Short pyrosequencing reads suffice for accurate microbial community analysis.
Short pyrosequencing reads suffice for accurate microbial community analysis.
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DOI：
10.1093/nar/gkm541
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发表时间：
2007
影响因子：
14.9
通讯作者：
Knight R
中科院分区：
文献类型：
--
作者：
Liu Z;Lozupone C;Hamady M;Bushman FD;Knight R
焦磷酸测序技术使我们能够利用16S核糖体RNA（rRNA）序列来表征微生物群落，其速度比以往可能的情况快几个数量级，且成本更低。然而，使用焦磷酸测序和传统测序的不同研究结果往往难以比较，因为覆盖rRNA不同区域的扩增子可能会得出不同的结论。我们使用来自全球200多个不同环境的序列来测试使用相似引物的研究是否会错误地聚在一起，而不考虑环境因素。然后我们使用UniFrac（我们最近开发的用于比较微生物群落的方法）来测试引物选择是否会影响基于序列的群落分析。我们进行了三项引物效应测试。我们测试了对于最近三项关于小鼠和人类肠道以及格雷罗内格罗微生物垫的微生物群落的大规模研究，不同的模拟扩增子是否能产生与近乎全长序列相同的UniFrac聚类结果。然后我们对类似于焦磷酸测序产生的短序列（100、150、200和250个碱基的读长）重复了这一分析。结果表明，如果引物选择得当，测序工作最好集中在收集更多的短序列而非更少的长序列上，而且像UniFrac这样的群落比较方法对测序区域的变化具有惊人的稳健性。
Pyrosequencing technology allows us to characterize microbial communities using 16S ribosomal RNA (rRNA) sequences orders of magnitude faster and more cheaply than has previously been possible. However, results from different studies using pyrosequencing and traditional sequencing are often difficult to compare, because amplicons covering different regions of the rRNA might yield different conclusions. We used sequences from over 200 globally dispersed environments to test whether studies that used similar primers clustered together mistakenly, without regard to environment. We then tested whether primer choice affects sequence-based community analyses using UniFrac, our recently-developed method for comparing microbial communities. We performed three tests of primer effects. We tested whether different simulated amplicons generated the same UniFrac clustering results as near-full-length sequences for three recent large-scale studies of microbial communities in the mouse and human gut, and the Guerrero Negro microbial mat. We then repeated this analysis for short sequences (100-, 150-, 200- and 250-base reads) resembling those produced by pyrosequencing. The results show that sequencing effort is best focused on gathering more short sequences rather than fewer longer ones, provided that the primers are chosen wisely, and that community comparison methods such as UniFrac are surprisingly robust to variation in the region sequenced.
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影响因子：
14.9
作者：
Ludwig, W;Strunk, O;Schleifer, KH
通讯作者：
Schleifer, KH
影响因子：
14.9
作者：
WOESE, CR;MAGRUM, LJ;NOLLER, HF
通讯作者：
NOLLER, HF
DOI：
10.1073/pnas.0504978102
发表时间：
2005-08-02
影响因子：
11.1
作者：
Ley, RE;Bäckhed, F;Gordon, JI
通讯作者：
Gordon, JI
影响因子：
10.7
作者：
SAITOU, N;NEI, M
通讯作者：
NEI, M
影响因子：
3
作者：
Lozupone C;Hamady M;Knight R
通讯作者：
Knight R