Thünen Institut für Biodiversität, Johann Heinrich von Thünen Institut, Braunschweig 38116, Germany.
Institut für Geoökologie, Technische Universität Braunschweig, Braunschweig 38106, Germany.
FEMS Microbiol Ecol. 2024 Feb 14;100(3). doi: 10.1093/femsec/fiae019.
Alpha-diversity indices are an essential tool for describing and comparing biodiversity. Microbial ecologists apply indices originally intended for, or adopted by, macroecology to address questions relating to taxonomy (conserved marker) and function (metagenome-based data). In this Perspective piece, I begin by discussing the nature and mathematical quirks important for interpreting routinely employed alpha-diversity indices. Secondly, I propose a metagenomic alpha-diversity index (MD) that measures the (dis)similarity of protein-encoding genes within a community. MD has defined limits, whereby a community comprised mostly of similar, poorly diverse protein-encoding genes pulls the index to the lower limit, while a community rich in divergent homologs and unique genes drives it toward the upper limit. With data acquired from an in silico and three in situ metagenome studies, I derive MD and typical alpha-diversity indices applied to taxonomic (ribosomal rRNA) and functional (all protein-encoding) genes, and discuss their relationships with each other. Not all alpha-diversity indices detect biological trends, and taxonomic does not necessarily follow functional biodiversity. Throughout, I explain that protein Richness and MD provide complementary and easily interpreted information, while probability-based indices do not. Finally, considerations regarding the unique nature of microbial metagenomic data and its relevance for describing functional biodiversity are discussed.
α多样性指数是描述和比较生物多样性的重要工具。微生物生态学家应用最初针对或被宏观生态学采用的指数来解决与分类学（保守标记）和功能（基于宏基因组的数据）相关的问题。在这篇观点文章中，我首先讨论了解释常用α多样性指数时重要的性质和数学怪癖。其次，我提出了一个衡量群落中编码蛋白基因（dis）相似性的宏基因组α多样性指数（MD）。MD 具有定义的极限，即由相似、多样性差的编码蛋白基因组成的群落将指数拉向低值，而富含不同同源物和独特基因的群落则将其推向高值。我利用来自一个计算机模拟和三个原位宏基因组研究的数据，推导出 MD 和典型的应用于分类学（核糖体 rRNA）和功能（所有编码蛋白）基因的α多样性指数，并讨论它们之间的关系。并非所有的α多样性指数都能检测到生物学趋势，而且分类学不一定遵循功能生物多样性。在整个讨论中，我解释说蛋白质丰富度和 MD 提供了互补且易于解释的信息，而基于概率的指数则不能。最后，还讨论了微生物宏基因组数据的独特性质及其对功能生物多样性描述的相关性。
