CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction.
CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction.
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DOI：
10.1186/2049-2618-2-11
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发表时间：
2014
期刊：
影响因子：
15.5
通讯作者：
Tyson GW
中科院分区：
文献类型：
--
作者：
Angly FE;Dennis PG;Skarshewski A;Vanwonterghem I;Hugenholtz P;Tyson GW
由于物种间基因拷贝数的差异，针对保守的标记基因，尤其是16S rRNA的独立于培养的分子调查，以评估微生物多样性仍然是半定量的。基于2900个已测序的参考基因组，我们发现16S rRNA基因拷贝数(GCN)与微生物系统发育分类密切相关，在扩增微生物谱中可能不能代表古生菌。利用这种关系，我们在系统发育框架内推断了格林数据库中所有细菌和古细菌谱系的GCN。我们创建了Copyright，这是一种新的软件，它使用这些估计来校正16S rRNA扩增微生物图谱和相关的定量(Q)PCR总丰度。著作权人解析微生物图谱，因为GCN估计是对参考分类中的所有分类群预先计算的，所以迅速纠正了GCN偏见。在电子计算机和体外模拟群落中进行的软件验证表明，GCN校正导致了对微生物相对丰度的更准确估计，并改善了元基因组和扩增子图谱之间的一致性。对人类相关和厌氧消化器微生物群的分析表明，校正使qPCR总丰度、α和β多样性的估计发生了明显变化，并可能显著改变生物学解释。例如，经过GCN校正后，来自双胞胎的人类肠道微生物群被重新分类为三种肠道类型，而不是两种肠道类型。利用版权生物信息学工具，可以在微生物调查中快速修正全球生物信息网，从而改进对微生物丰度、α和β多样性的估计。
Culture-independent molecular surveys targeting conserved marker genes, most notably 16S rRNA, to assess microbial diversity remain semi-quantitative due to variations in the number of gene copies between species. Based on 2,900 sequenced reference genomes, we show that 16S rRNA gene copy number (GCN) is strongly linked to microbial phylogenetic taxonomy, potentially under-representing Archaea in amplicon microbial profiles. Using this relationship, we inferred the GCN of all bacterial and archaeal lineages in the Greengenes database within a phylogenetic framework. We created CopyRighter, new software which uses these estimates to correct 16S rRNA amplicon microbial profiles and associated quantitative (q)PCR total abundance. CopyRighter parses microbial profiles and, because GCN estimates are pre-computed for all taxa in the reference taxonomy, rapidly corrects GCN bias. Software validation with in silico and in vitro mock communities indicated that GCN correction results in more accurate estimates of microbial relative abundance and improves the agreement between metagenomic and amplicon profiles. Analyses of human-associated and anaerobic digester microbiomes illustrate that correction makes tangible changes to estimates of qPCR total abundance, α and β diversity, and can significantly change biological interpretation. For example, human gut microbiomes from twins were reclassified into three rather than two enterotypes after GCN correction. The CopyRighter bioinformatic tools permits rapid correction of GCN in microbial surveys, resulting in improved estimates of microbial abundance, α and β diversity.
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影响因子：
64.8
作者：
Arumugam, Manimozhiyan;Raes, Jeroen;Pelletier, Eric;Le Paslier, Denis;Yamada, Takuji;Mende, Daniel R.;Fernandes, Gabriel R.;Tap, Julien;Bruls, Thomas;Batto, Jean-Michel;Bertalan, Marcelo;Borruel, Natalia;Casellas, Francesc;Fernandez, Leyden;Gautier, Laurent;Hansen, Torben;Hattori, Masahira;Hayashi, Tetsuya;Kleerebezem, Michiel;Kurokawa, Ken;Leclerc, Marion;Levenez, Florence;Manichanh, Chaysavanh;Nielsen, H. Bjorn;Nielsen, Trine;Pons, Nicolas;Poulain, Julie;Qin, Junjie;Sicheritz-Ponten, Thomas;Tims, Sebastian;Torrents, David;Ugarte, Edgardo;Zoetendal, Erwin G.;Wang, Jun;Guarner, Francisco;Pedersen, Oluf;de Vos, Willem M.;Brunak, Soren;Dore, Joel;Weissenbach, Jean;Ehrlich, S. Dusko;Bork, Peer
通讯作者：
Bork, Peer
影响因子：
5.8
作者：
Kembel, Steven W.;Cowan, Peter D.;Webb, Campbell O.
通讯作者：
Webb, Campbell O.
影响因子：
56.9
作者：
Barabási, AL;Albert, R
通讯作者：
Albert, R
影响因子：
11.8
作者：
Bishara, Jihad;Farah, Raymond;Nseir, William
通讯作者：
Nseir, William
影响因子：
7
作者：
Giardine, B;Riemer, C;Nekrutenko, A
通讯作者：
Nekrutenko, A