Diversity of Yeasts and Molds by Culture-Dependent and Culture-Independent Methods for Mycobiome Surveillance of Traditionally Prepared Dried Starters for the Production of Indian Alcoholic Beverages

Unveiling the microbial communities and metabolic pathways of Keem, a traditional starter culture, through whole-genome sequencing

Traditional alcoholic beverages have played a significant role in the cultural, social, and culinary fabric of societies worldwide for centuries. Studying the microbial community structure and their metabolic potential in such beverages is necessary to define product quality, safety, and consistency, as well as to explore associated biotechnological applications. In the present investigation, Illumina-based (MiSeq system) whole-genome shotgun sequencing was utilized to characterize the microbial diversity and conduct predictive gene function analysis of keem, a starter culture employed by the Jaunsari tribal community in India for producing various traditional alcoholic beverages. A total of 8,665,213 sequences, with an average base length of 151 bps, were analyzed using MG-RAST. The analysis revealed the dominance of bacteria (95.81%), followed by eukaryotes (4.11%), archaea (0.05%), and viruses (0.03%). At the phylum level, Actinobacteria (81.18%) was the most abundant, followed by Firmicutes (10.56%), Proteobacteria (4.00%), and Ascomycota (3.02%). The most predominant genera were Saccharopolyspora (36.31%), followed by Brevibacterium (15.49%), Streptomyces (9.52%), Staphylococcus (8.75%), Bacillus (4.59%), and Brachybacterium (3.42%). At the species level, the bacterial, fungal, and viral populations of the keem sample could be categorized into 3347, 57, and 106 species, respectively. Various functional attributes to the sequenced data were assigned using Cluster of Orthologous Groups (COG), Non-supervised Orthologous Groups (NOG), subsystem, and KEGG Orthology (KO) annotations. The most prevalent metabolic pathways included carbohydrate, lipid, and amino acid metabolism, as well as the biosynthesis of glycans, secondary metabolites, and xenobiotic biodegradation. Given the rich microbial diversity and its associated metabolic potential, investigating the transition of keem from a traditional starter culture to an industrial one presents a compelling avenue for future research.

Developing a novel selection method for alcoholic fermentation starters by exploring wine yeast microbiota from Greece

The selection of native yeast for alcoholic fermentation in wine focuses on ensuring the success of the process and promoting the quality of the final product. The purpose of this study was firstly to create a large collection of new yeast isolates and categorize them based on their oenological potential. Additionally, the geographical distribution of the most dominant species, Saccharomyces cerevisiae, was further explored. Towards this direction, fourteen spontaneously fermented wines from different regions of Greece were collected for yeast typing. The yeast isolates were subjected in molecular analyses and identification at species level. RAPD (Random Amplified Polymorphic DNA) genomic fingerprinting with the oligo-nucleotide primer M13 was used, combined with Matrix Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) technique. All yeast isolates were scrutinized for their sensitivity to killer toxin, production of non-desirable metabolites such as acetic acid and H2S, β-glucosidase production and resistance to the antimicrobial agent; SO2. In parallel, S. cerevisiae isolates were typed at strain level by interdelta - PCR genomic fingerprinting. S. cerevisiae strains were examined for their fermentative capacity in laboratory scale fermentation on pasteurized grape must. Glucose and fructose consumption was monitored daily and at the final point a free sorting task was conducted to categorize the samples according to their organoleptic profile. According to our results, among the 190 isolates, S. cerevisiae was the most dominant species while some less common non-Saccharomyces species such as Trigonopsis californica, Priceomyces carsonii, Zygosaccharomyces bailii, Brettanomyces bruxellensis and Pichia manshurica were identified in minor abundancies. According to phenotypic typing, most isolates were neutral to killer toxin test and exhibited low acetic acid production. Hierarchical Cluster Analysis revealed the presence of four yeast groups based on phenotypic fingerprinting. Strain level typing reported 20 different S. cerevisiae strains from which 65% indicated fermentative capacity and led to dry wines. Sensory evaluation results clearly discriminated the produced wines and consequently, the proposed yeast categorization was confirmed. A novel approach that employs biostatistical tools for a rapid screening and classification of indigenous wine yeasts with oenological potential, allowing a more efficient preliminary selection or rejection of isolates is proposed.

Fruit waste: a current perspective for the sustainable production of pharmacological, nutraceutical, and bioactive resources

Fruits are crucial components of a balanced diet and a good source of natural antioxidants, that have proven efficacy in various chronic illnesses. Various kinds of waste generated from fruit industries are considered a global concern. By utilizing this fruit waste, the international goal of "zero waste" can be achieved by sustainable utilization of these waste materials as a rich source of secondary metabolites. Moreover, to overcome this waste burden, research have focused on recovering the bioactive compounds from fruit industries and obtaining a new strategy to combat certain chronic diseases. The separation of high-value substances from fruit waste, including phytochemicals, dietary fibers, and polysaccharides which can then be used as functional ingredients for long-term health benefits. Several novel extraction technologies like ultrasound-assisted extraction (UAE), pressurized liquid extraction (PLE), and supercritical fluid extraction (SFE) could provide an alternative approach for successful extraction of the valuable bioactives from the fruit waste for their utilization as nutraceuticals, therapeutics, and value-added products. Most of these waste-derived secondary metabolites comprise polyphenols, which have been reported to have anti-inflammatory, insulin resistance-treating, cardiovascular disease-maintaining, probiotics-enhancing, or even anti-microbial and anti-viral capabilities. This review summarizes the current knowledge of fruit waste by-products in pharmacological, biological, and probiotic applications and highlights several methods for identifying efficacious bioactive compounds from fruit wastes.

Diversity, antimicrobial production, and seasonal variation of honey bee microbiota isolated from the honey stomachs of the domestic honey bee, Apis mellifera

The antimicrobial nature of honey and its related apiological origins typically focus on basic chemical analysis without attempting to understand the diversity of the microbial component. The antibacterial activity, chemical characterization, and diversity of bacteria isolated from Apis mellifera honey stomachs and hive honey collected throughout the honey production season are presented. After screening >2,000 isolates, 50 isolates were selected and characterized by 16S rRNA gene homology, Gram stain, catalase and protease tests, as well as for antibacterial activity against select indicators. Antibacterial-producing isolates were predominantly from the Pseudomonas, Paenibacillus, Lonsdalea, Serratia, and Bacillus genera. Isolates collected from honey stomachs in April displayed the highest level of activity (27%). While April isolates did not demonstrate activity against the Gram-negative bacteria tested. Whereas 59% of July isolates, 33% of September isolates, and 100% of the honey isolates did. The predominant honey stomach isolates were Pseudomonas spp. (April), Paenibacillus polymyxa (July, Sept.), and Lonsdalea iberica (Sept.). Chemical characterizations of the antimicrobial compounds show most to be antibiotic in nature with the minority being potential bacteriocins. This study offers the first glimpse into the variability and diversity of the bacteria/host interactions found within the honey stomach of the domestic honey bee while revealing a novel source of potentially beneficial antimicrobial compounds.

Physiological characterization and molecular identification of Saccharomycopsis fibuligera as the etiological agent of a skin lesion

Routine laboratory methods are not effective in identifying cryptic species resulting in the underreporting of infections caused by non-Candida yeasts. This paper presents the physiological characteristics and antifungal susceptibility of Saccharomycopsis fibuligera 12-771, isolated from a tinea-like lesion. Isolate 12-771 was identified by ITS and D1/D2 analysis as S. fibuligera. The isolate presented an auxonogram profile similar to Candida utilis, as well as protease, esterase and hemolysin activity. MICs were of 0.25 ​μg/mL for amphotericin B, 1-2 ​μg/mL for echinocandins, and 16 ​μg/mL for fluconazole. This work represents the first record in America of S. fibuligera as an infectious agent.

Changes in Microbial Diversity and Nutritional Components of Mare Milk Before and After Traditional Fermentation

The formation and quality of nutrients before and after fermentation depends on microbial community dynamics. In this study, the nutrients and microflora of mare milk were studied before and after traditional fermentation. To achieve this goal, ultra-performance liquid chromatography-mass spectrometry and Illumina MiSeq sequencing were used to study the changes in the main nutrients and microbial communities, respectively, before and after mare milk traditional fermentation. A total of 81 nutrients were identified before and after the fermentation of mare milk into koumiss; among these, 6 compounds [citraconic acid, 6-hydroxycaproic acid, creatine, adenine, d-(+)-proline, and histamine] were differentially upregulated. Histamine levels increased after traditional fermentation, whereas Lactobacillus, Dekkera, and Acetobacter grew rapidly and became the dominant microorganisms in the fermentation process. These three genera were positively correlated with creatine and proline levels, whereas Lelliottia was negatively correlated with citraconic acid and proline levels. Prediction of the functions of bacteria and fungi in the mare milk before and after fermentation included carbohydrate metabolism, cofactors and nutrition, and plant pathogens. The results of this study provide new insights into the formation of nutrients in koumiss; it is important to study changes in bacteria and fungi before and after traditional fermentation.

Revealing Probiotic Potential of Enterococcus Strains Isolated From Traditionally Fermented Chhurpi and Healthy Human Gut

In this study, the two lactic acid bacterial strains Enterococcus durans and Enterococcus lactis previously isolated from soft chhurpi, a traditionally fermented milk product prepared by the indigenous community of Sikkim Himalayas and healthy human gut were used. In this study, we attempted to investigate the probiotic attributes, safety, and health beneficial role, and hypercholesterolemia of Enterococcus durans and Enterococcus lactis. Both probiotic potential strains showed good hypocholesterolemic activity in vitro along with tolerance to acid pH (2 and 2.5), tolerance to three bile salts, oxbile, cholic acid, and taurocholic acid (0.5 and 1%), presence of BSH enzyme and its activity, and cell surface adherence. On assessing for safety, both LAB strains were sensitive to antibiotics and exhibited no hemolytic activity. The probiotic strains were tested in vivo in the Sprague–Dawley rats which were divided into five experimental groups: Normal Control (ND), probiotic strain Enterococcus durans HS03 (BSH-negative) and high-cholesterol diet (HCD1), probiotic strain Enterococcus lactis YY1 (BSH-positive) and high-cholesterol diet (HCD2), and a combination of both strains and high-cholesterol diet (HCD3) and Negative Control (HCD). The probiotic-treated groups HCD1, HCD2, and HCD3 showed a decrease in serum cholesterol levels up to 22.55, 6.67, and 31.06%; the TG and VLDL concentrations were 25.39, 26.3, and 33.21%; reduction in LDL-cholesterol was 33.66, 28.50, and 35.87%; and increase of HDL was 38.32, 47.9, and 41.92%. Similarly, the effects of total cholesterol and TG in the liver, kidney and liver histopathology, liver and body lipid index, and oxidative stress in rat liver were also studied. The fecal lactobacilli were more in the samples of the probiotic-treated groups and their fecal coliform and E. coli counts decreased relatively as compared to the control groups in 0, 7, 14, and 21 days. This is the first report on the probiotic potential of Enterococcus durans HS03 and Enterococcus lactis YY1 strains that gives a new insight into the cholesterol-lowering and probiotic product development with wide health attributes.

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.

Constructing Micro-Landscapes: Management and Selection Practices on Microbial Communities in a Traditional Fermented Beverage

Colonche is a traditional beverage produced in Mexico by the fermentation of fruits of several cacti species. In the Meridional Central Plateau region of Mexico, where this study was conducted, it is mainly produced with fruits of Opuntia streptacantha; there, the producers perform spontaneous fermentation and/or fermentations through inoculums. Several factors can change the microbial community structure and dynamics through the fermentation process, but little attention has been directed to evaluate what type and extent of change the human practices have over the microbial communities. This study aims to assess the microbiota under spontaneous and inoculated fermentation techniques, the microorganisms present in the inoculums and containers, and the changes of microbiota during the process of producing colonche with different techniques. We used next-generation sequencing of the V3-V4 regions of the 16S rRNA gene and the ITS2, to characterize bacterial and fungal diversity associated with the different fermentation techniques. We identified 701 bacterial and 203 fungal amplicon sequence variants (ASVs) belonging to 173 bacterial and 187 fungal genera. The alpha and beta diversity analysis confirmed that both types of fermentation practices displayed differences in richness, diversity, and community structure. Richness of bacteria in spontaneous fermentation (0D = 136 ± 0.433) was higher than in the inoculated samples (0D = 128 ± 0.929), while fungal richness in the inoculated samples (0D = 32 ± 0.539) was higher than in spontaneous samples (0D = 19 ± 0.917). We identified bacterial groups like Lactobacillus, Leuconostoc, Pediococcus and the Saccharomyces yeast shared in ferments managed with different practices; these organisms are commonly related to the quality of the fermentation process. We identified that clay pots, where spontaneous fermentation is carried out, have an outstanding diversity of fungal and bacterial richness involved in fermentation, being valuable reservoirs of microorganisms for future fermentations. The inoculums displayed the lowest richness and diversity of bacterial and fungal communities suggesting unconscious selection on specific microbial consortia. The beta diversity analysis identified an overlap in microbial communities for both types of fermentation practices, which might reflect a shared composition of microorganisms occurring in the Opuntia streptacantha substrate. The variation in the spontaneous bacterial community is consistent with alpha diversity data, while fungal communities showed less differences among treatments, probably due to the high abundance and dominance of Saccharomyces. This information illustrates how traditional management guides selection and may drive changes in the microbial consortia to produce unique fermented beverages through specific fermentation practices. Although further studies are needed to analyze more specifically the advantages of each fermentation type over the quality of the product, our current analysis supports the role of traditional knowledge driving it and the relevance of plans for its conservation.

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.

"Ethno-microbiology" of ethnic Indian fermented foods and alcoholic beverages

The concept of "ethno-microbiology" is to understand the indigenous knowledge of the Indian people for production of culturally and organoleptically acceptable fermented foods by natural fermentation. About 1000 types of common, uncommon, rare, exotic and artisan fermented foods and beverages are prepared and consumed in different geographical regions by multi-ethnic communities in India. Indian fermented foods are mostly acidic and some are alkaline, along with various types of alcoholic beverages. A colossal diversity of microorganisms comprising bacteria mostly belongs to phylum Firmicutes, filamentous moulds and enzyme- and alcohol-producing yeasts under phyla Ascomycota and Mucoromycota, and few bacteriophages and archaea have been reported from Indian fermented foods. Some microorganisms associated with fermented foods have functionalities and health promoting benefits. "Ethno-microbiology" of ethnic Indian people has exhibited the proper utilisation of substrates either singly or in combination such as fermented cereal-legume mixture (idli, dosa and dhokla) in South and West India, sticky fermented soybean food (kinema and related foods), fermented perishable leafy vegetable (gundruk and related foods), fermented bamboo shoots (soibum and related foods) and fermented fish (ngari and others) in North East India, and fermented meat and sausage-like products in the Indian Himalayas, fermented coconut beverage (toddy) in coastal regions, and various types of naturally fermented milk products (dahi and related products) in different regions of India. This review has also highlighted the "ethno-microbiology" knowledge of the people involving the consortia of essential microorganisms in traditionally prepared amylolytic starters for production of cereal-based alcoholic beverages. The novelty of this review is the interpretation of ethno-microbiological knowledge innovated by ethnic Indian people on the use of beneficial microorganisms for food fermentation to obtain the desired fermented food products for consumption.

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.

Linking the Diversity of Yeasts Inherent in Starter Cultures to Quorum Sensing Mechanism in Ethnic Fermented Alcoholic Beverages of Northeast India

In this review, the relevance of diversity of yeasts and their interactive association in household ethnic fermentation are discussed. The longstanding traditional household fermentation practice involves preparation of fermented product such as alcoholic beverages from various indigenous agricultural products with the help of microorganisms cultivated from local environment and perpetuated for hundreds of years through generations indoctrinating an indigenous knowledge system. Northeast India is known for its rich physiographic and geo-demographic diversity and is home to several ethnicities who follow unique practices of household traditional fermentation. The diversity of yeasts present within the microbial inoculum used for fermentation by different indigenous communities has been keenly studied and reported to be unique in spite of their common source for starter substrates. Saccharomyces yeasts are primarily involved in alcoholic fermentation, whereas non-Saccharomyces yeasts, which are reportedly confined to a particular geographical region, have been reported to contribute toward the final outcome of fermentation produce. During fermentation, interaction among these large microbial communities and their resulting physiological expression within the fermentation micro-environment is believed to affect the final quality of the product. Mechanism of quorum sensing plays an important role in these interactions in order to maintain proportionality of different yeast populations wherein the quorum sensing molecules not only regulate population density but also effectively aid in enhancement of alcoholic fermentation. Additionally, various secondary metabolites, which are secreted as a result of inter-species interactions, have been found to affect the quality of beverages produced. This review concludes that diverse species of yeasts and their interaction within the fermentation micro-environment influence the sustainability and productivity of household ethnic fermentation.

Changes in microbial communities and their predictive functionalities during fermentation of toddy, an alcoholic beverage of India

Toddy is a traditional mild-alcoholic drink of India, which is produced from fresh palm saps by natural fermentation. We studied the successional changes in bacterial and fungal communities during the natural fermentation (0 h-96 h) of toddy. During fermentation, alcohol content of the fermenting saps increased significantly from 0.6 %±0.15 to 5.6 %±0.02, pH decreased from 6.33 %±0.02-3.93 ± 0.01, volatile and titratable acidity acidity (g/100 mL) increased from 0.17 ± 0.02 (0 h) to 0.48 ± 0.02 (96 h) and 1.30 ± 0.005 (0 h) to 2.47 ± 0.005 (96 h), respectively. Total sugar content and ˚BRIX also decreased during the fermentation. Firmicutes (78.25 %) was the most abundant phylum followed by Proteobacteria (21.57 %). Leuconostoc was the most abundant genus in the early stages of fermentation. However, Lactobacillus and Gluconoacetobacter were found abundant with increase in pH during the later phases of fermentation (72 h-96 h). Ascomycota (99.02 %) was the most abundant fungal phylum. Hanseniaspora was the abundant yeast in the initial stages of fermentation, whereas the population of Saccharomyces increased significantly after 24 h of fermentation. Torulaspora, Lachancea and Starmerella showed their heterogeneous distribution throughout the fermentation. Computational analysis of metagenomes based on KEGG and MetaCyc databases showed different predictive functional profiles such as folate biosynthesis, glutathione metabolism, terpenoids biosynthesis and biosynthesis of amino acids with significant differences between the fresh palm saps and fermenting saps during toddy fermentation.

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.

Assessing the Microbial Communities in Four Different Daqus by Using PCR-DGGE, PLFA, and Biolog Analyses

Daqu made from raw wheat, barley or pea is used as an inoculum for the fermentation of Chinese Baijiu. In this study, the microbial communities of four different types of Daqus (sauce-flavor Wuling Daqu, sauce and strong-flavor Baisha Daqu, strong-flavor Deshan Daqu, and light-flavor Niulanshan Daqu) were analyzed by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), phospholipid fatty acid (PLFA) analysis, and Biolog EcoPlates analysis (Biolog). Clear differences were seen between the microbial communities of the four Daqus. PCR-DGGE showed differences in the number and brightness of bands between the Daqus, indicating the presence of unique bacterial species in Deshan Daqu, Wuling Daqu, and Niulanshan Daqu. Lactobacillus sanfranciscensis, Bacillus thermoamylovorans, and some unclassified bacteria were unique to Wuling Daqu, Deshan Daqu, and Niulanshan Daqu, respectively. Moreover, some bacterial species were observed in all four Daqus. A total of 26 PLFAs between C12 to C20 were detected from the four Daqus by PLFA analysis. Wuling Daqu had the highest total and fungal biomasses, Baisha Daqu had the highest bacterial biomass, and Niulanshan Daqu had the highest ratio of fungal biomass to bacterial biomass. The Biolog results indicated differences in the carbon source use and mode of the four Daqus, and also demonstrated that each Daqu had varying abilities to utilize different types of carbon sources. The cluster analysis of the three methods showed that the microbial communities of the four Daqus were different. This study also demonstrates the applicability of the three analytical methods in the evaluating of the microbial communities of Daqus.

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.

Fermented foods in a global age: East meets West

Fermented foods and alcoholic beverages have long been an important part of the human diet in nearly every culture on every continent. These foods are often well-preserved and serve as stable and significant sources of proteins, vitamins, minerals, and other nutrients. Despite these common features, however, many differences exist with respect to substrates and products and the types of microbes involved in the manufacture of fermented foods and beverages produced globally. In this review, we describe these differences and consider the influence of geography and industrialization on fermented foods manufacture. Whereas fermented foods produced in Europe, North America, Australia, and New Zealand usually depend on defined starter cultures, those made in Asia and Africa often rely on spontaneous fermentation. Likewise, in developing countries, fermented foods are not often commercially produced on an industrial scale. Although many fermented products rely on autochthonous microbes present in the raw material, for other products, the introduction of starter culture technology has led to greater consistency, safety, and quality. The diversity and function of microbes present in a wide range of fermented foods can now be examined in detail using molecular and other omic approaches. The nutritional value of fermented foods is now well-appreciated, especially in resource-poor regions where yoghurt and other fermented foods can improve public health and provide opportunities for economic development. Manufacturers of fermented foods, whether small or large, should follow Good Manufacturing Practices and have sustainable development goals. Ultimately, preferences for fermented foods and beverages depend on dietary habits of consumers, as well as regional agricultural conditions and availability of resources.

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.

Current insights into fungal species diversity and perspective on naming the environmental DNA sequences of fungi

The global bio-diversity of fungi has been extensively investigated and their species number has been estimated. Notably, the development of molecular phylogeny has revealed an unexpected fungal diversity and utilisation of culture-independent approaches including high-throughput amplicon sequencing has dramatically increased number of fungal operational taxonomic units. A number of novel taxa including new divisions, classes, orders and new families have been established in last decade. Many cryptic species were identified by molecular phylogeny. Based on recently generated data from culture-dependent and -independent survey on same samples, the fungal species on the earth were estimated to be 12 (11.7-13.2) million compared to 2.2-3.8 million species recently estimated by a variety of the estimation techniques. Moreover, it has been speculated that the current use of high-throughput sequencing techniques would reveal an even higher diversity than our current estimation. Recently, the formal classification of environmental sequences and permission of DNA sequence data as fungal names' type were proposed but strongly objected by the mycologist community. Surveys on fungi in unusual niches have indicated that many previously regarded "unculturable fungi" could be cultured on certain substrates under specific conditions. Moreover, the high-throughput amplicon sequencing, shotgun metagenomics and a single-cell genomics could be a powerful means to detect novel taxa. Here, we propose to separate the fungal types into physical type based on specimen, genome DNA (gDNA) type based on complete genome sequence of culturable and uncluturable fungal specimen and digital type based on environmental DNA sequence data. The physical and gDNA type should have priority, while the digital type can be temporal supplementary before the physical type and gDNA type being available. The fungal name based on the "digital type" could be assigned as the "clade" name + species name. The "clade" name could be the name of genus, family or order, etc. which the sequence of digital type affiliates to. Facilitating future cultivation efforts should be encouraged. Also, with the advancement in knowledge of fungi inhabiting various environments mostly because of rapid development of new detection technologies, more information should be expected for fungal diversity on our planet.

Unraveling the Contribution of High Temperature Stage to Jiang-Flavor Daqu, a Liquor Starter for Production of Chinese Jiang-Flavor Baijiu, With Special Reference to Metatranscriptomics

Jiang-flavor (JF) daqu is a liquor starter used for production of JF baijiu, a well-known distilled liquor in China. Although a high temperature stage (70°C) is necessary for qualifying JF daqu, little is known regarding its active microbial community and functional enzymes, along with its role in generating flavor precursors for JF baijiu aroma. In this investigation, based on metatranscriptomics, fungi, such as Aspergillus and Penicillium, were identified as the most active microbial members and 230 carbohydrate-active enzymes were identified as potential saccharifying enzymes at 70°C of JF daqu. Notably, most of enzymes in identified carbohydrate and energy pathways showed lower expression levels at 70°C of JF daqu than those at the high temperature stage (62°C) of Nong-flavor (NF) daqu, indicating lowering capacities of saccharification and fermentation by high temperature stage. Moreover, many enzymes, especially those related to the degradation of aromatic compounds, were only detected with low expression levels at 70°C of JF daqu albeit not at 62°C of NF daqu, indicating enhancing capacities of generating special trace aroma compounds in JF daqu by high temperature stage. Additionally, most of enzymes related to those capacities were highly expressed at 70°C by fungal genus of Aspergillus, Coccidioides, Paracoccidioides, Penicillium, and Rasamsonia. Therefore, this study not only sheds light on the crucial functions of high temperature stage but also paves the way to improve the quality of JF baijiu and provide active community and functional enzymes for other fermentation industries.

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.