Intra- and inter-species interactions drive early phases of invasion in mice gut microbiota

Abstract

AbstractThe stability and dynamics of ecological communities are dictated by interaction networks typically quantified at the level of species.1–10But how such networks are influenced by intra-species variation (ISV) is poorly understood.11–14Here, we use ~500,000 chromosomal barcodes to track high-resolution intra-species clonal lineages ofEscherichia coliinvading mice gut with the increasing complexity of gut microbiome: germ-free, antibiotic-perturbed, and innate microbiota. By co-clustering the dynamics of intra-species clonal lineages and those of gut bacteria from 16S rRNA profiling, we show the emergence of complex time-dependent interactions betweenE. coliclones and resident gut bacteria. With a new approach, dynamic covariance mapping (DCM), we differentiate three phases of invasion in susceptible communities: 1) initial loss of community stability asE. colienters; 2) recolonization of some gut bacteria; and 3) recovery of stability withE. colicoexisting with resident bacteria in a quasi-steady state. Comparison of the dynamics, stability and fitness from experimental replicates and different cohorts suggest that phase 1 is driven by mutations inE. colibefore colonization, while phase 3 is byde novomutations. Our results highlight the transient nature of interaction networks in microbiomes driven by the persistent coupling of ecological and evolutionary dynamics.One-Sentence SummaryHigh-resolution lineage tracking and dynamic covariance mapping (DCM) define three distinct phases during early gut microbiome invasion.