Gentamicin degradation and changes in fungal diversity and physicochemical properties during composting of gentamicin production residue

Antibiotics and antibiotic resistance gene dynamics in the composting of antibiotic fermentation waste - A review

Fate of antibiotics and antibiotic resistance genes (ARGs) during composting of antibiotic fermentation waste (AFW) is a major concern. This review article focuses on recent literature published on this subject. The key findings are that antibiotics can be removed effectively during AFW composting, with higher temperatures, appropriate bulking agents, and suitable pretreatments improving their degradation. ARGs dynamics during composting are related to bacteria and mobile genetic elements (MGEs). Higher temperatures, suitable bulking agents and an appropriate C/N ratio (30:1) lead to more efficient removal of ARGs/MGEs by shaping the bacterial composition. Keeping materials dry (moisture less than 30%) and maintaining pH stable around 7.5 after composting could inhibit the rebound of ARGs. Overall, safer utilization of AFW can be realized by optimizing composting conditions. However, further removal of antibiotics and ARGs at low levels, degradation mechanism of antibiotics, and spread mechanism of ARGs during AFW composting require further investigation.

Composting reduces the risks of antibiotic resistance genes in maize seeds posed by gentamicin fermentation waste

Using high-throughput quantitative PCR and next generation sequencing, the impact of land application of raw and composted gentamicin fermentation waste (GFW) on antibiotic resistance genes (ARGs) in maize seeds was studied in a three-year field trial. The raw and composted GFW changed both the bacterial community composition and the ARGs diversity in the maize seeds compared to non-amended controls and chemical fertilizer. The abundance of ARGs after raw GFW amendment was significantly higher than other treatments because of a high abundance of aadA1, qacEdeltal and aph(2')-Id-02; probably induced by gentamicin selection pressure in maize tissues. Meanwhile, the potential host of these three ARGs, pathogenic bacteria Tenacibaculum, also increased significantly in maize seeds after the application of raw GFW. But our result proved that composting could weaken the risk posed by GFW. We further reveal that the key biotic driver for shaping the ARG profiles in maize seeds is bacterial community followed by heavy metal resistance genes, and ARGs are more likely located on bacterial chromosomes. Our findings provide new insight into ARGs dispersal mechanism in maize seeds after long-term GFW application, demonstrate the potential benefits of composting the GFW to reduce risks as well as the potential efficient management method to GFW.

Effect of inoculation with newly isolated thermotolerant ammonia-oxidizing bacteria on nitrogen conversion and microbial community during cattle manure composting

Nitrogen loss during composting is closely related to NH₄⁺-N conversion, and ammonia-oxidizing bacteria (AOB) are important microorganisms that promote NH₄⁺-N conversion. Since the biological activity of conventional AOB agents used for compost inoculation declines rapidly during the thermophilic phase of composting, new compound inoculants should be developed that are active during that phase. In the current study, the effects of inoculating cattle manure compost with newly isolated AOB (5%, v/w) [thermotolerant AOB X-2 strain (T-AOB-2), mesophilic AOB X-4 strain (M-AOB-4), and AOB X-2 combined with AOB X-4 (MT-AOB-2-4)] on the conversion of nitrogen, compost maturity, and the resident microbial community were studied. During 35 days of composting, compared with the control, AOB inoculation reduced NH₃ emissions by 29.98-46.94%, accelerated the conversion of NH₄⁺-N to NO₂^--N, increased seed germination values by 13.00-25.90%, and increased the abundance of the microbial community at the thermophilic phase (16.38-68.81%). Network analysis revealed that Bacillaceae play a crucial role in the composting process, with the correlation coefficients: 0.83 (p < 0.05) with NH₃, 0.64 (p < 0.05) with NH₄⁺-N, and 0.81 (p < 0.05) with NO₂^--N. In addition, inoculation with MT-AOB-2-4 notably increased the total nitrogen content of compost, prolonged the sanitation stage, and promoted compost maturity. Hence, MT-AOB-2-4 may be used to increase the microbial community abundance and improve the efficiency of cattle manure composting.

Migration and toxicity of toltrazuril and its main metabolites in the environment

Veterinary drugs heavily used in livestock are passed into the environment through different ways, resulting in risks to terrestrial environments and humans. The migration of toltrazuril (TOL), an important anticoccidial drug used intensively in livestock, and its main metabolites between the chicken manure compost, soil and vegetables was investigated, and then the impacts of TOL on the soil bacterial community and ARGs, soil enzyme activities and phytotoxicity were detected. In the process of aerobic composting for 80 days, except for toltrazuril sulfoxide (the degradation half-life was 59.74 d), TOL and ponazuril (PON) were not significantly degraded. However, TOL and its metabolites were significantly degraded in fertilized soil, and the degradation half-life was 28.17-346.50 d. Among the three drugs, only PON could migrate from soil to vegetables, and the residual concentrations of PON in lettuce and radish were 2.64-70.02 μg kg-1 and 0-2.80 μg kg-1, respectively. Moreover, TOL and its main metabolisms had no significant effect on the bacterial community structure and the abundance of antibiotic resistance genes during composting, but affected the microbial activity in the soil. The presence of TOL and its main metabolites reduced soil urease activity, increased catalase activity, and decreased alkaline phosphatase activity at the beginning and then increased slightly. They had negative effects on plant growth. Compared with the control group, the inhibition rates of TOL and its metabolites on lettuce and radish seed germination were 8.33% and 26.74% respectively, and the inhibition rates of root elongation length were 25.88% and 34.45% respectively. These results showed that TOL and its main metabolites were ineffectively removed by aerobic composting, and could be migrated from composting to soil and vegetables, which had adverse effects on soil enzyme activity and plant growth. Therefore, its environmental ecological risk and human health risk needs to be further evaluated.

An Efficient High-Throughput Screening of High Gentamicin-Producing Mutants Based on Titer Determination Using an Integrated Computer-Aided Vision Technology and Machine Learning

The "design-build-test-learn" (DBTL) cycle has been adopted in rational high-throughput screening to obtain high-yield industrial strains. However, the mismatch between build and test slows the DBTL cycle due to the lack of high-throughput analytical technologies. In this study, a highly efficient, accurate, and noninvasive detection method of gentamicin (GM) was developed, which can provide timely feedback for the high-throughput screening of high-yield strains. First, a self-made tool was established to obtain data sets in 24-well plates based on the color of the cells. Subsequently, the random forest (RF) algorithm was found to have the highest prediction accuracy with an R² value of 0.98430 for the same batch. Finally, a stable genetically high-yield strain (998 U/mL) was successfully screened out from 3005 mutants, which was verified to improve the titer by 72.7% in a 5 L bioreactor. Moreover, the verified new data sets were updated on the model database in order to improve the learning ability of the DBTL cycle.

Fate of bacterial community, antibiotic resistance genes and gentamicin residues in soil after three-year amendment using gentamicin fermentation waste

Over a three-year field trial, the impacts of composted and raw gentamicin fermentation waste (GFW) application to land on residual soil gentamicin levels, physicochemical properties, bacterial community composition, and antibiotic resistance genes (ARGs) were assessed. In the saline-alkali soil tested, GFW application decreased electrical conductivity (EC) and pH. Importantly, there was no measurable long-term accumulation of gentamicin as a result of GFW addition. Changes in the abundance of Bacillus was primarily associated with degradation of gentamicin in soil, whereas wider (i.e. more general) shifts in bacterial communities over the treatments was linked to alteration of soil physicochemical properties, particularly pH, total nitrogen, dissolved organic carbon, EC, NO₃^--N and NH₄⁺-N. Compared with other treatments, soils receiving composted GFW harbored more types of ARGs and significantly higher (P < 0.05) abundances of mobile genes elements (MGEs) (especially IncQ and Int1) and aminoglycoside ARGs (especially aminoglycoside phosphotransferases genes, APH). Finally, the abundances of ARGs in soils receiving raw and composted GFW were 59.60% and 50.26% higher than that in soils only receiving chemical fertilizer, respectively. Specifically, the abundances of APH, especially strB, were significantly higher than other kinds of ARGs (P < 0.05). The results of linear regression and partial least squares path model showed that MGEs, including plasmids, integrons, and transposons, along with soil properties (EC and NH₄⁺-N) were the main factors associated with change in ARGs. Furthermore, different MGEs were involved in different transfer mechanisms of specific ARGs. Our findings demonstrated the potential risks of using raw and composted GFW as fertilizer, and suggest potential solutions to this problem.

Cattle manure compost humification process by inoculation ammonia-oxidizing bacteria

The effectiveness of newly isolated ammonia-oxidizing bacteria (AOBs; T-AOB-2, M-AOB-4 and MT-AOB-2-4) in promoting organic matter degradation and humification of cattle manure compost was explored. The results show that, compared with the control, the inoculation of AOBs (5%, v/w) promoted the humification process, particularly in the MT-AOB-2-4, which showed the lowest total organic carbon (19.13%) and dissolved organic carbon (2.61%), whereby humic substances (C_EX) and humic acid (C_HA) increased to 89.84 g/kg and 85.20 g/kg, and fulvic acid (C_FA) decreased to 4.63 g/kg. The high-throughput sequencing and quantitative PCR showed that the abundance of Bacillaceae, amoA and nirS had a significant correlation with humification factors. Among the treatments, the inoculation of MT-AOB-2-4 provided the driving force for the composting process by enhancing the bacterial activity and had the most significant effect on the formation of humic substances and the efficiency of organic matter decomposition.

Algal-based system for removal of emerging pollutants from wastewater: A review

The bioremediation of emerging pollutants in wastewater via algal biotechnology has been emerging as a cost-effective and low-energy input technological solution. However, the algal bioremediation technology is still not fully developed at a commercial level. The development of different technologies and new strategies to cater specific needs have been studied. The existence of multiple emerging pollutants and the selection of microalgal species is a major concern. The rate of algal bioremediation is influenced by various factors, including accidental contaminations and operational conditions in the pilot-scale studies. Algal-bioremediation can be combined with existing treatment technologies for efficient removal of emerging pollutants from wastewater. This review mainly focuses on algal-bioremediation systems for wastewater treatment and pollutant removal, the impact of emerging pollutants in the environment, selection of potential microalgal species, mechanisms involved, and challenges in removing emerging pollutants using algal-bioremediation systems.

Research trend analysis of composting based on Web of Science database

Bibliometric analysis was used in this study for the quantitative evaluation of current research trends on composting. The research articles indexed from the Science Citation Index-Expanded in Web of Science database published from 2000 to 2019 were investigated. The USA, China and Spain were the top three countries considering the number of papers. Amongst the research institutes, CSIC of Spain, Chinese Academy of Sciences and Agriculture & Agri-Food Canada ranked the top three in total publication amount. Journals that published a significant number of literature regarding topics of composting included Environmental Sciences & Ecology, Agriculture and Engineering. In terms of research content, keywords such as heavy metal, heavy metal and biodegradation appeared frequently. In addition, the analysis of keywords revealed the following research hotspots in future studies: investigation of heavy metal passivator, optimisation of composting conditioner, development of all kinds of microorganisms, rational management of the composting process and improvement of solid waste life cycle assessment. To some extent, it helps to understand the current global status and trends of the related research.

Effects of multi-phase inoculation on the fungal community related with the improvement of medicinal herbal residues composting

Composting has become the most important way to recycle medicinal herbal residues (MHRs). The traditional composting method, adding a microbial agent at one time, has been greatly limited due to its low composting efficiency, mutual influence of microbial agents, and unstable compost products. This study was conducted to assess the effect of multi-phase inoculation on the lignocellulose degradation, enzyme activities, and fungal community during MHRs composting. The results showed that multi-phase inoculation treatment had the highest thermophilic temperature (68.2 °C) and germination index (102.68%), significantly improved available phosphorus content, humic acid, and humic substances concentration, accelerated the degradation of cellulose and lignin, and increased the activities of cellulase in the mature phase, xylanase, manganese peroxidase, and utilization of phenolic compounds. Furthermore, the non-metric multi-dimensional scaling showed that the composting process and inoculation significantly influenced fungal community composition. In multi-phase inoculation treatment, Thermomyces in mesophilic, thermophilic, and mature phase, unclassified_Sordariales, and Coprinopsis in mature phase were the dominant genus that might be the main functional groups to degrade lignocellulose and improve the MHRs composting process.

Comprehensive analysis of environmental factors mediated microbial community succession in nitrogen conversion and utilization of ex situ fermentation system

An ex situ fermentation system (EFS) can efficiently transform and utilize nitrogen in swine wastewater and reduce environmental pollution. High-throughput sequencing was used to study the relationship between the succession of total bacteria, fungi, and functional bacteria in a swine wastewater EFS, as well as nitrogen metabolism and environmental factors. During the fermentation process, inorganic nitrogen gradually accumulated and the pH changed rapidly from weakly acidic to alkaline. The dominant genera of bacteria, fungi and functional bacteria carrying amoA, nirK, and nosZ genes changed gradually, and Clostridium sensu stricto 1, Thermomyces, Nitrosomonas, Mesorhizobium, and Pseudomonas genera became the most abundant, which showed positive correlations with temperature, pH, and nitrogen levels. Other changed populations showed different correlations with environmental factors, and physical-chemical factors explained more variation of microorganisms than nitrogen resources. These findings contribute to a comprehensive understanding of nitrogen metabolism in EFSs from a molecular micro-ecology perspective.

Novel strains with superior degrading efficiency for lincomycin manufacturing biowaste

As the antibiotic pollution source in the environment, a large amount of biowastes generated from antibiotic fermentation manufacture needs proper disposal. Recycling the biowaste as resources and nutrients is of great interest. Besides, degradation or removal of antibiotics is indispensable for the reclamation of antibiotic manufacturing biowaste. To establish environmentally friendly disposal strategies for lincomycin manufacturing biowaste (LMB), we screened the microbial strains that could efficiently degrade lincomycin from the antibiotic wastewater treatment plant. Among them, three novel strains were identified as Bacillus subtilis (strain LMB-A), Rhodotorula mucilaginosa (strain LMB-D) and Penicillium oxalicum (strain LMB-E), respectively. LMB-A and LMB-D could degrade 92.69% and 74.05% of lincomycin with an initial concentration of 1117.55 mg/L in 144 h, respectively. The lincomycin degradation products were formed by the breakage of amide bond or losing N-demethyl/thiomethyl group from the pyrrolidine/pyranose ringcata cata catalyzed by the strains. Moreover, LMB-A could decontaminate LMB, and the decontaminated LMB could be used as a nitrogen source to culture salt-resistant bacteria and other useful microorganisms. LMB-A and LMB-D have the potential to be used for the bioremediation of water and soil polluted by lincomycin and its analogs. LMB-E could degrade 88.20% LMB after 144-h cultivation. In summary, this study gives an insight into the green disposal of LMB, and the established strategy has potential application for biotreatment of other antibiotic fermentation manufacturing biowastes.

Changes in microbial community structure during pig manure composting and its relationship to the fate of antibiotics and antibiotic resistance genes

Animal manure containing veterinary antibiotics is a significant source of microbial antibiotic resistance genes (ARGs). Composting of animal manure with wheat straw and sawdust was explored as a means to reduce ARGs load in the final material. The effects of ciprofloxacin, oxytetracycline, sulfamerazine on the bacterial community composition, and how this then affected the removal of seven tetracycline resistance genes (TARGs), four sulfonamide resistance genes (SARGs), and two fluoroquinolone resistance genes (QARGs) were investigated. Treatments receiving either ciprofloxacin or the three mixed antibiotics had reduced bacterial alpha-diversity and displayed shifts in the abundance of Proteobacteria and Firmicutes. This demonstrated that different antibiotics played an important role in bacterial community composition. Furthermore, variation in the physicochemical properties of compost, particularly pH and temperature, was also strongly linked to shifts in bacterial composition over time. Based on network analysis, the reduction of TARGs were associated with loss of Pseudomonas, Pseudoxanthomonas, Pusillimonas, Aquamicrobium, Ureibacillus, Lysinibacillus, Bacillus and Brachybacterium during the thermophilic stage. However, QARGs and SARGs were more strongly affected by the presence of multiple antibiotics. Our results have important implications for reducing the spread of certain ARGs by controlling the composting temperature, pH or the antibiotics species used in husbandry.

Zoonosis: An Emerging Link to Antibiotic Resistance Under "One Health Approach"

Current scenario in communicable diseases has generated new era that identifies the "One health" approach to understand the sharing and management of etiological agents with its impact on ecosystem. Under this context the relevance of zoonotic diseases generates major concern. The indiscriminate and higher use of antibiotics in animal husbandry creates substantial pressure on the gut microbiome for development of resistance due to shorter generation time and high density. Thus, gut works as a bioreactor for the breeding of ARBs in this scenario and are continuously released in different niches. These ARBs transfer resistance genes among native flora through horizontal gene transfer events, vectors and quorum sensing. About 60% of infectious diseases in human are caused by zoonotic pathogens have potential to carry ARGs which could be transmitted to humans. The well documented zoonotic diseases are anthrax cause by Bacillus anthracis, bovine tuberculosis by Mycobacterium tuberculosis, brucellosis by Brucella abortus, and hemorrhagic colitis by Escherichia coli. Similarly, most of the antibiotics are not completely metabolized and released in unmetabolized forms which enters the food chain and affect various ecological niches through bioaccumulation. The persistence period of antibiotics ranges from < 1 to 3466 days in environment. The consequences of misusing the antibiotic in livestock and their fate in various ecological niches have been discussed in this review. Further the light sheds on antibiotics persistence and it biodegradation through different abiotic and biotic approaches in environment. The knowledge on personnel hygiene and strong surveillance system for zoonotic disease including ARBs transmission, prevention and control measures should be established to regulate the spread of AMR in the environment and subsequently to the human being through a food web.

Biodegradation of polyaromatic hydrocarbons and the influence of environmental factors during the co-composting of sewage sludge and green forest waste

The main aim of this research was to study the biodegradation of polycyclic aromatic hydrocarbons (PAHs) and the influence of environmental factors during composting in order to realize the utilization of PAHs contaminated sewage sludge. A production scale compost experiment was conducted with three mixtures of sewage sludge (SS): green forest waste (GFW) at quality ratios of 3:1 (T1), 3:2 (T2) and 3:3 (T3). The residual concentration of PAHs in the three treatments met the permissible limit prescribed by the Agricultural Sludge Pollutant Control Standard (GB 4284-2018). The biodegradation rates of PAHs were 0.0280, 0.0281 and 0.0218 mg/d, and removal efficiencies were 70.7%, 75.2% and 62.4% in T1, T2, T3, respectively, which followed the first-order rate kinetics. The residual concentration of PAHs in T2 was the lowest (1.81 mg/kg), while the germination index (GI) of Tall Fescues (~0.9) was the highest during 50 days of co-composting. The bacterial diversity negatively correlated with the residual PAHs content. The main genus, Bacillus, Pseudomonas and Methylotenera, with cellulose-degrading and PAHs co-metabolizing functions contributed significantly to sludge maturation and PAHs degradation. The dominant microorganisms, Pseudomonas, Sphingobacterium and Chitinophagaceae_uncultured, could support the high removal rate of PAHs in T2. Temperature, pH, total organic carbon (TOC), total nitrogen (TN) and carbon/nitrogen (C/N) ratio had significant positive effect on the compost maturity and quality, and these parameters correlated with the PAHs biodegradation efficiency during composting, especially in T2.

Succession of fungal dynamics and their influence on physicochemical parameters during pig manure composting employing with pine leaf biochar

The effects of pine leaf biochar (PLB) on fungal community during pig manure composting were investigated. Five different doses of PLB [0% (T1), 2.5% (T2), 5% (T3), 10% (T4) and 15% (T5)] were mixed with mixture of pig manure and sawdust (2:1) for 50 days of composting. The present results indicated that fungal diversity increased more obvious in biochar amendment treatments than control (T1) and that the highest was recorded in T4 treatment. Basidiomycota, Ascomycota and Mucoromycota were the most three abundant phyla in all the treatments, while Heterobasidion, Pezoloma, Mucor, Geastrum, Talaromyces and Cystofilobasidium were the richness genera. In addition, network analysis indicated that fungal community abundance was significantly (p < 0.05) associated with temperature, pH, CO₂ and CH₄ emission and the seed germination index. In summary, the 10% PLB amendment (T4) was a potential option to strengthen fungal diversity and improve the composting efficiency as well as compost quality.

Effects of inoculation with lignocellulose-degrading microorganisms on antibiotic resistance genes and the bacterial community during co-composting of swine manure with spent mushroom substrate

Composting is usually employed to treat livestock manure, and inoculation with lignocellulose-degrading microorganisms can enhance the quality of compost. In this study, lignocellulose-degrading microorganisms were inoculated at two levels (uninoculated control = 0%, and T treatment = 10%) during co-composting of swine manure with spent mushroom substrate, and their effects on antibiotic resistance genes (ARGs) and the bacterial community were investigated. Inoculation with lignocellulose-degrading microorganisms caused greater decreases in 6/11 ARGs and 3/4 mobile genetic elements than the control. The total relative abundances of ARGs increased by 0.23 logs in the control but decreased by 0.08 logs in the T treatment after co-composting. The bacterial community was clustered according to the composting time in the two treatments, where inoculation mainly affected the bacterial community during the mesophilic phase. Redundancy analysis and network analysis showed that the bacterial community succession had important effects on the variations in ARGs. Inoculation with lignocellulose-degrading microorganisms led to the reduction of ARGs, which was significantly correlated with the abundances of potential host bacteria for ARGs. Thus, inoculation with lignocellulose-degrading microorganisms could decrease the risk of ARGs spreading and make compost products more security.

Dynamics of fungal diversity and interactions with environmental elements in response to wheat straw biochar amended poultry manure composting

The fungal dynamics and its correlation with physicochemical and gaseous emission were investigated using metagenomics and Heat map illustrator (HEMI). Five different concentrations of wheat straw biochar (WSB) were applied to poultry manure (PM) and composted for 50 days; those without the WSB treatment were used as a control. The results revealed the dominant phyla to be Chytridiomycota, Mucoromycota, Ascomycota and Basidiomycota, while Batrachochytrium, Rhizophagus, Mucor, and Puccinia were the superior genera. In particular, the diversity of Chytridiomycota and Ascomycota was more abundant among all of the treatments. Overall, the diversity of the fungal species was correspondent, but relative abundance varied significantly among all of the composts. Principle Coordinate Analysis (PCoA) and Non-Metric Multi- Dimensional Scaling (NMDS) indicated that different concentrations of WSB applied treatments have significantly distinct fungal communities. In addition, correlation analyses of fungal interactions with environmental elements via HEMI also indicate a clear difference among the treatments. Ultimately, the relative abundance of fungal composition significantly influenced the PM compost treated by the WSB.

Effects of co-composting of lincomycin mycelia dregs with furfural slag on lincomycin degradation, degradation products, antibiotic resistance genes and bacterial community

This study explored the effects of co-composting of lincomycin mycelia dregs (LMDs) with furfural slag on variations in antibiotic resistance genes (ARGs) and the bacterial community. The results showed that more than 99% lincomycin was reduced after composting. Moreover, the total absolute and relative abundance of ARGs increased by 180 and 5 times, respectively. The gene lnuA was detected in the LMDs compost and it was proved to participate in lincomycin biodegradation based on the analysis of Pearson's correlation and the lincomycin degradation byproducts. Redundancy analysis showed the succession of the bacterial community had a greater influence than the environmental parameters (residual lincomycin, C/N, pH and temperature) on the variation of ARGs during composting. Composting was not effective in reducing most of the ARGs and intI1 and thus the LMDs compost is dangerous to the ecological environment.

Performance evaluation of gaseous emissions and Zn speciation during Zn-rich antibiotic manufacturing wastes and pig manure composting

In this study, the co-composting performance of Zn-rich antibiotic manufacturing wastes (AMW) and pig manure (PM) was evaluated. Four treatments, representing 2.5%, 5%, 10% and 20% of AMW (of PM dry weight) and control without AMW, were established during composting. Results suggested that the temperature, pH, electrical conductivity, NH₄⁺-N and germination index in end product met the maturity and sanitation requirement. More than 99% of residual antibiotic was removed. Compared with PM composting alone, the cumulative CH₄ and N₂O emissions in AMW composting increased by 13.46-79.00% and 10.78-65.12%, respectively. While the higher mixing ratios of AMW (10% and 20%) presented a negative impact on composing by inhibiting organic matter (OM) degradation and higher NH₃ emissions. The AMW had highly bioavailable Zn, but the exchangeable faction of Zn significantly decreased with the composting progress.

Dynamics of bacterial composition and the fate of antibiotic resistance genes and mobile genetic elements during the co-composting with gentamicin fermentation residue and lovastatin fermentation residue

Dynamics in bacterial community composition, along with 13 antibiotic resistance genes (ARGs) and eight mobile genetic elements (MGEs), were assessed during co-composting with gentamicin and lovastatin fermentation residue (GFR and LFR, respectively). Using next generation sequencing, the key bacterial taxa associated with the different stages of composting were identified. Most importantly, Bacillus, belonging to Phylum Firmicutes, was associated with enhanced degradation of gentamicin, decomposition of organic matter (OM) and dissolved organic carbon (DOC), and also extension of the thermophilic phase of the composting cycle. During the course of composting, the patterns of different ARGs/MGEs varied. However, the total and the normalized (to bacterial numbers) copies both remained high. The abundance of various ARGs was related to bacterial abundance and community composition, and the changing pattern of individual ARGs was influenced by the selectivity of MGEs and bacteria.