Quantifying Shared and Unique Gene Content across 17 Microbial Ecosystems

Measuring microbial diversity is traditionally based on microbe taxonomy. Here, in contrast, we aimed to quantify heterogeneity in microbial gene content across 14,183 metagenomic samples spanning 17 ecologies, including 6 human associated, 7 nonhuman host associated, and 4 in other nonhuman host environments. In total, we identified 117,629,181 nonredundant genes. The vast majority of genes (66%) occurred in only one sample (i.e., singletons). In contrast, we found 1,864 sequences present in every metagenome, but not necessarily every bacterial genome. Additionally, we report data sets of other ecology-associated genes (e.g., abundant in only gut ecosystems) and simultaneously demonstrated that prior microbiome gene catalogs are both incomplete and inaccurately cluster microbial genetic life (e.g., at gene sequence identities that are too restrictive). We provide our results and the sets of environmentally differentiating genes described above at http://www.microbial-genes.bio.

Automated summary

This study quantified the heterogeneity in microbial gene content across different ecological environments. The researchers identified a large number of nonredundant genes, with the majority occurring in only one sample. They also discovered sets of genes associated with specific ecological environments and highlighted the incompleteness and inaccuracy of previous microbiome gene catalogs.