Source: europepmc · Zeng X, Meng X, Weakley AM, Higginbottom SK, Lopez EM, Cabrera AV, Gray I, DeFelice B, Terasaki M, Zhao A, Hall KR, Levi · bioRxiv · 2026-05-25
URL: https://europepmc.org/article/PPR/PPR1238454
AI rationale (5/5, tier: emerging): Defined community dropout screen directly tests keystone species, colonisation dynamics, and community-level metabolic mechanisms in germ-free mice.
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 community's 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.