Contents lists available at ScienceDirect Bioresource Technology journal homepage: www.elsevier.com/locate/biortech Effect of mesophilic anaerobic digestion on the resistome profile of dairy manure Daniel Flores-Orozco a, ⁎ , Rakesh Patidar b , David B. Levin a , Richard Sparling b , Ayush Kumar b , Nazim Çiçek a a Department of Biosystems Engineering, University of Manitoba, Winnipeg, Manitoba R3T 5V6, Canada b Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T 5V6, Canada GRAPHICAL ABSTRACT ARTICLE INFO Keywords: Anaerobic digestion Dairy manure Antibiotic resistance genes Resistome Metagenomics ABSTRACT The effect of mesophilic anaerobic digestion (AD) on the resistome profile of manures from two different dairy farms was evaluated using a metagenomic approach. A total of 187 unique Antibiotic resistance genes (ARGs) for 17 different classes of antibiotics were detected in raw (undigested) manures. The results indicate that regardless of the origin of the dairy manure, mesophilic AD was capable of reducing or enriching the relative abundance of some ARGs. The main driver of these changes was strongly correlated with the evolution of the microbial community during the AD process. Putative ARG hosts were suggested by analyses of the co-occurrence of microbial groups and ARGs. Finally, network analyses revealed that mesophilic AD could also reduce the co- occurrence of different groups of ARGs potentially located in the same genetic elements. Our results provide valuable insights into the microbial mechanisms driving the diversity and abundance of ARGs during mesophilic AD. 1. Introduction Livestock production is considered one of the main sources of emission of antibiotics into the environment, as most of the antibiotics consumed globally are destined for veterinary applications (Kumar et al., 2012). Veterinary antibiotics are not only used as a treatment of infectious diseases, but are also used in subtherapeutic doses in healthy animals, because they enhance feed efficiency and serve as prophylactic therapies (Kumar et al., 2012). However, antibiotics are poorly absorbed in the body and more than 50% of the dose is excreted in urine and feces in the original form or as secondary metabolites that maintain biological activity (Jjemba, 2002). For instance, several stu- dies have documented high concentrations of residual antibiotics, in the order of mg/kg, in a variety of animal manures (Wohde et al., 2016). This represents a serious problem because a large fraction of the live- stock manure produced globally is used as a soil amendment in agri- cultural soils (FAO, 2019). There is an increasing concern about the potential impact of https://doi.org/10.1016/j.biortech.2020.123889 Received 9 June 2020; Received in revised form 15 July 2020; Accepted 16 July 2020 ⁎ Corresponding author. E-mail addresses: floresod@myumanitoba.ca (D. Flores-Orozco), Rakesh.Patidar@umanitoba.ca (R. Patidar), David.Levin@umanitoba.ca (D.B. Levin), Richard.Sparling@umanitoba.ca (R. Sparling), Ayush.Kumar@umanitoba.ca (A. Kumar), Nazim.Cicek@umanitoba.ca (N. Çiçek). Bioresource Technology 315 (2020) 123889 Available online 21 July 2020 0960-8524/ © 2020 Elsevier Ltd. All rights reserved. T