当前位置:科学网首页 > 小柯机器人 >详情
科学家开发出量化测序时空变异性的新方法
来源:小柯机器人 发布时间:2019/8/4 11:27:00

美国哥伦比亚大学Dennis Vitkup和Harris H. Wang团队合作开发了利用重复取样进行绝对微生物组丰度中时空变异性与噪声的量化。相关论文发表在2019年8月出版的《自然—方法学》上。

研究人员开发了一种基于重复采样和加标测序的方法,即通过重复采样的方差分解(DIVERS)。这个方法能够量化时间动态、空间抽样变异性以及技术背景噪声对绝对细菌丰度方差与协方差的贡献程度。研究人员利用DIVERS来研究了人体肠道微生物组的高分辨率时间序列以及曼哈顿中央公园土壤细菌群体的空间调查。他们的分析表明,肠道中的技术背景噪声占据了检测类群中近一半的丰度变化。DIVERS还揭示了肠道微生物菌群具有大量空间异质性,以及拟杆菌门中具有分类群的高时间协方差。在土壤菌群中,空间变异性主要导致在短时间尺度(数周)内的丰富波动,而时间变异性主要反映在长时间尺度中(几个月)。

据悉,宏基因组测序已经能够对不同的微生物群落进行详细研究,但了解它们的时空变化仍然是一个重要的挑战。
 

附:英文原文

Title: Quantifying spatiotemporal variability and noise in absolute microbiota abundances using replicate sampling

Author: Brian W. Ji, Ravi U. Sheth, Purushottam D. Dixit, Yiming Huang, Andrew Kaufman, Harris H. Wang, Dennis Vitkup

Issue&Volume: Volume 16 Issue 8

Abstract: 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 Manhattans 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).

DOI: 10.1038/s41592-019-0467-y

Source:https://www.nature.com/articles/s41592-019-0467-y

期刊信息

Nature Methods:《自然—方法学》,创刊于2004年。隶属于施普林格·自然出版集团,最新IF:28.467
官方网址:https://www.nature.com/nmeth/
投稿链接:https://mts-nmeth.nature.com/cgi-bin/main.plex


本期文章:《自然—方法学》:Volume 16 Issue 8