Plant secondary compound- and antibiotic-induced community disturbances improve the establishment of foreign gut microbiota.

Fecal transplants are a powerful tool for manipulating the gut microbial community, but how these non-native communities establish in the presence of an intact host gut microbiome is poorly understood. We explored the microbiome of desert woodrats (Neotoma lepida) to determine whether disrupting existing microbial communities using plant secondary compounds (PSCs) or antibiotics increases the establishment of foreign microbes. We administered two fecal transplants between natural populations of adult woodrats that harbor distinct gut microbiota and have different natural dietary exposure to PSCs. First, we administered fecal transplants to recipients given creosote resin, a toxin found in the natural diet of our "donor" population, and compared the gut microbial communities to animals given fecal transplants and control diet using 16S rRNA gene sequencing. Second, we disrupted the gut microbial community of the same recipients with an antibiotic prior to fecal transplants. We found that gut microbial communities of woodrats disrupted with PSCs or antibiotics resembled that of donors more closely than control groups. PSC treatment also enriched microbes associated with metabolizing dietary toxins in transplant recipients. These results demonstrate that microbial community disturbances by PSCs or antibiotics are sufficient to facilitate establishment of foreign microbes in animals with intact microbiomes.