Unveiling the relationship between phylogeny and function of the microbiome is crucial to determine its contribution to ecosystem functioning. However, while there is a considerable amount of information on microbial phylogenetic diversity, our understanding of its relationship to functional diversity is still scarce. Here we predicted the total microbiome functions of bacteria and fungi on Earth using the total known functions from level 3 of KEGG Orthology by modelling the increase of functions with increasing diversity of bacteria or fungi. For bacteria and fungi, the unsaturated model described the data significantly better (for both P <2.2e-16), suggesting the presence of two types of functions. Widespread functions ubiquitous in every living organism that make up two thirds of our current knowledge of microbiome functions are separated from rare functions from specialised enzymes present in only a few species. Given previous estimates on species richness, we predicted a global total of 35.5 million functions in bacteria and 3.2 million in fungi; of which only 0.02% and 0.14% are known today. Our approach highlights the necessity of novel and more sophisticated methods to unveil the entirety of rare functions to fully understand the involvement of the microbiome in ecosystem functioning. SIGNIFICANCE: The functionality of and within a microbial community is generally inferred based on the taxonomic annotation of the organism. However, our understanding of functional diversity and how it relates to taxonomy is still limited. Here we predict the total microbiome functionality in bacteria and fungi on Earth using known and annotated protein-coding sequences in species accumulation curves. Our estimates reveal that the majority of functionality (>99%) could be assigned to yet unknown and rare functions, highlighting that our current knowledge is incomplete and functional inference is thus lackluster.

中文翻译：

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总微生物组在细菌和真菌中起作用。

揭示系统发育与微生物组功能之间的关系对于确定其对生态系统功能的贡献至关重要。然而，尽管关于微生物系统发生多样性的信息很多，但我们对其功能多样性的关系的了解仍然很少。在这里，我们通过使用KEGG Orthology的第3级已知的总功能预测了细菌和真菌多样性的增加，从而预测了地球上细菌和真菌的总微生物组功能。对于细菌和真菌，非饱和模型描述的数据明显更好（对于P <2.2e-16），表明存在两种类型的功能。构成我们目前微生物组功能知识的三分之二的每个生物体中普遍存在的广泛功能，与仅在少数物种中存在的专门酶中的稀有功能区分开。根据先前对物种丰富度的估计，我们预测全球细菌共有3550万种功能，真菌共有320万种功能。今天只知道其中的0.02％和0.14％。我们的方法强调了新颖和更复杂的方法来揭示所有稀有功能的必要性，以充分了解微生物组在生态系统功能中的参与。意义：微生物群落及其内部的功能通常是根据生物的生物分类标记来推断的。但是，我们对功能多样性及其与分类法的关系的理解仍然有限。在这里，我们使用物种积累曲线中已知的和带注释的蛋白质编码序列来预测地球上细菌和真菌中的总微生物组功能。我们的估计表明，大多数功能（> 99％）可以分配给尚不为人所知和稀有的功能，这突出说明我们目前的知识是不完整的，因此功能推论不那么光彩。