**1. Introduction**

Certain microorganisms have the unique ability to populate the human gastrointestinal tract and thus generally referred as gut microbiota. Gut microbiota is always non-pathological, and hence, the immune system is not triggered because of their presence. Humans co-evolved with a huge number of intestinal microbial species that offer to the host certain benefits by playing an important role in preventing them from pathogenic activities [1]. In addition to metabolic benefits, symbiotic bacteria benefit the host with various functions like boosting the immune homeostasis and inhibiting the colonization by other pathogenic microorganisms. The ability of symbiotic bacteria to inhibit pathogen colonization particularly in the gut is mediated

via several mechanisms including direct killing of pathogen, competition for limited nutrients, and enhancement of immune responses [2]. The intestinal microorganisms also co-evolved and have strong affiliations and association towards each other. In this evolutionary process, the persistent and enduring members of this microflora become more competent during unsettling influences and thereby become essential for human health [3]. Definite composition of human microbiome varies between individuals [4] particularly among lean and obese people. The microbiome is also affected by the dietary modifications adapted for the weight loss [5]. Examination of metabolic profiles of human infant microbiota revealed that ingestion, storage and digestion of dietary lipids were explicitly regulated by the microbiome [6, 7].

The human gut microbial communities are a mixture of microorganisms. The classes of microbes that constitute the gut microbiome communities differ between hosts. The difference is attributed to factors such as, inability of a microorganism to migrate between different hosts, intense environmental conditions inside and outside host's gut and host inconsistency in terms of genotype, diet, and colonization history [8]. The co-evolution of humans and their symbiotic microorganism has created bilateral interactions which are important for the health of humans, and any genetic or ecological change in this bilateral interaction can result in pathological conditions like infection [8]. Gut microbial communities are important for diverse host functions, including metabolism, fertility, development, immunity, and even antioxidant activities which promote health and fitness of the host [9–12]. The gut microbiome has a much larger genetic variety compared to the genome of the host, e.g., human genome is comprised of 20-25,000 genes whereas microbiome inhabiting the body is estimated to be in trillions. Almost 1010 microorganisms enter the human body daily and with the progress of co-evolution of gut microbes in humans, the capability of microbes to exchange their genes and associated functions with the environment are some of the main factors leading to host adaptation. Therefore, the "hologenome" model appraises the host and its microbes genomes as one unit under assortment [13, 14]. It is acknowledged that host-symbiont co-evolution is accountable for basic biological aspects. In this chapter we aim to discuss the importance of gut microbiomes as a new organ system because of its association with the genetics and its role in the disease and health condition of the host. Moreover, the involvement of these microbiomes in shaping the overall health and constructing a symbiotic relationship with their host species is discussed as well as the co-evolution of gut microbes with the human body.
