Housefly larvae gut microbiome may attenuate veterinary antibiotics and alter the resistome in swine manure

Abstract:

[Objective] The overuse of antibiotics as veterinary feed additives is contributing to a significant reservoir of antibiotic resistance in livestock manure. A housefly larvae (Musca domestica) vermireactor has been increasingly adopted for swine manure value-added bioconversion and pollution control. In order to investigate its efficiency on attenuations of antibiotic and the associated resistome during manure vermicomposting, we implemented dynamic sampling during a typical cycle (6 days). [Methods] High-capacity qPCR, liquid chromatography-electrospray ionization tandem mass spectrometry, the isotope-labeled internal standard method and Illumina Hiseq sequencer were used to explore the effectiveness of antibiotic degradation and microbial mechanisms on dynamics of the associated resistome of full-scale larvae manure vermicomposting. [Results] Nine antibiotics (tetracycline, oxytetracycline, chlortetracycline, doxycycline, sulfadiazine, norfloxacin, ofloxacin, ciprofloxacin and enrofloxacin) were dramatically removed. The cumulative removal of these tested antibiotics reached 34.3%-58.1%, along with the daily reduction percentages ranging from 7.8% to 57.4%. In total, 113 of 158 antibiotic resistance genes (ARGs) were significantly attenuated (by 79.3%), while 23 were significantly enriched (3.48-fold) following vermicomposting. The manure-borne bacterial community showed a decrease in the relative abundance of Bacteroidetes, and an increase in Proteobacteria, specifically Ignatzschineria, following gut transit, while ARG attenuation was significantly correlated with changes in microbial community structure. Bacteria correlated with attenuated ARGs mainly belonged to order Clostridiales and Bacteroidales. Enriched ARGs, were mostly correlated with family Alcaligenaceae,[Weeksellaceae] and order Bacillales. [Conclusion] Housefly larvae vermicomposting is an efficient way to attenuate antibiotics and ARGs in swine manure within the 6-day treatment.