Comparative diversity of microbiomes and Resistomes in beef feedlots, downstream environments and urban sewage influent
Abstract Background Comparative knowledge of microbiomes and resistomes across environmental interfaces between animal production systems and urban settings is lacking. In this study, we executed a comparative analysis of the microbiota and resistomes of metagenomes from cattle feces, catch basin wa...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2019-08-01
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| Series: | BMC Microbiology |
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| Online Access: | http://link.springer.com/article/10.1186/s12866-019-1548-x |
| _version_ | 1818276420807294976 |
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| author | Rahat Zaheer Steven M. Lakin Rodrigo Ortega Polo Shaun R. Cook Francis J. Larney Paul S. Morley Calvin W. Booker Sherry J. Hannon Gary Van Domselaar Ron R. Read Tim A. McAllister |
| author_facet | Rahat Zaheer Steven M. Lakin Rodrigo Ortega Polo Shaun R. Cook Francis J. Larney Paul S. Morley Calvin W. Booker Sherry J. Hannon Gary Van Domselaar Ron R. Read Tim A. McAllister |
| author_sort | Rahat Zaheer |
| collection | DOAJ |
| description | Abstract Background Comparative knowledge of microbiomes and resistomes across environmental interfaces between animal production systems and urban settings is lacking. In this study, we executed a comparative analysis of the microbiota and resistomes of metagenomes from cattle feces, catch basin water, manured agricultural soil and urban sewage. Results Metagenomic DNA from composite fecal samples (FC; n = 12) collected from penned cattle at four feedlots in Alberta, Canada, along with water from adjacent catchment basins (CB; n = 13), soil (n = 4) from fields in the vicinity of one of the feedlots and urban sewage influent (SI; n = 6) from two municipalities were subjected to Illumina HiSeq2000 sequencing. Firmicutes exhibited the highest prevalence (40%) in FC, whereas Proteobacteria were most abundant in CB (64%), soil (60%) and SI (83%). Among sample types, SI had the highest diversity of antimicrobial resistance (AMR), and metal and biocide resistance (MBR) classes (13 & 15) followed by FC (10 & 8), CB (8 & 4), and soil (6 & 1). The highest antimicrobial resistant (AMR) gene (ARG) abundance was harboured by FC, whereas soil samples had a very small, but unique resistome which did not overlap with FC & CB resistomes. In the beef production system, tetracycline resistance predominated followed by macrolide resistance. The SI resistome harboured β-lactam, macrolide, tetracycline, aminoglycoside, fluoroquinolone and fosfomycin resistance determinants. Metal and biocide resistance accounted for 26% of the SI resistome with a predominance of mercury resistance. Conclusions This study demonstrates an increasing divergence in the nature of the microbiome and resistome as the distance from the feedlot increases. Consistent with antimicrobial use, tetracycline and macrolide resistance genes were predominant in the beef production system. One of the feedlots contributed both conventional (raised with antibiotics) and natural (raised without antibiotics) pens samples. Although natural pen samples exhibited a microbiota composition that was similar to samples from conventional pens, their resistome was less complex. Similarly, the SI resistome was indicative of drug classes used in humans and the greater abundance of mercury resistance may be associated with contamination of municipal water with household and industrial products. |
| first_indexed | 2024-12-12T22:45:22Z |
| format | Article |
| id | doaj.art-40eb08bdbfa94eb7a98269130180d86b |
| institution | Directory Open Access Journal |
| issn | 1471-2180 |
| language | English |
| last_indexed | 2024-12-12T22:45:22Z |
| publishDate | 2019-08-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Microbiology |
| spelling | doaj.art-40eb08bdbfa94eb7a98269130180d86b2022-12-22T00:09:13ZengBMCBMC Microbiology1471-21802019-08-0119111710.1186/s12866-019-1548-xComparative diversity of microbiomes and Resistomes in beef feedlots, downstream environments and urban sewage influentRahat Zaheer0Steven M. Lakin1Rodrigo Ortega Polo2Shaun R. Cook3Francis J. Larney4Paul S. Morley5Calvin W. Booker6Sherry J. Hannon7Gary Van Domselaar8Ron R. Read9Tim A. McAllister10Agriculture and Agri-Food Canada, Lethbridge Research and Development CentreDepartment of Clinical Sciences, Colorado State UniversityAgriculture and Agri-Food Canada, Lethbridge Research and Development CentreAlberta Agriculture and ForestryAgriculture and Agri-Food Canada, Lethbridge Research and Development CentreDepartment of Clinical Sciences, Colorado State UniversityFeedlot Health Management ServicesFeedlot Health Management ServicesNational Microbiology Laboratory, Public Health Agency of CanadaCumming School of Medicine, University of CalgaryAgriculture and Agri-Food Canada, Lethbridge Research and Development CentreAbstract Background Comparative knowledge of microbiomes and resistomes across environmental interfaces between animal production systems and urban settings is lacking. In this study, we executed a comparative analysis of the microbiota and resistomes of metagenomes from cattle feces, catch basin water, manured agricultural soil and urban sewage. Results Metagenomic DNA from composite fecal samples (FC; n = 12) collected from penned cattle at four feedlots in Alberta, Canada, along with water from adjacent catchment basins (CB; n = 13), soil (n = 4) from fields in the vicinity of one of the feedlots and urban sewage influent (SI; n = 6) from two municipalities were subjected to Illumina HiSeq2000 sequencing. Firmicutes exhibited the highest prevalence (40%) in FC, whereas Proteobacteria were most abundant in CB (64%), soil (60%) and SI (83%). Among sample types, SI had the highest diversity of antimicrobial resistance (AMR), and metal and biocide resistance (MBR) classes (13 & 15) followed by FC (10 & 8), CB (8 & 4), and soil (6 & 1). The highest antimicrobial resistant (AMR) gene (ARG) abundance was harboured by FC, whereas soil samples had a very small, but unique resistome which did not overlap with FC & CB resistomes. In the beef production system, tetracycline resistance predominated followed by macrolide resistance. The SI resistome harboured β-lactam, macrolide, tetracycline, aminoglycoside, fluoroquinolone and fosfomycin resistance determinants. Metal and biocide resistance accounted for 26% of the SI resistome with a predominance of mercury resistance. Conclusions This study demonstrates an increasing divergence in the nature of the microbiome and resistome as the distance from the feedlot increases. Consistent with antimicrobial use, tetracycline and macrolide resistance genes were predominant in the beef production system. One of the feedlots contributed both conventional (raised with antibiotics) and natural (raised without antibiotics) pens samples. Although natural pen samples exhibited a microbiota composition that was similar to samples from conventional pens, their resistome was less complex. Similarly, the SI resistome was indicative of drug classes used in humans and the greater abundance of mercury resistance may be associated with contamination of municipal water with household and industrial products.http://link.springer.com/article/10.1186/s12866-019-1548-xMicrobiomeAntimicrobial resistanceMetal and biocide resistanceCattle productionWastewater |
| spellingShingle | Rahat Zaheer Steven M. Lakin Rodrigo Ortega Polo Shaun R. Cook Francis J. Larney Paul S. Morley Calvin W. Booker Sherry J. Hannon Gary Van Domselaar Ron R. Read Tim A. McAllister Comparative diversity of microbiomes and Resistomes in beef feedlots, downstream environments and urban sewage influent BMC Microbiology Microbiome Antimicrobial resistance Metal and biocide resistance Cattle production Wastewater |
| title | Comparative diversity of microbiomes and Resistomes in beef feedlots, downstream environments and urban sewage influent |
| title_full | Comparative diversity of microbiomes and Resistomes in beef feedlots, downstream environments and urban sewage influent |
| title_fullStr | Comparative diversity of microbiomes and Resistomes in beef feedlots, downstream environments and urban sewage influent |
| title_full_unstemmed | Comparative diversity of microbiomes and Resistomes in beef feedlots, downstream environments and urban sewage influent |
| title_short | Comparative diversity of microbiomes and Resistomes in beef feedlots, downstream environments and urban sewage influent |
| title_sort | comparative diversity of microbiomes and resistomes in beef feedlots downstream environments and urban sewage influent |
| topic | Microbiome Antimicrobial resistance Metal and biocide resistance Cattle production Wastewater |
| url | http://link.springer.com/article/10.1186/s12866-019-1548-x |
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