Metagenomics analysis of microbial communities associated with a traditional rice wine starter culture (Xaj-pitha) of Assam, India

Novel Strain Leuconostoc lactis DMLL10 from Traditional Korean Fermented Kimchi as a Starter Candidate for Fermented Foods

Leuconostoc lactis strain DMLL10 was isolated from kimchi, a fermented vegetable, as a starter candidate through safety and technological assessments. Strain DMLL10 was susceptible to ampicillin, chloramphenicol, clindamycin, erythromycin, gentamicin, kanamycin, streptomycin, and tetracycline. It did not show any hemolytic activity. Regarding its phenotypic results related to its safety properties, genomic analysis revealed that strain DMLL10 did not encode for any toxin genes such as hemolysin found in the same genus. It did not acquire antibiotic resistance genes either. Strain DMLL10 showed protease activity on agar containing NaCl up to 3%. The genome of DMLL10 encoded for protease genes and possessed genes associated with hetero- and homo-lactic fermentative pathways for lactate production. Finally, strain DMLL10 showed antibacterial activity against seven common foodborne pathogens, although bacteriocin genes were not identified from its genome. These results indicates that strain DMLL10 is a novel starter candidate with safety, enzyme activity, and bacteriocin activity. The complete genomic sequence of DMLL10 will contribute to our understanding of the genetic basis of probiotic properties and allow for assessment of the effectiveness of this strain as a starter or probiotic for use in the food industry.

Synbiotic Effects of Fermented Rice on Human Health and Wellness: A Natural Beverage That Boosts Immunity

Fermented foods have been an important component of the human diet from the time immemorial. It contains a high amount of probiotics that have been associated to a wide range of health benefits, including improved digestion and immunity. This review focuses on the indigenously prepared prebiotic- and probiotic-containing functional fermented rice (named Xaj-pani) by the Ahom Community from Assam, in Northeast India, including all the beneficial and potential effects on human health. Literature was searched from scientific databases such as PubMed, ScienceDirect and Google Scholar. Glutinous rice (commonly known as bora rice of sali variety) is primarily employed to prepare beverages that are recovered through the filtration process. The beer is normally consumed during religious rites, festivals and ritual practices, as well as being used as a refreshing healthy drink. Traditionally, it is prepared by incorporating a variety of medicinal herbs into their starter culture (Xaj-pitha) inoculum which is rich in yeasts, molds and lactic acid bacteria (LAB) and then incorporated in alcoholic beverage fermentation. The Ahom communities routinely consume this traditionally prepared alcoholic drink with no understanding of its quality and shelf life. Additionally, a finally produced dried cake, known as vekur pitha act as a source of Saccharomyces cerevisiae and can be stored for future use. Despite the rampant use in this community, the relationship between Xaj-pani's consumption, immunological response, infectious and inflammatory processes remains unknown in the presence of factors unrelated or indirectly connected to immune function. Overall, this review provides the guidelines to promote the development of prebiotic- and probiotic-containing functional fermented rice that could significantly have an impact on the health of the consumers.

Amylolytic Fungi in the Ethnic Beer Starter “emao” and Their Beer-Producing Attributes

Naturally occurring autochthonous microbes associated with ethnic beer starters are diverse and important as they play different functional roles in beer fermentations. The study on culturable microbes from the ethnic rice beer starter “emao” of the Bodo community of Assam is limited. Here we isolated and identified the culturable fungal diversity associated with emao and screened them for beer-producing capability from glucose and starch substrates. Based on morphology and molecular characterization, the species identified were Candida glabrata (Cgla_RF2), Cyberlindnera fabianii (Cfab_RF37), Hyphopichia burtonii (Hbur_RF19), Mucor circinelloides (Mcir_RF48), Mucor indicus (Mind_RF25), Penicillium citrinum (Pcit_RF32), Rhodosporidiobolus ruineniae (Rrui_RF4 & Rrui_RF43), Saccharomyces cerevisiae (Scer_RF6), Saccharomycopsis fibuligera (Sfib_RF11), and Wickerhamomyces anomalus (Wano_RF3) among which the relative abundance (RA) of W. anomalus was the highest (24%) followed by C. glabrata and H. burtonii (16% in each). Five (Hbur_RF19, Sfib_RF11, Mind_RF25, Mcir_RF48, and Pcit_RF32) of eleven isolates showed amylase positive in the starch medium. Scer_RF6 showed the highest ethanol tolerance (14% v/v) followed by Hbur_RF19 (12% v/v), Cgla_RF2 (11% v/v) and Wano_RF3 (11% v/v). The amylase-positive strains produced beer-containing ethanol in the range of 3.17–7.3 (% v/v) from rice substrate. Although the rice beer produced by amylase-positive strains showed negligible pH difference, other parameters like ethanol, ascorbic acid, total phenol, and antioxidant properties were varied from beer to beer. Antibacterial activities shown by Mcir_RF48 and Pcit_RF32 against the test bacteria were higher with a 23–35 mm zone of inhibition than the other isolates. The present findings reveal the presence of fungi with antibacterial, amylolytic, ethanol fermenting, and antioxidant producing capacity in emao which could the source for future bioprospection.

A review on the application of bioinformatics tools in food microbiome studies

There is currently a transformed interest toward understanding the impact of fermentation on functional food development due to growing consumer interest on modified health benefits of sustainable foods. In this review, we attempt to summarize recent findings regarding the impact of Next-generation sequencing and other bioinformatics methods in the food microbiome and use prediction software to understand the critical role of microbes in producing fermented foods. Traditionally, fermentation methods and starter culture development were considered conventional methods needing optimization to eliminate errors in technique and were influenced by technical knowledge of fermentation. Recent advances in high-output omics innovations permit the implementation of additional logical tactics for developing fermentation methods. Further, the review describes the multiple functions of the predictions based on docking studies and the correlation of genomic and metabolomic analysis to develop trends to understand the potential food microbiome interactions and associated products to become a part of a healthy diet.

Bacterial Communities and Prediction of Microbial Metabolic Pathway in Rice Wine Koji From Different Regions in China

Rice wine koji, a traditional homemade starter culture in China, is nutritious and delicious. The final quality of rice wine koji is closely related to the structure of its microbial community. However, the diversity of natural microorganisms in rice wine koji from different regions has not been evaluated. In this study, the microbial population of 92 naturally fermented rice koji samples collected from Hubei, Guangxi, and Sichuan was systematically analyzed by high-throughput sequencing. From all the rice wine koji samples, 22 phyla and 479 bacterial genera were identified. Weissella, Pediococcus, Lactobacillus, Enterobacter, Lactococcus, Pantoea, Bacillus, Staphylococcus, and Leuconostoc were the dominant genera in rice wine koji. The bacterial community structure of rice wine koji samples from different regions was significantly different (p < 0.05). The bacterial community composition of the samples from Hubei and Guangxi was similar, but significantly different from that of SC samples (p < 0.05). These differences may be caused by variations in geography, environment, or manufacturing. In addition, the results of microbial phenotype prediction by BugBase and bacterial functional potential prediction by PICRUSt showed that eight of the nine predicted phenotypic functions of rice wine koji samples from different regions were significantly different (p < 0.05) and that vigorous bacterial metabolism occurred in rice wine koji samples.

Molecular tools for the analysis of the microbiota involved in malolactic fermentation: from microbial diversity to selection of lactic acid bacteria of enological interest

Winemaking is a complex process involving two successive fermentations: alcoholic fermentation, by yeasts, and malolactic fermentation (MLF), by lactic acid bacteria (LAB). During MLF, LAB can contribute positively to wine flavor through decarboxylation of malic acid with acidity reduction and other numerous enzymatic reactions. However, some microorganisms can have a negative impact on the quality of the wine through processes such as biogenic amine production. For these reasons, monitoring the bacterial community profiles during MLF can predict and control the quality of the final product. In addition, the selection of LAB from a wine-producing area is necessary for the formulation of native malolactic starter cultures well adapted to local winemaking practices and able to enhance the regional wine typicality. In this sense, molecular biology techniques are fundamental tools to decipher the native microbiome involved in MLF and to select bacterial strains with potential to function as starter cultures, given their enological and technological characteristics. In this context, this work reviews the different molecular tools (both culture-dependent and -independent) that can be applied to the study of MLF, either in bacterial isolates or in the microbial community of wine, and of its dynamics during the process.

Diversity of beneficial microorganisms and their functionalities in community-specific ethnic fermented foods of the Eastern Himalayas

The Eastern Himalayan regions of India, Nepal and Bhutan have more than 200 varieties of unsurpassed ethnic fermented foods and alcoholic beverages, which are lesser known outside the world. However, these ethnic foods are region- and community-specific, unique and some are exotic and rare, which include fermented vegetables, bamboo shoots, soybeans, cereals, milk (cow and yak), meats, fishes, and cereal-based alcoholic beverages and drinks. Ethnic communities living in the Eastern Himalayas have invented the indigenous knowledge of utilization of unseen microorganisms present in and around the environment for preservation and fermentation of perishable plant or animal substrates to obtain organoleptically desirable and culturally acceptable ethnic fermented food and alcoholic beverages. Some ethnic fermented products and traditionally prepared dry starters for production of alcoholic beverages of North Eastern states of India and Nepal were scientifically studied and reported till date, and however, limited publications are available on microbiological and nutritional aspects of ethnic fermented foods of Bhutan except on few products. Most of the beneficial microorganisms isolated from some ethnic fermented foods of the EH are listed in microbial food cultures (MFC) safe inventory. This study is aimed to review the updates on the beneficial importance of abundant microbiota and health-promoting benefits and functionalities of some ethnic fermented foods of the Eastern Himalayan regions of North East India, Nepal and Bhutan.

Community structure and metabolic potentials of the traditional rice beer starter 'emao'

The emao, a traditional beer starter used in the North-East regions of India produces a high quality of beer from rice substrates; however, its microbial community structure and functional metabolic modules remain unknown. To address this gap, we have used shot-gun whole-metagenome sequencing technology; accordingly, we have detected several enzymes that are known to catalyze saccharification, lignocellulose degradation, and biofuel production indicating the presence of metabolic functionome in the emao. The abundance of eukaryotic microorganisms, specifically the members of Mucoromycota and Ascomycota, dominated over the prokaryotes in the emao compared to previous metagenomic studies on such traditional starters where the relative abundance of prokaryotes occurred higher than the eukaryotes. The family Rhizopodaceae (64.5%) and its genus Rhizopus (64%) were the most dominant ones, followed by Phaffomycetaceae (11.14%) and its genus Wickerhamomyces (10.03%). The family Leuconostocaceae (6.09%) represented by two genera (Leuconostoc and Weissella) was dominant over the other bacteria, and it was the third-highest in overall relative abundance in the emao. The comprehensive microbial species diversity, community structure, and metabolic modules found in the emao are of practical value in the formulation of mixed-microbial cultures for biofuel production from plant-based feedstocks.

Specific metagenomic asset drives the spontaneous fermentation of Italian sausages

Metagenomics is a powerful tool to study and understand the microbial dynamics that occur during food fermentation and allows to close the link between microbial diversity and final sensory characteristics. Each food matrix can be colonized by different microbes, but also by different strains of the same species. In this study, using an innovative integrated approach combining culture-dependent method with a shotgun sequencing, we were able to show how strain-level biodiversity could influence the quality characteristics of the final product. The attention was placed on a model food fermentation process: Salame Piemonte, a Protected Geographical Indication (PGI) Italian fermented sausage. Three independent batches produced in February, March and May 2018 were analysed. The sausages were manufactured, following the production specification, in a local meat factory in the area of Turin (Italy) without the use of starter cultures. A pangenomic approach was applied in order to identify and evaluate the lactic acid bacteria (LAB) population driving the fermentation process. It was observed that all batches were characterized by the presence of few LAB species, namely Pediococcus pentosaceus, Latilactobacillus curvatus and Latilactobacillus sakei. Sausages from the different batches were different when the volatilome was taken into consideration, and a strong association between quality attributes and strains present was determined. In particular, different strains of L. sakei, showing heterogeneity at genomic level, colonized the meat at the beginning of each production and deeply influenced the fermentation process by distinctive metabolic pathways that affected the fermentation process and the final sensory aspects.

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

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

Screening and evaluation of Monascus purpureus FJMR24 for enhancing the raw material utilization rate in rice wine brewing

BACKGROUND

The rapid development of the rice wine industry has increased the demand for raw materials worldwide. A fungal strain with good adaptability to rice wine brewing conditions, which can also enhance the utilization rate of raw materials (URRM), thus increasing the production efficiency, was sought in the present research.

RESULTS

The strain FJMR24 was successfully isolated and screened from 35 fermentation starters and exhibited high amylase activity (2200.9 ± 18.5 U g^-1 ) and high glucoamylase activity (2330.4 ± 31.9 U g^-1 ). Based on a morphological examination and a sequence analysis of the internal transcribed spacer (ITS) gene and β-tubulin gene, FJMR24 was identified as Monascus purpureus, which is an edible and versatile fungus that plays a dominant role in the processing of Hong Qu. A moderate pH of 5-6 under incubation at 35 °C for 5-6 days was favorable for the growth and enzyme production of FJMR24. The strain could also tolerate the extreme conditions of 15-45 °C, 18% ethanol (v/v), and an acidity of pH 2. The excellent fermentation adaptability of FJMR24 might enable it to retain high enzyme activity during rice wine brewing. As a result of the action of FJMR24, the URRM of the base liquor increased by around 26% due to increased starch hydrolysis efficiency, which was mainly due to the high unit enzyme activity of FJMR24.

CONCLUSION

This study provides perspectives for the application of a M. purpureus strain with high starch hydrolysis activity for enhancing the URRM in traditional rice wine brewing. © 2020 Society of Chemical Industry.

Probiotic properties of lactic acid bacteria isolated from traditionally prepared dry starters of the Eastern Himalayas

The Himalayan people prepare dry and oval to round-shaped starter cultures to ferment cereals into mild-alcoholic beverages, which contain lactic acid bacteria (LAB) as one of the essential microbiota. There is no report on probiotic characters of LAB isolated from dry starters. Hence, we screened the probiotic and some functional properties of 37 LAB strains isolated from dry starters of the Eastern Himalayas viz. marcha, phab, paa, pee and phut. About 38% of the LAB strains showed high survival rate (> 50%) at pH 3 and 0.3% bile salts. Enterococcus durans BPB21 and SMB7 showed the highest hydrophobicity percentage of 98%. E. durans DMB4 and SMB7 showed maximum cholesterol assimilation activity. About 65% of the LAB strains showed the ability to produce β galactosidase. Majority of the strains showed phytase activity, whereas none of the strain showed amylase activity. About 86% of LAB strains showed an optimum tolerance of 10% ethanol concentration. Genetic screening of some probiotic and functional marker genes have also been analysed. The occurrence of clp L gene, agu A gene (survival of gastrointestinal tract conditions), apf, mub1 and map A gene (adhesion genes) was higher compared to other genes. The occurrence of bsh gene (bile salt tolerance) was detected in Pediococcus pentosaceus SMB13-1 and Enterococcus faecium BPB11. Gene ped B for pediocin with amplicon size of 375 bp was detected in E. durans DMB13 and Pediococcus acidilactici AKB3. Detection of nutritional marker gene rib A and fol P in some strains showed the potential ability to synthesize riboflavin and folic acid. LAB with probiotic and functional properties may be explored for food industry in future.

Fermentative Foods: Microbiology, Biochemistry, Potential Human Health Benefits and Public Health Issues

Fermented foods identify cultures and civilizations. History, climate and the particulars of local production of raw materials have urged humanity to exploit various pathways of fermentation to produce a wide variety of traditional edible products which represent adaptations to specific conditions. Nowadays, industrial-scale production has flooded the markets with ferments. According to recent estimates, the current size of the global market of fermented foods is in the vicinity of USD 30 billion, with increasing trends. Modern challenges include tailor-made fermented foods for people with special dietary needs, such as patients suffering from Crohn's disease or other ailments. Another major challenge concerns the safety of artisan fermented products, an issue that could be tackled with the aid of molecular biology and concerns not only the presence of pathogens but also the foodborne microbial resistance. The basis of all these is, of course, the microbiome, an aggregation of different species of bacteria and yeasts that thrives on the carbohydrates of the raw materials. In this review, the microbiology of fermented foods is discussed with a special reference to groups of products and to specific products indicative of the diversity that a fermentation process can take. Their impact is also discussed with emphasis on health and oral health status. From Hippocrates until modern approaches to disease therapy, diet was thought to be of the most important factors for health stability of the human natural microbiome. After all, to quote Pasteur, "Gentlemen, the microbes will have the last word for human health." In that sense, it is the microbiomes of fermented foods that will acquire a leading role in future nutrition and therapeutics.

Snails as Taxis for a Large Yeast Biodiversity

Yeasts are unicellular fungi that harbour a large biodiversity of thousands of species, of which particularly ascomycetous yeasts are instrumental to human food and beverage production. There is already a large body of evidence showing that insects play an important role for yeast ecology, for their dispersal to new habitats and for breeding and overwintering opportunities. Here, we sought to investigate a potential role of the terrestrial snails Cepaea hortensis and C. nemoralis, which in Europe are often found in association with human settlements and gardens, in yeast ecology. Surprisingly, even in a relatively limited culture-dependent sampling size of over 150 isolates, we found a variety of yeast genera, including species frequently isolated from grape must such as Hanseniaspora, Metschnikowia, Meyerozyma and Pichia in snail excrements. We typed the isolates using standard ITS-PCR-sequencing, sequenced the genomes of three non-conventional yeasts H. uvarum, Meyerozyma guilliermondii and P. kudriavzevii and characterized the fermentation performance of these three strains in grape must highlighting their potential to contribute to novel beverage fermentations. Aggravatingly, however, we also retrieved several human fungal pathogen isolates from snail excrements belonging to the Candida clade, namely Ca. glabrata and Ca. lusitaniae. Overall, our results indicate that diverse yeasts can utilise snails as taxis for dispersal. This courier service may be largely non-selective and thus depend on the diet available to the snails.

Traditional rice beer depletes butyric acid-producing gut bacteria Faecalibacterium and Roseburia along with fecal butyrate levels in the ethnic groups of Northeast India

Ethnicity, geography, and dietary habits are known to have dominant roles in modulating the gut microbiota. Two major ethnic groups Ahom and Bodo in the north-east of India consume traditionally prepared rice beer which contains various microbes and substances that promote the growth of such microbes, known as prebiotics. This study aimed to understand the effect of traditionally prepared rice beer on gut microbiota. A total of 134 (67 from each group) volunteers including non-drinkers and drinkers from three locations were recruited. Fecal and blood samples were collected to study fecal bacterial and metabolite profiles and biochemical markers, respectively. Amplicon 16S rRNA gene sequencing (region V3-V4) by next-generation sequencing showed similar alpha and beta diversities in both the ethnic groups. However, with rice beer consumption the abundance of Firmicutes, Bacteroidetes, Fusobacteria phyla was higher in the drinkers (p < 0.05) of Ahom whereas only Firmicutes were higher in Bodo ethnic group. At the genus level, the bacterial abundance of Faecalibacterium and Roseburia were lower in the drinkers (p < 0.05) of both communities. Gas chromatography-mass spectrometry for the detection of fecal metabolites also revealed lower butyric acid in the feces of drinkers (p < 0.05). This study showed the effects of traditionally prepared rice beer on human gut microbiota and fecal metabolites. Further research is required to understand their effect on health.

Diversity of Filamentous Fungi Isolated From Some Amylase and Alcohol-Producing Starters of India

Filamentous fungi are important organisms in traditionally prepared amylase and alcohol-producing dry starters in India. We collected 40 diverse types of amylase and alcohol-producing starters from eight states in North East India viz. marcha, thiat, humao, hamei, chowan, phut, dawdim, and khekhrii. The average fungal population was 4.9 × 10⁵ cfu/g with an average of pH 5.3 and 10.7%, respectively. In the present study, 131 fungal isolates were isolated and characterized based on macroscopic and microscopic characteristics and were grouped into 44 representative fungal strains. Based on results of morphological characteristics and ITS gene sequencing, 44 fungal strains were grouped into three phyla represented by Ascomycota (48%), Mucoromycota (38%), and Basidiomycota (14%). Taxonomical keys to species level was illustrated on the basis of morphological characteristics and ITS gene sequencing, aligned to the fungal database of NCBI GenBank, which showed seven genera with 16 species represented by Mucor circinelloides (20%), Aspergillus sydowii (11%), Penicillium chrysogenum (11%), Bjerkandera adusta (11%), Penicillium citrinum (7%), Rhizopus oryzae (7%), Aspergillus niger (5%), Aspergillus flavus (5%), Mucor indicus (5%) Rhizopus microsporus (5%), Rhizopus delemar (2%), Aspergillus versicolor (2%), Penicillium oxalicum (2%), Penicillium polonicum (2%), Trametes hirsuta (2%), and Cladosporium parahalotolerans (2%). The highest Shannon diversity index H was recorded in marcha of Sikkim (H: 1.74) and the lowest in hamei of Manipur (H: 0.69). Fungal species present in these amylolytic starters are morphologically, ecologically and phylogenetically diverse and showed high diversity within the community.

Major Metabolites and Microbial Community of Fermented Black Glutinous Rice Wine With Different Starters

Black glutinous rice wine (BGRW) is a traditional Chinese rice wine that is brewed using multiple strains. However, the roles of these microorganisms, particularly their contributions to aroma formation, are poorly understood. Accordingly, the main goal of this study was to determine the microbial communities and major metabolites of different traditional fermentation starters. Anshun (AS) starter and Xingyi (XY) starter were used for BGRW to provide insight into their potential contributions to the variation in flavor and aroma. High-throughput sequencing of the microbial community using the Illumina MiSeq platform revealed significant differences during fermentation between the two starter groups. Pediococcus, Leuconostoc, and Bacillus were the dominant bacterial genera in the AS group, whereas Leuconostoc, Pediococcus, and Gluconobacter were the dominant genera in the XY group. In addition, Rhizopus, Saccharomyces, and Saccharomycopsis were the predominant fungal genera detected in both samples. The major metabolites in the two groups were identified by high-performance liquid chromatography and headspace-solid-phase microextraction gas chromatography–mass spectrometry. A total of seven organic acids along with 47 (AS) and 43 (XY) volatile metabolites were detected, among which lactic acid was the primary organic acid, and esters were the largest group in both types of wine. Principal components analysis further revealed significant differences in the dynamic succession of metabolites between the two samples. Correlation analysis showed that 22 and 17 microorganisms were strongly correlated with the production of major metabolites in AS and XY, respectively. Among them, Pediococcus, Leuconostoc, Lactobacillus, Lactococcus, and Streptococcus were shown to play crucial roles in metabolite synthesis. Overall, this study can provide a valuable resource for the further development and utilization of starters to improve the aromatic quality of BGRW.

Microbial Diversity and Metabolite Profiles of Palm Wine Produced From Three Different Palm Tree Species in Côte d'Ivoire

Palm wine, the most commonly consumed traditional alcoholic beverage in Western Africa, harbours a complex microbiota and metabolites, which plays a crucial role in the overall quality and value of the product. In the present study, a combined metagenomic and metabolomic approach was applied to describe the microbial community structure and metabolites profile of fermented saps from three palm species (Elaeis guineensis, Raphia hookeri, Borassus aethiopum) in Côte d'Ivoire. Lactobacillaceae (47%), Leuconostocaceae (16%) and Acetobacteriaceae (28%) were the most abundant bacteria and Saccharomyces cerevisiae (87%) the predominant yeasts in these beverages. The microbial community structure of Raphia wine was distinctly different from the others. Multivariate analysis based on the metabolites profile clearly separated the three palm wine types. The main differentiating metabolites were putatively identified as gevotroline hydrochloride, sesartemin and methylisocitrate in Elaeis wine; derivative of homoserine, mitoxantrone in Raphia wine; pyrimidine nucleotide sugars (UDP-D-galacturonate) and myo-Inositol derivatives in Borassus wine. The enriched presence of gevotroline (an antipsychotic agent) and mitoxantrone (an anticancer drug) in palm wine supports its therapeutic potential. This work provides a valuable insight into the microbiology and biochemistry of palm wines and a rationale for selecting functional microorganisms for potential biotechnology applications.

High-throughput Sequencing-based Analysis of Microbial Diversity in Rice Wine Koji from Different Areas

Rice wine, a traditional fermented alcoholic beverage in China, is produced with grains such as rice, which are fermented with saccharifying starter-koji. Its flavor quality is closely associated to the starter culture-koji, which is made by mixing botanical materials with high-class glutinous rice in certain ecological context. However, there are few reports on the microbial community structure of rice wine koji. In this paper, bacterial community structures of rice wine koji were analyzed using 16S rRNA gene sequencing based on Illumina MiSeq high-throughput technology in 20 samples collected from Xiaogan area, Hubei province and Dazhu area, Sichuan province (10 from each area). We found rice wine koji flora mainly consisted of Weissella, Lactobacillus, Lactococcus, Bacillus, Enterococcus, and Cronobacter, with relative abundances of 29.49%, 10.93%, 8.85%, 4.75%, 1.16% and 1.15%, respectively, as well as an accumulative average relative abundance of 58.71%. They all belonged to Firmicutes and Proteobacteria-the two known dominant genus. Genus-level PCA (Principal component analysis) and OTU-level PCoA (Principal coordinates analysis) based on unweighted UniFrac distances showed that the bacterial community structure differed significantly between the samples from the 2 areas. 7 OTUs were detected in all samples, accounting for 4.4% of the total qualified assembly. Among the 7 OTUs, 3 OTUs were identified as Enterococcus, 2 OTUs were identified as Cronobacter, 1 OTU was identified as Bacillus and 1 OTU was identified as Alkaliphilus. Fifty-eight lactic acid bacteria (LAB) strains were isolated from the 20 koji samples with traditional microbial methods. Among them, Enterococcus faecium and Pediococcus pentosaceus were the dominant LAB isolates, with relative abundances of 51.72% and 31.03%. Despite the differences, a large number of shared bacteria were detected in samples from the two areas.

Phenotypic and Genotypic Identification of Bacteria Isolated From Traditionally Prepared Dry Starters of the Eastern Himalayas

Preparation of dry starters for alcohol production is an age-old traditional technology in the Eastern Himalayan regions of east Nepal, the Darjeeling hills, Sikkim, and Arunachal Pradesh in India, and Bhutan. We studied the bacterial diversity in 35 samples of traditionally prepared dry starters, represented by marcha of Nepal, Sikkim, the Darjeeling hills, and Bhutan, phab of Bhutan, and paa, pee, and phut of Arunachal Pradesh, respectively. Populations of bacteria in these starters were 105 to 108 cfu/g. A total of 201 bacterial strains were isolated from starter samples, phenotypically characterized, and their identities confirmed by the 16S rRNA sanger sequencing method. The dominant phylum was Firmicutes (85%), followed by Proteobacteria (9%), and Actinobacteria (6%). Lactic acid bacteria (LAB) (59%) formed the most abundant group, followed by non-LAB (32%) and Gram-negative bacteria (9%). Based on the 16S rRNA gene sequencing result, we identified LAB: Enterococcus durans, E. faecium, E. fecalis, E. hirae, E. lactis, Pediococcus acidilactici, P. pentosaceus, Lactobacillus plantarum subsp. plantarum, Lb. pentosus, Leuconostoc mesenteroides, and Weissella cibaria; non-LAB: Bacillus subtilis subsp. inaquosorum, B. circulans, B. albus, B. cereus, B. nakamurai, B. nitratireducens, B. pseudomycoides, B. zhangzhouensis, Kocuria rosea, Staphylococcus hominis subsp. hominis, S. warneri, S. gallinarum, S. sciuri, Lysinibacillus boronitolerans, Brevibacterium frigoritolerans, and Micrococcus yunnanensis; Gram-negative bacteria: Pseudomonas putida, Klebsiella pneumoniae, Enterobacter hormaechei subsp. xiangfangensis, E. hormaechei subsp. steigerwaltii, and Stenotrophomonas maltophilia. We characterized diversity indexes of the bacterial community present in traditionally prepared dry starters. This is the first report on the bacterial diversity of traditionally dry starters of the Eastern Himalayas by sanger sequencing.

Shotgun Metagenomics of a Water Kefir Fermentation Ecosystem Reveals a Novel Oenococcus Species

Water kefir is a fruity, sour, slightly alcoholic and carbonated beverage, which is made by fermentation of an aqueous sucrose solution in the presence of dried figs and water kefir grains. These polysaccharide grains contain lactic acid bacteria (LAB), yeasts, and sometimes bifidobacteria and/or acetic acid bacteria, which consume sucrose to produce exopolysaccharides, lactic acid, acetic acid, ethanol, and carbon dioxide. Shotgun metagenomic sequencing was used to examine the microbial species diversity present at two time points during water kefir fermentation in detail, both in the water kefir liquor and on the water kefir grains, hence representing four samples. Lactobacillus harbinensis, Lactobacillus hilgardii, Lactobacillus nagelii, Lactobacillus paracasei, and a Lactobacillus species similar to Lactobacillus hordei/mali were present in the water kefir examined, along with Bifidobacterium aquikefiri and two yeast species, namely Saccharomyces cerevisiae and Dekkera bruxellensis. In addition, evidence for a novel Oenococcus species related to Oenococcus oeni and Oenococcus kitaharae was found. Its genome was derived from the metagenome and made available under the name of Candidatus Oenococcus aquikefiri. Through functional analysis of the four metagenomic data sets, it was possible to link the production of lactic acid, acetic acid, ethanol, and carbon dioxide to subgroups of the microbial species found. In particular, the production of mannitol from fructose was linked to L. hilgardii, Candidatus O. aquikefiri, and B. aquikefiri, whereas glycerol production was associated with S. cerevisiae. Also, there were indications of cross-feeding, for instance in the case of amino acid supply. Few bacterial species could synthesize a limited number of cofactors, making them reliant on the figs or S. cerevisiae. The LAB species in turn were found to be capable of contributing to water kefir grain growth, as dextransucrase-encoding genes were attributed to L. hilgardii, L. hordei/mali, and Candidatus O. aquikefiri.

Mycobiome Diversity in Traditionally Prepared Starters for Alcoholic Beverages in India by High-Throughput Sequencing Method

Chowan, dawdim, humao, hamei, khekhrii, and phut are sun-dried starters used for preparation of alcoholic beverages in North East regions of India. We attempted to profile the mycobiome community in these starters by high-throughput sequencing (HTS) method. All fungal populations were found to be restricted to Ascomycota (67-99%), Zygomycota (0.7-29%), Basidiomycota (0.03-7%), and Chytridiomycota (0.0003%). We found 45 core operational taxonomic units (OTUs) which were universally present and were further weighed to 41 genera level and 22 species level taxonomy. A total number of 594 fungal species were detected by HTS including common species (224), unique species (133) and rare-species (237) in samples of starters. Unique species were recorded in phut (40 species), khekhrii (28), hamei (23), dawdim (21), chowan (13), and humao (8), respectively. Most of the fungal families were found to correlate to a type of nutritional mode and growth morphologies of the community, where saprotrophic mode of mold species were more dominant, whereas morphotypes were more dominant in yeast species.

Detection of an amplification bias associated to Leuconostocaceae family with a universal primer routinely used for monitoring microbial community structures within food products

Objectives

Sequencing of 16S rDNA V3–V4 region is widely applied for food community profiling. However, two different universal forward primers (named here MUYZER-primer1 and KLINDWORTH-primer2) targeting an identical conservative sequence upstream of the V3 region of 16S rRNA gene, and only distinguished by a single mismatch are both used. This study was carried out to compare whether the accuracy of food microbiota analysis would depend on the choice of one of these two primers.

Results

Alignment of both primers with common food-borne bacteria 16S sequences revealed that the mismatch between both primers might specifically affect the amplification of Leuconostoc, Oenococcus and Fructobacillus species but not Weissella species. Food products containing either Leuconostoc and/or Weissella were selected for a detection test. As expected from our in silico analysis, our study showed that this mismatch induced a strong biased amplification specifically associated to the OTUs belonging to the genus Leuconostoc but not to the genus Weissella. In presence of Muyzer-primer1, none of the sequences expected for Leuconostoc genus was detected whereas those sequences were correctly amplified with Klindworth-primer2. Since Leuconostoc is an important genus in food, agro-environments and in digestive tract of animals, we recommend that Muyzer-primer1 should thus be abandoned for the bacterial characterization of their associated microbiota.

Comprehensive analysis of fungal diversity and enzyme activity in nuruk, a Korean fermenting starter, for acquiring useful fungi

Nuruk is a fermenting starter that is involved in the production of alcoholic beverages, and has been used in South Korea for a very long time. To analyze the fungal diversity, we collected a total of 59 nuruk samples from several companies and persons in 2013 to 2014, and obtained 364 isolates. All of the single isolated fungi were identified, both morphologically and molecularly, based on the sequences of ribosomal RNA gene [18S, ITS1-5.8S-ITS2, and 26S (D1/D2 region)]. In 46 nuruk samples out of 59 (78%), Saccharomycopsis fibuligera, a dimorphic yeast, was most frequently isolated. Among the filamentous fungi, Aspergillus and Lichtheimia were found in more than 50% of the samples with lower colony forming unit (CFU/g of sample) than those of yeasts. The yeasts S. fibuligera and Wickerhamomyces anomalus were counted with maximum 1.3-1.8 × 10⁸ CFU/g. Among Mucorales fungi, Lichtheimia and Mucor were isolated in much higher numbers than Rhizopus and Rhizomucor. Overall, the home-made nuruks tend to contain more diverse filamentous fungi than the commercial nuruks. To acquire industrially useful filamentous fungi and yeasts, we analyzed the enzyme activities of α-amylase, glucoamylase and acid protease associated with brewing properties for 131 strains. Aspergillus oryzae and S. fibuligera had high α- and glucoamylase activities and most isolates of Lichtheimia ramosa had high acid protease activity. For further applications, 27 fungal strains were chosen based on isolation frequencies from nuruk, and the ability to produce useful enzyme.

Next-generation sequencing approaches for improvement of lactic acid bacteria-fermented plant-based beverages

Plant-based beverages and milk alternatives produced from cereals and legumes have grown in popularity in recent years due to a range of consumer concerns over dairy products. These plant-based products can often have undesirable physiochemical properties related to flavour, texture, and nutrient availability and/or deficiencies. Lactic acid bacteria (LAB) fermentation offers potential remediation for many of these issues, and allows consumers to retain their perception of the resultant products as natural and additive-free. Using next-generation sequencing (NGS) or omics approaches to characterize LAB isolates to find those that will improve properties of plant-based beverages is the most direct way to product improvement. Although NGS/omics approaches have been extensively used for selection of LAB for use in the dairy industry, a comparable effort has not occurred for selecting LAB for fermenting plant raw substrates, save those used in producing wine and certain types of beer. Here we review the few and recent applications of NGS/omics to profile and improve LAB fermentation of various plant-based substrates for beverage production. We also identify specific issues in the production of various LAB fermented plant-based beverages that such NGS/omics applications have the power to resolve.