Quantifying spatiotemporal variability and noise in absolute microbiota abundances using replicate sampling
Quantifying spatiotemporal variability and noise in absolute microbiota abundances using replicate sampling
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DOI：
10.1038/s41592-019-0467-y
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发表时间：
2019-08-01
期刊：
影响因子：
48
通讯作者：
Vitkup, Dennis
中科院分区：
文献类型：
--
作者：
Ji, Brian W.;Sheth, Ravi U.;Vitkup, Dennis
宏基因组测序已经能够对不同的微生物群落进行详细的研究，但了解它们的时空变异性仍然是一个重要的挑战。在这里，我们提出了使用重复抽样（DIVERS），重复抽样和穗在测序的基础上的方法的方差分解。该方法量化了时间动态，空间采样变异性和技术噪声的绝对细菌丰度的方差和协方差的贡献。我们应用DIVERS研究了人类肠道微生物组的高分辨率时间序列和曼哈顿中央公园土壤细菌群落的空间调查。我们的分析表明，在肠道，技术噪音占主导地位的丰度变异近一半的检测到的类群。DIVERS还揭示了肠道微生物群的巨大空间异质性，以及拟杆菌门内分类群的高时间协方差。在土壤群落中，空间变异主要是在短时间尺度（周）的丰度波动，而在较长的时间尺度（几个月）的时间变异占主导地位。
Metagenomic sequencing has enabled detailed investigation of diverse microbial communities, but understanding their spatiotemporal variability remains an important challenge. Here, we present decomposition of variance using replicate sampling (DIVERS), a method based on replicate sampling and spike-in sequencing. The method quantifies the contributions of temporal dynamics, spatial sampling variability, and technical noise to the variances and covariances of absolute bacterial abundances. We applied DIVERS to investigate a high-resolution time series of the human gut microbiome and a spatial survey of a soil bacterial community in Manhattan's Central Park. Our analysis showed that in the gut, technical noise dominated the abundance variability for nearly half of the detected taxa. DIVERS also revealed substantial spatial heterogeneity of gut microbiota, and high temporal covariances of taxa within the Bacteroidetes phylum. In the soil community, spatial variability primarily contributed to abundance fluctuations at short time scales (weeks), while temporal variability dominated at longer time scales (several months).