Do you cov me? Effect of coverage reduction on metagenome shotgun sequencing studies
Do you cov me? Effect of coverage reduction on metagenome shotgun sequencing studies
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作者：
F. Cattonaro;Alessandro Spadotto;S. Radovic;F. Marroni
霰弹枪宏基因组测序是表征复杂生物基质的强大工具，能够在单个实验中分析原核和真核生物和病毒，并有可能重新构建整个宏基因组或一组感兴趣的基因。限制在大规模项目中使用霰弹枪宏基因组学的主要因素之一是与该方法相关的高成本。我们开始确定是否有可能使用浅鸟枪宏基因组学来表征复杂的生物基质，同时降低成本。我们使用交错模拟群落来估计物种检测的最佳阈值。我们测量了几个汇总统计的变化，模拟了测序深度的减少，随机抽样了一些读数。比较的主要统计数据是多样性估计、物种丰度和从头重建宏基因组的长度和完整性的能力。我们的研究结果表明，复杂的原核生物、真核生物和病毒群落的多样性指数可以用50万或更少的reads准确估计，尽管特别复杂的样本可能需要100万reads。相反，任何涉及宏基因组重建的任务都表现不佳，即使是最大的模拟子样本（1,000,000次读取）。重建片段的长度小于完整数据集获得的长度，并且与完整样本相比，在元基因组中鉴定的保守基因比例大大减少。浅散弹枪宏基因组是描述复杂矩阵结构的有用工具，但它不足以重建-甚至部分重建-宏基因组。
Shotgun metagenomics sequencing is a powerful tool for the characterization of complex biological matrices, enabling analysis of prokaryotic and eukaryotic organisms and viruses in a single experiment, with the possibility of reconstructing de novo the whole metagenome or a set of genes of interest. One of the main factors limiting the use of shotgun metagenomics on wide scale projects is the high cost associated with the approach. We set out to determine if it is possible to use shallow shotgun metagenomics to characterize complex biological matrices while reducing costs. We used a staggered mock community to estimate the optimal threshold for species detection. We measured the variation of several summary statistics simulating a decrease in sequencing depth by randomly subsampling a number of reads. The main statistics that were compared are diversity estimates, species abundance, and ability of reconstructing de novo the metagenome in terms of length and completeness. Our results show that diversity indices of complex prokaryotic, eukaryotic and viral communities can be accurately estimated with 500,000 reads or less, although particularly complex samples may require 1,000,000 reads. On the contrary, any task involving the reconstruction of the metagenome performed poorly, even with the largest simulated subsample (1,000,000 reads). The length of the reconstructed assembly was smaller than the length obtained with the full dataset, and the proportion of conserved genes that were identified in the meta-genome was drastically reduced compared to the full sample. Shallow shotgun metagenomics can be a useful tool to describe the structure of complex matrices, but it is not adequate to reconstruct—even partially—the metagenome.
DOI：
10.1016/j.bbrc.2015.12.083
发表时间：
2016-01-22
影响因子：
3.1
作者：
Ranjan R;Rani A;Metwally A;McGee HS;Perkins DL
通讯作者：
Perkins DL
DOI：
10.1056/nejmoa1401268
发表时间：
2014-06-19
期刊：
The New England journal of medicine
影响因子：
--
作者：
Wilson MR;Naccache SN;Samayoa E;Biagtan M;Bashir H;Yu G;Salamat SM;Somasekar S;Federman S;Miller S;Sokolic R;Garabedian E;Candotti F;Buckley RH;Reed KD;Meyer TL;Seroogy CM;Galloway R;Henderson SL;Gern JE;DeRisi JL;Chiu CY
通讯作者：
Chiu CY
DOI：
10.1073/pnas.1117018109
发表时间：
2012-04-17
影响因子：
11.1
作者：
Schoch, Conrad L.;Seifert, Keith A.;Schindel, David
通讯作者：
Schindel, David