Quantifying diversity is of central importance for the study of structure, function and evolution of microbial communities. The estimation of microbial diversity has received renewed attention with the advent of large-scale metagenomic studies. Here, we consider what the diversity observed in a sample tells us about the diversity of the community being sampled. First, we argue that one cannot reliably estimate the absolute and relative number of microbial species present in a community without making unsupported assumptions about species abundance distributions. The reason for this is that sample data do not contain information about the number of rare species in the tail of species abundance distributions. We illustrate the difficulty in comparing species richness estimates by applying Chao's estimator of species richness to a set of in silico communities: they are ranked incorrectly in the presence of large numbers of rare species. Next, we extend our analysis to a general family of diversity metrics ("Hill diversities"), and construct lower and upper estimates of diversity values consistent with the sample data. The theory generalizes Chao's estimator, which we retrieve as the lower estimate of species richness. We show that Shannon and Simpson diversity can be robustly estimated for the in silico communities. We analyze nine metagenomic data sets from a wide range of environments, and show that our findings are relevant for empirically-sampled communities. Hence, we recommend the use of Shannon and Simpson diversity rather than species richness in efforts to quantify and compare microbial diversity.
Towards a Taxonomical Consensus: Diversity and Richness Inference from Large Scale rRNA gene Analysis
种群分析一直具有挑战性，但重要的是，导致确定微生物群落成员的多样性和功能预测。在这里，我们详细介绍了我们的生物信息学方法，用于分析大型微生物群落的种群分布和多样性。这是通过以下方式实现的：（i）基于同源性的方法，用于稳健的多态性类型确定，等同于核糖体数据库项目（RDP）分类器的分类准确度，但提供了密切相关序列的改进的关联;（ii）比较不同的聚类方法，用于实现更准确的丰富度估计。我们的方法，我们开发的RDP审查16 S rRNA基因序列集，通过测试它对一个大的16 S rRNA基因数据集的约2300个序列，我们从土壤微生物群落研究。我们的结论是，最好的方法，以获得准确的微生物群落的遗传学概况的基础上，16 S rRNA基因序列信息，是应用优化的爆破分类。这种方法得到了使用完整连锁聚类对密切相关序列进行分组的补充，以计算群落的丰富度和均匀度指数。
Cross-feeding Creates Tipping Points in Microbiome Diversity
Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg（奥尔登堡大学赫尔霍兹功能海洋生物多样性研究所）；Alfred Wegner institute（阿尔弗雷德·韦格纳研究所）；ICBM, University of Oldenburg（奥尔登堡大学国际与比较生物学中心）
A 454 survey of the community composition and core microbiome of the common bed bug, Cimex lectularius, reveals significant microbial community structure across an urban landscape
阐明与节肢动物宿主相关的微生物群落的空间动态和核心成分对于可能传播人类或农业病原体的昆虫至关重要。嗜血的温带臭虫（Cimex lectularius）被称为常见的臭虫，最近在北美和全世界死灰复燃，这可能是由于旅行增加和对杀虫剂的抗药性。迄今为止，尚未对臭虫微生物组进行全面调查，也没有对其微生物组的空间动态进行评估。在这里，我们提出了一个调查臭虫微生物群落扩增的V4-V6高变区的16 S rDNA基因区，然后454钛测序使用31个人从8个自然种群收集的住宅在辛辛那提，OH。在所有样品中，97%的微生物群落由两种主要OTU组成，被鉴定为α-变形杆菌Wolbachia和来自肠杆菌科的未命名的γ-变形杆菌。微生物群落在宿主种群中的群落多样性的措施，并表现出显着的人口结构。我们还发现了两种主要OTU丰度的强烈负相关性，这表明它们可能扮演着与营养互惠者相似的角色。这项广泛的调查代表了迄今为止对与臭虫相关的微生物的最全面的评估，并揭示了臭虫微生物组两个主要成员之间潜在拮抗作用的证据。
Microbiome association diversity reflects proximity to the edge of instability
Instituto Carlos I de Física Teórica y Computacional, Universidad de Granada（格拉纳达大学卡洛斯一世理论与计算物理研究所）；Departamento de Electromagnetismo y Física de la Materia, Universidad de Granada（格拉纳达大学电磁与物质物理系）；Institute of Functional Biology & Genomics, CSIC - Universidad de Salamanca（萨拉曼塔大学/西班牙国家研究委员会功能生物学与基因组学研究所）；Universidad Carlos III de Madrid（马德里卡洛斯三世大学）；Grupo Interdisciplinar de Sistemas Complejos (GISC)（复杂系统跨学科小组（GISC））；Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza（萨拉戈萨大学生物计算与复杂系统物理研究所（BIFI））
