Homo sapiens

Recent studies based on molecular approaches (independent of “in vitro” culture of bacteria) confirms that the great majority of bacterial diversity in the microflora of the human digestive tract is totally unknown (Suau et al., 1999; Bonnet et al., 2001).
Each individual has his/her own profile of dominant microbial species, which is unique and stable over time (Zoetendahl, 1998; Sutren et al., 2000). More than 80% of these bacterial species in healthy adults (more than 90% in the elderly) have no identifiable representative in international strain collections (unpublished work).
Constraints linked to the nature of the digestive ecosystem itself, problems in accessibility, and its limited size, as well as the physiologic specificities of the intestinal microflora and notably the obligate anaerobes, make this biologic reservoir difficult to study.
However, the intestinal microflora is implicated in the nutrition and health of the host, and for several years already, has been suspected to be involved in triggering and maintaining degenerative and inflammatory digestive pathologies, which are presently on the rise in industrialized countries (Efson 1995; Sartor 1997, 1998; Duchman 1999). Molecular studies have recently confirmed that primary alterations of the composition of the human fecal microflora are associated with Crohn’s disease, an incurable chronic inflammatory disease of the intestine (Seksik et al., 2003; Mangin et al., soumis). Furthermore, functional alterations of the flora have been demonstrated in this disease (Favier 1997).

Using existing metagenome extraction technologies, and by creating and exploiting DNA libraries, the project aims to access the ensemble of functionalities of the dominant intestinal microflora in order to be able to totally interface the two human genomes (our eukaryotic genome and the metagenome of our flora) for which the intimate interrelationships are an essential factor in the maintenance of good health.

A unique access to a global functional analysis of the intestinal ecosystem will make it possible to determine :

1. The functional homogeneity of the fecal microbial community in humans (between individuals) and its stability over time.
2. The key components in the interaction between microflora and epithelial and/or immune cells of the digestive system.
3. The functional specificity of fecal microbial communities asociated with selected digestive pathologies (inflammation, cancer).

Decisions and recommendations in the field of human nutrition or public health (in which the digestive flora often plays a decisive role) are greatly limited by our biased and fragmented knowledge of the dominant flora based on anaerobic culture :

• In preventive nutrition: whereas the marketing of functional nutrients is increasing, their health benefits are often poorly supported scientifically.
• In the medical domain, when a role of the digestive microflora is suspected in certain diseases such as inflammatory disorders of the digestibe tube or certain cancers, we do not have the tools to test these hypotheses.

The functional understanding of the intestinal ecosystem and its dynamic surveillance is a present-day challenge. It is therefore of fundamental importance to be able to measure effectively the functional diversity of dominant species of the digestive flora of humans, to determine its regulatory modes and to develop tools for its dynamic surveillance (in space and in time).

The economic effects as well as the public health consequences of such a program will be extremely pertinent. The information obtained will serve as databases for the creation of DNA networks which will make it possible to improve our understanding of the function of the human intestinal ecosystem, and will also lead to the development of multiple diagnostic applications in nutrition and in human health.

Genoscope is undertaking the sequencing of 200 fosmids from a metagenomic library created from total DNA from a bacterial fraction associated with healthy human ileal mucosa.

r each fosmid, a plasmid library (3 kb inserts) will be created in pcdna2.1 and 1,500 clones from each library will be sequenced at both ends, for an expected sequencing volume of 600,000 reads.

All the fosmids will be assembled in phase 2, and after analysis, certain interesting fosmids will undergo a finishing stage.

Contacts:
Sylvie Samain (Genoscope) - Joël Doré (INRA)