Question

微生物多样性（扩增子/16S rDNA测序）—α多样性分析方法描述

Answer 1

​一、α多样性指数分析内容及意义

a) 群落生态学中研究微生物多样性，通过单样品的多样性分析（α[Alpha]多样性）可以反映微生物群落的丰度和多样性，包括一系列统计学分析指数估计环境群落的物种丰度和多样性。 

b) α多样性指分析主要包括：

①菌群丰度（Community richness）指数计算：Chao、Ace指数；

②菌群多样性（Community diversity）指数计算：Shannon、Simpson指数。

    ——获得指数计算汇总表格。

稀释性曲线（Rarefraction Curve）；Shannon-Wiener曲线；Rank-Abundance曲线；Specaccum曲线

二、α多样性分析在科技论文中的描述

a) 稀释性曲线和Shannon-Wiener曲线结合使用：

例如1：Shannon and Rarefaction analysis showed that, although new phylotypes can be obtained by additional sequencing, most of the gut microbial diversity in each sample was captured with the current sequencing depth. After rarefying the sequencing depth among all the samples using bootstrap (XX,XXX reads per sample), Shannon diversity index and rarefaction OTU estimates were calculated. There was no significant difference in the richness (as indicated by rarefaction OTU estimates) and diversity between Group A and Group B in this study.

如有显著差异：while Group B significantly reduced both the richness and diversity of the microbiota(P<0.05 OR Show in fig.)。

  例 如2：The richness of oral bacterial communities in three oral habitats of periodontitis patients and the control cohort were estimated by rarefaction and Chao 1, and diversity was estimated by Shannon diversity index and Simpson diversity. The shape of the rarefaction curves indicated new phylotypes would be expected with additional sequencing. However, the Shannon diversity index curves of all samples reached plateaus with the current sequencing, suggesting that most diversity had already been captured.

b) Rank-abundance曲线：

例如1：Rank-abundance curves reflect the fact that a few dominant phylotypes comprise the major proportion of the A communities whereas a more even community is seen in XXX.

例如2：Bacterial communities were also similar in their structure, exhibiting comparable trends for both rank frequency and abundance across the soils sampled.

c) 物种累积曲线：

例如：According to the sample number and species OTUs, we calculated the species accumulation curve of all participants. In this study, the curve had reached a plateau, and the species had no more obvious increase as the sample number increased, which indicated that the sample volume in our study was relatively large enough to reflect the species richness.

d) α多样性指数比较：

  例 如：We compared the α-diversity of microbiota between XX and XX samples using the chao1, ACE, observed species, Shannon and Simpson index, and found that all five indexes showed significant difference (P = XXX, XXX, XXX, XXX, and XXX, respectively). The XXX samples had a significantly higher α-diversity.

温馨提示：

文章写作时，使用α多样性指数种类和方式，需根据文章表述需求进行选择，因此， α多样性指数的差异分析需根据提供的α多样指数汇总表自行完成。