Phytase is added to swine diets to improve the utilization of phytate-bound P. This provides financial and environmental benefits to the pig industry. It is unclear if phytase works equally well under all dietary circumstances. The objective was to determine if insoluble fiber impacts the efficacy of the phytase enzyme in nursery pigs when fed diets limiting in P content. A total of 480 pigs (initial BW 5.48 ± 0.14 kg) were blocked by BW and randomly assigned to treatment within block. A common nutrient-adequate diet was fed from d -14 to -5, and 2 basal P deficient diets (either a corn-soy diet containing 0.16% standardized total tract digestible [STTD] P [LF], or a corn-soybean meal plus 20% corn bran containing 0.14% STTD P [HF]) were fed from d -5 to 0 to acclimate pigs to a P deficient diet. From d 0-21, pigs received 8 dietary treatments (6 pens per treatment: n=6). Experimental diets consisted of LF supplemented with one of 4 levels of added phytase (0, 109, 218, and 327 phytase units [FTU]/kg; Quantum Blue 5 G, AB Vista, Wiltshire, UK) expected to provide 0.16, 0.21, 0.26, and 0.31% STTD P, respectively, or HF supplemented with one of the same 4 levels of added phytase. Titanium dioxide was added to the diet at 0.4% as an indigestible marker. On d 21, one pig representing the average BW for each pen was euthanized, and fibulae were collected and analyzed for bone ash. Fecal samples were collected from each pen on d 19-20. Data were analyzed using PROC MIXED of SAS. There were no interactions between insoluble fiber and phytase for any of the variables evaluated. For d 0 - 21, adding phytase increased ADG (P < 0.001) with the response being linear (P < 0.001), whereas insoluble fiber decreased ADG (P = 0.033). There were no effects of phytase or insoluble fiber on ADFI (P = 0.381 and P = 0.632, respectively). Phytase improved G:F ratio (P < 0.001) with the response being linear (P < 0.001). Insoluble fiber tended to decrease G:F ratio (P = 0.097). Phytase increased bone ash (P = 0.005) with the response being linear (P = 0.001), but there was no effect of insoluble fiber (P = 0.949). Phytase did not affect the apparent total tract digestibility of DM, NDF, or ADF (P > 0.050), whereas insoluble fiber decreased the ATTD of DM (P < 0.001), NDF (P < 0.001), and ADF (P < 0.001). In conclusion, the addition of insoluble fiber did not affect the ability of phytase to improve growth performance and bone mineralization in nursery pigs fed a P deficient diet.

Heat stress (HS) negatively impacts animal productivity and welfare. Precisely studying HS typically requires expensive climate-controlled facilities, resources often inaccessible to most scientists. Thus, it is of interest to develop and validate alternative and cost-effective models to study HS and to assess nutritional HS mitigation strategies using this model in lactating dairy cows. Many of the negative consequences of HS appears to be mediated by intestine-derived lipopolysaccharide (LPS) and thus HS biology can be modeled by infusing LPS. Administrating LPS decreases circulating calcium (Ca) and decreases markedly both feed intake and milk yield in dairy cows. The current dissertation centered on developing, evaluating, and validating an alternative model to study HS and identifying nutritional management strategies to ameliorate negative consequences of both heat-stressed and immune-challenged dairy cows.

In studies 1 and 2 (Chapters 2 and 3), we evaluated the efficacy of using an electric heat blanket (EHB) as an alternative method to study HS and we observed similar changes in body temperature indices, production and metabolism to natural and climate-controlled HS experiments. Additionally, we validated the EHB model (using a pair-feeding design) and confirmed that lowered nutritional plane explains only ~50% of the decreased milk yield.

In study 3 (Chapter 4), we evaluated a dietary electrolyte, osmolyte, and energetic compounds (EOEC) on physiological parameters in heat-stressed cows using the EHB model. Feeding EOEC appears to increase heat dissipation by increasing skin temperature. Additionally, dietary EOEC altered metabolic and the blood gas profile in heat-stressed cows and thus is a promising nutritional strategy to utilize during the warm summer months.

In study 4 (Chapter 5), we examined a dietary Saccharomyces cerevisiae fermentation product (SCFP) on body temperature indices, metabolism, and acute phase protein response (APPR) in heat-stressed dairy cows using the EHB model. Results demonstrated that HS caused an APPR and that feeding SCFP could be beneficial at reducing circulating cortisol and the APPR.

In study 5 (Chapter 6), we investigated the effects of providing an oral supplement containing Ca and live yeast on circulating Ca and production parameters in immune-challenged dairy cows. Results suggest that increased circulating Ca improves production parameters during inflammation. Overall, utilizing an oral supplement may be a valuable management strategy to improve animal welfare and productivity during and following immunoactivation.

In conclusion, employing the EHB model provides an excellent new platform for discovery research and for evaluating pragmatic HS mitigation strategies. Results demonstrated that feeding EOEC could benefit heat dissipation and metabolism. In addition, feeding SCFP may be useful at reducing the amount of “stress” and immune activation during HS. Furthermore, infusing i.v. LPS appears to be an effective technique to model hypocalcemia and to evaluate dietary strategies aimed at increasing circulating Ca in periparturient lactating dairy cows. Collectively, understanding the biology of HS is important for identifying mitigation strategies aimed at ameliorating the negative consequences of HS in dairy cow.

Onion powder and talc were inoculated with one of three groups of Salmonella enterica or a putative surrogate, Enterococcus faecium NRRL B-2354, and the radiation sensitivity of S. enterica was compared to E. faecium. For both inoculated onion powder and inoculated talc, D10-values were greater for E. faecium than any of the three groups of S. enterica. The survival of E. faecium in irradiated talc was used to estimate the potential survival of S. enterica in irradiated spices. Onion powder, dried oregano, whole cumin seeds or peppercorns were mixed with talc inoculated with either S. enterica (previously associated with a foodborne disease outbreak) or E. faecium and irradiated. The D10-values were calculated for each bacterial group and compared between E. faecium and S. enterica within each spice. For each spice, the D10-value for E. faecium was either not statistically different from (P < 0.05) S. entericaor greater than that of S. enterica (onion powder). Quadratic and linear models were developed to allow the estimation of potential surviving populations, and potential decimal reductions of S. enterica, based on surviving populations and decimal reductions determined with E. faecium. The use of E. faecium and these mathematical models would allow a processor to validate an irradiation process by estimating the reduction in S. enterica, based on the population reductions of E. faecium.

Background: Our understanding of the pig transcriptome is limited. RNA transcript diversity among nine tissues was assessed using poly(A) selected single-molecule long-read isoform sequencing (Iso-seq) and Illumina RNA sequencing (RNA-seq) from a single White cross-bred pig.

Results: Across tissues, a total of 67,746 unique transcripts were observed, including 60.5% predicted proteincoding, 36.2% long non-coding RNA and 3.3% nonsense-mediated decay transcripts. On average, 90% of the splice junctions were supported by RNA-seq within tissue. A large proportion (80%) represented novel transcripts, mostly produced by known protein-coding genes (70%), while 17% corresponded to novel genes. On average, four transcripts per known gene (tpg) were identified; an increase over current EBI (1.9 tpg) and NCBI (2.9 tpg) annotations and closer to the number reported in human genome (4.2 tpg). Our new pig genome annotation extended more than 6000 known gene borders (5′ end extension, 3′ end extension, or both) compared to EBI or NCBI annotations. We validated a large proportion of these extensions by independent pig poly(A) selected 3′-RNAseq data, or human FANTOM5 Cap Analysis of Gene Expression data. Further, we detected 10,465 novel genes (81% non-coding) not reported in current pig genome annotations. More than 80% of these novel genes had transcripts detected in > 1 tissue. In addition, more than 80% of novel intergenic genes with at least one transcript detected in liver tissue had H3K4me3 or H3K36me3 peaks mapping to their promoter and gene body, respectively, in independent liver chromatin immunoprecipitation data.

Conclusions: These validated results show significant improvement over current pig genome annotations.

The wealth of information deliverable from transcriptome sequencing (RNA-seq) is significant, however current applications for variant detection still remain a challenge due to the complexity of the transcriptome. Given the ability of RNA-seq to reveal active regions of the genome, detection of RNA-seq SNPs can prove valuable in understanding the phenotypic diversity between populations. Thus, we present a novel computational workflow named VAP (Variant Analysis Pipeline) that takes advantage of multiple RNA-seq splice aware aligners to call SNPs in non-human models using RNA-seq data only. We applied VAP to RNA-seq from a highly inbred chicken line and achieved high accuracy when compared with the matching whole genome sequencing (WGS) data. Over 65% of WGS coding variants were identified from RNA-seq. Further, our results discovered SNPs resulting from post transcriptional modifications, such as RNA editing, which may reveal potentially functional variation that would have otherwise been missed in genomic data. Even with the limitation in detecting variants in expressed regions only, our method proves to be a reliable alternative for SNP identification using RNA-seq data. The source code and user manuals are available at https://modupeore.github.io/VAP/.

The genus Brevibacterium harbors many members important for cheese ripening. We performed real-time quantitative PCR (qPCR) to determine the abundance of Brevibacterium on rinds of Vorarlberger Bergkäse, an Austrian artisanal washed-rind hard cheese, over 160 days of ripening. Our results show that Brevibacterium are abundant on Vorarlberger Bergkäse rinds throughout the ripening time. To elucidate the impact of Brevibacterium on cheese production, we analysed the genomes of three cheese rind isolates, L261, S111, and S22. L261 belongs to Brevibacterium aurantiacum, whereas S111 and S22 represent novel species within the genus Brevibacterium based on 16S rRNA gene similarity and average nucleotide identity. Our comparative genomic analysis showed that important cheese ripening enzymes are conserved among the genus Brevibacterium. Strain S22 harbors a 22 kb circular plasmid which encodes putative iron and hydroxymethylpyrimidine/thiamine transporters. Histamine formation in fermented foods can cause histamine intoxication. We revealed the presence of a putative metabolic pathway for histamine degradation. Growth experiments showed that the three Brevibacterium strains can utilize histamine as the sole carbon source. The capability to utilize histamine, possibly encoded by the putative histamine degradation pathway, highlights the importance of Brevibacterium as key cheese ripening cultures beyond their contribution to cheese flavor production.

Leg lameness is a prevalent welfare concern in broiler chickens, and biologically-relevant environmental enrichment designed to increase physical activity and decrease leg disorders is lacking. Therefore, a novel enrichment device was developed with the objective to motivate broilers to voluntarily move, thus improving leg health, production outcomes, and overall animal well-being. Research completed thus far has shown that the enrichment device was successful in improving performance. The work described here aims to validate that the change in these performance outcomes, particularly feed intake, was due to the enrichment itself, and to study if the device directly led to the birds to the feeder. Results show that in the first 9 days, 71% of birds went to the feeder during 4-min enrichment periods or within 5 mins following enrichment. Over weeks 1-6, 61% of birds went to the feeder during or within 5 mins after the enrichment periods. These data indicate that the environmental enrichment was successful in leading birds to the feeder and improving performance.

There is limited scientific knowledge in the literature that provides producers with effective handling tools for moving a non-ambulatory grow-finish pig on-farm that accounts for caretaker safety and pig welfare. Two objectives were defined to meet this goal: 1) determine durability, caretaker physiology, movement ease, overall time, and caretaker preference for sked, deer sled, modified deer sled, and wean-to-finish mat when moving 18 grow-finish pig cadavers on-farm, 2) evaluate durability, pig physiology and behavior, and overall time for the sked, revised deer sled, and ice fishing sled when moving 18 non-ambulatory grow-finish pigs on-farm.

Observed results from these studies showed that this version of a modified wean-to-finish mat and modified deer sled is not a suitable handling tool for manually moving grow-finish pig cadavers and we suggest that it will also not be suitable for moving non-ambulatory grow-finish pigs on a commercial farm. However, this version of the sked and deer sled are suitable handling tools for manually moving grow-finish pig cadavers on a commercial farm. In addition, this version of the sked, revised deer sled and ice fishing sled are suitable handling tools for manually moving non-ambulatory grow-finish pigs on a commercial farm. In conclusion, this research team supports four handling tools for manually moving non-ambulatory grow-finish pigs on-farm.

The objective of this study was to estimate the impact of a single injection of extended-release eprinomectin on economically relevant production variables in beef cows and calves as well as subsequent feedlot health, performance, and carcass traits of calves compared with a traditional, short duration anthelmintic. Animals from 13 cooperator herds across seven states were stratified within herd and assigned to one of two treatments; injectable doramectin (DOR; Dectomax; n = 828) or injectable eprinomection (EPR; Longrange; n = 832). Fecal samples were randomly collected from a subset of cows at both treatment and the end of grazing to evaluate fecal egg count (FEC). Continuous and categorical data were analyzed using the MIXED and GLIMMIX procedures of SAS, respectively. Cow treatment body weight (BW) and final BW were not different (P ≥ 0.40) between treatments. There were no differences (P ≥ 0.12) between treatments in cow ADG, change in BW, or body condition scores during the grazing season. While FEC at treatment did not differ (P = 0.18), cows treated with EPR had lower final FEC at the end of the grazing season (P = 0.02) and a greater reduction of FEC over the grazing season (P = 0.01). Calf treatment BW, weaning BW, and ADG did not differ between treatments (P ≥ 0.34). Incidence of pinkeye tended to be less (P = 0.06) for cows treated with EPR but was not different for calves (P = 0.43). Conception to AI, overall pregnancy rates, and calving interval were not different between treatments (P ≥ 0.45). A subset of calves from each herd was sent to Tri-County Steer Carcass Futurity (TCSCF) feedlot for the finishing phase. Calf BW did not differ at initiation of feeding (P = 0.20). While EPR calves tended to be heavier at reimplantation (P = 0.07), final BW and overall ADG were not different between treatments (P ≥ 0.13). Health records indicated lower morbidity for EPR calves (P = 0.05). Carcass performance including HCW, dressing percent, backfat, KPH, REA, YG, were not different between treatment groups (P ≥ 0.12). However, EPR calves had a greater marbling score, greater average quality grade (P < 0.01), and higher proportion of calves that graded average choice or greater (P = 0.03). Results of this study indicate no difference in cow or preweaning calf performance, however, carcass quality in the feedlot phase was improved. Thus, economic analysis indicates opportunities for return on investment if animals treated with EPR have improved health status and/or carcass quality during the feeding phase.

Economic losses in the nursery phase of pork production can largely be attributed to the underdeveloped gastrointestinal tract (GIT) and immune system of weaned pigs, which greatly increases their susceptibility to potential pathogens. Enterotoxigenic Escherichia coli (ETEC) is a common enteric pathogen that results in secretory diarrhea and leads to reductions in growth performance and increases in mortality, morbidity, and treatment costs. Vaccinations and antibiotics have traditionally been used as means of prevent or mitigating ETEC infections; however, with the increase in antibiotic resistant pathogens and pressure from the consumer population, pork producers are in need of alternative strategies. Dietary inclusion of direct-fed microbials have been proposed as a potential dietary strategy to prevent or mitigate the negative effects associated with weaning and ETEC infections due to their suggested ability to exert beneficial effects on the host’s GIT, immune system, and microbial population. Nonetheless, having an understanding of how disease physiologically impacts the pig is essential to developing effective alternative dietary technologies to prevent or mitigate disease. Therefore, the objectives of this thesis were to characterize the impact of an ETEC challenge in weaned pigs on growth, intestinal function, immune response, and mucosal microbiota, and to evaluate the potential beneficial effects of Bacillus-based DFMs under normal physiological and ETEC challenge conditions.

To achieve our objective, two experiments were conducted. The results of Experiment 1 (Chapter 2) revealed that Bacillus-based DFMs did not affect body weight or growth performance of healthy nursery pigs housed in a commercial-like environment compared to the control diet, which may be a result of contrasting effects of the DFM products and dietary ingredients, such as zinc oxide. Experiment 2 (Chapters 3 and 4) investigated the impact of an F18 ETEC challenge on growth performance, intestinal function, immune response, and mucosal microbiota of weaned pigs, as well as evaluated the potential protective effects of two Bacillus-based DFMs (DFM1 And DFM2). The ETEC challenge increased fecal scores, reduced rectal temperature, impaired intestinal barrier integrity, altered immune response, resulting in reduced growth performance during 10-d post-challenge period. The ETEC challenge also induced dysbiosis in the mucosa-associated microbiota by increasing the abundance of potentially pathogenic bacteria and reducing the abundance of beneficial microbes. Our results suggest that the supplementation of DFM2 may potentially alleviate negative impacts of an ETEC challenge by improving intestinal barrier integrity and reducing bacterial pathogen load in the GIT microbial population.