The dark matter of the human gut microbiome follows neutral ecological assembly rules

The discrepancy between the number of microbes that can be observed directly vs those that can be cultured has vexed scientists for decades. Here, we investigate whether yet-to-be-cultured microbes of the human gut microbiome are inherently different from cultured microbes. Using metagenomics from 22 fecal samples, we assembled 85 complete, previously unsequenced genomes from uncultured microbes. We then explore the ecological assembly processes and functional characteristics among these organisms. Specifically, we test the hypothesis that culturing selects for microbes that occupy a stable metabolic niche, whereas microbes that have yet to be cultured lack such a niche and assemble under stochastic, neutral processes (e.g. births, deaths, and migration). We find that neutral processes dominate in uncultured microbes and that functional predictions based on gene content fail to explain why they that have not been cultured. The findings from this study—which apply the tool of metagenomics to the problem of ecological assembly rules—may help lay the groundwork for understanding how the human gut microbiome is assembled, with important implications for health.