ArticleFrontiers in microbiology2020
Metagenomic Characterization of the Microbiome and Resistome of Retail Ground Beef Products.
Article in Frontiers in microbiology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 24 citations in OpenAlex.
- Article
- A Novel Real-Time SYBR Green PCR Assay for Integron Profiling inPathogens (Basel, Switzerland) · 2026Article
- Different DNA input amounts and library preparation kits yield comparable resistome characterization using target-enriched metagenomic sequencing.Frontiers in microbiology · 2026Article
- Antibiotic Resistance Genes and Microbiota inJournal of agricultural and food chemistry · 2025Article
- Antimicrobial resistance reservoirs in salmon and broiler processing environments, sidestreams, and waste discharges.Frontiers in microbiology · 2025Article
- Bioinformatic Pipeline for Profiling Foodborne Bacterial Ecology and Resistome from Short-Read Metagenomics.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Oxygen Sensor-Based Respirometry and the Landscape of Microbial Testing Methods as Applicable to Food and Beverage Matrices.Sensors (Basel, Switzerland) · 2023Review
- One Health: a holistic approach for food safety in livestock.Science in One Health · 2022Review
- Article
- Characterization of Escherichia coli harboring colibactin genes (clb) isolated from beef production and processing systems.Scientific reports · 2022Article
- Resistomes and microbiome of meat trimmings and colon content from culled cows raised in conventional and organic production systems.Animal microbiome · 2022Article
- A CURE for Meat: Comparing Bacterial Contaminants on Different Ground Beef Sources Emphasizes Process of Science and Quantitative Reasoning.Journal of microbiology & biology education · 2021Article
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Authors and funding
10 authors at 4 institutions in 1 country.
Funding
Abstract
Ground beef can be a reservoir for a variety of bacteria, including spoilage organisms, and pathogenic foodborne bacteria. These bacteria can exhibit antimicrobial resistance (AMR) which is a public health concern if resistance in pathogens leads to treatment failure in humans. Culture-dependent techniques are commonly used to study individual bacterial species, but these techniques are unable to describe the whole community of microbial species (microbiome) and the profile of AMR genes they carry (resistome), which is critical for getting a holistic perspective of AMR. The objective of this study was to characterize the microbiome and resistome of retail ground beef products labeled as coming from conventional or raised without antibiotics (RWA) production systems. Sixteen ground beef products were purchased from 6 retail grocery outlets in Fort Collins, CO, half of which were labeled as produced from cattle raised conventionally and half of products were from RWA production. Total DNA was extracted and isolated from each sample and subjected to 16S rRNA amplicon sequencing for microbiome characterization and target-enriched shotgun sequencing to characterize the resistome. Differences in the microbiome and resistome of RWA and conventional ground beef were analyzed using the R programming software. Our results suggest that the resistome and microbiome of retail ground beef products with RWA packaging labels do not differ from products that do not carry claims regarding antimicrobial drug exposures during cattle production. The resistome predominantly consisted of tetracycline resistance making up more than 90% of reads mapped to resistance gene accessions in our samples. Firmicutes and Proteobacteria predominated in the microbiome of all samples (69.6% and 29.0%, respectively), but Proteobacteria composed a higher proportion in ground beef from conventionally raised cattle. In addition, our results suggest that product management, such as packaging type, could exert a stronger influence on the microbiome than the resistome in consumer-ready products. Metagenomic analyses of ground beef is a promising tool to investigate community-wide shifts in retail ground beef. Importantly, however, results from metagenomic sequencing must be carefully considered in parallel with traditional methods to better characterize the risk of AMR in retail products.
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Registered trials
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