Prolonged delays in human microbiota transmission after a controlled antibiotic perturbation

Abstract

Humans constantly encounter new microbes, but few become long-term residents of the adult gut microbiome. Classical theories predict that colonization is determined by the availability of open niches, but it remains unclear whether other ecological barriers limit commensal colonization in natural settings. To disentangle these effects, we used a controlled perturbation with the antibiotic ciprofloxacin to investigate the dynamics of gut microbiome transmission in 22 households of healthy, cohabiting adults. Colonization was rare in three-quarters of antibiotic-taking subjects, whose resident strains rapidly recovered in the week after antibiotics ended. In contrast, the remaining subjects exhibited lasting responses to antibiotics, with extensive species losses and transient expansions of potential opportunistic pathogens. These subjects experienced elevated rates of commensal colonization, but only after long delays: many new colonizers underwent sudden, correlated expansions months after the antibiotic perturbation. Furthermore, strains that had previously transmitted between cohabiting partners rarely recolonized after antibiotic disruptions, showing that colonization displays substantial historical contingency. This work demonstrates that there remain substantial ecological barriers to colonization even after major microbiome disruptions, suggesting that dispersal interactions and priority effects limit the pace of community change.

Competition for shared resources increases dependence on initial population size during coalescence of gut microbial communities

“…1715 unique ASVs were detected across all samples, and 198 of these were present at ≥10 -3 relative abundance in at least one sample, which we estimated as the limit of detection. Although subjects from the same households often shared a higher proportion of gut microbial strains compared to subjects from different households 75 , we observed no differences in the proportion of ASVs shared in mixtures of communities from the same versus different households ( Extended Data Fig. 3 ).…”

“…Stool samples were collected as a part of a study 62 approved by the Stanford University Institutional Review Board under Protocol 54715. Informed written consent was obtained from all participants.…”

“…In vitro communities were derived from day 0 pre-antibiotic samples collected from healthy adults 75 .…”

Soil microbial community response to corrinoids is shaped by a natural reservoir of vitamin B12

“…We find that, while different corrinoids cause profound restructuring of both microcosm and enrichment communities, these corrinoid-dependent differences in community composition are transient. The soil community appeared initially sensitive to corrinoid addition and ultimately rebounded, analogous to the resilience of gut microbial communities to short-term antibiotic use [66]. The outcome of the added corrinoids remains unclear; they may be adsorbed by the soil and become inaccessible, or they could be remodeled into other corrinoids or degraded by yet unknown mechanisms.…”