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

<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>P...

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Autores principales:	Xing Yang, Lu Xie, Yixue Li, Chaochun Wei
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2009
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/8e094f57c3414cb7a3f2a00247e6f74e
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spelling	oai:doaj.org-article:8e094f57c3414cb7a3f2a00247e6f74e2021-11-25T06:21:51ZMore than 9,000,000 unique genes in human gut bacterial community: estimating gene numbers inside a human body.1932-620310.1371/journal.pone.0006074https://doaj.org/article/8e094f57c3414cb7a3f2a00247e6f74e2009-06-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/19562079/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203<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 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.<h4>Conclusion</h4>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.Xing YangLu XieYixue LiChaochun WeiPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 4, Iss 6, p e6074 (2009)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Xing Yang Lu Xie Yixue Li Chaochun Wei More than 9,000,000 unique genes in human gut bacterial community: estimating gene numbers inside a human body.
description	<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 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.<h4>Conclusion</h4>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.
format	article
author	Xing Yang Lu Xie Yixue Li Chaochun Wei
author_facet	Xing Yang Lu Xie Yixue Li Chaochun Wei
author_sort	Xing Yang
title	More than 9,000,000 unique genes in human gut bacterial community: estimating gene numbers inside a human body.
title_short	More than 9,000,000 unique genes in human gut bacterial community: estimating gene numbers inside a human body.
title_full	More than 9,000,000 unique genes in human gut bacterial community: estimating gene numbers inside a human body.
title_fullStr	More than 9,000,000 unique genes in human gut bacterial community: estimating gene numbers inside a human body.
title_full_unstemmed	More than 9,000,000 unique genes in human gut bacterial community: estimating gene numbers inside a human body.
title_sort	more than 9,000,000 unique genes in human gut bacterial community: estimating gene numbers inside a human body.
publisher	Public Library of Science (PLoS)
publishDate	2009
url	https://doaj.org/article/8e094f57c3414cb7a3f2a00247e6f74e
work_keys_str_mv	AT xingyang morethan9000000uniquegenesinhumangutbacterialcommunityestimatinggenenumbersinsideahumanbody AT luxie morethan9000000uniquegenesinhumangutbacterialcommunityestimatinggenenumbersinsideahumanbody AT yixueli morethan9000000uniquegenesinhumangutbacterialcommunityestimatinggenenumbersinsideahumanbody AT chaochunwei morethan9000000uniquegenesinhumangutbacterialcommunityestimatinggenenumbersinsideahumanbody
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More than 9,000,000 unique genes in human gut bacterial community: estimating gene numbers inside a human body.

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