Coordinating human microbiome research

Our bodies contain thousands of different bacterial species that cumulatively surpass in number the human cells. Their impact on physiology, immunity and nutrition is undisputed, but at the same time very complex.

The delineation of human microbial communities has been the subject of many different research studies. However, to compare data across studies and minimise variation, uniform protocols are required. The scope of the EU-funded 'International human microbiome standards' (IHMS) initiative is to standardise the procedures in human microbiome research.

In this context, participating groups will work to compare and optimise standard procedures and protocols in collecting samples, sequencing microbial genomes and analysing data. During the first project period, they reviewed current practices of more than 20 groups involved in human intestinal metagenomics.

Regarding sample collection, partners are optimising various parameters, including time and temperature of collection, storage and shipment on sample quality. Ideally, samples collected at home should be shipped within one day and preferably under cold conditions. To prohibit bacterial growth deterioration under ambient temperature, shipping under anaerobic conditions should be the preferred method. The IHMS-proposed method of sample collection and shipment guarantees preservation of microbial species for analysis.

So far, the consortium has sequenced the microbial DNA extracted from 24 stool samples and compared the abundance of over 3 million genes. Further to analysing and compiling this data, scientists also aim to perform phylogenetic evaluation by assessing the phylogenetic composition in each sample. This would constitute an important tool towards the characterisation of microbial communities.

IHMS research will identify how different genetic backgrounds, diets and, more generally, different life styles affect normal gut microbial communities. Through the design of novel pharmaceuticals to improve endogenous microbial fitness, it will also help improve or restore our health.