ArticleBMC microbiology2019
Comparative diversity of microbiomes and Resistomes in beef feedlots, downstream environments and urban sewage influent.
Article in BMC microbiology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers, 1 of them a synthesis that pooled it.
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Who cites it
32 citing papers in PubMed, 1 synthesis or guideline pooled it, 58 citations in OpenAlex.
- Quantifying antimicrobial resistance in food-producing animals in North America.Frontiers in microbiology · 2025Pooled it
- A preliminary metagenomic and metabolomic investigation into the effects of Aspergillus niger cultures on microbial homeostasis and antibiotic resistance gene profiles in the rumen of fattening sheep.Journal of animal science and biotechnology · 2026Article
- Enhanced metagenomic surveillance for bovine respiratory disease pathogens and antimicrobial resistance by hybridization capture sequencing.Applied and environmental microbiology · 2025Article
- Retrospective analysis of antimicrobial resistance associated with bovine respiratory disease.Applied and environmental microbiology · 2025Article
- Microbiota Composition Associates With Mosquito Productivity Outcomes in Belowground Larval Habitats.Molecular ecology · 2025Article
- Prevalences of respiratory viruses and bacteria in Western Canadian commercial feedlot calves detected using a single metagenomic sequencing protocol vary during the first two weeks of arrival and by age group.Frontiers in veterinary science · 2025Article
- Assessing antimicrobial resistance in pasture-based dairy farms: a 15-month surveillance study in New Zealand.Applied and environmental microbiology · 2024Article
- Accessory genes define species-specific routes to antibiotic resistance.Life science alliance · 2024Article
- Metagenomics reveals the temporal dynamics of the rumen resistome and microbiome in goat kids.Microbiome · 2024Article
- Altered microbiota, antimicrobial resistance genes, and functional enzyme profiles in the rumen of yak calves fed with milk replacer.Microbiology spectrum · 2024Article
- Recruitment of complete crAss-like phage genomes reveals their presence in chicken viromes, few human-specific phages, and lack of universal detection.The ISME journal · 2024Article
- Comparative microbiome analysis of beef cattle, the feedyard environment, and airborne particulate matter as a function of probiotic and antibiotic use, and change in pen environment.Frontiers in microbiology · 2024Article
- Article
- Effect of Antimicrobial Use in Conventional Versus Natural Cattle Feedlots on the Microbiome and Resistome.Microorganisms · 2023Article
- Clinically relevant antibiotic resistance genes are linked to a limited set of taxa within gut microbiome worldwide.Nature communications · 2023Article
- Microbiota and Resistome Analysis of Colostrum and Milk from Dairy Cows Treated with and without Dry Cow Therapies.Antibiotics (Basel, Switzerland) · 2023Article
- Isolation and characterisation of novel Methanocorpusculum species indicates the genus is ancestrally host-associated.BMC biology · 2023Article
- Driving forces shaping the microbial ecology in meat packing plants.Frontiers in microbiology · 2023Review
- Shifts of Antibiotic Resistomes in Soil Following Amendments of Antibiotics-Contained Dairy Manure.International journal of environmental research and public health · 2022Article
- FI: The Fecobiome Initiative.Foodborne pathogens and disease · 2022Article
Corrections and comments
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Authors and funding
11 authors at 6 institutions in 2 countries.
Funding
Abstract
backgroundComparative 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.
resultsMetagenomic 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.
conclusionsThis 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.
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