Inside a chicken #2: food safety and antibiotic resistance HD

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 agar 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 crucial 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 detrimental 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.

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