Volume 5, Issue 1-2 e70002
REVIEW ARTICLE
Open Access

A Review: Correlation Between Fermented Food and Human Microbiome

Rahel Debbarma

Rahel Debbarma

Department of Applied Biology, University of Science and Technology Meghalaya, Baridua, Meghalaya, India

Contribution: Conceptualization (equal), ​Investigation (equal), Writing - original draft (equal)

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Sony Kumari

Corresponding Author

Sony Kumari

Department of Applied Biology, University of Science and Technology Meghalaya, Baridua, Meghalaya, India

Contribution: Conceptualization (equal), ​Investigation (equal), Supervision (equal), Writing - original draft (equal)

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Doly Barman

Doly Barman

Department of Bioengineering and Technology, Gauhati University Institute of Science and Technology, Assam, India

Contribution: Validation (equal), Writing - original draft (equal)

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Rony Bhowal

Rony Bhowal

Department of Applied Biology, University of Science and Technology Meghalaya, Baridua, Meghalaya, India

Contribution: Data curation (equal), Writing - original draft (equal)

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Puja Roy

Puja Roy

Department of Microbiology, Gauhati University, Assam, India

Contribution: Visualization (equal), Writing - original draft (equal)

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First published: 07 April 2025

Funding: The authors received no specific funding for this work.

ABSTRACT

The symbiotic relationship between humans and microbes brings about a healthy lifestyle. The microbes reside all over the body. They have various key roles in maintaining metabolic activity by enhancing their catalytic role. Their beneficial perspective in human health is uplifting the immunological aspects. Microbes provide a fruitful diet in the form of fermented food, and it helps in enabling a good source for various metabolic disorders. Fermentative products have a distinct, able population of microorganisms. This microbe helps in interacting with the gut microbes, which makes them strong for digestion; ultimately, it boosts microbial distinctiveness and improves the immunological barrier. The fermentative food can also cause harmfulness and disturb the microbiome residing within the human body if the fermentation is carried out without proper implications, that is, pH and temperature. The current review considers the role of the microbial consortium of each part of the human body and its respective mechanism of action at various regions.

1 Introduction

Imagine a hectic morning filled with overloaded work and appointments. In the actual world, every morning is spent in such a rush. But if we examine the world at the microscopic level, a different kind of narrative emerges. At the microscopic level, we will observe that many bacterium species are active, reflecting the microbiome of an organism. Thousands of distinct species of microorganisms, often known as microbiota, make up the majority of the microbiome. The microbiome includes bacteria, fungi, viruses, and other parasites. In a healthy condition, the microorganisms exist mainly in the large and small intestine. They are also found throughout the body. The microbiome part of the human body is marked as the strongest positive support system; most of it is beneficial for health and plays important roles in enhancing and uplifting the immune system. The healthy immune cells are the key contributors to good health, which ultimately leads to a healthy life. There are certain groups of microbes that are still not explored. For instance, in the human gut, they are categorized into known and unknown members of the total microbiome. Age et al. [1] reported both the classes by taking results from a multi-body site large-scale metagenomic assembly study and a population-wide study. Both helpful and harmful microbes are the components of the microbiome. They are helpful when they are present in a balanced condition. Most of the members are symbiotic because both the human body and the microbiota exist together and are benefited. Some members are pathogenic as they are disease-promoting. Both microbiotas coexist peacefully, but the problem appears when there is an imbalance of microbiota, brought by illness, unhealthy diet, and prolonged use of antibiotics, and this ultimately leads our body to be susceptible to diseases [2].

Summary

  • The human microbiome plays a crucial role in metabolism, immunity, and overall health. Fermented foods, rich in probiotics, help maintain a balanced gut microbiota, which is essential for digestion and disease prevention. Foods like yogurt, kefir, kimchi, and sauerkraut introduce beneficial microbes that enhance gut diversity, support immune function, and improve metabolic processes. However, an imbalance in gut microbiota, often caused by poor diet, antibiotic overuse, or improper fermentation, can lead to health issues, such as obesity, diabetes, and bowel diseases. Although fermented foods have been linked to various health benefits, their preparation requires careful control of pH, temperature, and hygiene. Improperly fermented foods can harbor harmful bacteria, disrupting the microbiome and potentially leading to illness.
  • Research highlights the direct correlation between dietary choices and gut microbial diversity. Advances in microbiome analysis, such as 16S rRNA sequencing, provide deeper insights into how fermented foods influence microbial composition. Personal microbiome-based diets are emerging as a potential approach to managing health conditions. A well-balanced microbiome is essential for overall health, and consuming properly fermented foods can be a natural way to support gut health. However, ensuring safe fermentation practices is crucial to prevent unintended health risks.

The human gut microbiota is specific and varies from individual to individual, shaped during the early life period, which keeps on changing throughout our lifetime [3]. In adulthood, it usually stays fairly stable, but it can vary from person to person depending on their body type, level of exercise, and diet. Therefore, each individual may have a particular bacterial composition that is essential for good health. Many researchers are trying to understand how to change microbiome composition and the resulting impact on health and disease development [4]. It is unclear how microbe-containing supplements and diet modify the microbiome community, but promising research suggests that it is likely possible [5]. Until recently, fecal transplants have been the only way for effective modification of the human microbiome. However, a new drug that modifies gut microbiome has been approved in China to treat Alzheimer's disease, whereas there are some companies that offer personal microbiome analysis along with a personalized nutrition plan to control diabetes and have data to show effectiveness [5, 6]. Researchers are now highly interested in better understanding the function of microbes at the molecular level as well as their impact on signaling molecules in the surroundings. To solve these phenomena, the relationships between the microbes and the host organism and within the microbes have to be understood. These studies might help in understanding the interactions of both the microbiome. The host genetics may provide additional insight on disease diagnosis, treatment, and prevention at the same time [7, 8]. The technology behind the knowledge and understanding of the relationship between the microbes and host is important in microbiota relationship analysis. The advancements in sequencing technologies have played an important role in creating cost-effective methods in determining the microbial composition of any sample. However, each analysis step may comprise numerous technical variables and potentially introduce variability in the acquired data. The main steps include sample collection without any contamination, preparation of the collected sample, followed by preservation and storage. The final step involves DNA extraction and NGS sequencing [9].

2 Microbiota Diversity and Health

Good health is the basic requirement of healthy life. Certain factors influence the health quality; microbiome is one of them, with diversity at different regions of the human body. In diseased condition, the microbial diversity is disturbed, and beneficial microbes are suppressed by pathogenic microbes. For instance, lower microbial diversity can be observed among diseased people like people with diabetes, bowel disease, obesity, arthritis, and so forth, who have lower microbial diversity compared to healthy individuals. The correlation of microbiota diversity and disease is an indication of an unhealthy condition; it indicates a smaller number of microbial species residing internally, and healthy microbes are missing. The present microbes are compensating for the function of absent microbes in a dominating way. The indication of microbial diversity is generally representative of the healthier gut condition than the less diverse microbial condition [10, 11]. Diet is important for controlling the microbial diversity; it has been found that it is the general trend; increasing the consumption of dietary fiber in diet reduces the diversity of microbiome in that region. The microbes that use fiber to digest become specifically enriched, which then leads to a change in composition and, through competitive interactions, reduces diversity. By harnessing the technique of microbiota transplantation in fecal samples, it has been reported that human gut microbiome is functional [12], which is in routine use [13]. Fecal transplant method has been explored; however, it is not used in recent times in clinical practice [14]. The work of Kootte et al. [15] has shown the relationship between the host and the recipient during transplantation, from healthy to diseased host, indicating the better sensitivity in the syndrome host than in the normal [15].

3 History of Microbiome

The microbiota residing inside and on the human body provides a great opportunity for current research. Microorganisms are part of the human body; it was discovered when Theodor Escherich, an Austrian pediatrician, observed a bacterium (Escherichia coli) in the intestinal region of healthy children and diarrheal children. In addition to E. coli, followed by the isolation of other microorganisms over the perusing years, including in 1898 when Veillonella parvula (an anerobic, coccus-shaped, gram-negative bacterium) was found in the oral, digestive, urinary, and upper respiratory tracts. Later in the 1900s, Bifidobacteria were reported in the intestinal flora. Throughout the 20th century, microorganisms continued to be isolated from oral cavities, nasal passages, skin, the gastrointestinal tract, and the urogenital tract and characterized as part of the human microbiota [3].

The term “Microbiome” was coined in the year 2001 when Lederberg and McCray published their monumental paper [4]. The human “microbiome” was considered “the ecological community of microorganisms (commensal, symbiotic, and pathogenic type) that share human whole body” [6]. During the same period of time, the human genome project was published, which would involve an idea of microbial genes and genomes at the mouth, gut, vagina, and skin, where colonization of microbes occurs [7]. The microbes present in environment and inside human body are not new, even present when people were practicing the preparation of the fermentation process of products as shown in Figure 1, including beverages for thousands of years. The presence of microbes, evidenced by the use of fermented alcoholic beverages in Neolithic China, dates back to 7000–6600 bce, when they were made from fruit, honey, and rice.

Details are in the caption following the image
Some examples of food items involved in fermentation.

Fermenting the beverages in Babylon around 3000 bce and wine making in around 6000 bce in Georgia are strong evidence of the historical use of microbiome. The history of microbiome is even before the era of fermenting beverages. Human were making dairy products, which is also a good example of microbial use. Camels, goats, sheep, and cattle milk were fermented naturally as far back as 10,000 bce. The process of fermentation, which involves the use of microbes, is not intentional; it is thought to be a spontaneous process due to the natural presence of microflora in the milk. Climate has a great role in microbial diversity and its role. It is believed that dairy product formation by fermentation took place due to its subtropical climate because of the presence of thermophilic lactic acid fermentation. In North Africa, where temperatures average approximately 110°F, which is perfect for fermentation to take place, goats have been used to produce yogurt. Fermentation uses helpful microbes, which are also referred to as friendly bacteria. The advantages of eating friendly bacteria have been researched over the past 40 years. The beneficial bacteria help the body's cleansing and digesting processes, among other things. These probiotics are helpful for maintaining human health. These discoveries are reflected in modern food technology, which has led to the rise in popularity of “probiotic” products that contain beneficial bacteria [16].

4 Human Microbiome Projects

The project was announced in the year 2007 by the National Institutes of Health [17]. The project was designed in two phases, which included resources and methods linking between humans with microbiomes for health issues [19]. The key objective of the project was to explore the relation of genetic and physiological diversity of the microbiome. It also emphasized factors that influence the distribution and evolution of the constituent microbiota; the data were supposed to be used to identify new ways of determining many microbiomes related to predisposition to diseases. The project was also aimed at being involved in defining the parameters needed for designing, implementing, and monitoring the strategies for manipulation of the microbiota [18]. Knowledge of dynamic changes in the microbiome and hosts under three different conditions of pregnancy and preterm birth, including prediabetes and inflammatory bowel disease, was part of the Integrative Human Microbiome Project. The Human Microbiome Project has begun its second phase, which aims to explain the mechanism underlying host–microbiome interactions. The findings offer data sources for future multi-omics studies of the human microbiome for various studies [19]. The findings of the two-phase microbiome project have revealed much information on microbe–host interaction. The first phase findings have identified the ecological niches of the microbes at different organ locations such as the vagina and gut.

Another piece of information that can be gathered is nucleotide sequences of microbes from many isolates for future research works [20]. It has been found that the host microbiome can evolve throughout the lifespan of the human [17]. This has clearly explained that every human being appears to carry their own individualized composition of microbial strains. There is a direct correlation between the age and the microbial diversity of host. The initial bacteria, which are known as founder species in the newborn condition, are known to have simple composition and low diversity; however, with an increase in age, the microbes are found to be more diversified. It has been reported that a number of environmental factors are responsible for affecting the microbial diversity. It includes factors like mode of delivery, maternal colonization, diet, illness, and host genetic makeup [17, 21].

The project's first stage put forth the notion of the taxonomic makeup of the microbiome and emulated that molecular analysis is the indispensable tool for microbial taxonomic investigation. The second phase of the Human Microbiome Project has been designed in response to the first phase's findings, and it will inspect host–microbiome interactions as well as the molecular activity of the microbes [17]. The microbe genome analysis by the two-phase study in Human Microbiome Project has led to stored information with 42 TB of multi-omics data. These data are obtainable at the data management center for the National Institutes of Health (http://ihmpdcc.org).

5 Applications and Risks of Microbiome

The microbiome reflects the whole composition of the microbial community present in a region. They are highly beneficial and important for maintenance and control of host metabolism; it regulates the immune system of the host, combating pathogens; they have emerged as an advanced diagnosis tool for exploring host–microbiome relationships. The microbes directly work in human body by metabolizing molecules, which is very much essential for the metabolic reactions of body. Each and every region of the body is essential for proper metabolism; however, the intestinal microbiome is the most important one and is the key part of digestion and absorption of food. The digestion of food generally starts in the gut. The gut region microbiome provides additional nutrition for the host, including the degradation of protein and glycosaminoglycans. It produces short-chain fatty acids, amino acids, bile acids, and vitamins. Enzymes play a key role in digestive system for their complete digestion and absorption. Gut microbiome is the source of many enzymes, including primary and secondary metabolites. All the enzymes become active when catalysis is needed. Complete digestion is the combination of total enzyme catalysis. The biomolecules that are microbiome-derived are thought to be essential for metabolism [22]. In addition to digestion, the application of gut microbiome is immense in relation to fermented foods and beverages. Fermented food products have a consortium of microbes that are beneficial for human health. In fact, fermented foods serve as vehicles for probiotic strains and make available the microbes that might not be indigenous to that environment [23, 24]. The study of Lavermicocca et al. [23] on olive oil reported that the olives can be used in the form of fermented food for introducing probiotics safely through gastric transit. The study was carrying out the establishment of probiotic Lacticaseibacillus paracasei. They were subjected to the intestines of 5 humans, who were given 10–15 olives coated with 10 to the power 9–10 to the power 10 CFU of lactobacilli. The microbiome of the gut is not only essential for fermentation, but it also regulates the immune system. They influence the metabolic diseases by regulation of the immune cells and system. The microbial community may be beneficial or useful. Their regulation is directly related to the metabolic functions and disorders. For instance, the inflammation that is a symptom, induced by the disturbed microbiome, might be a regulator of some metabolic disease as the normal microbiome is disturbed [25]. Similarly, in many metabolic disorders, the low-grade systemic inflammation is identified, for example, in obesity, non-alcoholic fatty liver disease, and Type 2 diabetes, which was reported by Tran et al. [26]. Generally, inflammation is observed during infection, which is known as acute inflammation. The inflammation that is linked with metabolic diseases is usually chronic, and it affects body organs, mainly adipose tissue, the liver, and cardiovascular system. The application of microbiome is diversified and depends upon the metabolic status of the body and regulation.

The complete microbiome information gathered is the beneficial form of microbes. It is known that human is lined up with a million microorganisms collectively called a microbiome, which enhances our health. Human microbiome has been an area of interest over the past few years as the composition of microbiome is directly linked to human health. They are involved in digestion and boosting immune system. Unfortunately, the relation between human microbial consortium and health is still unknown and unexplored. The reduction in microbial diversity is actually linked to certain inflammatory diseases, such as eczema, asthma, diabetes, and obesity; allergies; and digestive tract disorders and irritable bowel syndrome [10, 2731].

6 Human Microbiota Composition

Microbiota of humans consists of different types of microorganisms. The composition of the microbial community varies according to the region of body part and its requirement. The microbiota has its impact in body and imparts special function in the respective region where it is found. For instance, oral microbiota exerts an important impact in the perception of flavor in the oral cavity. This implies that oral microbial composition is an important factor in modulating the flavor perception in mouth. The human microbiome composition of whole body is represented in Table 1.

TABLE 1. Microbiota composition at different locations of human body.
Sl. No. Location Microbiome References
1 Oral Streptococcus, Eubacteria, Fusobacterium, Capnocytophaga, Eubacteria, Staphylococcus, Eikenella, Porphyromona, Leptotrichia, Prevotella, Peptostreptococcus, Treponema, Actinomyces, Streptococcus, Granulicatella, Gemella, and Veillonella are predominant, but the majority are definite to certain sites [83]
2 Gut Bacteroidetes (including Bacteroides fragilis and B. thetaiotaomicron). Prevotella, Porphyromonas, Bacteroides, Fusobacterium and Peptostreptococcus spp. Microaerophilic and streptococci [37]
3 Intestine Peptostreptococcus sp., Eubacterium sp., Lactobacillus sp., and Clostridium sp. of genus Bacteroides [84]
4 Rectal Pseudomonas, Corynebacterium, Staphylococcus, Lactobacillus [46]
5 Colonic Bacteroides, anaerobic gram-positive cocci, such as Peptostreptococcus sp., Eubacterium sp., Lactobacillus sp., and Clostridium sp. [47]

The composition of oral microbiota introduces characteristics that can influence the relationship between chemo sensory organs and the oral microbiota [32]. The human oral cavity, as shown in Figure 2, is the habitat of thousands of microorganisms like bacteria, fungi, parasites, and viruses.

Details are in the caption following the image
Schematic representation of parts of human oral cavity.

The complete composition constitutes the oral microbiota. Streptococcus, Actinomyces species, and obligate anaerobes like Bacteroidaceae and Fuso bacteroidaceae are specifically common in oral microbiota with facultative anaerobic bacteria such as in sites with reduced oxygen. The oral microbial community, as described in Figure 3, is not constant; rather, it is developed throughout the life and is influenced by external factors. Saliva microbiota is the most important out of all of oral cavity colonization, as it is essential in maintaining the microorganisms and oral cavity due to the activities of many different proteins: lysozyme, immunoglobulins, lactoferrin, and peroxidase system [33]. Grassl et al. [34] reported that 50 different types of bacterial genera are found in oral cavity, 2000 proteins have been identified in saliva microbiota. The saliva microbiota is useful in solubilizing and transporting the nutrients that are used to be ingested during food intake to the different colonization sites in our mouth.

Details are in the caption following the image
Diagram representing the site of various microbes and enzymes of oral cavity.

Oral microbiome, as in Table 2, changes in relation with the change in host environment and activity [3], which is the symbiotic relation between the host and the microbiota based on their mutual benefits. The microbiota can become pathogenic if their composition is disturbed and after they reach the barrier of the commensals, causing infection and diseases [35].

TABLE 2. Bacterial genera of human oral cavity [68].
Type Gram-positive Gram-negative
Cocci Abiotrophia, Peptostreptococcus, Streptococcus, Stomatococcus Moraxella, Neisseria, Veillonella
Rods Actinomyces, Bifidobacterium, Cornybacterium, Eubacterium, Lactobacillus Campylobacter, Desulfobacter, Fusobacterium, Hemophilus, Prevotella

Gut microbiota consists of the microorganisms that survive in the human digestive tract. It includes bacteria and archaea that remain different at different regions of digestive tract. Engel et al. [36] report suggests that most of the bacteria in gut are anaerobes, which is over 99%; however, in the cecum region, the presence of aerobic bacteria is reported [36]. Bile acid that is synthesized by liver is mainly catabolized by the gut microbiota, which conjugates with taurine or glycine before getting stored in the gall bladder and then secreted into duodenum for digestion, mainly for metabolism of cholesterol and lipid. In humans, the dominating microbe is Bacteroidetes [37]. The perception of gut–brain axis has been established, and it has been found that gut microbiota composition has effect on the brain and the central nervous system in interaction. The study results in showing a link for establishing diet as an impact factor on the gut microbiota composition and consequently on the brain and eventually on the homeostasis of the organism [38, 39].

Bacteria found in intestine are incredibly important for human health. The main bacteria found is Bifidobacteria, which are y-shaped and predominantly found in the intestines. Like other parts of human body, intestine is a reservoir of different microbial composition. Around 50 different beneficial bacterial species, all of which are thought to possess different functions at their level and have health-beneficial properties, are conserved in intestinal region [40]. Out of the total, in adult gut microbiota, only Bifidobacteria make up approximately less than 10% of the bacteria [41]. The main function of such bacteria in humans is digestion of fibers and complex carbohydrates that cannot be digested by human body [42]. The bacteria digest fiber by secreting some chemicals essential for fiber digestion [42, 43]. The work of Fukuda et al. [44] has reported that such a mechanism is helpful against other bacterial infections (E. coli infection). This is possible because certain chemicals are produced during the process that does not allow toxins to pass into the blood. As probiotics are composed of live microorganisms that can provide a specific health benefit to humans when consumed, they can be used as probiotics, which will be important for health and, hence, used as probiotics in supplements.

Rectal microbiome is reflected by the fecal microbial composition of an individual. Contijoch et al. [45] have reported that the bacterial density of fecal specimens, in fact, the density of the region, is highly variable and the main species present are Pseudomonas, Staphylococcus, Corynebacterium, and Lactobacillus [46]. As other parts of the body's microbial colony are found in the colon part of human. However, the colonic microbial community is the largest population of microbes that has been colonizing human body since birth. The microbiome is useful in prospect as the microbiome provides nutritional uptake, metabolic signal, and beneficial protective layer. In contrast, depending on the host's susceptibility, it might be a risk factor for disease. Colonic bacteria causing irritable bowel syndrome, inflammatory bowel disease, and colon cancer can also have serious environmental risks. Different forms of microbiota can be observed in colonic part; out of all bacteria, which are mostly found, they are mainly obligate anaerobes and anaerobic gram-positive in nature [47]. Bacteria predominantly found in colon part are Lactobacillaceae, Fusobacteriaceae, Eubacteriaceae, Bifidobacteriaceae, Enterobacteriaceae, Clostridiaceae, and so forth. The complete microbiome composition of human colon helps in the digestion of certain complex carbohydrates. Some factors are responsible for microbial changes in intestine. Tuddenham and Sears [48] reported that age is the most common factor influencing the microbiota. For instance, the number and proportion of Firmicutes family, Bifidobacteria, and Faecalibacterium prausnitzii decrease, whereas with increasing age the proportions of E. coli, other Proteobacteria, and staphylococci increase. The other factor influencing the microbial change is diet, which shapes the composition and functional metabolism of microbial community [12]. The use of antibiotics also influences the type and composition of human microbiota. Changes in gut community membership and composition have been reported [49]. Not only the type but also the dosses of courses influence the community type in gut and intestine, as reported by Jernberg et al. [50].

7 Effects on Gut Microbiota

The diversity of the microbiota and human health are directly correlated. The bacteria just assist in the regulation and process of metabolism. The sort of food we consume affects both human health and microbial diversity. The usage of artificial sweeteners is one of the best illustrations of the relationship between the food ingested and the effect of microbial diversity. They are frequently used as sugar substitutes because of their low-calorie content and perceived safety. But according to the 2016 investigation by Nettleton et al. [51], sugar substitutes may have a deleterious impact on the microbiota in the stomach. Sucralose, aspartame, and saccharin, which are sugar derivatives, have reportedly been implicated in upsetting the diversity and equilibrium of the gut's microbiota. The use of sucralose had significantly shown that the concentration of aerobic bacteria and clostridia in guts is higher; pH has also been reported to be higher in feces of those treated with sucralose than in those without sucralose [52]. In a similar way, mice dosed with sucralose for half a year increased expression in the gut of bacterial pro-inflammatory genes and disrupted fecal metabolites [53]. In addition to sweeteners and food emulsifiers, which are common food additives in food processing, have been found to affect the gut microbiota in animals [54]. Lowering the concentrations of emulsifiers, that is, carboxymethylcellulose and polysorbate-80 in mice, has been found to be reducing the diversity in microbiome; mainly, Verrucomicrobia and Bacteroidales were decreased, and Proteobacteria, which is linked with inflammation in mucus, was enriched. Raw cooked food and vegan diets are also effective in altering the microbial diversity in humans.

7.1 Fermented Foods and Beverages

Due to their distinctive flavor and refreshing taste, many people prefer fermented foods. The preparation and consumption of such food from various raw materials is thought to be a tribal custom inherent in its people. In the process of creating beverages and other products, natural herbs are combined with the beginning cake. They are referred to as the category of foods that are created through the enzymatic breakdown of dietary components in well-regulated microbial environments [55]. Fermented foods are not only good in taste, but they are also the health immune boosters. In recent time, they are not limited to tribal. However, they are at the peak of popularity due to its health benefits. People are much concerned with their health and lifestyle; hence, they mainly opt fermented foods as one the key element of meal over others. Fermented foods are not the recent concept. Food items for instance fish, meat, legumes, soybean, vegetables, cereals, fruits, and so forth, have got fermented naturally and are very common concept of daily meal. The significance of fermented products is that they are free of spoilage microbes and can be preserved for a longer period. They have antimicrobial properties, which enhance the health value of the foods. They are rich in probiotics, which in turn enhances health condition. Kefir, kombucha, sauerkraut, tempeh, natto, miso, kimchi, and so forth are some of the examples of fermented foods; they can exert high rates of health values with the richness of probiotics [2].

7.2 Effects of Fermented Food in Human Microbiome

Human internal tract and organs are full of microbes. The function of a complete microbiome is in a balancing manner. The harmful microbes are in balance with the useful microbiomes. Hence, they cannot cause any health issue. However, if the balance is disturbed and the harmful microbes start dominating the good microbes, there might be health issues. Fermented foods are performing the task of good or useful microbes, as they possess many of the good microbes. The microbial composition of some common fermented food products with their origin is represented in Table 3. Clinical evidence proves the effect of fermented food consumption on internal gastrointestinal health conditions and related diseases. These studies are limited in this regard; findings have proved some fermented foods to be beneficial and others to be harmful. Kefir is a fermented food that is synthesized by the addition of a starter culture called kefir grain, lactose-fermenting yeasts (e.g., Kluyveromyces lactis), and non-lactose fermenting yeasts, for example, Saccharomyces unisporus and Saccharomyces cerevisiae [56]. Kefir consumption is very much beneficial for people with lactose malabsorption [2].

TABLE 3. Fermented food, origin, and their microbial composition.
Fermented food Origin Raw ingredients Microbial components References
Fermented milk (kefir) Eastern Europe Kefir grains Lactobacillus brevis, Lacticaseibacillus casei, Bifidobacterium longum, and Streptococcus thermophilus; Bifidobacterium animalis and S. thermophilus [35, 6971]
Yogurt Turkey Raw milk cultured with Lactobacillus bulgaricus and S. thermophilus Lactobacillus acidophilus, Bifidobacterium lactis, L. bulgaricus [72, 73]
Camembert cheese Northern France Warmed cow milk with mesophilic bacteria such as Flora Danica S. thermophilus, Lactococcus lactis, Leuconostoc, Hafnia alvei, and Geotrichum [47]
Kimchi Korea Cabbage, radish, cucumber; red pepper, ginger, leek, mustard, black pepper, onion, and cinnamon Lactobacillus spp. [66]
Sauerkraut China and Germany Cabbage and salt Lactobacillus spp. (Lactiplantibacillus Plantarum and L. brevis), Leuconostoc spp., Weissella confusa, L. lactis, and Enterobacteriaceae [67]
Fermented tea China Yeast, sugar, and black tea; mixture is set aside for one week or more Aspergillus luchuensis var kawachii kitahara, Lactobacillus spp. (Latilactobacillus sakei, L. acidophilus, L. casei [74]
Fermented soybean milk China Sterilizedsoy milk, Lactobacillus, Bifidobacterium, or other suitable bacteria Lactobacillus paracasei, L. casei, Lactobacillus mali, and Bifidobacterium breve [75]

Fermented food mainly its component has been found to be of at most importance, they act as potential and beneficial enhancers and modulators in gut microbiota of human. The microbiota has been reported to be effective for the management of metabolic non-communicable diseases. The fermented food consumption shows direct connection between the type of microbial composition of any part of body as shown in Figure 4. The microbes are specific to body locations, and they are linked to the type of the food consumed. As fermented foods have their specific beneficial microbiota, they play a contributing role for good health.

Details are in the caption following the image
The effect of fermented food at organ level in humans.

The composition and type of the microbiota are analyzed by 16s rRNA sequencing. Lactic acid bacteria families have been found in mostly vegetable-based fermented products. Lactiplantibacillus bacteria can produce lactic acid and are found in different fermented products that are vegetable-based, for instance, sauerkraut and kimchi [57]. The bacterial compositions that are beneficial for health act as probiotics; for example, Lacticaseibacillus and Latilactobacillus. They can be explored from fermented foods, as they are readily available in them. Along with these two genera, some other bacteria are present that are considered good for health and hence are probiotics. Pediococcus is a bacterial genus that is used as a food preservative. It can decrease the pH of food by converting the sugars found into lactic acid in fresh vegetables; hence, it prevents food spoilage [58]. Other than the mentioned species found in fermented vegetables, like in sauerkraut, Lactococcus and Weissella are prominent. It can also synthesize lactic acid like others by glucose fermentation. Species of Weissella, as reported, are also present in other fermented foods along with sauerkraut, and most of them can make exopolysaccharide, which is required for adhering to surfaces; it also maintains the viscosity and structure of fermented food [59]. As mentioned, Lactococcus species are found in sauerkraut; in addition, they have a great scope in dairy product formation.

8 Beneficial Effect of Fermented Food

Consumption of fermented food is health beneficial and regulates the immune system for maintaining good health. They possess a long shelf life and are generally believed to result in health benefits and have a positive effect on health. The processed or fermented foods are easy to use and handle. With simple traditional technology, fermented foods can be formed by exploiting raw unprocessed raw materials as ingredients. They do not contain any chemical preservative or any coloring agent. They are produced naturally with long shelf-life properties, which is highly essential for future sustainable development. Fermented products are a new concept of live food, as they contain useful microbiota; they contain natural and diverse microbiota [24], toward which consumers are effectively attracted for maintaining good health. People are highly concerned with health maintain parameters like weight, cholesterol, fat, and calories. Fermented foods are found to be related to good health maintenance by reducing weight. There is a very strong association and correlation between dairy product consumption and body weight control [60]. Fermented food reduces mortality rate along with disease like cardiovascular disease and diabetes [61, 62]; it enhances metabolism of glucose and reduces soreness of muscle [63].

The benefit of fermented foods in human is well proved and documented. As the gut microbiota is also the main part of total microbiome of an individual which maintains most of the body mechanisms. Fermented foods have the ability to boost up the gut microbiome. There is a positive effect on microbial metabolism when fermented plant is consumed than in fermented food nonconsumers. Pseudomonas spp., Dorea spp., L., Prevotella spp., Alistipes putredinis, Oscillospira spp., Enterobacteriaceae, Clostridium clostridioforme, Fusobacterium spp., Actinomyces spp., Bacteroides spp., Achromobacter spp., F. prausnitzii, Bacteroides uniformis, Clostridiales, and Delftia spp. were the microbes detected in fermented product consumers [64]. Yogurt is a very common fermented milk product, which is consumed by many people. The metagenomic study evidenced the changes in microbial diversity changes. It was found to be changing the microbial diversity of gut part of healthy human. Microbiome analysis is considered the most advanced tool which involves 16s rRNA sequencing analysis study. The pieces of evidence for gut microbe changes are the results of such metagenomic studies. For the yogurt consumption analysis, larger 16s cohort studies reflect that alpha diversity is more in yogurt eaters than those nonconsumers [65].

Northeast India is a home of different types of fermented foods. The tribes have their own traditional recipes for making enormous types of fermented products. Different types of raw materials are used with specific starter cultures to prepare fermented food and beverages. For instance, fermented kimchi has shown a relative rise in Bacteroides and Prevotella and a relative decrease in Blautia [66]. Sauerkraut, a very famous fermented cabbage product both in pasteurized and unpasteurized forms, is preferable. It has been reported that there is a greater number of sauerkraut-associated LAB (Lactiplantibacillus plantarum and Lactobacillus brevis) in unpasteurized compared to pasteurized milk [67].

9 Health Issues of Fermented Food Consumption

Generally, fermented food is beneficial to health. It contains microbial consortium of useful bacteria, essential for good health. The microbial composition is correct only if the condition in which fermented product is formed is proper. The microbial composition is seen to be become resistant in some cases and fermented foods are one of the reasons. The resistance of gut microbiota with their resistance mechanism in presented in Table 4.

TABLE 4. Resistance mechanism of gut microbiota.
Colonization resistance Resistance mechanisms References
Direct gut microbiota and pathogen interaction Niche exclusion, fermentation products, antimicrobial property, and antibiotic production [76-79]
Gut microbiota enhances the host defense mechanisms Interactions with local pattern recognition receptors, IgA secretion induction, pro-inflammatory cytokines, and recruiting immune cells interacting with exterminate pathogens [80-82]

Three factors mostly determine the perfect fermented food production, that is, salt level, temperature, and hygiene. In most of the fermented food preparation salt is used, the level of salt used in critical. If the level of the salt is not maintained, then the useful probiotic bacteria will be hampered [68-73]. Similarly, if temperature of condition is not maintained at the optimum temperature of fermenting bacteria, then again, the product will be altered. Increase in temperature can ferment food at higher rate, but gradually it will be spoiled at faster rate. Generally, the optimum temperature to be maintained for proper fermentation is 36°C [74-78]. Hygiene is essential in fermentation as it controls the growth of unwanted and pathogenic bacteria. Like any other food, which is prepared with proper hygiene, fermented food also needs proper care [79-82].

10 Conclusion

The diversity of microbiome is the key measure in a line of defense of human. The consortium of microbes is one key that enhance the defensive system within the hosts system. Internal tract of human being is filled with microbes from which some are beneficial and some are harmful. They maintain the integrity by benefitting microbes due to which immunity of human get promoted. Different groups of microbes are found in different location. Gut microbiota makes the environment more resistance against the pathogens. They are also consumed as a probiotic and prebiotic, and known for their catalytic activity to maintain the metabolic activity by adding them in a normal diet in fermented form. Fermented food promotes the growth of microbes in gut. But if fermentation is carried out in unhygienically without maintaining temperature, pH, and so forth, can triggers the growth of unwanted or harmful microbes. So, it is very important to maintain the existence of hygienic substances otherwise they can terminate the activity of pathogenic microbes.

Author Contributions

Rahel Debbarma: conceptualization (equal), investigation (equal), writing–original draft (equal). Sony Kumari: conceptualization (equal), investigation (equal), supervision (equal), writing–original draft (equal). Doly Barman: validation (equal), writing–original draft (equal). Rony Bhowal: data curation (equal), writing–original draft (equal). Puja Roy: visualization (equal), writing–original draft (equal).

Acknowledgments

The authors declare that no funds, grants, were received during the preparation of this manuscript. Authors are thankful to the Department of Applied Biology, University of Science and Technology Meghalaya, India, for providing research facilities.

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