More than 9,000,000 unique genes in human gut bacterial community: estimating gene numbers inside a human body.
BACKGROUND
Estimating the number of genes in human genome has been long an important problem in computational biology. With the new conception of considering human as a super-organism, it is also interesting to estimate the number of genes in this human super-organism.


RESULTS
We presented our estimation of gene numbers in the human gut bacterial community, the largest microbial community inside the human super-organism. We got 552,700 unique genes from 202 complete human gut bacteria genomes. Then, a novel gene counting model was built to check the total number of genes by combining culture-independent sequence data and those complete genomes. 16S rRNAs were used to construct a three-level tree and different counting methods were introduced for the three levels: strain-to-species, species-to-genus, and genus-and-up. The model estimates that the total number of genes is about 9,000,000 after those with identity percentage of 97% or up were merged.


CONCLUSIONS
By combining completed genomes currently available and culture-independent sequencing data, we built a model to estimate the number of genes in human gut bacterial community. The total number of genes is estimated to be about 9 million. Although this number is huge, we believe it is underestimated. This is an initial step to tackle this gene counting problem for the human super-organism. It will still be an open problem in the near future. The list of genomes used in this paper can be found in the supplementary table.
Yang
Xing
X
Shanghai Center for Bioinformation Technology, Shanghai, China.
Xie
Lu
L
Li
Yixue
Y
Wei
Chaochun
C
D019295:Computational Biology; D005798:Genes, Bacterial / Q000235:genetics*; D016680:Genome, Bacterial; D006801:Humans; D007422:Intestines / Q000382:microbiology*; D008957:Models, Genetic; D008962:Models, Theoretical; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012984:Software
D012336:RNA, Ribosomal, 16S