‘The processes required for fermented foods were present on earth when man appeared on the scene… When we study these foods, we are in fact studying the most intimate relationships
between man, microbe and foods.’ 
Prof. Keith H. Steinkraus, Cornell University, 1993
Functional microorganisms transform the chemical constituents of raw materials of plant/animal sources during food fermentation thereby enhancing the bio-availability of nutrients, enriching sensory quality of the food, imparting bio-preservative effects and improvement of food safety, degrading toxic components and anti-nutritive factors, producing antioxidant and antimicrobial compounds, stimulating the probiotic functions, and fortifying with some health-promoting bioactive compounds (Tamang et al., 2009, 2016; Farhad et al., 2010; Bourdichon et al., 2012; Thapa and Tamang, 2015).
Lactic acid bacteria present in fermented foods may decrease number of incidence, duration and severity of some gastrointestinal disorders (Verna and Lucak, 2010). Administration of some strains of Lactobacillus improves the inflammatory bowel disease, paucities and ulcerative colitis (Orel and Trop, 2014). L. rhamnosus GG is effective in the treatment of acute diarrhea (Szajewska et al., 2007) and administration of L. helveticus-fermented milk in healthy older adults produced improvements in cognition function (Chung et al., 2014). Consumption of fermented milk products containing live bacteria has immunomodulation capacity (Granier et al., 2013), and cures diarrhea (Balamurugan et al., 2014). Korean kimchi is suitable for control of inflammatory bowel diseases (Lim et al., 2011).
Citation: Tamang JP, Shin D-H, Jung S-J and Chae S-W (2016) Functional Properties of Microorganisms in Fermented Foods. Front. Microbiol. 7:578. doi: 10.3389/fmicb.2016.00578
Modern advances in chemical preservation, refrigeration, and transportation efficiency have not resulted in the abandonment of fermented foods. At least in traditional dietary practices, fermented foods and beverages remain widespread, currently accounting for approximately one-third of the human diet globally . Moreover, as scientists continue to uncover health-promoting properties of ancestral dietary patterns (for example, the Mediterranean diet, the traditional Japanese diet, and hunter-gatherer diets), by extension there is a renewed examination of the fermented foods that are so often a part of such ancient diets . Emerging research, as reviewed here, indicates that fermentation may magnify the known benefits of a wide variety of foods and herbs, influencing the bioavailability and activity of the chemical constituents. In addition, as our knowledge of the human microbiome increases (the intestinal microbiota in particular), it is becoming increasingly clear that there are untold connections between the ways in which microbes act upon dietary items pre-consumption, and in turn, the ways in which these fermented dietary items influence our own microbiota.
Selhub EM, Logan AC, Bested AC. Fermented foods, microbiota, and mental health: ancient practice meets nutritional psychiatry. Journal of Physiological Anthropology. 2014;33(1):2. doi:10.1186/1880-6805-33-2.
Modern lifestyles tend to impose stress on systems genetically adapted over millions of years. The consumption of food containing microorganisms has dramatically reduced, and as a consequence, the developing mucosal immune systems are faced with different microflora, particularly fewer pathogens than paleolithic man. Increases in observed incidence and severity of allergies and conditions such as IBD in the Western world have been linked with increases in standards of hygiene and sanitation, which have occurred concomitantly with decreases in the number and range of infectious challenges encountered by the growing and developing host. This lack of immune education impairs the development of the immune system and allows the host to over-react to non-pathogenic antigen-containing commensal flora, resulting in inflammatory damage, allergy and/or autoimmunity . To combat these trends directly, the World Health Organisation currently advocates the implementation of alternative disease control strategies, such as exploiting the prophylactic and therapeutic potential of probiotic bacteria . Most of these probiotic microorganisms, isolated from such sources as faeces of healthy individuals, are safe for human consumption and are available over the counter. Because of continued scepticism of such products, European Union funded research groups including medical, scientific and industrial interests, have agreed on criteria for selection and assessment of probiotics.
Co-evolution led to a symbiotic relationship between eukaryotes and prokaryotes with the development of sophisticated by-directional signaling systems of mucosal epithelia and lymphocytes in the intestinal tract . It is estimated that over 400 species of bacteria, separated into two broad categories, namely beneficial (e.g., Bifidobacterium and Lactobacillus) and those considered detrimental (e.g., Enterobacteriaceae and Clostridium spp.) inhabit the human gastrointestinal tract. Bacterial end products of fermentation are essential mucosal nutrients including amino acids (arginine, cysteine and glutamine) and short chain fatty acids (SCFA: acetate, propionate and butyrate) . These SCFAs serve as an energy source for the host, providing 10–30% of basal metabolic requirements including energy for liver cells, colonocytes and peripheral tissues with only about 5% excreted in the feces . Besides fermentation, the metabolic products of the microflora includes vitamins K and B complex, secondary bile acid production, neutralization of dietary carcinogens such as nitrosamines, and conversion to active metabolites of some prodrugs. The indigenous intestinal (autochthonous) microbiota act as a further barrier against any transient (allochthonous) potential pathogens by competing for nutrients and mucosal adherence and by production of antigens (bacteriocins), which are active against pathogens. Furthermore, it has been clearly established that the gastrointestinal flora are essential for mucosal protection and immune education as it has been described as the most adaptable and renewable metabolic organ of the body. The composition and activities of gastrointestinal flora affect both intestinal and systemic physiology. The complex gastrointestinal microbial load is required for normal development and homeostasis of the humoral and cellular immune system. It is the interaction between the mucosal immune system and the enteric microflora which maintains the physiologically normal state or activation of immune organ, the latter resulting in secretion of antibodies against harmful antigens (pathogenic microorganisms) .
Cencic A, Chingwaru W. The Role of Functional Foods, Nutraceuticals, and Food Supplements in Intestinal Health. Nutrients. 2010;2(6):611-625. doi:10.3390/nu2060611.
To understand how probiotics work, it is important to understand a little about the physiology, microbiology of GI tract and the digestive process. The digestive process begins as soon as food enters the mouth and to stomach, the microbes present in the GI tract have the potential to act in a favourable, a deleterious or a neutral manner. Microbes in small intestine and in the large intestine complete the digestion process.
Certain intestinal microbes are known to produce vitamins and they are nonpathogenic, their metabolism is non-putrefactive, and their presence is correlated with a healthy intestinal flora. The metabolic end products of their growth are organic acids (lactic and acetic acids) that tend to lower the pH of the intestinal contents, creating conditions less desirable for harmful bacteria. Probiotics may also influence other protective functions of the intestinal mucosa including synthesis and secretion of antibacterial peptides, mucins. The GI tract also serves as a large mucosal surface that bridges the gap between ‘inside the body’ and ‘outside the body’. Along this mucosal interface, microbes and foreign antigens colonizing or passing through the GI tract interact with important components of the immune system. This interaction serves to prime or stimulate the immune system for optimal functioning. Normal microbial inhabitants of the GI tract also reinforce the barrier function of the intestinal lining, decreasing ‘translocation’ or passage of bacteria or antigens from the intestine into the blood stream. This function has been suggested to decrease infections and possibly allergic reactions to food antigens.
Lactic acid bacteria are known to release various enzymes and vitamins into the intestinal lumen. This exert synergistic effects on digestion, alleviating symptoms of intestinal malabsorption, and produced lactic acid, which lowers the pH of the intestinal content and helps to inhibit the development of invasive pathogens such as Salmonella spp. or strains of E. coli (Mallett et al. 1989; Mack et al. 1999). Bacterial enzymatic hydrolysis may enhance the bioavailability of protein and fat (Fernandes et al. 1987) and increase the production of free amino acids, short chain fatty acids (SCFA), lactic acid, propionic acid and butyric acid are also produced by lactic acid bacteria. When absorbed these SCFAs contribute to the available energy pool of the host (Rombeau et al. 1990; Rolfe 2000) and may protect against pathological changes in the colonic mucosa (Leavitt et al. 1978; Leopold and Eileler 2000). SCFA concentration helps to maintain an appropriate pH in the colonic lumen, which is critical in the expression of many bacterial enzymes and in foreign compound and carcinogen metabolism in the gut (Mallett et al. 1989).
In addition to nutrient synthesis, the action of micro-organisms either during the preparation of cultured foods or in the digestive tract can, to a limited extent, improve the digestibility of some dietary nutrients. Several lines of evidence show that the appropriate strain of lactic acid bacteria, in adequate amounts, can alleviate symptoms of lactose intolerance. Streptococcus thermophilus, Lactobacillus bulgaricus and other lactobacilli used in fermented milk products deliver enough bacterial lactase to the intestine and stomach where lactose is degraded to prevent symptoms in lactase nonpersistent individuals (Kilara and Shahani 1975; Martini et al. 1991).
Probiotic supplementation has both direct and indirect effects. Probiotics exhibit direct effects locally in the GI tract, including modulation of resident bacterial colonies and vitamin production. There are also indirect effects exerted at sites outside the GI tract, including the joints, lungs, and skin. Indirect effects most likely result from an impact on immunity, via changes in inflammatory mediators such as cytokines. Modulation of inflammatory responses may be related to regulating or modulating the immune system both locally in the GI tract.
It is speculated that inflammation associated with rheumatoid arthritis may be modulated by the use of probiotics (Marteau et al. 2001). Thirty patients with chronic juvenile arthritis were randomly allocated to receive Lactobacillus GG or bovine colostrum for a 2-week period (Malin et al. 1997). Immunological and nonimmunological gut defences were investigated in blood and faeces. It has been observed by different researchers that gut defence mechanisms are disturbed in chronic juvenile arthritis and suggested orally administered Lactobacillus GG has potential to reinforce mucosal barrier mechanisms in this disorder. When inflammed, the GI tract becomes permeable and serves as a link between inflammatory diseases of the GI tract and extra-inflammatory disorders such as arthritis. Modulation or downregulation of the immune system and subsequent reduction in GI permeability can result from consuming probiotics (Yukuchi et al. 1992; Vanderhoof 2000).
The potential of probiotics to control allergic inflammation at an early age was assessed in a randomized double-blind placebo-controlled study. The results provide the first clinical demonstration of specific probiotic strains modifying the changes related to allergic inflammation. The data further indicate that probiotics may counteract inflammatory responses beyond the intestinal milieu. The combined effects of these probiotic strains will guide infants through the weaning period, when sensitization to newly encountered antigens is initiated (Mack et al. 1999; Vanderhoof 2000).
In spite of inherent difficulties establishing good measures of probiotic efficacy (Rolfe 2000), studies on lactose intolerance, diarrhoea and colon cancer show that a daily dose of lactic acid bacteria is needed for any measurable effect (Rembacken et al. 1999).