Identifying biologically relevant differences between metagenomic communities
Identifying biologically relevant differences between metagenomic communities
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DOI：
10.1093/bioinformatics/btq041
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发表时间：
2010-03-15
期刊：
影响因子：
5.8
通讯作者：
Beiko, Robert G.
中科院分区：
文献类型：
--
作者：
Parks, Donovan H.;Beiko, Robert G.
动机：元基因组学是研究直接从环境样本中提取的遗传物质。后基因组样本之间的分类和功能差异可以突出生态因素对广泛生境中微生物生命模式的影响。统计假设检验可以帮助我们区分生态影响和抽样伪迹，但仅从统计假设检验中获得的P值知识不足以做出关于生物相关性的推断。结果：我们开发了一个新的比较元基因组学软件包STAMP，它支持分析和报告方面的最佳实践。对一对铁矿元基因组的研究表明，使用我们软件中可用的统计技术可以获得更深层次的生物学见解。对两个强化生物除磷Metagenome中‘Candidatus Acumulibacter Phatis’的功能潜力的分析发现，在这些相关群落中，有几个不同的磷假丝酵母菌株的子系统，包括磷酸盐代谢、分泌和金属运输。
Motivation: Metagenomics is the study of genetic material recovered directly from environmental samples. Taxonomic and functional differences between metagenomic samples can highlight the influence of ecological factors on patterns of microbial life in a wide range of habitats. Statistical hypothesis tests can help us distinguish ecological influences from sampling artifacts, but knowledge of only the P-value from a statistical hypothesis test is insufficient to make inferences about biological relevance. Current reporting practices for pairwise comparative metagenomics are inadequate, and better tools are needed for comparative metagenomic analysis.Results: We have developed a new software package, STAMP, for comparative metagenomics that supports best practices in analysis and reporting. Examination of a pair of iron mine metagenomes demonstrates that deeper biological insights can be gained using statistical techniques available in our software. An analysis of the functional potential of 'Candidatus Accumulibacter phosphatis' in two enhanced biological phosphorus removal metagenomes identified several subsystems that differ between the A. phosphatis stains in these related communities, including phosphate metabolism, secretion and metal transport.