We follow a two-pronged approach to generate the catalog of intestinal genes and genomes. One is to determine the complete sequence of genomes from bacteria that we know how to cultivate. As they represent only a minority, about 20 %, of all intestinal bacteria, we will also sequence the total bacterial DNA prepared from stool samples. This provides information about genes of bacteria that we cannot cultivate. 

Our objective is to sequence full genomes of 100 bacterial species and the total stool DNA of a cumulative length corresponding to some 1000 bacterial species. The first thirty cultivable species have been chosen, and their genomes were sequenced.  The choice of species has been coordinated within IHMC, and in particular the USA National Institutes of Health, which supports sequencing of intestinal bacterial species carried out within the Human Microbiome Project.

We wished to sequence total stool DNA from different individuals, in order to maximize  the reference gene catalog, as different individuals carry different microbiota. Bacterial diversity of 35 individuals from the IBD and obesity cohorts was examined and the 8 individuals with the most divergent microbiota were identified. The cumulative length of total stool DNA sequence determined thus far from these individuals corresponds to about 2 full human genomes or 2 000 bacterial genomes. We are also using deep metagenomic next generation sequencing for establishing a broad gene catalog. 

To establish the most extensive reference catalog of intestinal genes and genomes, which will be of  universal value, we plan to include sequence information generated not only in MetaHIT but also in other large metagenomic programs.