Chicken Gut: Microbial World Worth Exploring

UK - What lives inside a chicken? It might sound like a strange question to ask, but as the world's most abundant food animal and an incubator of many bacteria - both helpful and harmful - the chicken's gut is a microbial world worth exploring using the latest DNA sequencing technology.

5 April 2013

7 minute read

Europe

"We know more about the dark side of the moon than we do about what lives inside a chicken," says Professor Mark Pallen at the University of Warwick. "What we do know is that the chicken gut is home to a very rich microbial community. When high-throughput DNA sequencing arrived it became clear that the time was right to attempt a deep survey of this microbiome."

Charting the chicken microbiota touches upon many of BBSRC's strategic priorities: food security and food safety because we eat the chicken as well as its eggs; healthy ageing because the bird is an important model organism in which the fundamental bioscience of normal growth and development is recorded; finally, the chicken gut might be a source of new enzymes for industrial biotechnology.

More than a poultry matter

Poultry farming is a mega industry worldwide. [Image: USDA]

The chicken is undeniably the world's favourite food bird. An eye-popping 20Bn of them live on the planet at any one time, producing a jaw-dropping 1.2 trillion eggs^1,2. And its popularity is predicted to rise, as the developing world consumes more meat³, and because it is cheaper to produce and less energy intensive than rearing lamb, beef or pork, making it a healthy protein choice for meat eaters keen to reduce their carbon hoofprint^4,5.

To look at life inside the chicken, Professor Pallen, who started the chicken microbiome project at the University of Birmingham in 2010, and his colleagues adopted the 'metagenomics' approach, sequencing the DNA of all the organisms in the chicken gut. Because the technique does not rely on identifying only those bacteria that can be cultured, it offers a far more unbiased view of microbial communities.

"We know that most of these organisms are very difficult to grow or impossible to grow in a lab," said Professor Pallen. "We will grow as many as we can but we recognise that's not going to get us very far. That's why we're adopting this approach."

To identify the bacteria present among billions of cells, short stretches of DNA can act as 'molecular barcodes'. Just as barcodes on retail products can transmit information about the contents of a shopping basket, DNA barcodes can be matched to catalogues of living species, providing useful information about the components of complex microbial communities^6,7.

Fantastic voyage

In metagenomics, DNA sequencing technology can probe the organisms inside organisms. [Image: Hongiiv on Flickr]

In the first phase of the chicken microbiome project, molecular barcodes were recovered from bacteria in the chicken gut and then compared against known bacterial genetic sequences. Like most microbial ecologists, the Pallen team exploited sequences from bacterial 16S ribosomal RNA genes as barcodes because it's critical for protein synthesis and all bacteria have a variation of this sequence.

From samples taken from a region of the chicken gut where microbial load is highest, the caecum, more than 400,000 different 16S sequences were recovered. Sequences from 20 birds could be classified into nearly 800 different species, over half of which probably represent previously unknown species; each individual chicken carries around 200-350 different species.

"We were surprised to discover so many new species from such a commonplace environment", said Professor Pallen

The team then went on to sequence an entire DNA sample extracted from one chicken caecum. Of the 120 million 110-base-pair sequences that they obtained, more than 98 per cent were bacterial. Perhaps surprisingly, less than 1 per cent were from the chicken genome and fewer than one in a thousand were from other organisms, such as the cereal fungus Magnaporthe orazae, the alga Chlamydomonas reinharrdii (both likely from feed), bacteriophage or fowl adenovirus.

The analysis is still underway and full results have yet to be published. Professor Pallen said in looking at the chicken metagenome, he first hopes to complete a census of the microbial community before mapping the metabolic processes active in that community at various stages in the development of the chicken.

The metabolic processes that take place inside the chicken gut are of significant commercial interest - what enzymes and digestive pathways are chickens using to absorb their food, for example? With 57Bn chicken slaughtered in 2011, efficiency gains of 0.1 per cent could save huge amounts of money and energy because less feed would be needed per chicken.

In the past, antibiotics have been used as growth promoters in chickens, but this practice has now been banned in the EU since 2006 because of concerns that it could lead to antibiotic resistance, but it is still a huge source of antibiotic use in other countries^8,9 including the US, which has been slower to impose restrictions¹⁰.

Key questions remain regarding how antibiotics affect the gut microbial community and how the benefits could be achieved by other means. "If you give antibiotics how does that bacterial community change?" Professor Pallen asked. "Something good is happening in terms of growth but what is it… better recycling of nutrients? Or are 'bad' organisms suppressed or absent?"

The good, the bad and the unknown

Electron microscope image of Campylobacter jejuni bacteria. Microbes in chicken can be helpful and harmful. [Image: US Agricultural Research Service]

Professor Pallen and colleagues are keen to do comparative studies, including comparisons between birds at different ages as well as birds with and without Campylobacter. This bacterium is responsible for most cases of food poisoning in the UK (an estimated 321,000 cases in 2008), with contaminated poultry meat as the major source of infection. Although symptoms usually only last for a few days, on rare occasions there are serious and fatal complications¹¹.

The chicken microbiome project compliments a £4M initiative funded by BBSRC, Defra and the Food Standards Agency (FSA) to study Campylobacter in the food chain, from field to plate.

For these ongoing and future comparative studies on chicken metagenomics, Professor Pallen hopes to utilise even more powerful technology. "The chief problem is keeping up with the sequencing technology, which is advancing all the time," he explained. "A study done a year ago looks outdated. We used a 454 sequencer for the 16S studies and Illumina HiSeq for the metagenome, and we are moving towards using the Illumina MiSeq for 16S studies in the future. These technologies take us ever closer to a definitive catalogue of the chicken gut microbiome."