School of Animal Sciences
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The School of Animal Sciences merged Dairy Science and Animal and Poultry Science in 2022.
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Browsing School of Animal Sciences by Department "Civil and Environmental Engineering"
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- AgroSeek: a system for computational analysis of environmental metagenomic data and associated metadataLiang, Xiao; Akers, Kyle; Keenum, Ishi M.; Wind, Lauren L.; Gupta, Suraj; Chen, Chaoqi; Aldaihani, Reem; Pruden, Amy; Zhang, Liqing; Knowlton, Katharine F.; Xia, Kang; Heath, Lenwood S. (2021-03-10)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. Results Here we introduce AgroSeek, a centralized web-based system that provides computational tools for analysis and comparison of metagenomic data sets tailored specifically to researchers and other users in the agricultural sector interested in tracking and mitigating the spread of ARGs. AgroSeek draws from rich, user-provided metagenomic data and metadata to facilitate analysis, comparison, and prediction in a user-friendly fashion. Further, AgroSeek draws from publicly-contributed data sets to provide a point of comparison and context for data analysis. To incorporate metadata into our analysis and comparison procedures, we provide flexible metadata templates, including user-customized metadata attributes to facilitate data sharing, while maintaining the metadata in a comparable fashion for the broader user community and to support large-scale comparative and predictive analysis. Conclusion AgroSeek provides an easy-to-use tool for environmental metagenomic analysis and comparison, based on both gene annotations and associated metadata, with this initial demonstration focusing on control of antibiotic resistance in agricultural ecosystems. Agroseek creates a space for metagenomic data sharing and collaboration to assist policy makers, stakeholders, and the public in decision-making. AgroSeek is publicly-available at https://agroseek.cs.vt.edu/ .
- Combined effects of composting and antibiotic administration on cattle manure–borne antibiotic resistance genesKeenum, Ishi M.; Williams, Robert K.; Ray, Partha P.; Garner, Emily; Knowlton, Katharine F.; Pruden, Amy (2021-04-01)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. Results Progression of composting with time and succession of the corresponding bacterial microbiota was the overarching driver of the resistome composition (ANOSIM; R = 0.424, p = 0.001, respectively) in all composts at the small-scale. Reduction in relative abundance (16S rRNA gene normalized) of total ARGs in finished compost (day 42) versus day 0 was noted across all conditions (ANOSIM; R = 0.728, p = 0.001), except when externally heated. Sul1, intI1, beta-lactam ARGs, and plasmid-associated genes increased in all finished composts as compared with the initial condition. External heating more effectively reduced certain clinically relevant ARGs (blaOXA, blaCARB), fecal coliforms, and resistome risk scores, which take into account putative pathogen annotations. When manure was collected during antibiotic administration, taxonomic composition of the compost was distinct according to nonmetric multidimensional analysis and tet(W) decayed faster in the dairy manure with antibiotic condition and slower in the beef manure with antibiotic condition. Conclusions This comprehensive, integrated study revealed that composting had a dominant effect on corresponding resistome composition, while little difference was noted as a function of collecting manure during antibiotic administration. Reduction in total ARGs, tet(W), and resistome risk suggested that composting reduced some potential for antibiotic resistance to spread, but the increase and persistence of other indicators of antibiotic resistance were concerning. Results indicate that composting guidelines intended for pathogen reduction do not necessarily provide a comprehensive barrier to ARGs or their mobility prior to land application and additional mitigation measures should be considered.
- Dietary phosphorus effects on characteristics of mechanically separated dairy manureKnowlton, Katharine F.; Love, Nancy G.; Parsons, C. A. (American Society of Agricultural and Biological Engineers, 2005)One approach to reduce nutrient losses from livestock farms is to apply biological waste treatment systems such as biological nitrogen (N) removal or enhanced biological phosphorus (P) removal (EBPR) to reduce the nutrient content of land-applied waste. The EBPR process takes advantage of the ability of P-accumulating organisms (PAOs) to sequester excess P as polyphosphate granules in their cytoplasms, yielding a P-depleted liquid effluent and a P-enriched biomass. Biological N removal systems result in the conversion of organic or ammonia-N to innocuous N-2 gas. Understanding the variation in parameters such as chemical oxygen demand (COD), total and volatile suspended solids (TSS and VSS), and ammonia-N (NH3-N) is necessary to design these systems. Our objectives were to evaluate the effects of diet and manure separation on parameters important to reactor design. Waste was collected from nine cows fed a high P diet (0.47% P), a low P diet (0.32 % P), or low P with exogenous phytase plus cellulase (0.32 % P), in a replicated Latin square design (three 3 X 3 squares). Total collection of milk, urine, and feces was conducted on days 19 to 21 of each period, a mixed slurry (urine, feces, and water) was created, and slurry was separated mechanically to generate liquid effluent. Slurry contained more COD, solids, N, and P than liquid effluent, but the COD:P ratio was similar in the two wastes. The ratio of COD:N was higher in slurry than in separator effluent, but the ratio in both wastes was sufficient to support biological N removal. The P content of slurry, liquid effluent, and manure solids from cows fed low P was lower than from cows fed high P, and the COD content of effluent was higher with the low P diet. The COD:P ratio of all wastes was sufficient to support EBPR and biological N removal, but variation was observed with diet. Waste from cows fed low P had a higher COD:P ratio than that of cows fed high P, and waste from cows fed the enzyme-supplemented diet had a lower COD:N ration than that of cows fed the control diet. Dairy manure slurry and effluent will support EBPR and biological N removal. Dietary effects on parameters important to the design of advanced waste treatment systems were observed, but were not of a magnitude that would affect reactor design.
- Effect of composting and soil type on dissipation of veterinary antibiotics in land-applied manuresChen, Chaoqi; Ray, Partha P.; Knowlton, Katharine F.; Pruden, Amy; Xia, Kang (2018)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. Antibiotic dissipation in the raw manure-amended soils followed bi-phasic first order kinetics. The first phase half-lives for sulfamethazine, tylosin, chlortetracycline, and pirlimycin ranged from 6.0 to 18, 2.7 to 3.7, 23 to 25, and 5.5–8.2 d, respectively. During the second phase, dissipation of sulfamethazine was negligible, while the half-lives for tylosin, chlortetracycline, and pirlimycin ranged from 41 to 44, 75 to 144, and 87–142 d, respectively. By contrast, antibiotic dissipation in the compost-amended soils followed single-phase first order kinetics with negligible dissipation of sulfamethazine and half-lives of tylosin and chlortetracycline ranging from 15 to 16 and 49–104 d, respectively. Pirlimycin was below the detection limit in the compost-amended soils. After incubating 120 d, antibiotics in compost-amended soils (up to 3.1 μg kg−1) were significantly lower than in manure-amended soils (up to 19 μg kg−1, p < .0001), with no major effect of soil type on the dissipation. Risk assessment suggested that composting can reduce antibiotic resistance selection potential in manure-amended soils.
- The effects of dietary protein content and manure handling technique on ammonia emissions during short-term storage of dairy cow manureSparks, J. A.; Ogejo, Jactone Arogo; Cyriac, J.; Hanigan, Mark D.; Knowlton, Katharine F.; Gay, S. W.; Marr, Linsey C. (American Society of Agricultural and Biological Engineers, 2011)An improved understanding of the potential for dietary protein manipulation to reduce ammonia emissions from dairy farms during various stages of manure handling is needed for both modeling and policy-making efforts. The objective of this study was to assess the effects of dietary protein manipulation on ammonia emissions from relatively freshly voided dairy cow manure in three types of removal systems: scraped manure removal systems, flushed manure removal systems, and flushed manure removal systems with a solids separator. Emissions were measured using a dynamic flux chamber for 12 h or more. Ammonia fluxes and emission factors per mass of manure were not affected by dietary protein content because fluxes depended mainly on total ammoniacal nitrogen (TAN) concentration, which did not vary with diet. However, emissions on a per-cow basis were 12% lower with the diet containing 15.0% crude protein as compared to the one with 17.8% (a change in crude protein of 16%) due to reduced urine output. The largest absolute impact of dietary protein manipulation would be with separated liquids because their emission factor was approximately four times higher than for the other types of manure. While dietary protein manipulation can reduce ammonia emissions from manure during long-term storage, its effectiveness in the hours immediately after manure is excreted is limited because emissions are more sensitive to other factors, including temperature and extent of mixing of the manure, that vary widely under real operating conditions on a farm.
- Excretion of antibiotic resistance genes by dairy calves fed milk replacers with varying doses of antibioticsThames, Callie H.; Pruden, Amy; James, Robert E.; Ray, Partha P.; Knowlton, Katharine F. (Frontiers, 2012-01-01)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.
- Metagenomic Analysis of Antibiotic Resistance Genes in Dairy Cow Feces following Therapeutic Administration of Third Generation CephalosporinChambers, Lindsey R.; Yang, Ying; Littier, Heather; Ray, Partha P.; Zhang, Tong; Pruden, Amy; Strickland, Michael S.; Knowlton, Katharine F. (PLOS, 2015-08-10)Although dairy manure is widely applied to land, it is relatively understudied compared to other livestock as a potential source of antibiotic resistance genes (ARGs) to the environment and ultimately to human pathogens. Ceftiofur, the most widely used antibiotic used in U.S. dairy cows, is a 3rd generation cephalosporin, a critically important class of antibiotics to human health. The objective of this study was to evaluate the effect of typical ceftiofur antibiotic treatment on the prevalence of ARGs in the fecal microbiome of dairy cows using a metagenomics approach. β-lactam ARGs were found to be elevated in feces from Holstein cows administered ceftiofur (n = 3) relative to control cows (n = 3). However, total numbers of ARGs across all classes were not measurably affected by ceftiofur treatment, likely because of dominance of unaffected tetracycline ARGs in the metagenomics libraries. Functional analysis via MG-RAST further revealed that ceftiofur treatment resulted in increases in gene sequences associated with “phages, prophages, transposable elements, and plasmids”, suggesting that this treatment also enriched the ability to horizontally transfer ARGs. Additional functional shifts were noted with ceftiofur treatment (e.g., increase in genes associated with stress, chemotaxis, and resistance to toxic compounds; decrease in genes associated with metabolism of aromatic compounds and cell division and cell cycle), along with measureable taxonomic shifts (increase in Bacterioidia and decrease in Actinobacteria). This study demonstrates that ceftiofur has a broad, measureable and immediate effect on the cow fecal metagenome. Given the importance of 3rd generation cephalospirins to human medicine, their continued use in dairy cattle should be carefully considered and waste treatment strategies to slow ARG dissemination from dairy cattle manure should be explored.