A large part of my work as a GP is spent trying to persuade my patients that they will heal themselves, naturally, usually and possibly better than if we intervene with antibiotics. After all, they often cause unwanted side effects like diarrhoea, sore throat and thrush. The good news is it’s getting easier. People are more aware of the idea that they have a self-limiting condition (as we call it). There’s always an anxiety it may not work so I can understand the need to check with a professional – it’s part of being responsible for your health. Whilst I was researching around this topic I realised we have spent little time, energy and money in the area of our own flora and our symbiotic relationship. It took me a good deal of hunting to discover – a rough estimate of – the number of bugs in our GI tract (the long tube mouth to bottom): somewhere in the region of 100 trillion bacteria. That’s about ten times, TEN TIMES, more of them than us.

This led me to a recent New Scientist article about the work of Anders Hakansson. In short, bacteria are difficult to study in their normal environment. The studies we have of them ‘in vitro’ (test tube/lab etc) give a false impression of numbers and ‘behaviour’. He has pointed me towards what looks like the main site of interest in normal flora – see http://genome.wustl.edu/articles/detail/human-microbiome-project-leader-q-and-a/ and http://genome.wustl.edu/projects/detail/human-microbiome-project/.

The Human Microbiome Project is trying to get a better idea of the type and number of bugs ‘down there’. I quote from their front page (take a look at the link):

“Most of the microbes that we harbor do a lot for us – from helping to digest our food and absorbing nutrients we need, to churning out vitamins we can’t make ourselves and even protecting us from other harmful microbes that could make us sick. Many of these organisms are with us from birth to death and influence our growth and development. This is the impetus behind work like the Human Microbiome Project, which will help us understand more about these microscopic life forms that are so crucial to our survival…..

…..But now, with next generation sequencing techniques, it is possible to sequence hundreds of individual microorganisms’ genomes and do it in a reasonable amount of time and at a lower cost than ever before.

But there’s a catch – unlike animals and plants, a large proportion of microbes aren’t willing to give up their DNA so readily. In fact, many of the microbes in the human body depend on other surrounding microbes and nutrients for their survival and can’t grow on their own outside of that environment.

In order to figure out what kind of microbes live in the human body, researchers are taking samples from one of five predetermined body sites (mouth, nose, skin, vagina and gut). Since they can’t sequence each microbe’s genome separately, they sequence and study the entire microbial sample at once – a field called metagenomics. The samples may contain hundreds of different microbial species, each with their own unique genome. To identify the types of species present in the sample, the scientists use key genes that are known to be associated with certain microbes. They can then look up the genomes of other microbes that have already had their entire genomes sequenced. This allows them to compare and catalog many of the important genes and species that are in a given body site sample. The more deeply they sequence each sample, the more information they can obtain about the microbial make-up of that sample.

All in the Community

Studying microbes within their communities rather than individually plays a key role in understanding the human microbiome. A major goal of the Human Microbiome Project is to help researchers determine the similarities and differences among the microbiome of healthy and diseased individuals. They can then characterize these communities among groups of people, and determine how they change in different health and disease states.

With the development of more advanced sequencing technologies that shorten sequencing times and reduce costs, The Genome Institute is now able to more effectively sequence the massive amounts of genetic information present in the human microbiome and discover what types of microbes are important to our health and well-being and what types we should be targeting to prevent disease. As Dr. Weinstock explains: “The microbes inside our body have a huge impact on who we are, what we do, how we feel – and we have never really defined that very precisely. That’s what we need to do to truly understand the human microbiome.”