Review: Diversity of Microorganisms in Global Fermented Foods and Beverages

Culturalable and non-culturable microorganisms naturally ferment majority of global fermented foods and beverages. Traditional food fermentation represents an extremely valuable cultural heritage in most regions, and harbors a huge genetic potential of valuable but hitherto undiscovered strains. Holistic approaches for identification and complete profiling of both culturalable and non-culturable microorganisms in global fermented foods are of interest to food microbiologists. The application of culture-independent technique has thrown new light on the diversity of a number of hitherto unknown and non-cultural microorganisms in naturally fermented foods. Functional bacterial groups (“phylotypes”) may be reflected by their mRNA expression in a particular substrate and not by mere DNA-level detection. An attempt has been made to review the microbiology of some fermented foods and alcoholic beverages of the world.


INTRODUCTION
Traditionally, boiled rice is a staple diet with fermented and non-fermented legume (mostly soybeans) products, vegetables, pickles, fish, and meat in Far-East Asia, South Asia, North Asia, and the Indian subcontinent excluding Western and Northern India; while wheat/barley-based breads/loaves comprise a staple diet followed by milk and fermented milk products, meat, and fermented meats (sausages) in the Western and Northern part of India, West Asian continent, Europe, North America, and even in Australia and New Zealand (Tamang and Samuel, 2010). Sorghum/maize porridges, on the other hand, are the main courses of diet with many fermented and non-fermented sorghum/maize/millets, cassava, wild legume seeds, meat, and milk products in Africa and South America. Fermented foods are the hub of consortia of microorganisms, since they are either present as natural indigenous microbiota in uncooked plant or animal substrates, utensils, containers, earthen pots, and the environment (Hesseltine, 1979;Franz et al., 2014), or add starter culture(s) containing functional microorganisms (Holzapfel, 1997;Stevens and Nabors, 2009) which modify the substrates biochemically, and organoleptically into edible products that are culturally and socially acceptable to the consumers (Campbell-Platt, 1994;Steinkraus, 1997;Tamang, 2010b). Microorganisms convert the chemical composition of raw materials during fermentation, which enrich the nutritional value in some fermented foods, and impart health-benefits to the consumers (Steinkraus, 2002;Farhad et al., 2010;Tamang, 2015a).
Several researchers have reviewed the microbiology, biochemistry, and nutrition of fermented foods and beverages from different countries of Asia (Hesseltine, 1983;Steinkraus, 1994Steinkraus, , 1996Nout and Aidoo, 2002;Tamang et al., 2015); Africa (Odunfa and Oyewole, 1997;Olasupo et al., 2010;Franz et al., 2014); Europe (Pederson, 1979;Campbell-Platt, 1987;Wood, 1998); South America (Chaves-López et al., 2014), and North America (Doyle and Beuchat, 2013). Many genera/species of microorganisms have been reported in relation to various fermented foods and beverages across the world; the usage of molecular tools in recent years have helped to clarify, at least in part, the nomenclatural confusion and generalization caused by conventional (phenotypic) taxonomic methods. The present paper is an attempt to collate and review the updated information on microbiology of some globally fermented foods and beverages.
Bacillus is present in alkaline-fermented foods of Asia and Africa (Parkouda et al., 2009;Tamang, 2015b). Species of Bacillus that are present, mostly in legume-based fermented foods, are Bacillus amyloliquefaciens, Bacillus circulans, Bacillus coagulans, Bacillus firmus, Bacillus licheniformis, Bacillus megaterium, Bacillus pumilus, Bacillus subtilis, Bacillus subtilis variety natto, and Bacillus thuringiensis (Kiers et al., 2000;Kubo et al., 2011), while strains of Bacillus cereus have been isolated from the fermentation of Prosopis africana seeds for the production of okpehe in Nigeria (Oguntoyinbo et al., 2007). Some strains of B. subtilis produce λ-polyglutamic acid (PGA) which is an amino acid polymer commonly present in Asian fermented soybean foods, giving the characteristic of a sticky texture to the product (Urushibata et al., 2002;Nishito et al., 2010).
Major role of filamentous molds in fermented foods and alcoholic beverages is the production of enzymes and the degradation of anti-nutritive factors (Aidoo and Nout, 2010). Species of Actinomucor, Amylomyces, Aspergillus, Monascus, Mucor, Neurospora, Parcilomyces, Penicillium, Rhizopus, and Ustilago are reported for many fermented foods, Asian non-food amylolytic starters and alcoholic beverages (Nout and Aidoo, 2002;Chen et al., 2014).

TAXONOMIC TOOLS FOR IDENTIFICATION OF MICROORGANISMS FROM FERMENTED FOODS
Use of culture media may ignore several unknown non-culturable microorganisms that may play major or minor functional roles in production of fermented foods. Direct DNA extraction from samples of fermented foods, commonly known as cultureindependent methods, is nowadays frequently used in food microbiology to profile both culturable and non-culturable microbial populations from fermented foods (Cocolin and Ercolini, 2008;Alegría et al., 2011;Cocolin et al., 2013;Dolci et al., 2015), provided that the amplification efficiency is high enough. PCR-DGGE analysis is the most popular culture-independent technique used for detecting microorganisms in fermented foods and thereby profiling both bacterial populations (Cocolin et al., 2011;Tamang, 2014) and yeast populations in fermented foods (Cocolin et al., 2002;Jianzhonga et al., 2009). Both culturable and non-culturable microorganisms from any fermented food and beverage may be identified using culture-dependent and -independent methods to document a complete profile of microorganisms, and also to study both inter-and intra-species diversity within a particular genus or among genera (Ramos et al., 2010;Greppi et al., 2013a,b;Yan et al., 2013). A combination of Propidium MonoAzide (PMA) treatment on samples before DNA extraction and molecular quantifying method can be used to accurately enumerate the viable microorganisms in fermented foods (Desfossés-Foucault et al., 2012;Fujimoto and Watanabe, 2013). Molecular identification is emerging as an accurate and reliable identification tool, and is widely used in identification of both culture-dependent and culture-independent microorganisms from fermented foods (Giraffa and Carminati, 2008;Dolci et al., 2015). Species-specific PCR primers are used for species level identification ; this technique is widely applied in the identification of LAB isolated from fermented foods (Robert et al., 2009). The application of real-time quantitative PCR (qPCR) with specific primers enables the specific detection and quantification of LAB species in fermented foods . Random amplification of polymorphic DNA (RAPD) is a typing method based on the genomic DNA fragment profiles amplified by PCR, and is commonly used for disintegration of LAB strains from fermented foods (Coppola et al., 2006;Chao et al., 2008). The repetitive extragenic palindromic sequencebased PCR (rep-PCR) technique permits typing at subspecies level and reveals significant genotypic differences among strains of the same bacterial species from fermented food samples . Amplified fragment length polymorphism (AFLP) is a technique based on the selective amplification and separation of genomic restriction fragments, and its applicability in identification and to discriminate has been demonstrated for various LAB strains (Tanigawa and Watanabe, 2011).
Techniques of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) have been developed to profile microbial communities directly from fermented foods, and are based on sequence-specific distinctions of 16S rDNA and 26S rDNA amplicons produced by PCR (Ercolini, 2004;Flórez and Mayo, 2006;Alegría et al., 2011). However, DGGE has some disadvantages as well like it is time consuming, unable to determine the relative abundance of dominant species and distinguish between viable and nonviable cells, as well as it has difficulties in interpretation of multi-bands (Dolci et al., 2015). DGGE is also limited to detect specific species as it may only reveal some of the major bacterial species such as B. licheniformis and Bacillus thermoamylovorans in chungkokjang (sticky fermented soybean food of Korea) and not detect a large number of predominant or diverse rare bacterial species identified in pyrosequencing analysis (Nam et al., 2011).
The amplified ribosomal DNA restriction analysis (ARDRA) technique using restriction enzymes is also useful in identification of microorganisms from fermented foods (Jeyaram et al., 2010).
Effective tools of next generation sequencing (NGS) such as metagenomics, phylobiomics, and metatranscriptomics are nowadays applied for documentation of cultures in traditionally fermented products (Mozzi et al., 2013;van Hijum et al., 2013). However, NGS as a sophisticated tool needs well-trained hands and a well-equipped molecular laboratory, which may not always be available. Application of metagenomic approaches, by using parallel pyrosequencing of tagged 16S rRNA gene amplicons, provide information on microbial communities as profiled in kimchi, a naturally fermented vegetable product of Korea (Jung et al., 2011;Park et al., 2012), nukadoko, a fermented rice bran of Japan (Sakamoto et al., 2011), narezushi, a fermented salted fish and cooked rice of Japan (Kiyohara et al., 2012), and ben-saalga, a traditional gruel of pearl millet of Burkina Faso (Humblot and Guyot, 2009). Pyrosequencing has revealed the presence of numerous and even minor bacterial groups in fermented foods, but DNA-level detection does not distinguish between metabolically "active" and "passive" organisms. "Functionally relevant phylotypes" in an ecosystem may be specifically detected by, e.g., weighted UniFrac principal coordinate analysis based on 454 pyrosequencing of 16S rRNA genes, as applied in studies on gut microbiota (Wang et al., 2015). The 16S rRNA gene sequence based pyrosequencing method enables a comprehensive and high-throughput analysis of microbial ecology (Sakamoto et al., 2011), and this method has been applied to various traditionally fermented foods (Oki et al., 2014).
A proteomics identification method based on protein profiling using matrix-assisted laser desorption ionizing-time of flight mass spectrometry (MALDI-TOF MS) has been used to identify species of Bacillus in fermented foods of Africa (Savadogo et al., 2011), and species of LAB isolated from global fermented foods (Tanigawa et al., 2010;Dušková et al., 2012;Sato et al., 2012;Nguyen et al., 2013a;Kuda et al., 2014).

Global Fermented Foods
Campbell-Platt (1987) reported around 3500 global fermented foods and beverages, and had divided them into about 250 groups. There might be more than 5000 varieties of common and uncommon fermented foods and alcoholic beverages being consumed in the world today by billions of people, as staple and other food components (Tamang, 2010b). Global fermented foods are classified into nine major groups on the basis of substrates (raw materials) used from plant/animal sources: (1) fermented cereals, (2) fermented vegetables and bamboo shoots, (3) fermented legumes, (4) fermented roots/tubers, (5) fermented milk products, (6) fermented and preserved meat products, (7) fermented, dried and smoked fish products, (8) miscellaneous fermented products, and (9) alcoholic beverages (Steinkraus, 1997;Tamang, 2010b,c).

Fermented Milk Products
Fermented milk products ( Table 1) are classified into two major groups on the basis of microorganisms: (A) lactic fermentation, dominated by species of LAB, comprising the "thermophilic" type (e.g., yogurt, Bulgarian buttermilk), probiotic type (e.g., acidophilus milk, bifidus milk), and the mesophilic type (e.g., natural fermented milk, cultured milk, cultured cream, cultured buttermilk); and (B) fungal-lactic fermentations, where LAB and yeasts cooperate to generate the final product, which include alcoholic milks (e.g., acidophilus-yeast milk, kefir, koumiss), and moldy milks (e.g., viili; Mayo et al., 2010). Natural fermentation is one of the oldest methods of milk processing using raw and boiled milk to ferment spontaneously, or of using the back-slopping method where a part of the previous batch of a fermented product is used to inoculate the new batch (Holzapfel, 2002;Josephsen and Jespersen, 2004). Cheese and cheese products derived from the fermentation of milk are of major nutritional and commercial importance throughout the world (de Ramesh et al., 2006)  1 | Microorganisms isolated from some common and uncommon fermented milk products of the world.

Fermented Cereal Foods
In most of the Asian countries, rice is fermented either by using mixed-culture(s) into alcoholic beverages or by using food beverages (Tamang, 2010c), whereas in Europe, America, and Australia, most cereals like wheat, rye, barley and maize are fermented by natural fermentation or by adding commercial baker's yeast into the batter for dough breads/loaves (Guyot, 2010). In Africa, fermented cereal foods are traditionally used as staples as well as complementary and weaning foods for infants and young children (Tou et al., 2007). In Europe, people still practice the old traditional method of preparation of breads or loaves without using any commercial strains of baker's yeast (Hammes and Ganzle, 1998). Yeasts and LAB conduct dough fermentation, mostly San Francisco sourdough, and the resultant products are generally called sourdough breads because they have higher contents of lactic acid and acetic acid due to the bacterial growth (Brandt, 2007;). Cereal fermentation is mainly represented by species of LAB and yeasts (Corsetti and Settanni, 2007). Enterococcus, Lactococcus, Lactobacillus, Leuconostoc, Pediococcus, Streptococcus, and Weissella are common bacteria associated with cereal fermentations ( Table 2; Guyot, 2010;Moroni et al., 2011). Native strains of Saccharomyces cerevisiae are the principal yeast of most bread fermentations (Hammes et al., 2005), but other non-Saccharomyces yeasts are also significant in many cereal fermentations including Candida, Debaryomyces, Hansenula, Kazachstania, Pichia, Trichosporon, and Yarrowia (Iacumin et al., 2009;Weckx et al., 2010;Johnson and Echavarri-Erasun, 2011).

Fermented Vegetable Foods
Perishable and seasonal leafy vegetables, radish, cucumbers including young edible bamboo tender shoots are traditionally fermented into edible products ( Table 3). Fermentation of vegetables is mostly dominated by species of Lactobacillus and Pediococcus, followed by Leuconostoc, Weissella, Tetragenococcus, and Lactococcus Watanabe et al., 2009a). A complete microbial profile of LAB in kimchi has been characterized using different molecular identification tools (Shin   Nam et al., 2009;Park et al., 2010;Jung et al., 2011Jung et al., , 2013a. Natural fermentations during production of sauerkraut, a fermented cabbage product of Germany, had been studied and a species of LAB were reported. (Johanningsmeier et al., 2007;Plengvidhya et al., 2007). Species of LAB constitute the native population in the Himalayan fermented vegetable products such as gundruk, sinki, goyang, khalpi, and inziangsang (Karki et al., 1983;Tamang et al., 2005Tamang, 2007, 2010) and in several naturally fermented bamboo products of India and Nepal (Tamang and Sarkar, 1996;Tamang et al., 2008;Jeyaram et al., 2010;Sonar and Halami, 2014).

Fermented Meat Products
Fermented meat products are divided into two categories: those made from whole meat pieces or slices such as dried meat and jerky; and those made by chopping or comminuting the meat,  Merican and Yeoh, 1989 usually called sausages (Adams, 2010). Traditionally fermented meat products of many countries have been well-documented (Table 6), such as fermented sausages (Lücke, 2015) and salami (Toldra, 2007) of Europe, jerky of America and Africa (Baruzzi et al., 2006), nham of Thailand (Chokesajjawatee et al., 2009), and nem chua of Vietnam (Nguyen et al., 2013b). The main microbial groups involved in meat fermentation are LAB (Albano et al., 2009;Cocolin et al., 2011;Khanh et al., 2011;Nguyen et al., 2013b), followed by coagulase-negative staphylococci, micrococci and Enterobacteriaceae (Cocolin et al., 2011;Marty et al., 2011), and depending on the product, some species of yeasts (Encinas et al., 2000;Tamang and Fleet, 2009), and molds, which may play a role in meat ripening (Lücke, 2015).

Fermented Fish Products
Preservation of fish through fermentation, sun/smoke drying and salting (Table 7) is traditionally practiced by people living nearby coastal regions, lakes, and rivers and is consumed as seasoning, condiments, and side dishes (Salampessy et al., 2010). Several species of bacteria and yeasts have been reported from fermented and traditionally preserved fish products of the world (Kobayashi et al., 2000a,b,c;Wu et al., 2000;Thapa et al., , 2007Saithong et al., 2010;Hwanhlem et al., 2011;Romi et al., 2015).
Pidan is a preserved egg prepared from alkali-treated fresh duck eggs and is consumed by the Chinese, and has a strong hydrogen sulfide and ammonia smell (Ganasen and Benjakul, 2010). The main alkaline chemical reagent used for making pidan is sodium hydroxide, which is produced by the reaction of sodium carbonate, water, and calcium oxide of pickle or coating mud. B. cereus, B. macerans, Staph. cohnii, Staph. epidermidis, Staph. Haemolyticus, and Staph. warneri are predominant in pidan (Wang and Fung, 1996).

Amylolytic Starters
Traditional way of culturing the essential microorganisms (consortia of filamentous molds, amylolytic, and alcoholproducing yeasts and LAB) with rice or wheat as the base in the form of dry, flattened or round balls, for production of alcoholic beverages is a remarkable discovery in the food history of Asian people, which is exclusively practiced in South-East Asia including the Himalayan regions of India, Nepal, Bhutan, and China (Tibet; Hesseltine, 1983;Tamang, 2010a). Around 1-2% of previously prepared amylolytic starters are inoculated into the dough, and mixed cultures are allowed to develop for a short time, then dried, and used to make either alcohol or fermented foods from starchy materials . Asian amylolytic starters have different vernacular names such as marcha in India and Nepal; hamei, humao, phab in India; mana and manapu of Nepal; men in Vietnam; ragi in Indonesia; bubod in Philippines; chiu/chu in China and Taiwan; loogpang in Thailand; mae/dombae/buh/puh in Cambodia; and nuruk in Korea (Hesseltine and Kurtzman, 1990;Nikkuni et al., 1996;Sujaya et al., 2004;Thanh et al., 2008;Yamamoto and Matsumoto, 2011;Tamang et al., 2012).
A combination of Asp. oryzae and Asp. sojae is used in koji in Japan to produce alcoholic beverages including saké (Zhu and Trampe, 2013). Koji (Chinese chu, shi, or qu) also produces amylases that convert starch to fermentable sugars, which are then used for the second stage yeast fermentation to make nonalcoholic fermented soybean miso and shoyu (Sugawara, 2010). Asp. awamori, Asp. kawachii, Asp. oryzae, Asp. shirousamii, and Asp. sojae have been widely used as the starter in preparation of koji for production of miso, saké, shoyu, shochu (Suganuma et al., 2007).

Non-distilled Mild-Alcoholic Food Beverages Produced by Amylolytic Starters
The biological process of liquefaction and saccharification of cereal starch by filamentous molds and yeasts, supplemented by amylolytic starters, under solid-state fermentation is one of the two major stages of production of alcoholic beverages in Asia (Tamang, 2010c). These alcoholic beverages are mostly considered as food beverage and eaten as staple food with high calorie in many parts of Asia, e.g., kodo ko jaanr of the Himalayan regions in India, Nepal, Bhutan, and China (Tibet) with 5% alcohol content . Saccharifying activities are mostly shown by Rhizopus spp. and Sm. fibuligera whereas, liquefying activities are shown by Sm. fibuligera and Sacch. cerevisiae . Rhizopus, Amylomyces, Torulopsis, and Hansenula are present in lao-chao, a popular ethnic fermented rice beverage of China (Wei and Jong, 1983). During fermentation of Korean makgeolli (prepared from rice by amylolytic starter nuruk), the proportion of the Saccharomycetaceae family increases significantly and the major bacterial phylum of the samples shifts from γ-Proteobacteria to Firmicutes (Jung et al., 2012).

Non-Distilled and Filtered Alcoholic Beverages Produced by Amylolytic Starters
Alcoholic beverages produced by amylolytic starter (koji) are not distilled but the extract of fermented cereals is filtered into clarified high alcohol-content liquor, like in sake, which is a national drink of Japan containing 15-20% alcohol (Tamang, 2010c). Improved strains of Asp. oryzae are used for saké production in industrial scale (Kotaka et al., 2008;Hirasawa et al., 2009).

Distilled Alcoholic Beverages Produced by Amylolytic Starters
This category of alcoholic drinks is the clear distillate of high alcohol content prepared as drink from fermented cereal beverages by using amylolytic starters. Raksi is an ethnic alcoholic (22-27% v/v) drink of the Himalayas with aromatic characteristic, and distilled from the traditionally fermented cereal beverages (Kozaki et al., 2000).

Alcoholic Beverages Produced by Malting or Germination
Bantu beer or sorghum beer of Bantu tribes of South Africa is an alcoholic beverage produced by malting or germination process (Taylor, 2003). Malted beer is common in Africa with different names e.g., as bushera or muramba in Uganda, chibuku in Zimbabwe, dolo, burkutu, and pito in West Africa and ikigage in Rwanda (Myuanja et al., 2003;Sawadogo-Lingani et al., 2007;Lyumugabe et al., 2012). Sorghum (Sorghum caffrorum or S. vulgare) is malted (Kutyauripo et al., 2009), characterized by a two-stage (lactic followed by alcoholic) fermentation, with Lb. fermentum as the dominating LAB species (Sawadogo-Lingani et al., 2007).

Alcoholic Beverages Produced from Fruits without Distillation
The most common example of alcoholic beverages produced from fruits without distillation is wine, which is initiated by the growth of various species of Saccharomyces and non-Saccharomyces (so-called "wild") yeasts (e.g., Candida colliculosa, C. stellata, Hanseniaspora uvarum, Kloeckera apiculata, Kl. thermotolerans, Torulaspora delbrueckii, Metschnikowia pulcherrima; Pretorius, 2000;Moreira et al., 2005;Sun et al., 2014;Walker, 2014). Candida sp. and Cladosporium sp. were isolated from fermenting white wine using mCOLD-PCR-DGGE, but had not been detected by conventional PCR . Sacch. cerevisiae strains developed during wine fermentations play an active role in developing the characteristics of a wine (Capece et al., 2013). Saccharomyces Genome Database (SGD; www.yeastgenome.org) provides free of charge access or links to comprehensive datasets comprising genomic, transcriptomic, proteomic and metabolomic information (Pretorius et al., 2015).

CONCLUSIONS
Every community in the world has distinct food culture including fermented foods and alcoholic beverages, symbolizing the heritage and socio-cultural aspects of the ethnicity. The word "culture" denotes food habits of ethnicity; another meaning for the same word "culture" is a cluster of microbial cells or inoculum, an essential biota for fermentation, often used in the microbiology. The diversity of functional microorganisms ranges from filamentous molds to enzyme-producing and alcoholproducing yeasts, and from Gram-positive to a few Gramnegative bacteria, while even Archaea has been ascribed roles in some fermented foods and alcoholic beverages. However, consumption of lesser known and uncommon ethnic fermented foods is declining due to the change in lifestyles that is shifting from cultural food habits to commercial foodstuffs and fast foods, drastically affecting traditional culinary practices, and also due to the climate change in some environments such as the Sahel region in Africa and the vast areas adjacent to the Gobi desert in Asia.

AUTHOR CONTRIBUTIONS
JT: contributed 50% of review works. WH, contributed 25% of review. KW contributed 25% of review.