Catalog of genes
We established a broad catalogue of microbial genes from the intestinal tract. This was achieved by the cutting edge sequencing technology, which allows to generate tens and even hundreds of millions short sequences in parallel for any DNA sample. We determined a total of some 540 Gb of DNA sequence prepared from stool samples, a value approaching that of 200 human genomes. In a break-through manner, we succeeded to connect these short snippets into much longer DNA stretches, where we could identify the genes present in the intestinal microbes.
We analyzed samples from 124 individuals that participate in our studies. They were of Danish and Spanish origin, some were healthy and some sick, suffering from IBD or obesity. In this way, we expected to identify the largest possible gene number, not missing those that could possibly be less frequent or even absent in a given group of individuals. An extensive bio-informatics analysis has shown that there is a staggering number of some 3.3 million different genes among the individuals that we analyzed, 150-fold more than in our own genome! We have identified at least 85 % of all the frequent genes that the 124 individuals carry, the value determined by an appropriate statistical analysis. Some 99 % of the genes were of bacterial origin, in keeping with the predominance of bacteria among the intestinal microbes. From the gene number we deduce that there are at least a 1000 bacterial species frequent in our gut.
How many of the 1000 are present in each individual? We find that a person carries, on average, 540 000 genes, a value that corresponds to some 160 species. Inevitably, different individuals have many of the bacterial species in common - there are no more than a 1000 to go around and everyone has at least 160. We found some 60 species that are present in at least half of the individuals of the cohort, in keeping with the fact that about 40 % of the genes of each individual are present in at least 50% of other individuals.
Does our catalog contain the genes from individuals other than those that we have studied? The answer is definitely yes - we find over 80 % of the sequences from 18 US individuals and over 70 % from 12 Japanese individuals, determined in previous studies of a smaller scope in the catalog. Clearly, a majority of genes of the human intestinal bacteria are well represented. Collectively, they have been dubbed “our other genome” on the cover of a recent Nature issue where these results were published.