ARGem: a new metagenomics pipeline for antibiotic resistance genes: metadata, analysis, and visualization.

Antibiotic resistance is of crucial interest to both human and animal medicine. It has been recognized that increased environmental monitoring of antibiotic resistance is needed. Metagenomic DNA sequencing is becoming an attractive method to profile antibiotic resistance genes (ARGs), including a special focus on pathogens.

To Treat or Not to Treat: Public Attitudes on the Therapeutic Use of Antibiotics in the Dairy Industry-A Qualitative Study.

This paper describes the views of 779 U.S. residents on questions related to therapeutic antibiotic use in dairy cattle.

Microbiomes of Various Maternal Body Systems Are Predictive of Calf Digestive Bacterial Ecology.

Body systems once thought sterile at birth instead have complex and sometimes abundant microbial ecosystems. However, relationships between dam and calf microbial ecosystems are still unclear. The objectives of this study were to (1) characterize the various maternal and calf microbiomes during peri-partum and post-partum periods and (2) examine the influence of the maternal microbiome on calf fecal microbiome composition during the pre-weaning phase.

Combined effects of composting and antibiotic administration on cattle manure-borne antibiotic resistance genes.

Background: Research is needed to delineate the relative and combined effects of different antibiotic administration and manure management practices in either amplifying or attenuating the potential for antibiotic resistance to spread. Here, we carried out a comprehensive parallel examination of the effects of small-scale (> 55 °C × 3 days) static and turned composting of manures from dairy and beef cattle collected during standard antibiotic administration (cephapirin/pirlimycin or sulfamethazine/chlortetracycline/tylosin, respectively), versus from untreated cattle, on "resistomes" (total antibiotic resistance genes (ARGs) determined via shotgun metagenomic sequencing), bacterial microbiota, and indicator ARGs enumerated via quantitative polymerase chain reaction. To gain insight into the role of the thermophilic phase, compost was also externally heated to > 55 °C × 15 days.

AgroSeek: a system for computational analysis of environmental metagenomic data and associated metadata.

Background: Metagenomics is gaining attention as a powerful tool for identifying how agricultural management practices influence human and animal health, especially in terms of potential to contribute to the spread of antibiotic resistance. However, the ability to compare the distribution and prevalence of antibiotic resistance genes (ARGs) across multiple studies and environments is currently impossible without a complete re-analysis of published datasets. This challenge must be addressed for metagenomics to realize its potential for helping guide effective policy and practice measures relevant to agricultural ecosystems, for example, identifying critical control points for mitigating the spread of antibiotic resistance.

Fate of pirlimycin and antibiotic resistance genes in dairy manure slurries in response to temperature and pH adjustment.

Quantifying the fate of antibiotics and antibiotic resistance genes (ARGs) in response to physicochemical factors during storage of manure slurries will aid in efforts to reduce the spread of resistance when manure is land-applied. The objectives of this study were to determine the effects of temperature (10, 35, and 55 °C) and initial pH (5, 7, 9, and 12) on the removal of pirlimycin and prevalence of ARGs during storage of dairy manure slurries. We collected and homogenized feces and urine from five lactating dairy cows treated with pirlimycin and prepared slurries by mixing manure and sterile water.

Short communication: Increasing temperature and pH can facilitate reductions of cephapirin and antibiotic resistance genes in dairy manure slurries.

Quantifying antibiotics and antibiotic resistance genes (ARG) in manure exposed to various temperature and pH treatments could guide the development of cost-effective manure handling methods to minimize the spread of antibiotic resistance following land application of manure. This study aimed to investigate the effect of various temperatures and initial pH shocks on the persistence of a cephalosporin antibiotic and ARG in dairy manure slurries. Feces and urine were collected from 5 healthy dairy cows administered with cephapirin (cephalosporin antibiotic) at dry-off via intramammary infusion and were mixed with sterile water to generate manure slurries.

Prolonged exposure to manure from livestock-administered antibiotics decreases ecosystem carbon-use efficiency and alters nitrogen cycling.

Microbial communities drive soil ecosystem function but are also susceptible to environmental disturbances. We investigated whether exposure to manure sourced from cattle either administered or not administered antibiotics affected microbially mediated terrestrial ecosystem function. We quantified changes in microbial community composition via amplicon sequencing, and terrestrial elemental cycling via a stable isotope pulse-chase.

Effect of composting and soil type on dissipation of veterinary antibiotics in land-applied manures.

The objective of this study was to determine the fate of commonly used veterinary antibiotics in their naturally excreted form when manure-based amendments are applied to soil. Beef cattle were administered sulfamethazine, tylosin, and chlortetracycline and dairy cows were treated with pirlimycin. The resulting manure was composted for 42 d under static or turned conditions and applied at agronomic N rates to sandy, silt, and silty clay loam soils and compared with amendment with corresponding raw manures in sacrificial microcosms over a 120-day period.

Exposure to dairy manure leads to greater antibiotic resistance and increased mass-specific respiration in soil microbial communities.

Intensifying livestock production to meet the demands of a growing global population coincides with increases in both the administration of veterinary antibiotics and manure inputs to soils. These trends have the potential to increase antibiotic resistance in soil microbial communities. The effect of maintaining increased antibiotic resistance on soil microbial communities and the ecosystem processes they regulate is unknown.

Fate and Effect of Antibiotics in Beef and Dairy Manure during Static and Turned Composting.

Manure composting has general benefits for production of soil amendment, but the effects of composting on antibiotic persistence and effects of antibiotics on the composting process are not well-characterized, especially for antibiotics commonly used in dairy cattle. This study provides a comprehensive, head-to-head, replicated comparison of the effect of static and turned composting on typical antibiotics used in beef and dairy cattle in their actual excreted form and corresponding influence on composting efficacy. Manure from steers (with or without chlortetracycline, sulfamethazine, and tylosin feeding) and dairy cows (with or without pirlimycin and cephapirin administration) were composted at small scale (wet mass: 20-22 kg) in triplicate under static and turned conditions adapted to represent US Food and Drug Administration guidelines.

Milk protein composition and stability changes affected by iron in water sources.

Water makes up more than 80% of the total weight of milk. However, the influence of water chemistry on the milk proteome has not been extensively studied. The objective was to evaluate interaction of water-sourced iron (low, medium, and high levels) on milk proteome and implications on milk oxidative state and mineral content.

Method development and validation: solid Phase extraction-ultra performance liquid chromatography-tandem mass spectrometry quantification of pirlimycin in bovine feces and urine.

Pirlimycin, a lincosamide antibiotic, is one of the most commonly used antibiotics for the treatment of mastitis in dairy cows. Assessment of pirlimycin loadingto the environment via fecal and urinary excretion is critical to develop efficient management strategies to reduce environmental pollution by the livestock industry. Therefore, the aim of this study was to develop and validate an analytical method to identify and quantify pirlimycin in bovine feces and urine.

Development and validation of a UPLC-MS/MS method to monitor cephapirin excretion in dairy cows following intramammary infusion.

Cephapirin, a cephalosporin antibiotic, is used by the majority of dairy farms in the US. Fecal and urinary excretion of cephapirin could introduce this compound into the environment when manure is land applied as fertilizer, and may cause development of bacterial resistance to antibiotics critical for human health. The environmental loading of cephapirin by the livestock industry remains un-assessed, largely due to a lack of appropriate analytical methods.

Polyphosphate- and glycogen-accumulating organisms in one EBPR system for liquid dairy manure.

Two enhanced biological phosphorus removal (EBPR) sequencing batch reactors (SBR1, SBR2) treating liquid dairy manure were operated with the same hydraulic retention time (HRT) and solids retention time (SRT), but with different aeration cycles. During eight months of operation, both SBRs achieved good removal of total phosphorus (P) (TP; 56.8 and 73.

Excretion of antibiotic resistance genes by dairy calves fed milk replacers with varying doses of antibiotics.

Elevated levels of antibiotic resistance genes (ARGs) in soil and water have been linked to livestock farms and in some cases feed antibiotics may select for antibiotic resistant gut microbiota. The purpose of this study was to examine the establishment of ARGs in the feces of calves receiving milk replacer containing no antibiotics versus subtherapeutic or therapeutic doses of tetracycline and neomycin. The effect of antibiotics on calf health was also of interest.

Occurrence, fate and removal of synthetic oral contraceptives (SOCs) in the natural environment: a review.

Synthetic oral contraceptives (SOCs) are a group of compounds with progestagenic and/or androgenic activities, with some also possessing estrogenic activities. Recent research has documented that some of these emerging contaminants have adverse effects on aquatic organisms at very low concentrations. To facilitate the evaluation of their latent risks, published works on their occurrence and fate in the environment are reviewed.

Effects of reducing dietary nitrogen on ammonia emissions from manure on the floor of a naturally ventilated free stall dairy barn at low (0-20 degrees C) temperatures.

This study was conducted to determine the potential for reducing ammonia (NH3) emissions from manure deposited on the floor of a naturally ventilated free stall barn by mid-lactation dairy cows fed reduced or normal N diets. Two crude protein (CP) diets (178 g kg(-1) [high] and 159 g kg(-1) [low] dry matter ), were used. The diets were fed to 48 Holstein cows in a replicated crossover design with two pens per diet.

Prefermentation of liquid dairy manure to support biological nutrient removal.

A continuously operated, intermittently fed reactor (fermenter) system with a 2-d solids retention time was proposed for supporting biological nutrient removal from liquid dairy manure. The first objective of this study was to select a material with high fermentation potential to be used as the fermenter feed. Primary sludge, liquid separated dairy manure, and flushed dairy manure were investigated for their fermentation potential.

Biochemical and biological assays of endocrine disrupting compounds in various manure matrices.

Wastes generated by animal agriculture have complex matrices and present a significant challenge for achieving accurate measurements of estrogens. The objective of this study was to compare two different extraction methods and two different biochemical and biological estrogen assays on two dairy manure matrices. The two extraction methods studied in this research were a two-step base-toluene extraction and a one-step cyclohexane extraction.

Effect of relocation on locomotion and cleanliness in dairy cows.

This study was conducted to determine the effect that relocation to a new free stall barn had on locomotion and cleanliness of two breeds of dairy cows. The original facility before relocation had cows housed in an 8-row free stall barn. Cows were allocated in a new 4-row free stall facility: cows of two breeds (n=22 Holsteins and 22 Jerseys) were intermixed in the northwest section.

A novel test for measuring and managing potential phosphorus loss from dairy cattle feces.

Pollution of waters resulting from phosphorus (P) runoff from agricultural land receiving long-term manure application is one of the most serious threats to water quality in many regions of the world. Of various approaches to alleviate the problem, reducing P surplus on animal farms through optimizing P intake and minimizing P excretion in manure offers a great opportunity. Here, we present a fecal P test method that has the potential to identify over-feeding of P in dairy cattle.

Reducing phosphorus runoff from dairy farms.

Phosphorus (P) runoff from manure can lead to eutrophication of surface water and algae growth. This study evaluates the impacts of alternative P reduction practices on dairy farm net returns and on potential P runoff. The P control practices include dairy herd nutrient management, crop nutrient management, and runoff and erosion control.

Phosphorus characteristics of dairy feces affected by diets.

Phosphorus (P) surplus on dairy farms, especially confined operations, contributes to P buildup in soils with increased potential for P loss to waters. One approach to reduce P surplus and improve water quality is to optimize P feeding and improve P balance on farms. Here we report how varying P concentrations in lactating cow diets affects the amount as well as the chemical forms and fraction distribution of P in fecal excretion, and the environmental implications of this effect.