Exploring inner space: the chicken gut microbiome (and another job opportunity!)

Nick is going to post very soon on the application of high-throughput sequencing to microbial community profiling using 16S rDNA sequences and the insights he gained into this process from a recent workshop. In the meantime, allow me to wax lyrical on the contents of chicken shit...!

More seriously, why should anyone be interested in the microbial community that inhabits the chicken caecum? Here are a few reasons that I put forward in our recent successful grant application:

The importance of chickens. 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 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; across the globe, the health of chickens contributes to the wealth of nations. Chickens provide a case study in domestication, a process began >7,000 years ago in South-East Asia. There are now hundreds of breeds—some generalist or show breeds, but many specialised for either egg production or rapid growth and meat production (“broilers”). At any one time, the UK is home to ~29 million egg-laying chickens and >100 million broilers.

Chickens have also played a key role in the history of science—from Aristotle’s description of a chick embryo to Darwin’s account of their domestication. The chicken has been adopted as a laboratory organism for research in genetics, embryology, development, immunology, virology and cancer. The completion of the chicken genome sequence was a landmark in basic and applied biology, providing a new platform for the functional and comparative genomics of birds. However, the nuclear and mitochondrial genomes of the chicken remain represent just a small part of the gene pool associated with this bird and it is premature to celebrate the completion of the chicken genome, when the vast “genomic ocean” of the chicken microbiome remains largely uncharted and unexplored.

The importance of the chicken caecal microbiome. The chicken gastrointestinal tract is home to a complex microbial community that underpins the links between diet and health and is of key scientific, medical and agricultural interest for numerous reasons:
• It is rich in microbial biodiversity, playing home to ≥500 phylotypes or ~1 million bacterial genes, which equates to 40-50 times the number in the chicken nuclear genome! Most bacteria in the chicken caecum have never been cultured in the laboratory—they are accessible only through molecular-biological approaches.
• These bacteria play important roles in the assimilation of nutrients from food, particularly through the release of energy from dietary fibre—in effect, the gut microbiome acts as an additional organ, as complex as, say, the avian liver.
• The normal bowel microbiota exerts a colonisation resistance that prevents harmful pathogens from gaining a foothold. The chicken gut microbiome also acts as source of human infections (e.g. Salmonella, Campylobacter) and as a reservoir of antibiotic-resistance determinants. A sub-optimal gut microbiome can impede agricultural productivity, as evidenced by the ability of antibiotics to promote growth in chicks. The microbiome is essential for development of the gut epithelium and mucosal immunity.
• This rich collection of genes is likely to include many sequences of scientific interest and biotechnological potential. In addition, the caecal metagenome is likely to shed light on the evolution of bacterial interactions with other organisms, including their role in maintenance of health and pathogenesis of disease.
• The chicken gut microbiome represents an ideal test case for the study of bacteria in their natural environments and will facilitate comparative studies with other avian and mammalian gut microbiomes (particularly with the wealth of data coming from the human microbiome project: http://nihroadmap.nih.gov/hmp/).

So, it may be chicken shit, but it feeds the world!

Unfortunately, all previous attempts to profile the chicken gut microbiome or its genes have exploited underpowered technologies that can never hope to achieve anything like global coverage, particularly when the most plentiful microbial species are several orders of magnitude more abundant than the rarer, but perhaps still crucial, minority components of the community. Fortunately, high-throughput sequencing provides a fresh opportunity to obtain deep and definitive catalogues of bacteria and bacterial genes in complex communities that will deliver key insights into their ecology, evolution and genomic diversity and prime the formulation of many new hypotheses.

Over the next three years, thanks to a project grant from the BBSRC, we aim to use high-throughput sequencing to perform a census of the chicken caecal microbiome, determine how it responds to change and make progress in working out what it does. In support of this goal, we are looking to recruit a Research Fellow in Bioinformatics, who will bring relevant experience and enthusiasm to this project. You can access the job description here and find out how to apply here. Closing Date: 9th July. Interview Date: 22nd july 2010. Informal enquiries to m.pallen@bham.ac.uk. Forward this blog post to anyone who might be interested!