Anaerobic Chamber For Cultivation of Poultry Probiotic Strains to Improve Gut Health and Homeostasis.

The long-term over-arching goal of this project is to use anaerobic cultivation techniques to bring naturally-occurring strains of bacteria found in the poultry GI tract into axenic culture in the lab. Through time, this approach will build strain libraries that can be used to construct synthetic poultry gastrointestinal (GI) microbiomes with the goal of 1- improving gut health by excluding pathogens such as Clostridium perfringens and 2-providing alternatives to antibiotics still commonly used in poultry feed. Combined, these results will improve animal health.Poultry production is the most efficient form of terrestrial animal protein production, but diseases such as necrotic enteritis (NE) reduce production, increase costs, and negatively influence animal welfare. The best independent estimates of the global burden of the cost of NE range from $2-$5B USD annually. As water, land, and greenhouse emissions increasingly constrain food production for a growing human population, the
health and productivity of broiler chickens are critical elements of agricultural sustainability, competitiveness, and global food security.The U.S. broiler chicken industry has typically relied on in-feed antibiotic growth promoters (AGPs) to manage gut health and improve growth performance, but as the chronic sub-therapeutic use of AGPs in agriculture has selected for widespread antibiotic resistance, the practice is increasingly negatively perceived by regulators and consumers and has led to a search for viable alternatives. In 2006, the European Union mandated the removal of antibiotics from animal feed, and in 2014, the U.S. Food and Drug Administration released similar new guidance. Finding alternatives to AGPs is a very timely topic and one which will require new strategies and approaches to maintain animal health, optimize nutrition, and control foodborne pathogens.In our previous work using next-generation DNA sequencing taxonomic and metagenomic surveys of the chicken GI
microbiome , we have shown that a limited number of metabolic functions are performed by a variety of bacterial taxa. Based on this observation, we hypothesize that recapitulating the functional output of a natural community can be done with relatively few strains. We reason that such a multi-strain mixture can be rationally selected by screening strain libraries produced from cultivation of naturally occurring bacteria in the poultry GI tract. Our own preliminary data has provided proof of concept that naturally-occurring GI bacterial communities can be optimized to function as probiotic supplements that can match or exceed the performance benefits of antibiotics and exclude undesirable animal and human pathogens in the gut.To achieve our goal, we will begin with the first objective to identify the core metabolic and taxonomic groups within the broiler chicken GI microbiome and recapitulate these functions with a simple consortium of strains, referred to as a synthetic microbiome. A
key rationale for this approach is the phenomenon of niche-exclusion, in which a closely-related strain can outcompete an undesirable strain such as C. perfringens. A bioinformatics-based approach will first involve summarizing our own and others publically-available data to identify core metabolic pathways of the microbiome during the six week broiler chicken growth cycle. These data will then be used to screen strains that we culture in the lab. This objective thus has three steps, with the critical experimental step requiring an anaerobic growth environment:Objective 1: Identify core metabolic functions of the GI microbiome at key life stages and recapitulate these functions with simple consortia of strains. This will be done in three steps:Identify a core set of microbial taxa in the GI microbiome from our own and others data. Build strain libraries via anaerobic cultivation targeted to taxonomic groups identified above. Screen strain library against the core sets of taxa and
metabolic functions to identify candidate strains that can be assembled to recapitulate these functions.