19The intestinal microbiota contains beneficial microorganisms that protect against pathogen 20 colonization. Antibiotics can disrupt the microbiota and compromise colonization 21 resistance. Here, we determine how the exchange of microbes between hosts impacts the 22 resilience of the gut microbiota to resist colonization after antibiotic-induced dysbiosis. We 23 assess the functional consequences of dysbiosis using a mouse model of colonization 24 resistance against an invading Escherichia coli. Antibiotics caused the stochastic loss of 25 microbiota members, but the microbiotas of co-housed animals remained more similar to 26 each other than those among singly housed animals. Strikingly, co-housed animals 27 maintained colonization resistance after antibiotics, whereas most singly housed mice 28 were susceptible to invasion by E. coli. The ability to retain or share a particular 29 commensal, Klebsiella michiganensis, a related member of the same family 30 Enterobacteriaceae, was sufficient for colonization resistance after antibiotic-induced 31 dysbiosis. K. michiganensis generally outcompeted E. coli in vitro, but in vivo administration 32 of galactitol to bi-colonized gnotobiotic mice, a nutrient that supports only E. coli growth in 33 vitro, abolished the colonization resistance capacity of K. michiganensis against E. coli, 34 supporting nutrient competition as the primary mechanism for their interaction. K. 35 michiganensis also hampered colonization of the enteric Enterobacteriaceae pathogen 36 Salmonella enterica serovar Typhimurium and prolonged host survival. Our results address 37 the functional consequences of the stochastic effects of antibiotic treatments, whereby 38 microbial transmission through host interactions can facilitate the reacquisition of 39 beneficial commensals and thus minimize the negative impact of antibiotics. 40 57 Proteobacteria (e.g. from the Enterobacteriaceae family Escherichia and Salmonella in 58 particular) and Firmicutes (e.g. Clostridia) 4,19 . These known mechanisms of colonization 59 resistance mainly involve (1) metabolic processes 20 , involving competition for nutritional 60 niches 21-24 ; (2) production of inhibitory or signaling molecules 25-33 ; and (3) contact-61 dependent killing 34,35 . Antibiotics disrupt the microbiota and potentially affect all of these 62 mechanisms, possibly accounting for the breakdown of colonization resistance against 63 4 intestinal pathogens. Identification of environmental factors that minimize loss of 64 protective bacteria upon perturbations can facilitate the development of general strategies 65 to attenuate the negative impact of antibiotics and other drugs. 66 67 In the gut, competition for nutrients is highly shaped by diet and cross-feeding among 68 established species, to optimize the available resources 36,37 . This competition poses a 69 challenge for invading species, since unutilized niches are unlikely to exist. Dietary fiber 70 and mucus polysaccharides are mostly degraded by strict anaerobes, and the release...
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