Only Simpson Diversity can be Estimated Accurately from Microbial Community Fingerprints
Only Simpson Diversity can be Estimated Accurately from Microbial Community Fingerprints
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DOI：
10.1007/s00248-014-0394-5
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发表时间：
2014-08-01
影响因子：
3.6
通讯作者：
Hamelin, Jerome
中科院分区：
文献类型：
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作者：
Haegeman, Bart;Sen, Biswarup;Hamelin, Jerome
Lalande等人。(Microb.伊科。66(3)：647-658,2013)提出了一种从指纹图谱量化微生物多样性的有前景的方法。他们的分析是基于将指纹中可检测到的系统类型的丰度外推到群落的稀有系统类型。通过考虑一组重建的社区，Lalande等人。获得了系统类型丰富度、香农多样性和辛普森多样性的一系列估计。他们报告的范围很窄，表明估计准确，特别是香农和辛普森的多样性。在这里，我们展示了比Lalande等人所考虑的要大得多的重建社区集。与指纹相符。我们发现，对种型丰富度和香农多样性的估计在数量级上有所不同，但对辛普森多样性的估计局限在一个很窄的范围内(约10%)。我们的结论是，只有辛普森多样性才能从指纹中准确地估计出来。
Lalande et al. (Microb. Ecol. 66(3):647-658, 2013) introduced a promising approach to quantify microbial diversity from fingerprinting profiles. Their analysis is based on extrapolating the abundance of the phylotypes detectable in a fingerprint towards the rare phylotypes of the community. By considering a set of reconstructed communities, Lalande et al. obtained a range of estimates for phylotype richness, Shannon diversity and Simpson diversity. They reported narrow ranges indicating accurate estimation, especially for Shannon and Simpson diversities. Here, we show that a much larger set of reconstructed communities than the one considered by Lalande et al. is consistent with the fingerprint. We find that the estimates for phylotype richness and Shannon diversity vary over orders of magnitude, but that the estimates for Simpson diversity are restricted to a narrow range (around 10 %). We conclude that only Simpson diversity can be estimated accurately from fingerprints.