The intestinal microbiota of beef cattle are important for animal health, food safety, and methane emissions. This full-length sequencing survey of 11,171 16S rRNA genes reveals animal-to-animal variation in communities that cannot be attributed to breed, gender, diet, age, or weather. Beef communities differ from those of dairy. Core bovine taxa are identified.

There is concern that antibiotic resistance can potentially be transferred from animals to humans through the food chain. The relationship between specific antibiotic resistant bacteria and the genes they carry remains to be described. Few details are known about the ecology of antibiotic resistant genes and bacteria in food production systems, or how antibiotic resistance genes in food animals compare to antibiotic resistance genes in other ecosystems. Here we report the distribution of antibiotic resistant genes in publicly available agricultural and non-agricultural metagenomic samples and identify which bacteria are likely to be carrying those genes. Antibiotic resistance, as coded for in the genes used in this study, is a process that was associated with all natural, agricultural, and human-impacted ecosystems examined, with between 0.7 to 4.4% of all classified genes in each habitat coding for resistance to antibiotic and toxic compounds (RATC). Agricultural, human, and coastal-marine metagenomes have characteristic distributions of antibiotic resistance genes, and different bacteria that carry the genes. There is a larger percentage of the total genome associated with antibiotic resistance in gastrointestinal-associated and agricultural metagenomes compared to marine and Antarctic samples. Since antibiotic resistance genes are a natural part of both human-impacted and pristine habitats, presence of these resistance genes in any specific habitat is therefore not sufficient to indicate or determine impact of anthropogenic antibiotic use. We recommend that baseline studies and control samples be taken in order to determine natural background levels of antibiotic resistant bacteria and/or antibiotic resistance genes when investigating the impacts of veterinary use of antibiotics on human health. We raise questions regarding whether the underlying biology of each type of bacteria contributes to the likelihood of transfer via the food chain.

Domestic and industrial wastewater discharges harbor rich bacterial communities, including both pathogenic and commensal organisms that are antibiotic-resistant (AR). AR pathogens pose a potential threat to human and animal health. In wastewater treatment plants (WWTP), bacteria encounter environments suitable for horizontal gene transfer, providing an opportunity for bacterial cells to acquire new antibiotic-resistant genes. With many entry points to environmental components, especially water and soil, WWTPs are considered a critical control point for antibiotic resistance. The primary and secondary units of conventional WWTPs are not designed for the reduction of resistant microbes. Constructed wetlands (CWs) are viable wastewater treatment options with the potential for mitigating AR bacteria, their genes, pathogens, and general pollutants. Encouraging performance for the removal of AR (2–4 logs) has highlighted the applicability of CW on fields. Their low cost of construction, operation and maintenance makes them well suited for applications across the globe, especially in developing and low-income countries. The present review highlights a better understanding of the performance efficiency of conventional treatment plants and CWs for the elimination/reduction of AR from wastewater. They are viable alternatives that can be used for secondary/tertiary treatment or effluent polishing in combination with WWTP or in a decentralized manner.

Emerging molecular, animal model and epidemiologic evidence suggests that Shiga-toxigenic Escherichia coli O157:H7 (STEC O157) isolates vary in their capacity to cause human infection and disease. The translocated intimin receptor (tir) and intimin (eae) are virulence factors and bacterial receptor-ligand proteins responsible for tight STEC O157 adherence to intestinal epithelial cells. They represent logical genomic targets to investigate the role of sequence variation in STEC O157 pathogenesis and molecular epidemiology. The purposes of this study were (1) to identify tir and eae polymorphisms in diverse STEC O157 isolates derived from clinically ill humans and healthy cattle (the dominant zoonotic reservoir) and (2) to test any observed tir and eae polymorphisms for association with human (vs bovine) isolate source.