Effect of mesophilic anaerobic digestion on the resistome profile of dairy manure

Daniel Flores-Orozco; Rakesh Patidar; David B Levin; Richard Sparling; Ayush Kumar; Nazim Çiçek

doi:10.1016/j.biortech.2020.123889

Effect of mesophilic anaerobic digestion on the resistome profile of dairy manure

Bioresour Technol. 2020 Nov:315:123889. doi: 10.1016/j.biortech.2020.123889. Epub 2020 Jul 21.

Authors

Daniel Flores-Orozco¹, Rakesh Patidar², David B Levin³, Richard Sparling⁴, Ayush Kumar⁵, Nazim Çiçek⁶

Affiliations

¹ Department of Biosystems Engineering, University of Manitoba, Winnipeg, Manitoba R3T 5V6, Canada. Electronic address: floresod@myumanitoba.ca.
² Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T 5V6, Canada. Electronic address: Rakesh.Patidar@umanitoba.ca.
³ Department of Biosystems Engineering, University of Manitoba, Winnipeg, Manitoba R3T 5V6, Canada. Electronic address: David.Levin@umanitoba.ca.
⁴ Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T 5V6, Canada. Electronic address: Richard.Sparling@umanitoba.ca.
⁵ Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T 5V6, Canada. Electronic address: Ayush.Kumar@umanitoba.ca.
⁶ Department of Biosystems Engineering, University of Manitoba, Winnipeg, Manitoba R3T 5V6, Canada. Electronic address: Nazim.Cicek@umanitoba.ca.

PMID: 32717520
DOI: 10.1016/j.biortech.2020.123889

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.

Keywords: Anaerobic digestion; Antibiotic resistance genes; Dairy manure; Metagenomics; Resistome.

MeSH terms

Anaerobiosis
Anti-Bacterial Agents / pharmacology
Drug Resistance, Microbial / drug effects
Genes, Bacterial
Manure*
Microbiota / drug effects*

Substances

Anti-Bacterial Agents
Manure