Video transcript: Inside a chicken #2: food safety and antibiotic resistance

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June 2013

Video shows chickens.

Professor Mark Pallen, The University of Warwick
So to investigate the chicken gut we've been taking largely culture independent approaches, so generally microbiology people, in particular, bacteriology people try and grow things on eggar plates. The problem with that approach is it only recovers a small fraction of the organisms that are living in that environment and so we have to go beyond that. So we are doing a bit of culture but we are mainly relying on sequence-dependent approaches, so we extract DNA from the contents of the chicken gut and then we take one of two approaches: we either look for a molecular bar code which is present in all bacteria, or we try and amplify and extract that from that population and that gives us a kind of sense of population and a profile of what's living there. We actually also do what we call metagenomics where we are just sequencing that DNA on mass and so that allows us to recover genome level information on many of the inhabitants of the chicken gut, particularly the most abundant inhabitants we can effectively get genome sequences through that approach. And what that allows us to do is then reconstruct the metabolic pathways, those organisms using how nutrients are being cycled and recycled through that gut community largely to the benefit, we hope, of the chicken but sometimes we have the chance to understand disease states where these don't go so well.

The chicken food industry is of massive industry and if you can achieve improvements of only a few per cent in the growth rates of chickens, the final weight that they reach in their efficiency of producing eggs. These have tremendous effects on economic affects and in terms of food security when we are going to have to feed 9 billion people, squeezing more out of these food systems is crutial so that is motivating us. In years gone by people used to use additives in the form of antibiotics in the chicken diet and that did produce an increase in growth weight, it acted as growth enhancers, but they have been banned in most of the developed world now and so what we hope to do is to try and work out what went on when antibiotics were used, to give that growth advantage, and see if there are other ways in which you can manipulate this microbial community because the antibiotics were certainly having their effect primarily my manipulating that microbial community. If we can reconstitute that effect, but without using antibiotics that might then have detrital effects in selecting antibiotics organisms that then get into the food chain and into human health. The main interest in the chicken gut community, in terms of human health, is that it is a reservoir of human pathogens. Campylobacter is probably the most important one but salmonella is also very important. There are some multi-driving systems we see in hospitals, where sometimes the finger is pointed at the human food chain and the use of antibiotics in chickens. There is also this concern that the chicken gut might be a repository of antibiotic resistance genes that actually find their way into the human food chain and find their way into our gut.

We have been very grateful that the BBSRC have supported this project. It obviously speaks to the BBSRC's interest in food security, in healthy food and avoiding pathogens getting into the human food chain. There are implications obviously for modern organism biology and how a chicken develops and so forth, and we also have a biotechnological spin and as I say we have potential to get enzymes that would be useful coming out of this community.



Hen and chicken footage courtesy of The Roslin Institute.

DNA sample, DNA animationsm chicken bacteria and bacteria animations from www.sciencephoto.com.

Music 'Jellyland' and 'Uncovering the mole' from cinephonix.com

BBSRC ident from biganimal.co.uk