The deposed data are from the experiment describing the results of the synergistic effect of antibiotics on anaerobic digestion of cattle manure. The raw sequencing data of metagenomic analysis of cattle manure digestate

This study examined the long-term synergistic effects of amoxicillin (AMO), enrofloxacin (ENR), and metronidazole (MET) on the anaerobic digestion (AD) process of cattle manure. The prevalence of antibiotic resistance genes (ARGs) and changes of microbial biodiversity in the presence of combinations of antimicrobials were investigated with a metagenomic approach. The anaerobic chambers were loaded with substrate supplemented with a mixture of AMO, ENRO, and MET, and substrate without antibiotics addition (control sample, CS). The study was divided into seven experimental series (series I – VII, S I – S VII, respectively), depending on the concentration of the antimicrobials. The experiment lasted 417 days. During the experiment, the production of methane (CH4) and volatile fatty acids (VFAs) was monitored. In each experimental series, at least 2 digestate samples were collected in duplicate. One sample from the I, IV, and last VII experimental series were selected from the control anaerobic chamber (control sample I, control sample IV, control sample VII, CS I, CS IV, CS VII, respectively). A total of 21 samples were collected and subjected to metagenomic sequencing. The mixture of AMO, ENRO and MET administered over a long period of time and in variable, increasing concentrations to biomass resulted in a temporary reduction in the volume of CH4 produced due to the limited growth and development of methanogens. Among the identified microorganisms, bacteria belonging to the types Bacteroidetes, Firmicutes and Actinobacteria were the most numerous in the digestate samples. Among the Archaea, methanogens belonging to the genera Methanothrix, Methanosarcina and Methanomassiliicoccales dominated. In total, 17 types of ARGs were detected and classified. The most abundant types of ARGs in the samples were tetracyclines, multi-drug resistance genes, macrolides-lincosamides-streptogramins, and aminoglycosides. The study showed that the mixture of antibiotics added to biomass affects homoacetogenic bacteria and methanogens, which may consequently inhibit the production of CH4. Nevertheless, microorganisms with high drug resistance in AD chambers reduced the negative effect of antibiotics on CH 4 production.