Gut microbiota is a complex and highly diverse community of trillions of microorganisms that live in the digestive tracts of humans and animals, including insects [11,12]. Microbiota are ten times more abundant than our somatic and germ line cells of the body [13]. The human gut microbiota consists of several types of microbes including bacteria, archaea, eukarya, viruses and parasites [14] that weigh approximately 1 kg and represents the first protection system of the gastrointestinal (GI) apparatus. The microenvironment of the gut favors the growth of bacteria from seven predominant divisions (Firmicutes, Bacteroidetes, Actinobacteria, Fusobacteria, Proteobacteria, Verrucomicrobia and Cyanobacteria) [15]. Among these, more than 90% of the total population is made up of the Bacteroidetes and Firmicutes [13]. The presence of the microbiota differs within the parts of the GI tract, from few micro-organisms in the stomach and small intestine, up to a concentration of approximately 10¹² bacteria in the colon [16,17]. In humans, the gut microbiota has the biggest quantities of microorganisms, and the greatest number of species compared to other parts of the body [18].

Microbiota acquired at birth develop in parallel with the host and maintains its temporal stability and diversity through adulthood until death [19]. The gut microbiota forms an integral part of the human body [13] and plays a significant role in its normal functioning [11].

Though the gut microbiota is dynamic, it performs some basic immunological, metabolic, structural and neurological functions [13]. The metabolic role consists of the conversion of dietary elements into bioactive food components [8]. The gut microbiota scavenge about 10–30% of energy from the dietary fibers in the colon and the rest is excreted as feces [20]. Gut microbes possess an array of enzymes enabling the utilization of carbohydrates resistant to digestion by host digestive enzymes such as lignin, non-starch polysaccharides, resistant starch and oligosaccharides. Gut microbiota of the lower intestines ferments all of the dietary fibers, which results in the release of gases, short chain fatty acids (SCFAs), organic acids, and alcohols. SCFAs, the most prevalent being acetate, propionate and butyrate, meet about 10% of caloric demand of the host [21] and their main producers are Roseburia spp., Eubacterium rectale, Faecalibacterium prausnitzii and Clostridium spp. [22]. SCFAs also have promising anti-inflammatory and chemo-preventive properties [23]. According to the MEROPS database, gut microbiota have various peptidase and protease enzymes. Clostridium spp., Bacteroides spp. and Lactobacillus spp. are of special importance because of the diversity of possessed enzymes [24]. Some gut bacteria take part in the transformation of bile acids—their bile salt hydrolase deconjugates the unabsorbed bile salt and produces deoxycholate, ursodeoxycholate and lithocholate [8]. Gut microbiota executes its protective role by occupying intestinal surfaces and preventing the invasion of pathogenic microorganisms through creating a stable system. The epithelial cells of the mucosal barrier use the SCFAs as an energy source. Gut microbiota exhibit a significant impact on bone growth and development though SCFAs, regulation of calcium and phosphorus absorption from the diet and immunoregulation by the Lactobacillus spp. of the osteoclast-osteoblast mediated bone remodeling process [8]. Gut microbiota can control both the central and enteric nervous system through various mechanisms such as the production and expression of neurotransmitters and neurotrophic factors, modulating the enteric sensory afferents, metabolite production, immunoregulation of mucosa and maintaining the integrity of the intestinal barrier and tight junctions.

There are several factors that can change the gut microbiota composition and function. Numerous studies have indicated that host genetics influences the composition of the gut microbiome [25]. Pattern recognition receptors modulate microbiome composition and the diseases associated with it. After birth, gut microbiota is shaped mainly by diet as the microbiome adjust to absorbed nutrients. Firstly, it is enriched in genes involved in the metabolism of breast milk’s oligosaccharides, whereas later in the ones associated with the digestion of polysaccharides and vitamins [26]. The method of feeding the newborn significantly influences the microbiome composition—breast-fed infants exhibit an overgrowth of Actinobacteria and an inhibition of Firmicutes and Proteobacteria, whereas formula-fed infants experience an increase of Clostridium, Streptococci, Bacteroides and Enterobacteriaceae [27]. Vegetarians exhibit the dominance of Firmicutes and Bacteroidetes [8]. The abundance of bile-tolerant species (Bacteroides, Bilophila and Alistipes) and suppression of Firmicutes have been correlated with a diet rich in protein and fats. Another factors significantly affecting the microbiota composition is age. The first year of age is considered to be the most important period of development. Taxonomic diversity is low at birth, but increases over time. Firmicutes and Bacteroidetes are dominating the adult gut microbiota, while the elderly exhibit a decrease in Bacteroidetes to Firmicutes ratio, a reduction in Bifidobacterium, amylolytic activity and SCFAs production and an abundance of Enterobacteriaceae [28]. Exercise increases the diversity of microflora by both internal and external factors such as overall healthy lifestyle, intrinsic adaptation to training, lower levels of inflammation, reduced morbidity and improved metabolic markers. Greater amounts of Firmicutes and a lower amount of Bacteroidetes were found in athletes as compared to non-athletes [8]. What is more, the antibiotics destroy both pathogenic and beneficial microbes causing dysbiosis—a disturbance of gut microbiota [29]. The kind of antibiotic and the length of the treatment are associated with the effect on gut microbiota. Moreover, studies have demonstrated an impact of smoking on microbiota composition, with the most significant impact observed in the oral cavity [30].

The disturbance of the gut microbiota population associated with the alteration of the microbial composition was proven to be related with diverse pathological conditions, i.e., inflammatory bowel diseases (IBD) [31], obesity and diabetes [32], allergy [33], autoimmune diseases [34] and cardiovascular disease [35]. Examples of changes in the composition of gut microbiota correlated with various diseases are shown in Table 1.

The human gut microbiota has received considerable interest in recent years and our knowledge about the species and their potential applications is increasing with the increasing number of metagenomics studies [11].