Explorative Meta-Analysis of 377 Extant Fungal Genomes Predicted a Total Mycobiome Functionality of 42.4 Million KEGG Functions

Abstract

Unveiling the relationship between taxonomy 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 taxonomic diversity, our understanding of its relationship to functional diversity is still scarce. Here, we used a meta-analysis of completely annotated extant genomes of 377 taxonomically distinct fungal species to predict the total fungal microbiome functionality on Earth with accumulation curves (ACs) of all known functions from the level 3 of KEGG Orthology using both parametric and non-parametric estimates in an explorative data-mining approach. The unsaturated model extrapolating functional diversity as a function of species richness described the ACs significantly better than the saturated model that assumed a limited total number of functions, which suggested the presence of widespread and rare functions. Based on previous estimates of 3.8 million fungal species on Earth, we propagated the unsaturated model to predict a total of 42.4 ± 0.5 million KEGG level 3 functions of which only 0.06% are known today. Our approach not only highlights the presence of widespread and rare functions but points toward the necessity of novel and more sophisticated methods to unveil the entirety of functions to fully understand the involvement of the fungal microbiome in ecosystem functioning.

Explorative Analysis of 60 Metagenomes to Unveil the Abundance of Widespread Functions in the Environment and Its Weight on Functional Indices

“…Both functional redundancy and richness increased with increasing metagenome depth, implying unlimited potential of functional diversity with metagenome depth. Adding more organisms will not only add more rare functions but also increase the chances of the addition of already present widespread (or rare) functions [8,9] that, in turn, will increase both functional redundancy and richness.…”

“…We hypothesize that (i) functionality in aquatic and terrestrial ecosystems will be higher than in aerial metagenomes with generally low biomass [11]. Functionality in both bacteria [8] and fungi [8,9] will be dominated by widespread functions, making up roughly 60% of the entire functionality which is why we further hypothesize that (ii) removing the widespread functiome will result in different estimates of functional indices, potentially resulting in varying differences among the three ecosystems. ), the correlation of diversity to metagenome depth was not significant (Adj.…”

“…Problematically, the vast majority of organisms were not yet studied [5,6] and their annotations are based on their similarity to the genomes of the very few studied model organisms, potentially yielding flawed annotations [7]. Recently, the total functional richness of bacteria [8] and fungi [8,9] was predicted to be millions of KEGG level 3 functions but locally, only a subset of the functions will be available [10]. However, widespread functions present in all metagenomes with abundances depending on the local metagenome density could potentially impact functional indices.…”

Explorative Meta-Analysis of 417 Extant Archaeal Genomes to Predict Their Contribution to the Total Microbiome Functionality

“…Indeed, interspecies redundancy was reported to be very high with several hundreds to thousands of different taxa to express the same function in a habitat [ 11 ]. These functions can be statistically inferred based on the homology to experimentally characterized genes and proteins in specific organisms to find orthologs present in a microbiome [ 12 , 13 , 14 ]. This ortholog annotation is used by KEGG Orthology [ 15 , 16 ], which covers a wide range of functional classes (level 1 of KEGG) comprising cellular processes, environmental information processing, genetic information processing, human diseases, metabolism, organismal system, brite hierarchies, and functions not included in the annotation of the two databases pathway or brite.…”

“…Hence, the lower the share of known species or the higher the predicted total diversity, the weaker the prediction itself. Problematically, the vast majority of organisms have not yet been studied [ 17 , 18 ] which is why the annotation is based on the similarity to the genomes of the very few studied model organisms [ 12 , 13 , 14 ]. Consequentially, microbiome functionality is inferred based on the taxonomic composition of the community and its relation to functional parameters [ 19 ], indicated by the frequent use of the 16S rRNA gene metabarcoding to describe the prokaryotic community.…”