The Chicken Microbiome Project

INTRODUCTION

The domestic chicken occupies a special place in science and society. It is the most common domesticated animal, the most important food production animal and the most abundant and widely distributed bird in the world, with ~ 30 billion individuals scattered across islands and continents from the Arctic to the Falklands. Chickens are a major source of energy and protein for humans worldwide, with billions of birds used in meat and egg production each year. Apollo astronauts even ate chicken stew on the Moon! In the UK, chicken farming remains crucial to the rural economy and contributes significantly to the balance of trade.

Despite their prevalence and economic importance, relatively little is known about the bacteria present in their gastro-intestinal tract (microbiome). Yet the composition of the microbiome directly affects the health of the chicken, acting in effect as an extra organ. It is responsible for the digestion of compounds such as cellulose, protection against pathogens, as well as other functions. The importance of the correct composition of the microbiome has long been appreciated, indeed antibiotics which alter the microbiome have often been used as growth promoters. However, exactly what changes take place and what constitutes an effective micobiome is poorly understood. Therefore a thorough knowledge of the composition and function of the microbiome is of key importance. We aim to achieve this primarily by 16S analysis using 454 next generation sequencing.

THE CHICKEN GASRTO-INTESTINAL TRACT

The bulk of analysis will be on the caeca - although the microbial contents of all the other parts of the digestive tract will also be profiled since little is known about their true microbial content and the effect it may have on the health of the chicken.

The crop is basically a pocket in the oesophagus where feed and liquids are stored until required by the digestive system. Very little digestion takes place in the crop and the microbial load is very low. The proventriculus (true stomach) acts in a similar way to the human stomach, the low pH and gastric enzymes begin the digestion process, very few bacteria reside in the stomach. The Gizzard is highly muscular organ and is where food is mechanically ground. It can also contain grit which aids grinding. The microbial content of the gizzard and crop have been investigated and found to contain low levels of aerobic bacteria including E. coli and Campylobacter. However, such experiments used conventional culture techniques, so the true bacterial content is unknown. Bile and digestive enzymes in the duodenum further aid digestion and the rest of the small intestine is mainly involved in absorption of nutrients. The bacterial load in the small intestine is usually kept in check, since overgrowth of bacteria would deprive the host chicken of nutrients. The large intestine contains two large, blind pouches and this is where the highest concentration of bacteria reside (10¹¹ per gram of contents). Unlike the rest of the digestive system, in which transit time is rapid, contents of the caeaca can remain for longer than 24 hours and it believed to have the following functions

• Break down of urea which is involved in nitrogen cycling
• Cellulose degradation
• Exerts a colonization resistance which prevents harmful pathogens from establishing in the gut
• Fermentation to produce organic acids especially butyric acid

Progress