Performing Department
CVM
Non Technical Summary
Necrotic enteritis (NE) is the most economically important animal health problem facing the broiler industry. The goal of this project is to culture bacterial strains that can be used to construct a synthetic poultry gastrointestinal (GI) microbiome to improve gut health by excluding pathogens and improving nutrient utilization and feed efficiency, and thereby increasing the sustainability of poultry production. Recent research has shown that the GI microbiota play critical roles in gut health, nutrition and growth and is thus a logical area to focus efforts to improve animal health.One key element required for constructing such a synthetic microbiome will be the ability to culture naturally occurring members of the GI microbiome in the lab. This will require anaerobic cultivation techniques and proper anaerobic facilities. The approach proposed here is to use anaerobic cultivation techniques to build a library of strains that naturally occur in the poultry GI tract, and then to screen this library of strains using bioinformatics to identify potential probiotic bacterial species that can exclude pathogens.By developing products and tools to manage the microbiome of food animals to increase exclude pathogens and reduce reliance on antibiotics, this project has the potential to support the sustainable food and agriculture by increasing farm efficiency and profitability and improving food safety. This project may also help ensure U.S. agricultural resources contribute to enhanced global food security.
Animal Health Component
100%
Research Effort Categories
Basic
100%
Applied
(N/A)
Developmental
(N/A)
Goals / Objectives
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.
Project Methods
The majority of the wet bench methods used for this project will involve basic aspects of anaerobic microbiology. Samples will be regularly collected from poultry gastrointestinal samples and cultured anaerobically on a variety of growth media. Some of the media will be non-selective and some will be specifically targeted to the phylogenetic groups identified bioinformatically from previous data.Efforts will also be directed to mentoring of students in the technical skills required for proper use of the anaerobic chamber and for engaging in a broader associated research project.Evaluation of the cultivation efforts will be done by screening of the strains recovered using sequence data to confirm we are recovering the desired taxonomic and metabolic. Evaluation of mentoring efforts will be done by monitoring of the number of student presentations, publications, and exit surveys of students following engagement in research programs.