Mechanisms for more efficient antibiotics and antibiotic resistance genes removal during industrialized treatment of over 200 tons of tylosin and spectinomycin mycelial dregs by integrated meta-omics.

To mitigate the environmental risks posed by the accumulation of antibiotic mycelial dregs (AMDs), this study first attempted over 200 tons of mass production fermentation (MP) using tylosin and spectinomycin mycelial dregs alongside pilot-scale fermentation (PS) for comparison, utilizing the integrated-omics and qPCR approaches. Co-fermentation results showed that both antibiotics were effectively removed in all treatments, with an average removal rate of 92%. Antibiotic resistance gene (ARG)-related metabolic pathways showed that rapid degradation of antibiotics was associated with enzymes that inactivate macrolides and aminoglycosides (e.g., K06979, K07027, K05593). Interestingly, MP fermentations with optimized conditions had more efficient ARGs removal because homogenization permitted faster microbial succession, with more stable removal of antibiotic resistant bacteria and mobile genetic elements. Moreover, Bacillus reached 75% and secreted antioxidant enzymes that might inhibit horizontal gene transfer of ARGs. The findings confirmed the advantages of MP fermentation and provided a scientific basis for other AMDs.

Integrated meta-omics study on rapid tylosin removal mechanism and dynamics of antibiotic resistance genes during aerobic thermophilic fermentation of tylosin mycelial dregs.

For efficient treatment of tylosin mycelial dregs (TMDs), rapid tylosin removal mechanism and dynamics of ARGs during TMDs fermentation were investigated using integrated meta-omics (genomics, metaproteomics and metabolomics) and qPCR approaches. The results showed that over 86% of tylosin was degraded on day 7 regardless of the type of bulking agents. The rapid removal of tylosin was mainly attributed to de-mycarose reaction (GH3) and esterase hydrolysis (C7MYQ7) of Saccharomonospora, and catalase-peroxidase oxidation of Bacillus (A0A077JB13). In addition, the moisture content and mobile genetic elements were vital to control the rebound of ARGs. The removal efficiency of antibiotic resistant bacteria (Streptomyces, Pseudomonas, norank_f__Sphingobacteriaceae, and Paenalcaligenes) and Intl1 (98.8%) in fermentation treatment TC21 with corncob as the bulking agent was significantly higher than that in other three treatments (88.3%). Thus, appropriate bulking agents could constrain the abundance of antibiotic resistant bacteria and Intl1, which is crucial to effectively reduce the resistance.

Dynamics and removal mechanisms of antibiotic and antibiotic resistance genes during the fermentation process of spectinomycin mycelial dregs: An integrated meta-omics study.

Antibiotic mycelial dregs (AMDs) have been listed as industrial hazardous wastes. With the aim of reducing the environmental risk, the integrated-omics and qPCR approaches were used to reveal the dynamics and removal mechanisms of antibiotic and antibiotic resistance genes (ARGs) during the fermentation of different spectinomycin mycelial dregs (SMDs). The results showed that the removal efficiency of antibiotic in the fermentation of high moisture SMDs reached up to 98%. The high abundance of aadA1 gene encoded by Streptomyces, Lactobacillus, and Pseudomonas was associated with the efficient degradation of spectinomycin, and the inactivating enzymes secreted by degradative bacteria were identified. Furthermore, the dominant microbiota was impacted by moisture content significantly under high temperature environments. In the fermentation of low moisture SMDs, Saccharopolyspora was the dominant microbiota which secreted S8 endopeptidase, M14, M15, S10, S13 carboxypeptidases, M1, M28, S15 aminopeptidases, and antioxidant enzymes, while in the fermentation of high moisture SMDs, Bacillus and Cerasibacillus were dominant genera which mainly secreted S8 endopeptidase and antioxidant enzymes. The abundance of ARGs and mobile genetic elements decreased significantly at thermophilic phase, with maximum drops of 93.7% and 99.9%, respectively. Maintaining moisture content below 30% at the end phase could prevent the transmission of ARGs effectively.

Aerobic composting as an effective cow manure management strategy for reducing the dissemination of antibiotic resistance genes: An integrated meta-omics study.

Livestock manure is considered as an important source for spreading antibiotic resistance genes (ARGs) into the environment, and therefore poses a direct threat to public health. Whereas the effects of reused manure on soil microbial communities and ARGs have been studied extensively, comprehensive characterizations of microbial communities and ARGs of manure produced by different management methods are not well understood. Here, we analyzed the fate of microbial communities and ARGs of cow manure treated by three conventional management strategies: aerobic composting, mechanical drying and precipitation, applying an integrated-omics approach combining metagenomics and metaproteomics. Integrated-omics demonstrated that composted manure contained the lowest diversity of microbial community and ARGs compared with manure treated by other two strategies. Quantitative PCR methods revealed that the abundances of ARGs were reduced by over 83 % after composting for 14 days, regardless of the season. Besides, the potential ARG hosts Acinetobacter and Pseudomonas dominating mechanical drying process were sharply decreased in abundances after composting. The significant co-occurrence networks among bacteria, ARGs and transposase gene tnpA-01 in composting samples indicated the important role of these bacteria in the dissemination of ARGs. These findings offer insight into potential strategies to control the spread of ARGs during livestock manure reuse.