A single-strain dropout screen reveals mechanistic links between microbial ecology and metabolism
Zeng, X.; Meng, X.; Weakley, A. M.; Higginbottom, S. K.; Lopez, E. M.; Cabrera, A. V.; Gray, I.; DeFelice, B.; Terasaki, M.; Zhao, A.; Hall, K. R.; Levia, M.; Arreola, J.; Fischbach, M. A.
Show abstract
The complexity of the gut microbiome has made it challenging to define the role of individual species in community-level function. Here, we constructed 56 single-strain dropout variants of a defined 118-member community and used each one to colonize a group of germ-free mice. In many cases, removing a single strain triggered a large reordering of a small group of species, which in turn altered the communitys metabolic output. En bloc removal of the eight-strain acetogen compartment markedly reduced acetate production and caused intestinal H2 accumulation and bloating; a specific subset of four acetogens was sufficient to relieve bloating and restore acetate production. Together, these data show that small disturbances in community composition can trigger a confined ecological reorganization with a large chemical phenotype, and they reveal novel strategies for engineering communities with altered metabolic output.
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