molds and yeasts play an irreplaceable role in the formation of flavor substances and the production of functional components in fermented foods. The research progress of molds and yeasts in traditional Chinese fermented foods from traditional to modern is reviewed, including the research on the diversity, and population structure of molds and yeasts in fermented foods. The interaction between fermenting mold and yeast and the latest research results and application development prospects of related industries were discussed.

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.

Yeasts Inhabiting Extreme Environments and Their Biotechnological Applications

Yeasts are microscopic fungi inhabiting all Earth environments, including those inhospitable for most life forms, considered extreme environments. According to their habitats, yeasts could be extremotolerant or extremophiles. Some are polyextremophiles, depending on their growth capacity, tolerance, and survival in the face of their habitat's physical and chemical constitution. The extreme yeasts are relevant for the industrial production of value-added compounds, such as biofuels, lipids, carotenoids, recombinant proteins, enzymes, among others. This review calls attention to the importance of yeasts inhabiting extreme environments, including metabolic and adaptive aspects to tolerate conditions of cold, heat, water availability, pH, salinity, osmolarity, UV radiation, and metal toxicity, which are relevant for biotechnological applications. We explore the habitats of extreme yeasts, highlighting key species, physiology, adaptations, and molecular identification. Finally, we summarize several findings related to the industrially-important extremophilic yeasts and describe current trends in biotechnological applications that will impact the bioeconomy.

Advances in Kombucha Tea Fermentation: A Review

Kombucha is a carbonated, slightly acidic beverage traditionally produced by the fermentation of sweetened tea by a symbiotic culture of bacteria and yeast (SCOBY). The microbial community of kombucha is a complex one, whose dynamics are still not fully understood; however, the emergence of culture-independent techniques has allowed a more comprehensive insight into kombucha microbiota. In recent times, advancements have been made towards the optimisation of the fermentation process, including the use of alternative substrates, defined starter cultures and the modification of fermentation parameters, with the aim of producing an innovative beverage that is improved in terms of its physiochemical, sensory and bioactive properties. The global kombucha market is rapidly increasing, with the rising popularity of the tea attributed in part to its purported health benefits, despite the lack of research in human subjects to substantiate such claims. Accordingly, the incidence of kombucha home-brewing has increased, meaning there is a requirement for individuals to recognise the potential hazards associated with fermentation and the relevant preventative measures to be undertaken to ensure the safe preparation of kombucha. The aim of this review is to provide an update regarding the current knowledge of kombucha production, microbiology, safety and marketing.

Shotgun metagenomics of Cheonggukjang, a fermented soybean food of Korea: Community structure, predictive functionalities and amino acids profile

Cheonggukjang is a naturally fermented soybean food of Korea. The present study was aimed to reveal the whole microbial community structure of naturally fermented cheonggukjang along with the prediction of microbial functional profiles by shotgun metagenomic sequence analysis. Metataxonomic profile of cheonggukjang samples showed different domains viz. bacteria (95.83%), virus (2.26%), unclassified (1.84%), eukaryotes (0.05%) and archaea (0.005%). Overall, 44 phyla, 286 families, 722 genera and 1437 species were identified. Firmicutes was the most abundant phylum (98.04%) followed by Proteobacteria (1.49%), Deinococcus-Thermus (0.14%). Bacillus thermoamylovorans was the most abundant species in cheonggukjang followed by Bacillus licheniformis, Bacillus glycinifermentans, Bacillus subtilis, Bacillus paralicheniformis, Bacillus amyloliquifaciens, Brevibacillus borstelensis, Brevibacillus sonorensis Brevibacillus, Acinetobacter, Carnobacterium, Paenibacillus, Cronobacter Enterococcus, Enterobacter, Terriglobus, Psychrobacter and Virgibacillus. A colossal diversity of the genus Bacillus was detected with 150 species. Functional analysis of cheonggukjang metagenome revealed the genes for the synthesis and metabolism of wide range of bioactive compounds including, various essential amino acids, conjugated amino acids, different vitamins, flavonoids, and enzymes. Amino acid profiles obtained from KEGG annotation in cheonggukjang were validated with experimental result of amino acid profiles.

Evolution of Food Fermentation Processes and the Use of Multi-Omics in Deciphering the Roles of the Microbiota

Food fermentation has been practised since ancient times to improve sensory properties and food preservation. This review discusses the process of fermentation, which has undergone remarkable improvement over the years, from relying on natural microbes and spontaneous fermentation to back-slopping and the use of starter cultures. Modern biotechnological approaches, including genome editing using CRISPR/Cas9, have been investigated and hold promise for improving the fermentation process. The invention of next-generation sequencing techniques and the rise of meta-omics tools have advanced our knowledge on the characterisation of microbiomes involved in food fermentation and their functional roles. The contribution and potential advantages of meta-omics technologies in understanding the process of fermentation and examples of recent studies utilising multi-omics approaches for studying food-fermentation microbiomes are reviewed. Recent technological advances in studying food fermentation have provided insights into the ancient wisdom in the practice of food fermentation, such as the choice of substrates and fermentation conditions leading to desirable properties. This review aims to stimulate research on the process of fermentation and the associated microbiomes to produce fermented food efficiently and sustainably. Prospects and the usefulness of recent advances in molecular tools and integrated multi-omics approaches are highlighted.

Effect of kombucha intake on the gut microbiota and obesity-related comorbidities: A systematic review

Kombucha is a fermented nonalcoholic tea-based beverage produced through a symbiotic culture of bacteria and yeasts. In vitro studies have demonstrated antimicrobial, antioxidant, antiproliferative, and anti-carcinogenic properties of kombucha. However, no systematic reviews have evaluated the effects of kombucha in vivo. Thus, we aimed to evaluate the evidence that exists so far about kombucha consumption on comorbidities associated with obesity as well as on the gut microbiota. The search was conducted in accordance with PRISMA and the protocol was registered in PROSPERO (registration number: CRD42020158917). The MEDLINE/PubMed, Web of Science, LILACS, SciELO, Scopus, and Science Direct databases were used in the search considering the following terms: "kombucha" OR "kombucha tea" OR "kombucha teas" OR "tea, kombucha" OR "teas, kombucha" NOT "review." Fifteen studies were included in this review. The results suggest that kombucha consumption attenuates oxidative stress and inflammation, improves the liver detoxification process, and reduces intestinal dysbiosis. There is evidence that kombucha consumption is beneficial for the control and treatment of obesity and associated comorbidities, as well as for the modulation of the gut microbiota in vivo.

Comparative Metagenomics Reveals Microbial Communities and Their Associated Functions in Two Types of Fuzhuan Brick Tea

Fuzhuan brick tea (FBT) is a unique post-fermented tea product, naturally co-fermented by microorganisms, and has gained global popularity due to its potential health benefits for humans. Considerable efforts have been made toward elucidating the microbial diversity within FBT, but an understanding of the underlying FBT community interactions and functions remains poorly studied. Consequently, the microbial communities of two types of FBT, originating from Hunan and Shaanxi provinces, were investigated using comparative shotgun metagenomic sequencing and functional annotations. Metagenomic analysis indicated that two communities shared similar taxonomic and functional attributes. Two samples shared 486 genera, in which Pseudomonas contributed most to the abundant functions within the two samples. The carbohydrate active enzyme functions of the communities primarily comprised GH (32.92%), GT (26.8%), CEs (20.43%), and AAs (18.04%). Furthermore, the overall metabolic pathways encoded by the metagenomes were largely associated with carbohydrate and amino acid metabolism, with nine metabolic pathways that were differential between two groups including penicillin and cephalosporin biosynthesis. Significantly, a total of 35 potential probiotics were inferred, with Pseudomonas putida being the most abundant inferred probiotic (80%) within the FBT communities. This study provides new insights into FBT microbial communities on their potential functions and roles in FBT characteristics.

Effect of freeze-dried kombucha culture on microbial composition and assessment of metabolic dynamics during fermentation

Kombucha is a traditional fermented beverage gaining popularity around the world. So far, few studies have investigated its microbiome using next-generation DNA sequencing, whereas the correlation between the microbial community and metabolites evolution along fermentation is still unclear. In this study, we explore this correlation in a traditionally produced kombucha by evaluating its microbial community and the main metabolites produced. We also investigated the effects of starter cultures processed in three different ways (control, starter culture without liquid suspension (CSC), and a freeze-dried starter culture (FDSC)) to evaluate changes in kombucha composition, such as antioxidant activity and sensory analysis. We identified seven genera of bacteria, including Komagataeibacter, Gluconacetobacter, Gluconobacter, Acetobacter, Liquorilactobacillus, Ligilactobacillus, and Zymomonas, and three genera of yeasts, Dekkera/Brettanomyces, Hanseniaspora, and Saccharomyces. Although there were no statistically significant differences in the acceptance test in sensory analysis, different starter cultures resulted in products showing different microbial and biochemical compositions. FDSC decreased Zymomonas and Acetobacter populations, allowing for Gluconobacter predominance, whereas in the control and CSC kombuchas the first two were the predominant genera. Results suggest that the freeze-drying cultures could be implemented to standardize the process and, despite it changes the microbial community, a lower alcohol content could be obtained.

Tailor-made microbial consortium for Kombucha fermentation: Microbiota-induced biochemical changes and biofilm formation

Kombucha is a very distinct naturally fermented sweetened tea that has been produced for thousands of years. Fermentation relies on metabolic activities of the complex autochthonous symbiotic microbiota embedded in a floating biofilm and used as a backslop for successive fermentations. Here, we designed a tailor-made microbial consortium representative of the core Kombucha microbiota to drive this fermentation. Microbial (counts, metagenetics), physico-chemical (pH, density) and biochemical (organic acids, volatile compounds) parameters were monitored as well as biofilm formation by confocal laser scanning microscopy and scanning electron microscopy. While nine species were co-inoculated, four (Dekkera bruxellensis, Hanseniaspora uvarum, Acetobacter okinawensis and Liquorilactobacillus nagelii) largely dominated. Microbial activities led to acetic, lactic, succinic and oxalic acids being produced right from the start of fermentation while gluconic and glucuronic acids progressively increased. A distinct shift in volatile profile was also observed with mainly aldehydes identified early on, then high abundances of fatty acids, ketones and esters at the end. Correlation analyses, combining metabolomic and microbial data also showed a shift in species abundances during fermentation. We also determined distinct bacteria-yeast co-occurence patterns in biofilms by microscopy. Our study provides clear evidence that a tailor-made consortium can be successfully used to drive Kombucha fermentations.