Abstract
Abstract
Background
The resistome describes the array of antibiotic resistant genes (ARGs) present within a microbial community. Recent research has documented the resistome in the rumen of ruminants and revealed that the type and abundance of ARGs could be affected by diet and/or antibiotic treatment. However, most of these studies only assessed ARGs using metagenomics, and expression of the resistome and its biological function within the microbiome remains largely unexplored.
Results
We characterized the pools of ARGs (resistome) and their activities in the rumen of 48 beef cattle belonging to three breeds (Angus, Charolais, Kinsella composite hybrid), using shotgun metagenomics and metatranscriptomics. Sixty (including 20 plasmid-associated) ARGs were expressed which accounted for about 30% of the total number of ARGs (187) identified in metagenomic datasets, with tetW and mefA exhibiting the highest level of expression. In addition, the bacterial hosts of 17 expressed ARGs were identified. The active resistome was less diverse in Kinsella composite hybrid than Angus, however, expression of ARGs did not differ among breeds. Although not associated with feed efficiency, the total abundance of expressed ARGs was positively correlated with metabolic pathways and ‘attenuation values’ (a measurement of stability) of the active rumen microbiome, suggesting that ARGs expression influences the stability and functionality of the rumen microbiome. Moreover, Ruminococcus spp., Prevotella ruminicola, Muribaculaceae spp. and Collinsella aerofaciens were all identified as hosts of expressed ARGs, possibly promoting the dominance of these carbohydrate degraders within the rumen microbiome.
Conclusions
Findings from this study provide new insight into the active rumen resistome in vivo, which may inform strategies to limit the spread of ubiquitously found ARGs from the rumen to the broader environment without negatively impacting the key functional outcomes of the rumen microbiome.
Funder
Central Public-interest Scientific Institution Basal Research Fund
Ministry of Agriculture, Forestry and Fisheries
Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada
Genome Alberta
Agricultural Science and Technology Innovation Program
Publisher
Springer Science and Business Media LLC
Reference76 articles.
1. Cogliani C, Goossens H, Greko C. Restricting antimicrobial use in food animals: lessons from Europe: banning nonessential antibiotic uses in food animals is intended to reduce pools of resistance genes. Microbe. 2011;6:274–9.
2. Van Boeckel TP, Brower C, Gilbert M, Grenfell BT, Levin SA, Robinson TP, et al. Global trends in antimicrobial use in food animals. Proc Natl Acad Sci. 2015;112:5649–54.
3. Campagnolo ER, Johnson KR, Karpati A, Rubin CS, Kolpin DW, Meyer MT, et al. Antimicrobial residues in animal waste and water resources proximal to large-scale swine and poultry feeding operations. Sci Total Environ. 2002;299:89–95.
4. Heuer H, Solehati Q, Zimmerling U, Kleineidam K, Schloter M, Müller T, et al. Accumulation of sulfonamide resistance genes in arable soils due to repeated application of manure containing sulfadiazine. Appl Environ Microbiol. 2011;77:2527–30.
5. Davies J, Davies D. Origins and Evolution of Antibiotic Resistance. Microbiol Mol Biol Rev. 2010;74:417–33.
Cited by
7 articles.
订阅此论文施引文献
订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献