MICROBIAL ECOLOGY OF THE GASTROINTESTINAL TRACT OF DOMESTICATED BIRDS

CHAPTER ONE
INTRODUCTION
1.1 Background of Study
The gastrointestinal tract is the major digestive and absorbing organ and it plays a crucial role in host immunomodulation and chicken growth. It hosts a complex microbial community that participates in several microbial processes (Tilocca et al 2016). The diversification of the intestinal microbiome allows innumerable interactions with the host to occur, thus exerting an important function for the growth of the animals while also contributing to their health (Oakley et al., 2014).
The microbial composition differs throughout the intestinal tract, that is, each section of the intestine has its own microenvironment, where the colonies of specific microorganisms that best identify with the site remain (Videnska et al., 2013a). In the duodenum, the pH is neutral and the microorganisms colonize this compartment, as well as the jejunum and ileum. While the cecum is considerably the site of higher colonization of microorganisms, being a large part of Gram positive and negative bacteria (Gabriel et al., 2006). The composition of the intestinal microbial community is influenced by a number of environmental factors, and it is therefore likely to find differences between poultry chickens and local chickens. Important differences between poultry chicken and local chicken are their environment and their feed. The gastrointestinal tracts (GITs) of chickens harbor microbial communities, or microbiomes, that play important roles in: growth and development, including the production of energy-rich short chain fatty acids (SCFA) (Dunkley et al., 2007); promotion of GIT villus and crypt morphology (Shakouri et al., 2009); nutrient utilization, including reduction in luminal viscosity (Shakouri et al., 2009), the deconstruction of dietary polysaccharides (Beckmann et al., 2006; Qu et al., 2008); nutrient absorption and well-being of their chicken hosts, including detoxification (Hai et al., 2010).
The chicken GIT is inhabited by various bacteria (Qu et al., 2008), methanogenic archaea (Saengkerdsub et al., 2007a, b), fungi, and viruses (Qu et al., 2008). Protists are more sparsely distributed and are generally regarded as pathogens (Qu et al., 2008). The composition of the GIT microbiome reflects co-evolution among the inhabiting microbes, genetic, immune, and metabolic interactions with the host, and environmental influences (Yeoman et al., 2011). Microbes are found across the entire length of the GIT, where they show spatial variation in community composition biogeographically (Gong et al., 2007), as well as between luminal and mucosa-associated populations (Gong et al., 2002).
Microbial diversity and abundance are most evident in the ceca (Gong et al., 2007), where more than 2200 operational taxonomic units (OTUs; 95% sequence ID) (Danzeisen et al., 2011) and as many as 3500 genotypes (Qu et al., 2008) have been predicted. Consistently, microbial fermentation is most active in this section of the GIT. As a result of issues that relate to zoonoses, food safety, animal nutrition, and health, the composition and function of the chicken GIT microbiome has received significant attention from researchers for almost 40 years. It is well known that the composition and structure of the feed as well as the housing conditions influences the composition of the intestinal microbial community of chickens (Apajalahti et al., 2004).
1.2 Statement of problem
Microorganisms are ubiquitous and have various potentials and functions. The health of humans and that of the environment is highly dependent on the surroundings, particularly the food we take in or consume. Many bacterial species inhabit the gastrointestinal tract of chickens and can thus
be introduce into the food chain where they can cause several infectious diseases if pathogenic example pneumonia, abscesses, vomiting, stomach upset, intra-abdominal, respiratory tract, and bloodstream infections in transplant recipients, etc. Environmental pollution is another area of concern when the droppings of these birds are release into the surroundings.
1.3 Justification of the study
Many species of birds are domesticated or raised for human consumption. These include local fowl and poultry chickens, both serving as food and having different feeding habit. While the local fowls’ feeds freely from the environment, pecking from the soil, woods, water, food items, etc. the poultry birds are confined and eats only special feeds compounded from different manufacturers. This is likely to make their nutrient as well as their intestinal flora different. Birds especially, poultry are widely eaten in our homes, eateries, roadsides, etc. Examination of the intestinal microflora of these birds becomes importance to provide caution on the composition and human health potentials since they can be introduced into the food chain. This study is also intended to provide information on the environmental significance of the isolated microorganisms. As the intestinal contents (excreta) serves as manure in agriculture (crop production).

1.4 Objectives of the study
The main objective of this work is to determine the microbial diversity of the intestinal tract of local fowl and poultry chicken. The specific objectives of this work are as follows: –
To determine the microbial load and diversity of the intestinal flora of local and poultry birds.
To determine the virulence factors of the isolates.
To determine the antibiotic susceptibility of the isolates.
To determine the probiotics potentials of the isolates.