Saturday, September 17, 2011

self portrait

Cheeky (?) monkey. Oblivious - occupied only with the present action of gratification through consumption.

somewhere in the forest 
Ubud 2008

Tuesday, September 13, 2011

Complex social networks in our guts

What's your enterotype?
Well... I'm attracted to open minded guts, those who enjoy the finer aspects of life...


Weekend reading has brought my attention to an impressive large-scale human study announced to by researchers at the European Molecular Biology Laboratory (EMBL) and the French National Institute for Agricultural Research (INRA). The aim of the study as stated in the information pack is to:

"Analyse the composition and function of gut microbial samples that will eventually contribute to an improved understanding of the balance between humans and their microorganisms, and its importance in health and disease."
Just scratching the surface: the bacterial social network of your skin (from Wikipedia)

This comes 3 years into the 5-year Human Microbiome Project (HMP) a global initiative by the NIH which aims to characterise the universe of microorganisms (bacteria, viruses, fungi and other protoctista) found in healthy human bodies and under pathological conditions.

Estimates of microbial cell numbers to ourselves are 10:1. Whichever way you look at it, we are outnumbered. The HMP is sampling the five 'hot spots' of your microbiome cohabitors: the nose, mouth, skin, gut and urogenital region.

The EMBL project is focusing to identify all the microbiota of our digestive tract. Entitled my.microbe (twitter follow here), Dr. Peer Bock and his crew want to know your enterotype. Their most recent findings (initially 39 Europeans, Americans and Japanese, and now extended to more than 400 samples) suggest we have one of three different gut ecosystems or enterotypes. These have been identified as Type I - III and describe the major population of microorganisms in our gut. What is striking in the findings is there are no links between our enteric ecosystem and age, sex, ethnicity, or health. Now the second phase of the study aims to sample 5000 more individuals' gut microbiomes.

The project is open to the public but with an upfront payment of 1400 euros plus shipping it may be difficult to get volunteers with sufficient disposable income and personal interest to collect a 'specimen' and send it across the world for sequencing and analysis. This is a lot to expect from any person- I wonder if they can find alternatives to reduce costs ie.change method of recruitment, or enlist satellite groups around the globe to perform sequencing (though that will create problems too) and upload to a database.

Is it really so important? Given our symbiotic relationship with microbes and their contribution of almost 2 kilograms of our body mass- the simple answer is yes. We need to understand the microbiome to help tailor better healthcare provision, find better ways to diagnose illness, treatment of disease. There are huge implications from this study and it'll be really interesting once the momentum picks up and helps us to appreciate the complex relationship with the organisms that help create equilibrium with our body.

Sunday, September 4, 2011

what's with skinny genes?

A few weeks ago, a publication in Nature titled: Mirror extreme BMI phenotypes associated with gene dosage at the chromosome 16p11.2 locus by researchers at Britain's Imperial College London and the University of Lausanne in Switzerland (a cast of 100+ authors) unveiled new information that duplicate copies of a portion found on chromosome 16 (16p11.2locus to be exact) have been identified to contribute to extreme thinness (BMI <18kg/square metre), failure to thrive and microcephaly- predominantly in males. They also reported previously that absence of this region/gene is associated with some forms of morbid obesity.

What does this mean?

This is exciting, but not unexpected news. Now with genome wide association studies in full force- we are witness to the explosion of discoveries of genetic factors contributing to a multitude of pathologies. Of course, this isn't the only answer. There are many cases of extreme obesity/thinness with unknown cause. Some will involve other genes yet to be discovered as well as the many epigenetic and environmental factors which influence and regulate phenotype.

Sure, there's promise of something big, but now comes the long, hard slog -  figuring out how these genes interact with their environment to bring about such phenotypes.

 There is much work ahead...