Horizontal gene transfer and shifts in linked bacterial community composition are associated with maintenance of antibiotic resistance genes during food waste composting

Liao, Hanpeng; Friman, Ville‐Petri; Geisen, Stefan; Zhao, Qian; Cui, Peng; Lü, Xiaomei; Chen, Zhi; Yu, Zhen; Zhou, Shungui

doi:10.1016/j.scitotenv.2018.12.353

Cited by 114 publications

(19 citation statements)

References 56 publications

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“…Han et al reported that community composition was the main factor driving changes in ARG abundance in a mariculture sediment 59 . Liao et al found that shifts in bacterial community composition were associated with the maintenance of ARGs in food waste composting 60 . Thus, further work is needed to better understand how bacterial community shift drive ARG alteration in the food samples.…”

Section: Discussionmentioning

confidence: 99%

Metagenomic characterization of bacterial community and antibiotic resistance genes in representative ready-to-eat food in southern China

Cao

Liang

et al. 2020

Sci Rep

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Ready-to-eat (RTE) foods have been considered to be reservoirs of antibiotic resistance bacteria, which constitute direct threat to human health, but the potential microbiological risks of RTE foods remain largely unexplored. In this study, the metagenomic approach was employed to characterize the comprehensive profiles of bacterial community and antibiotic resistance gene (ARG) in 18 RTE food samples (8 RTE meat, 7 RTE vegetables and 3 RTE fruit) in southern China. In total, the most abundant phyla in RTE foods were Proteobacteria, Firmicutes, Cyanobacteria, Bacteroidetes and Actinobacteria. 204 ARG subtypes belonging to 18 ARG types were detected with an abundance range between 2.81 × 10−5 and 7.7 × 10−1 copy of ARG per copy of 16S rRNA gene. Multidrug-resistant genes were the most predominant ARG type in the RTE foods. Chloramphenicol, macrolide-lincosamide-streptogramin, multidrug resistance, aminoglycoside, bacitracin, tetracycline and β-lactam resistance genes were dominant, which were also associated with antibiotics used extensively in human medicine or veterinary medicine/promoters. Variation partitioning analysis indicated that the join effect of bacterial community and mobile genetic elements (MGEs) played an important role in the resistome alteration. This study further deepens the comprehensive understanding of antibiotic resistome and the correlations among the antibiotic resistome, microbiota, and MGEs in the RTE foods.

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Section: Discussionmentioning

confidence: 99%

Metagenomic characterization of bacterial community and antibiotic resistance genes in representative ready-to-eat food in southern China

Cao

Liang

et al. 2020

Sci Rep

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“…Procrustes analysis for samples in the cattle study were performed by treatment group, and by time within each treatment group. Procrustes analysis has been previously applied in a number of studies including the characterization of resistomes and colocalization of resistant determinants and MGEs ( Noyes et al, 2016 ; Wu et al, 2017 , 2018 ; Zhu et al, 2017 ; Liao et al, 2019 ).…”

Section: Methodsmentioning

confidence: 99%

Mobilization of Antibiotic Resistance: Are Current Approaches for Colocalizing Resistomes and Mobilomes Useful?

et al. 2020

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Slizovskiy et al. Colocalization Analysis of Resistomes-Mobilomes that current alignment-and assembly-based methods estimating resistome mobility yield contradictory and incomplete results, likely constrained by approach-specific data inputs, and bioinformatic limitations. We discuss recent laboratory and computational advancements that may enhance resistome risk analysis in clinical, regulatory, and commercial applications.

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“…Spent coffee grounds (SCGs) are generated from approximately 91 wt% of the whole coffee bean in coffee processing [2]. SCGs are buried in landfills, causing environmental pollution such as soil, water and air pollution and the emission of greenhouse gases [3]. In addition, disposable coffee cups made of plastic have been associated with these forms of pollution [4].…”

Section: Introductionmentioning

confidence: 99%

Statistical Optimization of Alkali Pretreatment to Improve Sugars Recovery from Spent Coffee Grounds and Utilization in Lactic Acid Fermentation

et al. 2021

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Biorefinery, which utilizes carbon-neutral biomass as a resource, is attracting attention as a significant alternative in a modern society confronted with climate change. In this study, spent coffee grounds (SCGs) were used as the feedstock for lactic acid fermentation. In order to improve sugar conversion, alkali pretreatment was optimized by a statistical method, namely response surface methodology (RSM). The optimum conditions for the alkali pretreatment of SCGs were determined as follows: 75°C, 3% potassium hydroxide (KOH) and a time of 2.8 h. The optimum conditions for enzymatic hydrolysis of pretreated SCGs were determined as follows: enzyme complex loading of 30-unit cellulase, 15-unit cellobiase and 50-unit mannanase per g biomass and a reaction time of 96 h. SCG hydrolysates were used as the carbon source for Lactobacillus cultivation, and the conversions of lactic acid by L. brevis ATCC 8287 and L. parabuchneri ATCC 49374 were 40.1% and 55.8%, respectively. Finally, the maximum lactic acid production by L. parabuchneri ATCC 49374 was estimated to be 101.2 g based on 1000 g of SCGs through the optimization of alkali pretreatment and enzymatic hydrolysis.

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Horizontal gene transfer and shifts in linked bacterial community composition are associated with maintenance of antibiotic resistance genes during food waste composting

Abstract: This is a repository copy of Horizontal gene transfer and shifts in linked bacterial community composition are associated with maintenance of antibiotic resistance genes during food waste composting.

Cited by 114 publications

References 56 publications

Metagenomic characterization of bacterial community and antibiotic resistance genes in representative ready-to-eat food in southern China

Metagenomic characterization of bacterial community and antibiotic resistance genes in representative ready-to-eat food in southern China

Mobilization of Antibiotic Resistance: Are Current Approaches for Colocalizing Resistomes and Mobilomes Useful?

Statistical Optimization of Alkali Pretreatment to Improve Sugars Recovery from Spent Coffee Grounds and Utilization in Lactic Acid Fermentation

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