Review on Applied Applications of Microbiome on Human Lives

Abstract

It is imperative to say that we are immersed in a sea of microorganisms due to their ubiquitous presence on the planet, from soil to water and air. Human bodies harbor a vast array of microorganisms from both the inside and out called the human microbiome. It is composed of single-celled organisms, including archaea, fungi, viruses, and bacteria, including bacteriophages, where bacteria are the biggest players, and this is collectively referred to as the human microbiome. These organisms have a symbiotic relationship with humans and impact human physiology where they colonize various sites on and in the human body, adapting to specific features of each niche. However, dysbiosis, or the deviation from normal microbial composition, is associated with adverse health effects, disrupted ecosystems, and eco-imbalance in nature. In this review, we delve into the comprehensive oversight of bacteria, their cosmopolitan presence, and their additional applications affecting human lives.

1. Introduction

The origin of the ‘Microbial World’ dates back to the early 1900s, when the coexistence of a vast number of microorganisms, including bacteria, yeasts, and viruses, was reported on various sites on the human body and in and around its surroundings [1]. Microorganisms are ubiquitously found in soil, water, and air, including space [2]. The human and microbial world go hand in hand, and the human microbiome is often referred to as ‘the hidden organ’, which contributes over 150 times more genetic information than that of the entire human genome [3]. Recent advances in sequencing have enabled genome sequencing of the microorganisms and thus their understanding [4]. The composition of the microbiome varies from environment to environment and from site to site in the human body [5]. In the current review, our goal is to comprehensively focus on how the microbial world influences human lives in health and well being (Figure 1). Additionally, we provide a comprehensive overview of microorganisms of agricultural importance, biopesticides, biofertilizers, and nitrogen fixation, providing detailed accounts of PGPR (plant growth-promoting Rhizobacteria). We also discuss air, water, and soil pollution with regard to the microbial world. Then, we present a detailed account of microbial applications in the food industry and pharmaceutical industry. Furthermore, we discuss various probiotics and how they influence mental and reproductive health in human beings. As this is a very dynamic and diverse area of research, there is a significant requirement for advanced technologies, such next-generation sequencing and bioinformatics approaches, to completely understand the microbiome and how it influences human lives in different ways.

2. Beneficial Bacteria of Agricultural Importance

Microbes are tiny structures that are difficult to visualize with the naked eye and have variability starting from micrometers to millimeters in length. However, their small unicellular structures act as machinery for the production of several compounds that provides several benefits in the agricultural sector. Sometimes, their whole cells are also as useful as products in practical applications. Some of the frequent and paramount aspects of bacteria in the agricultural field are discussed here (Figure 1).

2.1. Decomposition of Organic Matters

The decomposition of organic materials is a fundamental ecological phenomenon in which nature recycles nutrients into the lithosphere and biosphere [6,7]. The conversion of soluble substances, like sugars and nitrogenous products, is the preliminary choice for conversion since they serve as the predominant energy source for bacteria [8]. They mainly turn into aliphatic acids (acetic, formic, etc.), hydroxy acids (citric, lactic, etc.), or alcohols (ethyl alcohol, etc.) by different groups of bacteria by simple oxidation processes. The decomposition of insoluble complex substances, like cellulose, which is broken down mostly into cellobiose and glucose, is further converted into organic acids [9]. Hemicellulose is broken down into component sugars and uranic acid, which are further metabolized to pentose and carbon dioxide [10,11]. Pectin is broken down into galacturonan or rhamnogalacturonan [12]. Lignin is broken down into hydroxy cinnamyl alcohols (or monolignols), coniferyl alcohol, and sinapyl alcohol, p-coumaryl alcohol [13]. Starch is broken down into glucose via amylose and amylopectin [14,15], xylan into xylose [8], chitin into n-acetyl D glucosamine and then fructose 6 phosphate [11], keratin into simple amino acid molecules [16], lipids into fatty acids and glycerol [17], and many more.

2.2. Soil Fertility/PGPR

The upper surface or crust of our earth is a breathing element continuously recycling nutrients, minerals, gases, and all kinds of life forms, which also aid the base for plants [18]. PGPR is an emerging group of organisms responsible for enhancing the growth and bodily functions of terrestrial autotrophs, viz., plants [19]. The direct PGPR machinery involves the fixation of molecular N₂, the production of siderophores, the mineralization of inorganic phosphates, the solubilization of potassium, and the production of growth hormones beneficial to the plants, whereas the indirect PGPR involves the secretion of antibiotics, the production of HCN, the release of hydrolytic enzymes, polysaccharide accumulation, and induced systemic resistance [19,20]. For example, a recent study identified two novel biofilm-forming PGPR strains, Bacillus subtilis-FAB1 and Pseudomonas azotoformans-FAP3, which resulted in improved growth and productivity of wheat under drought conditions [21,22]. Similar encouraging results were found in corn using PGPR mix formulation, which mainly comprised different Bacillus sp. [23]. In an earlier study, Dyadobacter sp. was used to enhance the growth of legumes and finger millets by fixing atmospheric N₂ and making it more available to plants [24,25].

When it comes to the demand of the growing population, an increase in population, decrease in agricultural land area, an increase in seasonal variations and different biotic and abiotic stresses which have brough down the food production annually are the most concerning factors. [19]. The emerging needs of microbes focus on PGPR as a boon in the agriculture sector that can increase the productivity and disease control in plants [21]. Beneficial free-living bacteria in soil are referred to as PGPR or yield-increasing bacteria (YIB) by one group of workers in China [22,26]. Currently, PGPR as a bioinoculant in sustainable farming practices has received greater attention [23]. PGPR stimulates plant growth through several mechanisms, either directly by supplying plants with phytohormones, phosphate solubilization, nitrogen fixation, and siderophore production, or indirectly by protecting plants from phytopathogens through different mechanisms [23]. The group of PGPR includes bacteria belonging to different genera, such as Acinetobacter, Agrobacterium, Arthobacter, Azobacter, Azospirillum, Burkholderia, Bradyrhizobium, Rhizoobium, Frankia, Serratia, Thiobacillus, Pseudomonads, and Bacillus [19,21].

2.2.1. PGPR by Phytohormone Production

Many PGPR are well known to secrete hormones and manipulate hormone balance in the plants to boost growth and stress response, which finally regulate root/shoot growth [27]. The hormones involved mostly include auxins, cytokinins, and ethylene and, to a lesser extent, gibberellins and abscisic acid [28].

Auxin Producing PGPR

Patten and Glick (1996) reported that around 80% of PGPR possess the ability to produce indole acetic acid (IAA) [29]. Indole acetic acid plays a vital role in the growth and developmental aspects of plants, such as the development of vascular tissues, lateral root formation, cell differentiation, apical dominance, etc. [29]. Two strains, Pseudomonas fluorescens (M4) and Serratia proteamaculans (M11), have shown 13.26 µg/mL and 19.19 µg/mL auxin production in presence of L-tryptophan, which showed an increase in plant height by 45%, fresh biomass by 56%, total chlorophyll content by 29%, total phenolic content by 59 to 73%, phosphorus content by 26%, potassium content by 50%, and protein content by 27% [30]. Similarly, a substantial increment in straw yield, cob length, cob weight, grain weight, and grain yield were recorded with inoculation of the Bacillus strain. IAA production with tryptophan was 57–288 µg/mL by Pseudomonas aeruginosa (CMG860), and the root elongation of germinating seeds and shoot lengths was the highest when inoculated with CMG860 [29]. IAA production by Azosprillum brasilense (DSM1690) is reported to be 32µg/mL. The maximum grain yield (13.8 g/plant) was seen when inoculated with isolate S54 [29,30].

Cytokinin-Producing PGPR

Cytokinins influence plant growth and development by cell division, the expansion of leaves, delaying leaf senescence, etioplast conversion to chloroplast, and chloroplast accumulation in leaves [31]. Cytokinins are plant hormones and in one of the research projects, it was found that wheat plants inoculated with Azospirillum brasilense (RA17) showed increased plant height, crop growth rate, relative growth rate, net assimilation rate, and leaf area index during different developmental stages of the plant [28,31]. It also showed an increase in proline content, endogenous hormones, and antioxidant enzyme activity in wheat kernels. Other physiological parameters like epicuticular wax, stomatal conductance, the photosynthetic rate, and chlorophyll contents were also found to improve [28]. Bacillus megaterium (UMCV1) increased root and shoot fresh weight in wild-type Arabidopsis thaliana [32]. One of the studies reveal that the AK1 strain of Pseudomonas fluorescens increased isopentanyl adenosine (IPA), dihydroxyzeatin riboside (DHZR), and zeatin riboside (ZR) production with time in pure cultures, i.e., at 12 h 2.1 pmol/mL and at 336 h 5.5 pmol/mL IPA at 96 h 0.2 pmol/mL, at 336 h 1.38 pmol/mL of DHZR, at 72 h 2.5 pmol/mL, and at 336 h 3.1 pmol/mL ZR. Inoculation with root exudates at 5.9 pmol/mL IPA and 2.6 pmol/mL ZR showed no significant difference in DHZR in treated and untreated plants [33]. The free-living bacteria Paenibacillus polymyxa produced isopentenyladenine during its stationary phase of growth [34].

ACC-Producing PGPR

Ethylene is a gaseous hormone that causes senescence and fruit ripening in plants [35]. 1-Aminocyclopropane 1-carboxylic acid (ACC) is a direct precursor of ethylene biosynthesis [36]. PGPR-producing ACC deaminase promotes plant growth by lowering plant ethylene levels. The inoculation of Glutamicibacter (YD01) species had the ability to produce ACC deaminase and had shown increased shoot height, root length, fresh weight, and dry weight, and enhanced salt tolerance in rice [37]. Brevibacterium iodinum (RS16), Bacillus licheniformis (RS656), and Zhihengliuela alba (RS111) have been shown to reduce ethylene production by 57%, 44%, and 53%, which helped in to reduce salt stress in red pepper plants [38]. Methylobacterium fujisawaense promoted root elongation in canola [39]. Pseudomonas sp. and Bradyrhizobium sp. enhanced nodulation in mung beans [40] and Pseudomonas plecoglossicida strain Pp20 plant photosynthesis in maize plants under saline stress [38].

PGPR-Producing Siderophores

Siderophores are low molecular weight iron chelating compounds synthesized by many bacteria, which form complexes with free iron [41]. These molecules are encoded by five genes in operon [41,42]. In addition, siderophore has applications in clinical, environmental fields, and phytoremediation [41]. Siderophore-producing bacteria have been shown to induce metal tolerance in plants [43]. Studies in Indian mustard have shown that Bacillus edaphicus stimulated plant growth, facilitated soil Pb mobilization, and enhanced Pb accumulation [35,44]. Streptomyces tendae F4 promoted plant growth, facilitated soil metal solubilization, and enhanced Cd and Fe uptake in sunflowers [45]. Streptomyces acidiscabies E13 protected plants from metal toxicity and enhanced the uptake of Al, Cu, Fe, Mn, Ni, and U in cowpeas [46]. Presently, 500 siderophores are reported from selected microorganisms. A great variation is seen in the siderophore structure from one species to another [41].

PGPR with Antifungal Properties

PGPR, having antifungal properties, can be used as bio-fungicides and to minimize yield loss and maximize crop productivity [47]. The plant growth-promoting rhizobacteria OUG38 strain has shown a high level of inhibition against Colletotrichum capscici (80%) and Rhizoctonia solani (76%), and OUG61 has shown a high level of inhibition against Fusarium oxysporum (78%) and Macrophomina phaseolena (78%). Pseudomonas aeruginosa (B7-1, B11-5, B3-, Rh-1, Rh-2) and Pseudomonas putida (B53) showed antifungal activity against Fusarium oxysporum [48,49,50]. Bacillus (Bac10) has shown the highest antifungal activity against Macrophomina, while Azotobacter (Azt12) has shown the highest antagonistic activity against Helminthosporium sp., and (Azt6) against Fusarium sp. Azotobacter (WR7) showed maximum inhibition against Rhizoctonia solani in wheat [49,51].

Phosphate Solubilizing PGPR

Phosphorus is the second most critical macronutrient after nitrogen required for the metabolism, growth, and development of plants [52]. Despite its abundance, it is mostly unavailable to plants [21]. The application of phosphate-solubilizing microorganisms in the soil is a promising approach to restoring soil health [53]. The solubilization index shown by Lysinibacillus pakistanensis (PCPSMR15) is 4.0 [54]. Mung beans inoculated with PCPSMR15 brought remarkable enhancement in the root (3.1 cm), stem (20.8 cm), and leaf (2.9 cm) length, as well as the control at 1.3 cm, 7.1 cm, and 1.6 cm, respectively [54,55]. Qualitative analysis reports that the phosphate solubilizing efficiency shown by the Bacillus subtilis strain 3 (PS4) is the highest, i.e., 50.9 and 10.22 µg/mL [56]. There is a diversity of phosphate-solubilizing microorganisms in the soil, which are nowadays used as biofertilizers [54]. The number of published articles on PSB from 2002 to 2022 is 1% to 13%. According to data obtained from the Web of Science (WOS) database, a total of 67 countries are involved in the publication of the topic on PSB, among which, 15 countries showed the highest number of publications, and there are 225 institutions involved in research [57]. Although PSB research is abundant, the isolation, identification, and selection of PSB strains have not yet been successfully commercialized; thus, the application is still found to be limited [21,28,58].

2.3. Nitrogen Fixation

Nitrogen is a significant component used for autotrophs and heterotrophs offered in assorted redox conditions, and its regulation for transport and assimilation might vary significantly, depending on the organism’s nature [59]. There is an unmet demand for nitrogen fertilizer to fulfill the requirement of nitrogen in agriculture. However, we do not have any options left but to depend on nature and microbes to fix them spontaneously. These biological fixations could be either symbiotic, free living, or associative in nature [25]. Numerous efforts have been made to make engineered plants that can directly fix nitrogen or enter an association with microbes (e.g., making non-leguminous plants compatible with symbiotic nitrogen-fixing bacteria). However, the results are still not promising enough to be introduced on a large scale to date [24,60]. In a recent study, bacterium, like Rhodobacter sphaeroides, can be seen fixing nitrogen along with the microalgae strain Coelastrella sp. in a mutual nutrient exchange understanding [61]. On the other hand, novel free-living bacteria, like Fundidesulfovibrio magnetotacticus, have been reported recently in rice fields capable of fixing significant amounts of nitrogen [62]. Newer approaches, like the isolation of plant tissue extract and subsequent 16 S rRNA gene profiling for total culture-independent bacterial microbiome revealing newer species, are capable of fixing nitrogen in association with plants, except for the formation of legumes [14].

2.4. As Biofertilizers

Biofertilizers are predominantly live organisms or their products and can be used to enhance the nutrient attributes of soil, thus improving its health and productivity. Biofertilizers can be bacteria, fungi, algae, or cyanobacteria, helping to recuperate the fertility of soil via mineral and organic matter recycling. However, biosafety trials with bacteria as bio-stimulants and biofertilizers should be based on bioassays rather than taxonomy [63]. Bacteria used as major biofertilizers include nitrogen fixers (as discussed in the previous section), cyanobacteria, phosphate, and potassium solubilizers. Proven nitrogen fixer biofertilizer bacteria may include but are not limited to Rhizobium sp., Bradyrhizobium sp., Streptomyces griseoflavus, Bacillus subtilis, Bacillus pumilus, Bacillus licheniformis, Kelbsiella pneumoniae, Azotobacter, Azospirillum, Nostoc, Anabaena, and many more [22,43,64,65]. Phosphate solubilizers showing great potential as biofertilizers may include but are not limited to Pseudomonas fluorescens, Sphingobacterium suaedae, Bacillus pimilus, Bacillus cereus, Bacillus endophyticus, Bacillus sphaericus, Bacillus megaterium, Virgibacillus sp., and Enterobacter aerogenes [21,53,58,66]. Potassium solubilizer bacteria are sometimes put under PGRP; however, their great potential might lead to them being prospective candidates in the biofertilizer market soon. A few important potassium solubilizing bacteria are Pseudomonas fluorescens, Pseudomonas putida, Enterobacter sp., Bacillus megaterium, Bacillus firmus, Pantoeaagglomeran, Bacillus pseudomycoides, and Bacillus cereus [67,68].

2.5. As Biopesticides

Biopesticides are naturally derived substances from animals, plants, bacteria, or certain minerals that can control pest infestation in an ecofriendly manner, whereas chemical pesticides have always been a concern for the environment, as they are recalcitrant xenobiotics and are prone to bioaccumulation and biomagnification [69]. Several bacteria have been reported to produce a lethal toxin capable of controlling pests, but they are nontoxic and nonpathogenic to animals and humans [69]. Bacillus thuringiensis, a Gram-positive, spore-forming soil organism, was first identified in the early 20th century in Japan and was commercialized as a biopesticide in the late 1930s in France [64]. The most widely studied and applied strains for Bacillus thuringiensis are kurstaki, galeriae, and dendrolimus, which secrete ‘Cry’ protein as an endotoxin; the gastrointestinal enzymes present in the gut of different insect larvae can activate the toxin, thus leading to subsequent gut paralysis and death of the insect [70,71]. Other agriculturally important bacteria used as biopesticides include (but are not limited to) cyclic lipopeptides (CLPs) producing Bacillus velezensis [72]; hydrogen sulfide producing Pseudoxanthomonas indica [73]; and Agrobacterium radiobacter (now Rhizobium rhizogenes), which produce agrocin, an antibiotic capable of controlling Crown Gall disease caused by Agrobacterium tumefaciens [74]. Pseudomonas aeruginosa is capable of producing shenqinmycin, an antifungal agent [75]. Pseudomonas fluorescens is capable of producing phenazine and others [33,76].

3. Bacteria: The Natural Scavenger of Environmental Pollutants

Rising contamination in the lithosphere, biosphere, hydrosphere, and atmosphere imposes a severe threat to public health and safety not only in underdeveloped countries but also in industrialized developing or developed countries, such as The United States of America, the European Union, China, and India [77]. The last few decades have shed some light on the eradication of contaminants from the soil, water, or air catalytic activities of microorganisms—specifically bacteria rather than relying solely on chemical methods [46]. Additionally, the inception of genetically modified organisms (GMOs) in the early 1980s has extended the opportunity to degrade or remove certain compounds, thus improving the scope for bacterial bioremediation [78].

3.1. In Water Pollution Control

Contamination of water has become a global concern, as major sources for such pollution are from the agricultural revolution (producing herbicides, pesticides, and chemical fertilizers), the industrial revolution (producing synthetic dyes, oil and grease, metals, chlorinated solvents, and toxic sludge), and the healthcare revolution (producing radioactive element and antibiotics), which are inevitable for the thriving of human civilization [79]. In 2018, fluoride was removed from water by nanoparticles synthesized using Bacillus subtilis as a microbial agent [80]. A study by Wan et al. showed that heterotrophic (Thauera and Ferritrophicum) and autotrophic bacteria (Chlorobaculum) can be useful for removing perchlorate and nitrate from water [81]. Various studies for synthetic dye (such as Malachite Green, Congo Red, Direct Green, Bromophenol Blue, Acid Red, Basic Blue, and many more) removal from water have been performed previously, which revealed that physicochemical parameters might be a crucial factor influencing removal percentage from aqueous solutions [4,82,83,84]. Recent studies have shown bacteria’s ability to remove antibiotics [85], chemical fertilizers [86], herbicides [78], pesticides [79], radioactive elements [87], oil and grease [88], and many more from water [89].

3.2. In Air Pollution Control

Air pollution is generally regarded as the admixture of harmful elements generated via any anthropogenic activity or natural sources, leading to ~4 million premature mortalities every year [90]. The principal causes behind air pollution are alleged to be PM_2.5 (particles whose diameter is less than 2.5 mm), as these can infiltrate the respiratory, cardiovascular, and circulatory systems, thus leading to several diseases, including cancer [90,91]. As per research data, the most susceptible groups affected by air pollution are pregnant women, adolescents, and elderly people in terms of their physical and mental health [91]. Moreover, flue gases such as CO, NO, SO₂, volatile organic compounds (VOCs), dioxin, and polycyclic aromatic hydrocarbons (PAHs) generated by combustion of fuels and flammable substances are equally poisonous to humans. Biofiltration is an emergent practice and is being used to remove air pollutants discharged by different industries. Several bacteria are being reported as competent biological agents to be used in biofilters to remove air pollutants [92]. In 2017, Bravo et al. exploited a non-culturable microbial community in an anaerobic bioscrubber and found that Methanosaeta sp., Methanospirillum sp., Methanobacterium sp., Geobacter sp., and Pelobacter sp. are predominant while removing volatile organic compounds (VOCs) [93]. In another study, three proteobacteria, viz., Thioalkalimicrobium cyclicum, Stappia sp., and Ochrobactrum sp., were predominantly found in bioscrubbers and were successfully involved in the desulfurization of biogas [94]. A recent study showed that Thiobacillus sp. can act as a better denitrifying agent in anaerobic conditions, whereas Cryseobacterium and unclassified Xanthomonadaceae can work as efficient sulfide oxidizing agents under aerobic conditions in bioscrubbers [95].

3.3. In Soil Pollution Control

Soil is a natural compound that mainly forms the loose surface of the earth and principally consists of five elements—minerals, organic matter, living microbes, gases, and water [40]. Among them, soil minerals are predominantly categorized into clay, silt, and sand, which vary in percentage to make different types of soil in general [14]. Rapid industrialization and the agricultural revolution continuously produce unusual environmental contaminants, like hydrocarbons, heavy metals, synthetic dyes, microplastics, and pesticides, whose cytotoxic and genotoxic effects are well known along with their non-biodegradability and advanced persistence [70,96,97]. Zhang et al., 2019, showed that the immobilization of bacterial cells in natural biochar can enhance the bioremediation of petroleum hydrocarbons from soil and has a potential for application in ex situ bioremediations [97]. A range of bacteria like Acinetobacter baumannii, Bacillus weihenstephanensis, Pseudomonas aeruginosa, Pseudomonas fluorescens, and Rhodococcus ruber can be useful for the biodegradation of microplastic and nanoplastic residues from the soil via biodeterioration, biofragmentation, assimilation, and mineralization [98]. Reports suggest that several bacteria such as Bacillus, Klebsiella, Mycobacterium, Pandoraea, Pseudomonas, Sphingomonas, Sphingopyxis, Rhodococcus, Sphingobium, and Phanerochaete chrysosporium are involved in the bioremediation of pesticide-contaminated soil, thus controlling soil toxicity and nutrient recycling [99]. However, an integrated approach may be taken among microbiological methods linked with field application design so that genetically modified or engineered microbial stains can be developed, achieving a more effective in situ and ex situ bioremediation of hazardous waste from the soil using recombinant bacterial cells [100].

4. Microbial Applications in the Food Industry

The contemporary food system depends on unsustainable practices and often fails to meet the food demand of a rapidly growing population [101]. Hence, there is an urgent demand for novel sustainable food systems and processes [63,101]. Microorganisms have gained significant attention as a new nutrition source owing to their low carbon footprints, low reliance on land and water, and seasonal variations coupled with a favorable nutrition profile [102]. With the emergence of new tools in synthetic biology, the use of microbes has expanded, showing tremendous potential to meet our global food requirement/demand [103]. Here, we present a detailed account of various applications of microbes in food, and we cover both the use of microbes to produce whole food out of their biomass and as cell factories in making highly functional and nutritional biomolecules.

4.1. Fermented Dairy Products

The fermentation of dairy products is accomplished through a diverse group of microbes. Along with the wide-range commercial production of fermented dairy products, the usage of starter and adjunct culture(s) has also gained application in the last century [104]. In recent years, severe investigations have also been carried out on the health benefits being conferred by various dairy products. Lactic acid bacteria (LAB) strains remove anti-nutritional factors, like lactose and glucose, from dairy products through their fermentative action [105]. The lactic acid bacteria develop flavor and texture and acidify milk through their proteolytic activities [106]. Some studies have demonstrated that kefir consumption has been found to have a positive impact on the metabolism and mineral density of bones [107]. Likewise, the consumption of yogurt is associated with a lower threat of type 2 diabetes [108]. The use of fermented milk products containing Bifidobacterium lactis CNCM I-2494 demonstrated a positive effect on the tolerance of a plant-based diet in patients with disorders in gut–brain interactions [109]. The most common starter cultures of Gram-positive lactic acid bacteria that are widely used are Streptococcus thermophilus, Lactobacillus helveticus, Lactobacillus lactis, and Lactobacillus delbruckii subsp. bulgaricus. Some of these strains also help in the preservation of fermented milk by producing bacteriocins [110]. Some specific lactic acid bacteria, like Fructilactobacillus, Lacticaseibacillus, Lactiplantibacillus, Lactobacillus, Lactococcus, Lactobacillus, Lentilactobacillus, Leuconostoc, Limosilactobacillus, Pediococcus, Streptococcus, Weissella sp., etc., synthesize exopolysaccharides (EPSs) that impart desirable physical properties to fermented dairy products [103].

4.2. Fermented Non-Dairy Products Based on Cereal and Vegetables

Around the world, the consumption of fermented cereals and vegetables constitutes a significant part of the human diet, with a substantial contribution to the food supply chain for a constantly growing world population [111]. Several different species of lactic acid bacteria (LAB) prevail in various fermented vegetables, depending on raw materials and environmental and physiochemical conditions during fermentation. Most predominant species in table olives are Lactobacillus pentosus and Lactobacillus plantarum [112]. Kimchi, a traditional South Korean fermented product, is made from cabbages, radish, and other vegetables and contains Weissella and Leuconostoc, along with Pediococcus, which is the predominant species [111]. Sauerkraut, a fermented food product made from cabbage, contains Lactobacillus and Leuconostoc as the dominant species during the early and middle/late stages of its fermentation. Streptococcus malefermentans was also found to play an important role in sauerkraut fermentation when carried out at lower temperatures [113]. During the production of pickled cucumbers, Pediococcus ethanolidurans, Enterococcus thailandicus, and diverse species of the genus Lactobacillus and Leuconostoc play a key role in the fermentation process [14,114].

In cereal fermentations, a key role is played by Bacillus and Lactobacillus species by hydrolyzing complex polyphenols to simpler and biologically active forms. Lactobacillus plantarum and Saccharomyces cerevisiae play a significant role in the fermentation of wheat noodles, affecting the structure and flavor. A significant effect was seen in the enhanced continuity of the gluten network and pore formation [14]. Many fermented food products made from cereals, like Akamu/ogi and Uji, a thin maize gruel, and ting, a fermented porridge, are used in African countries. LAB strains are mostly used in the fermentation of cereals but are sometimes mixed with the inoculum of other organisms like Candida spp., Saccharomyces cerevisiae, Streptococcus spp., and Acetobacter spp. [115].

4.3. In Industrial Breweries

Acetic acid bacteria have been associated with the production of vinegar and other fermented beverages [102]. A. pasteurianus, A. aceti, Komagataeibacter xylinus, K. europaeus, and K. hansenii are commonly used in vinegar production. K. xylinus, A. pasteurianus, K. hansenii, A. aceti, Gluconacetobacter saccharivorans, Acetobacter, Gluconobacter, and Gluconacetobacter spp. are involved in the production of a fermented beverage, kombucha [93,110]. Acetobacter lovaniensis, Acetobacter fabarum, Acetobacter cerevisiae, A. aceti, Acetobacter ghanensis, A. lovaniensis/fabarum, and Acetobacter sicerae are the predominant species during fermentation of water kefir [24]. A. lambici and G. cerevisiae are the significant species associated with the fermentation of lambic beer [4]. A study has demonstrated that Lactobacillus fermentum KKL1 exerts a substantial effect and enhances functional aspects during the preparation of haria, a rice-based beverage consumed by ethnic people of Central and Eastern India [116]. Cheka, Keribo, Borde, Areki, Tella, Shamita, Booka, and Korefe are some of the Ethiopian indigenous fermented beverages produced from several kinds of cereal. During the preparation of these beverages, lactic acid bacteria (LAB) species and Acetobacter species play a significant role in enhancing their organoleptic and nutritional properties and improving their bio-preservation [117]. Cauim (Kawi) is a non-alcoholic beverage of South American origin prepared from several substrates like banana, cotton seeds, maize, pumpkin, rice, cassava, etc. Lactic acid bacteria are the dominant species and play a significant role during cauim preparation. Among LAB, Lactobacillus pentosus and Lactobacillus plantarum are the most prevalent species. A few species of Bacillus are also present in small amounts [118]. Wine malolactic fermentation is carried out by Lactobacillus hilgardii [119].

4.4. In the Meat Industry and Related Products

Carnobacterium piscicola, C. divergens, Lactobacillus sakei, L. curvatus, L. plantarum, Leuconostoc mesenteroides, Le. Gelidum, and Le. carnosum are the natural strains of LAB present in meat and meat products. In fresh meat, LAB are responsible for mild fermentation changes without affecting organoleptic properties [120]. The bacteriocins (proteinaceous toxins) produced by many bacteria can inhibit the growth of other bacteria in meat and meat products, e.g., the bacteriocin produced by Pediococcus acidilactici inhibits the growth of L. monocytogenes in meat products stored under refrigerated conditions for about 28 days [4]. Likewise, bacteriocins of the genus Lactobacillus have shown antimicrobial effects against several Salmonella sps., such as Enteritidis, Heidelberg, Newport, and Typhimurium [4]. The bacteriocin nisin produced by Lactobacillus lactis has a positive effect on meat bio-preservation [120]. Lactobacillus sakei and L. curvatus are the main producers of bacteriocins among the LAB present in meat and meat products and produce sakacins and curvacins, respectively [121]. Studies have shown that a combination of garlic extract with Lactobacillus reuteri and L. plantarum from beef is known to inhibit Listeria monocytogenes by the production of antibacterial agents [122]. In beef sausage, bacteriocinogenic strains of Enterococcus mundtii, along with curing agents (3% sodium chloride, 0.02% sodium nitrate, 0.0075% ascorbic acid, 0.75% glucose and sucrose), have shown an inhibitory effect on Listeria monocytogenes [123]. Pediocin secreted by Pediococcus pentosaceus and extract from Murraya koenigii berries were demonstrated to reduce the growth of Listeria innocua in goat meat emulsion [124]. Fermented meat products like Arabic sausage, lean pork, and shrimp paste contain bacterial strains of Lactobacillus alimentarius, L. pentosus, L. plantarum, L. versmoldensis, Pediococcus acidilactici, P. pentosaceu, Stolephorus species, and Sardinella species, which help in the flavoring of meat products and increase their shelf life [125,126].

4.5. As Probiotics

Lactobacillus, Enterococcus, Streptococcus, Pediococcus, and Leuconostoc are some of the genera of lactic acid bacteria used as probiotics in the intestine [127]. Apart from these, some stains of genera Bacillus and bacteria Akkermansia muciniphilaare and Faecalibacterium prausnitzii have also been recognized as potential sources of probiotics [128]. Commercial probiotics food, e.g., BIO^®, Actimel^®, LC1^®, and Yakult^®, contain lactic acid bacterial strains Lactobacillus casei and Lactobacillus acidophilus. Probiotics enhance the nutritive value of food, improving the test. The fermented food doenjang/soybean paste contains bacterial strains of Bacillus species, Tetragenococcus, and Zygosaccharomyces, acting as probiotics. These bacterial strains enhance the activity of natural killer (NK) cells of the spleen. They can also improve the inhibitory effect of bioactive peptides on the angiotensin-converting enzyme (ACE) [129]. Fermented food products, like glutinous rice, tapioca, idli–dosa, kimchi, natto, sauerkraut, vinegar, etc., contain Lactobacillus that impart several health beneficiary effects, such as mitigating constipation and stimulating the human immune system. They also have antioxidant, antihypertensive, and anti-diabetic properties [4]. Studies have demonstrated that the introduction of antigens inside the human body along with probiotic bacteria can provide an effective means to attenuate autoimmune diseases, as this leads to the simultaneous suppression of both antibody and cell-mediated immune responses [130]. Some riboflavin-producing lactic acid bacteria strains, e.g., Lactobacillus plantarum, have also displayed probiotic traits. These are appealing from an industrial perspective as multifunctional adjunct cultures for the production of biofortified fermented edibles, and they exercise probiotic characteristics [119].

4.6. In the Pharmaceutical, Nutraceutical, and Cosmeceutical Industries

Many lactic acid bacteria possess beneficial properties of being, antagonistic, antioxidant, and antimicrobial, and they also have immunomodulatory properties [111]. So, they are widely used in the pharmaceutical industry. Bacteriocins produced by several bacteria, including LAB, are widely used in food processing industries [121,131]. Due to their promising anti-bacterial, anti-viral, and anti-cancer nature, these bacterial products are further studied for their use in the pharmaceutical and medical fields [110]. Several metabolites secreted by strains of Lactobacillus, Enterococcus, and Lactococcus have shown anti-proliferative impacts on distinct cancer cell lines by the induction of apoptosis [121,132]. Microbial by-products produced by S. epidermidis are known to inhibit the colonization of pathogenic Staphylococcus aureus responsible for several clinical conditions [133,134].

Nutraceuticals are natural compounds and have the properties of chemoprotection, antioxidation, and anti-inflammation, and they are derived from food or are part of the food [135]. A high-value bread was obtained with the fermentation of barley sourdough using the Pediococcus acidilactici LUHS29 strain that was immobilized in apple pomace [15]. It showed variable carbohydrate metabolism and better adaptability to acidic environments due to increased lactic acid production, β-glucan solubility, scavenging of free radicals, and an increase in total phenolic content by the bacterial strain [111]. An increase in vitamin B2 and B9 levels and elevated blood hemoglobin was detected when pasta fermentation was carried out with a mixed culture of Lactobacillus plantarum CRL 1964 and L. plantarum CRL 2107 [119]. Lactobacillus strains also display anti-colorectal cancer properties [119]. Lactobacillus plantarum, Pediococcus pentosaceus, and Lactobacillus rhamnosus are involved in the elimination of carcinogens and toxins from fecal material by modulating the mechanism and decreasing the pH [113].

The usage of Staphylococcus epidermidis for application in basic cosmetics as a beneficial bacterium for skin health is widely accepted [136]. S. epidermidis produces several metabolic products, like organic acids and glycerin, which help maintain skin health by retaining moisture, improving the rough texture of the skin, and maintaining low acidic conditions on the surface of the skin [134]. Further, it also has anti-aging properties due to the presence of superoxide dismutase, which destroys reactive oxygen intermediates [136,137]. Cutibacterium acnes secret propionic acid as one of the short-chain fatty acids (SCFAs) during triacylglycerol fermentation in the sebum [127]. Propionic acid keeps the pH of hair follicles of sebaceous glands at an acidic level, thereby controlling the growth of pathogenic bacteria [138,139].

5. Probiotic Bacteria and Their Benefits in Human Health

Probiotics are live, beneficial microorganisms, which include mostly bacteria and yeasts and are consumed or applied on the body and are proposed to improve or maintain our healthy lives [140]. The term symbiotics is used to define a combination of probiotics and prebiotics, the compounds used as a supplement with the probiotics that selectively favor the growth of beneficial bacteria and prevent the growth of harmful bacteria [140,141]. Probiotics play a critical role in the restoration of healthy gut microbiome communities that protect the gut by building a healthy intestinal mucous membrane, inhibiting the intestinal colonization of the pathogenic bacteria, ameliorating the host immunity, or preventing gut inflammation and systemic disease [109,141]. Apart from the promising role in the gut, the advantages of probiotics in human immune, reproductive, and respiratory systems, skin diseases, and oral and mental health have been demonstrated [142,143,144]. Lactic acid bacteria, a broad heterogeneous Gram-positive, spore-free bacteria, exist widely in the natural environment and include soil and fermented foods in or on the host body [105]. This group of bacteria plays a beneficial role in the host by regulating the microbiome in the gut [132]. Common strains of lactic acid bacteria, including L. acidophilus, L. rhamnosus, L. casei, L. delbrueckii, L. plantarum, L. reuteri, L. pracasei, B. bifidum, B. animalis, B. longum, B. infantis, B. adolescentis, etc., are used as probiotics for health benefits. C. butyricum, S. boulardii, S. cerevisiae, B. coagulans, and E. coli Nissle 1917 are widely used non-lactic acid bacteria and also have a probiotic effect on the hosts [42,116,132]. These microorganisms protect us from infections, hypertension, high blood cholesterol, diabetes, food allergies, oxidative stress, mutations, and carcinogens [145,146]. Here, we briefly summarize health-beneficial bacteria consumed by our body as probiotics for protection against several medical concerns.

5.1. Reproductive Health

Historically, it was thought that there were no native bacteria in the reproductive tract [147]. Many believed that microbes were only present during infection [148]. Several studies have demonstrated that the gut microbiome is an important regulatory component for sustaining the basal nourishing of the mammalian reproductive tract [130,132]. The healthy female reproductive tract has low bacterial diversity due to the main genus Lactobacillus spp. [147]. Probiotics and the molecules they produce help maintain a healthy reproductive tract by supporting healthy bacterial communities, inhibiting pathogen growth, maintaining the proper pH, and facilitating the immune system to function properly [147,149]. In the female reproductive tract, probiotics not only help to maintain an acidic pH but also can aid in fertilization by promoting epithelial barrier function and membrane integrity, which are essential for successful basculation and formation of the amnion, chorion, and placenta [91,147,150]. One example of the symbiotic relationship between microbes and hosts in the female reproductive tract is Lactobacillus spp., which metabolizes sugar glucose to produce energy and lactic acid [147]. This lactic acid then lowers the pH of the female reproductive tract and prevents pathogenic bacteria from growing, such as Gardnerella vaginalis [147].

5.2. Mental Health

An altered microbiome in the gut–brain axis has been associated with neuropsychological illnesses, including autism spectrum disorder and depression. Studies have also signified that the consumption of probiotics can modulate gut microbiomes that restore mental health. The beneficial effects of probiotics on the enteric nervous system and central nervous system have been reported by a series of investigations. For example, feeding L. reuteri to rats for 9 days elevated excitability and declined the slow afterhyperpolarization in sensory afterhyperpolarization neurons [151]. Similarly, a B. longum NCC3001-fermented medium inhibits the enteric nervous system neuron excitability [152]. Probiotic L. rhamnosus, ingested into healthy Balb/C mice, reduced emotional behavior, including anxiety and depression [153]. A study demonstrated that healthy women volunteers consumed 4 weeks of a fermented milk product containing B. animalis subsp. Lactis, L. lactis subsp. Lactis, L. bulgaricus, and S. thermophilus, resulting in induced brain activity in the emotional system [154]. Healthy volunteers improved their mood after drinking milk containing probiotic L. casei Shirota for 3 weeks [155]. One interesting study reported that 30 days of consumption of a formulated probiotic mixture consisting of L. helveticus R0052 and B. longum R0175 by healthy volunteers improved their psychological distress. Furthermore, this study also demonstrated that the daily administration of the same mixture of probiotics to rats for 2 weeks showed anxiolytic-like activity [156]. Taken together, probiotics play a vital role in protecting mental health.

5.3. Respiratory Health

Microbes occupy virtually all the surfaces of the human body, and the respiratory tract is not an exception [157,158]. Recent techniques of respiratory biology have begun to shed light on the microbial world of the respiratory tract, which was long considered to be a sterile environment [33,130]. It is clear that the human lungs are often exposed to live microbes and their by-products, and the nature of the lung microbiome is distinct from other microbial communities residing in our bodies, such as the gut [132]. The upper and lower respiratory tracts have different microbial compositions and biomasses. The upper tract is made up of the nasal cavity, paranasal sinuses, and pharynx, and the supraglottic portion of the larynx is primarily colonized with bacteria [157]. There are topographical differences in the microbial composition, and the nasal cavity and nasopharynx are dominated by Moraxella, Staphylococcus, Corynebacterium, Haemophilus, and Streptococcus species, while the oropharynx is dominated by Prevotella, Veillonella, Streptococcus, Leptotrichia, Rothia, Neisseria, and Haemophilus species [157]. On the contrary, the lower respiratory tract, which includes the trachea and lungs, exhibits low biomass due to rapid microbial clearance via several physiological mechanisms. It allows the lower tract to perform its most crucial function: the exchange of oxygen and carbon dioxide [33,42,130].

6. Summary and Conclusions

In this review, we highlighted the many ways by which microorganisms can influence their environment by altering the properties of their surroundings or by building microbial communities and structures. As environmental properties are also known to affect their surrounding microbial communities, the interaction between soil microbial community composition and soil microorganisms is reciprocal. Thus, microorganisms and their environmental interaction entail networks of causation of feedback, in which previously selected microorganisms drive environmental changes and, as a a consequence, microbially driven shifts in environmental properties subsequently shape microbial community composition and possibly evolutionary trajectories.

To advance the field, integrative research bridging soil sciences, ecology, biogeochemistry, evolution, and microbiology is paramount. Owing to the interconnected nature of microbial communities and soil properties, identifying the underlying mechanisms remains challenging. With the pressing need to protect and restore the environment, future approaches and steps should leverage insights gained from studying natural systems. Progress towards understanding the functional roles of the microbiome in shaping soil properties can also come from using more proactive approaches, whereby microbial communities are directly manipulated in controlled experiments. Such studies should include examining the evolutionary consequences of niche construction by microorganisms. Thus, the evidence outlined in this review shows that microbially driven shifts in environmental properties can also have practical applications, such as limiting soil erosion, promoting carbon sequestration, or restoring contaminated soil through bioremediation. The directed modification of the microbiome is an emerging research area that requires a better understanding of how microbially mediated shifts in properties can be used to combat threats to health and other environmental challenges.