The antibiotic-nanoparticle combinatorial effects on gut microbiome diversity, abundance, and antibiotic resistance remain largely unknown. In the present study, we investigated the potential impacts of biodegradable nanocarriers after one biocompatible dose that could promote sustainable treatment against enteropathogens. Enrofloxacin (Enro), a common antibiotic used in livestock, was loaded into biodegradable synthetic poly(lactic-co-glycolic) acid (PLGA) and plant-based Lignin (LIGNIN) nanoparticles. Anaerobic bioreactors containing fresh slurry collected from pig intestines were used to simulate the anaerobic gut microenvironment. Bioreactors were inoculated with empty NPs with concentrations identical to loaded nanoparticles and free Enro, PLGA (Enro) (PE), and LIGNIN(Enro) (LE) that present antimicrobial activity and non-cytotoxicity to pig intestinal cells. Slurry aliquots from the bioreactors were collected for RNA extraction after 24, 48, and 72 hours of exposure to the drug and nanocarriers for microbial 16S rRNA metatranscriptomics and resistome analysis. Our results showed that PLGA and PE microbial communities were similar over all periods despite containing Enro. The impact of LIGNIN on the microbial community was minimal since it was similar to the control. However, loaded LE significantly reduced the microbial diversity but maintained essential estimated metabolic functions. Free Enrofloxacin affected the microbial community the most by decreasing the core gut microbiome diversity. Our results indicate that NP encapsulation of antibiotics delayed the increase in antibiotic resistance genes (ARG) expression between 24 and 72 hours compared to free Enro. These results demonstrate that the antibiotic treatment conveyed by NPs slows the rate of expression of ARG and reduces the adverse antibiotic effects on the gut microbial community.

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