Disentangling the role of intestinal bacteria in human and animal health

In the last decade, the advent of the Next-Generation high throughput Sequencing (NGS) technologies allowed to shed light on the composition and functionality of the microbial populations inhabiting humans and other animals, i.e. microbiota. In humans, it has been estimated that 1014 microorganisms reside in several compartments of the body such as the surface of skin and in the gastrointestinal, genitourinary and respiratory tracts. The gastrointestinal tract, which has the large numbers of microorganisms in humans, included specific compartments such as mouth, esophagus, stomach, small intestine, large intestine (colon), rectum, and anus. The range of published studies focusing on this topic revealed that the gut microbiota is largely responsible for the overall health status of the host. In detail, the complex activities exerted by the gut microbiota impact on several functions of its host, including gut physiology, intestinal metabolism, and immune system modulation. While the gut microbiota composition is influenced by factors such as diet, lifestyle and environment, the alteration of the gut microbiota composition, i.e. dysbiosis, has been associated with a large array of human disorders and diseases such as inflammatory bowel diseases (IBD) and irritable bowel syndrome (IBS), colorectal cancer (CRC), metabolic diseases and allergic disease. The major role of the microbiota in defining the health status of the host led to extensive study of farm animals. The gut microbiota of healthy animals is supposed to exert a significant role in nutrient assimilation, vitamin and amino acid production as well as prevention of pathogens colonization. Moreover, the livestock animal gut microbiota may also act as a source of bacterial pathogens that can spread to human beings or to exploit a role as a reservoir of antibiotic-resistance determinants, which can be transferred to other microorganisms including opportunistic pathogens. The aim of this Ph.D. thesis is to explore the role of intestinal bacteria in human and animal health. In particular, it aims to investigate compositional and functional differences of poultry animals kept under different housing regimes and nutritional circumstances. Furthermore, focusing the interest on human beings, a comparison between all publicly available human gut shotgun metagenomic datasets corresponding to urbanized and pre-agricultural societies allowed to validate the assumption that urbanization/industrialization processes have significantly influenced the composition and functionality of the human gut microbiome. Additionally, these metagenomic data allowed genome reconstruction of bacterial taxa that seem to have been lost or gained by individuals living in urban-industrialized countries. Consequently, this PhD thesis also evaluates the correlation between human gut microbiota and diseases in order to identify possible microorganisms known as microbial biomarkers associated with a health/disease status.