Dataset Information

More than 9,000,000 unique genes in human gut bacterial community: estimating gene numbers inside a human body.

ABSTRACT:

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.

Principal findings

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.

Conclusion

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.

SUBMITTER: Yang X

PROVIDER: S-EPMC2699651 | biostudies-literature | 2009 Jun

REPOSITORIES: biostudies-literature

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Publications

More than 9,000,000 unique genes in human gut bacterial community: estimating gene numbers inside a human body.

Yang Xing X Xie Lu L Li Yixue Y Wei Chaochun C

PloS one 20090629 6

<h4>Background</h4>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.<h4>Principal findings</h4>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 hum ...[more]

PMID: 19562079

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Dataset Information

More than 9,000,000 unique genes in human gut bacterial community: estimating gene numbers inside a human body.

Background

Principal findings

Conclusion

Publications

More than 9,000,000 unique genes in human gut bacterial community: estimating gene numbers inside a human body.

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