Carbohydrates represent the largest components of swine diets in the U.S. due to the different chemical and physical characteristics among sources; carbohydrates can exert different effects in the gastrointestinal tract of pigs. The primary purpose of this dissertation was to improve our understanding of the role of simple and complex carbohydrates on various nutritional interventions for nursery and growing pigs. To achieve this objective 5 experiments were conducted. A set of three experiments were designed to determine the effect of a prototype Lactobacillus acidophilus fermentation product (FP). The first experiment evaluated the FP with and without dietary antibiotics on growth performance. Second, a similar experiment was performed to determine the effect of the FP and lactose (LA) level on growth performance in an antibiotic-free diet scenario. A more mechanistic experiment was conducted to determine the effects of LA and the FP, on diet digestibility, N balance and intestinal function of weaned pigs. A set of- two experiments were designed to investigate the role of insoluble in two scenarios. The first experiment evaluated the effect of insoluble fiber on the efficacy of the phytase enzyme in nursery pigs when fed diets limiting in P content. The second was designed to determine if the impact of increasing insoluble fiber level on the digestibility of energy and nutrients- differs when diets are adjusted to constant nutrient (CN) or to constant ingredient composition (CI). Results of Exp 1 supported the positive role of dietary antibiotics on the growth performance of nursery pigs. However, the addition of FP or increasing the level of LA (from 7.5 to 15%) were not effective strategies to improve these growth variables (Exp 1 and Exp 2). Results of Exp 3 showed that LA benefits the weaned pig by improving nutrient utilization rather than by improving gut function and structure. Results also showed a little benefit of using FP alone or in combination with LA and that there were no additive effects between the two (LA and FP), at least under the conditions of this study. Results of Exp 4 clearly showed that the efficacy of

phytase to release P from phytate is not impaired by insoluble fiber. Results of Exp 5 showed that increasing the insoluble fiber level in the form of DDGS decreased the digestibility of most dietary components. Results also showed that the use of the CI method for formulating diets resulted in a lower digestibility of insoluble fiber compared with diets formulated using the CN method. This demonstrated the bias that can be introduced into this type of experiment by the formulation method.

The approach of this experiment was to apply the regression method for the estimation of endogenous intestinal losses of ether extract (EEE) when pigs are fed complete diets ad libitum and using dietary levels of fat typical of those employed in commercial situations. A total of 40 gilts (PIC 337 sires × C22 or C29) were allotted to individual pens and randomly assigned to diets (8 pigs per treatment) with 5 different levels of acid hydrolyzed ether extract (AEE). The dietary treatments consisted of a corn-soybean meal diet with no added fat (L1); a corn-soy diet with 6% each of corn distiller’s dried grains with solubles (DDGS), corn germ meal, and wheat middlings (L2); the L2 diet but with 12% each of corn DDGS, corn germ meal, and wheat middlings (L3); the L2 diet plus soybean oil to equalize the NE concentration of the L2 diet with L1 (L4); and the L3 diet plus soybean oil to equalize the NE concentration of the L3 diet with L1 (L5). Pigs received feed and water ad libitum for the growing period (initial BW = 38.5 ± 1.2 kg) and the finishing period (initial BW = 73.82 ± 2.9 kg). A quadratic broken-line model was employed to estimate the response of apparent total tract digestibility (ATTD) of AEE to dietary AEE level. The average true total tract digestibility (TTTD) of AEE and endogenous losses of AEE were estimated using regression analysis of dietary AEE intake (g/kg of DM) against apparent digested AEE (g/kg of DMI). The ATTD of AEE increased in curvilinear fashion as dietary AEE level increased in growing and in finishing pigs (P < 0.001). This suggests an influence of EEE on the ATTD of AEE estimates. The linear regression of apparent digested AEE against dietary AEE intake (L1–L5; P < 0.001, R2 = 0.99 for growing pigs and P < 0.001, R2 = 0.99 for finishing pigs) estimated greater EEE (P < 0.05) and TTTD of AEE (P < 0.05) for growing than finishing pigs. Estimated EEE from growing pigs ranged between 18.1 and 20.2 g/kg of DMI, while TTTD of AEE ranged between 96.40% and 100.70%. In finishing pigs, EEE ranged between 21.6 and 23.8 g/kg of DMI and TTTD of AEE ranged between 91.30% and 95.25%. In conclusion, EEE under practical conditions is estimated to be 19.2 g/kg of DMI in growing and 22.7 g/kg of DMI in finishing pigs.

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.

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/.

Feed grains are processed to improve their value in pig diets by exposing kernel contents to enzymatic and microbial action. The objective of this study was to quantify the effect of reducing mean particle size (PS) of wheat grain ground with two different grinding methods (GMs) on the apparent total tract digestibility (ATTD) of nutrients and energy in growing and finishing pigs. Forty-eight barrows were housed in individual pens for 11 d for two periods. Pigs were randomly assigned to a 3 × 2 × 2 factorial experimental design: three target mean PS of wheat grain (300, 500, and 700 µm), two GMs (roller mill and hammermill), and two body weight (BW) periods (growing period; initial BW of 54.9 ± 0.6 kg and finishing period; initial BW of 110.7 ± 1.4 kg). Diets contained one of six hard red wheat grain samples, vitamins, minerals, and titanium dioxide as an indigestible marker. Feed allowance provided 2.5 (for the two lightest pigs in each treatment) or 2.7 (for the remaining six pigs in each treatment) times the estimated daily maintenance energy requirement for each growth stage. Fecal samples were collected for the last 3 d of each period. Data were analyzed as a linear mixed model with pig as a random effect and PS, GM, and BW period and their interactions as fixed effects utilizing the MIXED procedure of SAS. Growing pigs had greater (P < 0.05) ATTD of dry matter (DM), gross energy (GE), N, acid hydrolyzed ether extract (AEE), and neutral detergent fiber (NDF) by lowering mean PS from 700 to 500 μm using either a roller mill or a hammermill. However, digestibility did not increase when PS was reduced from 500 to 300 μm, except for AEE (P < 0.05). Finishing pigs had greater ATTD of DM, GE, N, AEE, and NDF by lowering mean PS with a hammermill from 700 to 500 μm (P < 0.05), but it was greater for 500 μm than for 300 μm (P < 0.05). Using a roller mill reduced the ATTD of DM and NDF by lowering PS from 700 to 300 μm (P < 0.05). The ATTD of GE decreased by lowering PS from 700 to 500 μm with a roller mill (P < 0.05) for finishing pigs. The ATTD of N and AEE for finishing pigs were similar from 700 to 300 μm when ground by a roller mill. These data suggest that the PS that maximized digestibility for a hammermill is 500 μm for both growing and finishing pigs. However, for the roller mill, the PS resulting in the best digestibility were 500 and 700 μm for growing and finishing pigs, respectively.

The experimental objective was to determine the role of mean particle size (PS), grinding method, and body weight (BW) category on nutrient, fiber, and energy digestibility of corn. A total of 48 barrows were housed in individual pens and randomly assigned to one of six dietary treatments for 11 d at two BW categories (55 kg and 110 kg). The six treatments consisted of corn ground at three different targeted mean PSs (300, 500, and 700 µm) using either a roller mill or a hammermill. Fecal samples were collected for the last 3 d of each feeding period. Titanium dioxide was used as an indigestible marker. Digestibility data were analyzed as a linear mixed model using the MIXED procedure of SAS. Finishing pigs had greater apparent total tract digestibility (ATTD) of dry matter (DM), gross energy (GE), and N than growing pigs (P = 0.02, P = 0.01, and P <0.01, respectively). The ATTD of DM, GE, and N was similar in pigs fed hammermilled corn across all PS treatments. However, in roller-milled corn, they increased as PS was reduced (P < 0.05). The ATTD of acid-hydrolyzed ether extract (AEE) in growing pigs was similar between corn ground at 700 and 500 µm, but it was increased by further reducing PS to 300 µm (P < 0.05). In finishing pigs, the ATTD of AEE increased as mean PS decreased from 700 to 300 µm (P < 0.05). The ATTD of AEE was similar in hammermilled corn at all three PS treatments. On the other hand, the ATTD of AEE was similar in corn ground in a roller mill to 700 and 500 µm, but it increased when PS was reduced to 300 µm (P < 0.05). In conclusion, reducing PS of corn with a roller mill increased digestibility of energy and nutrients, but there was less effect using a hammermill. It is possible that differences in SD, distribution, chemical composition, and the shape of the particles resulting from the two grinding processes help to explain the different response.

The objective of this study was to determine the impact of reducing the mean particle size (PS) of corn distillers dried grains with solubles (DDGS) with a hammermill (HM) or with a roller mill (RM) on the apparent total tract digestibility (ATTD) of dry matter (DM), gross energy (GE), N, acid hydrolyzed ether extract (AEE), and fiber components in growing and finishing pigs. Twenty-four growing barrows were housed in individual pens and were randomly assigned to a 3 × 2 factorial design (n = 8): three grinding methods [either corn DDGS ground with an HM to a PS of 450 μm; corn DDGS ground with an RM to a PS of 450 μm; and corn DDGS with a PS of 670 μm (not further ground)] and two body weight (BW) periods (growing pigs with an average initial BW of 54.7 ± 0.9 kg, and finishing pigs with an average initial BW of 107.8 ± 1.5 kg BW). Fecal samples were collected for each BW period in the last 3 d of an 11-d feeding period. Titanium dioxide was used as an indigestible marker. Digestibility data were analyzed using the MIXED procedure of SAS. Results showed that finishing pigs tended to have better ATTD of DM than growing pigs (P = 0.09) and had increased ATTD of GE and N than growing pigs (P = 0.03 and P < 0.01, respectively). On the other hand, growing pigs had better ATTD of AEE than finishing pigs (P = 0.01). Pig BW period did not affect the ATTD of neutral detergent fiber (NDF), acid detergent fiber (ADF), and hemicellulose. Reducing the mean PS of corn DDGS with either HM or RM (from 670 to 450 µm) improved the ATTD of DM and GE (P < 0.01 and P < 0.01), tended to improve the ATTD of N (P = 0.08), and improved the ATTD of AEE (P < 0.01). No effect of reducing PS was observed for the ATTD of NDF, ADF, or hemicellulose. There were no differences between HM and RM in any of the ATTD variables tested. In conclusion, reducing PS of corn DDGS from 670 to 450 μm either with an HM or with an RM improved the digestibility of DM, GE, and AEE and modestly improved the digestibility of N in growing and finishing pigs. However, reducing the PS of corn DDGS did not affect the digestibility of fiber components.

The objective of this study was to determine the differences in response to distillers dried grains with solubles (DDGS) level under constant nutrient or floating nutrient concentrations. A total of 21 ileal-cannulated gilts (33.1 ± 0.4 kg body weight) were randomly allotted to one of seven dietary treatments in a 3-period incomplete Latin square design (n = 9). Treatments consisted of a 0% DDGS basal diet, plus diets containing 15%, 30%, or 45% DDGS. Diets were formulated using one of two different formulation methods: 1) constant nutrient (CNU) where nutrients were held equal to the basal diet or 2) constant ingredients (CIN) where DDGS were added at the expense of corn and all other ingredients remained constant, so nutrient levels were allowed to “float.” Chromic oxide was added to the diets at 0.5% as an indigestible marker. Increasing the level of DDGS decreased the apparent ileal digestibility (AID) of dry matter (DM), gross energy (GE), starch, dispensable amino acids (AA), and fiber components (P < 0.050). The decrease in the AID of Lys, Met, Thr, and Trp was more pronounced under CNU compared with the CIN formulation method (P < 0.050). The decrease in the AID of hemicellulose was less pronounced under CNU compared with the CIN formulation method (P = 0.045). There was a DDGS level × formulation method interaction for the AID of acid hydrolyzed ether extract (AEE; P = 0.015); for the CNU formulation method, increasing level of DDGS decreased the AID of AEE from 0% to 30% and remained similar from 30% to 45% DDGS, whereas the CIN had no effect on the AID of AEE. Increasing the level of DDGS decreased the apparent total tract digestibility (ATTD) of DM, GE, and fiber components (P < 0.050), except for acid detergent fiber, which was not affected. The decrease in the ATTD of insoluble dietary fiber and total dietary fiber was less pronounced under CNU compared with CIN (P < 0.050). The ATTD of AEE decreased for CNU compared with CIN (P < 0.010). In conclusion, increasing the insoluble fiber level in the form of DDGS decreased the digestibility of most dietary components, including DM, GE, starch, insoluble fiber, and AA. The CNU and CIN formulation methods are equivalent when evaluating the digestibilities of DM, GE, starch, crude protein, and AA (when they were not added in purified synthetic forms). Differences between CNU and CIN formulation methods were detected for the digestibility of insoluble fiber, fat, and essential AA (when added as crystalline AA).

The objective of this study was to determine the effects of lactose (LA) and a prototype Lactobacillus acidophilus fermentation product (FP) on growth performance, diet digestibility, nitrogen (N) balance, and intestinal function of weaned pigs. Twenty-eight newly weaned pigs [approximately 21 d of age; initial body weight (BW) = 5.20 ± 0.15 kg] were housed in metabolism crates and assigned to one of four treatments (n = seven pigs per treatment) corresponding to a 2 × 2 factorial design: with (LA+; 15% inclusion) or without (LA−) LA and with (FP+) or without (FP−) the prototype FP (1 g of FP per kilogram of diet; Diamond V, Cedar Rapids, IA). Feed and water were provided ad libitum. At day 5, pigs were orally given lactulose and mannitol to assess small intestinal permeability. Fecal samples were collected on days 5–9 to determine the apparent total tract digestibility (ATTD) of dry matter (DM), gross energy (GE), and N. Total urine output and fecal samples were collected on days 10–13 to determine N retention. On day 15, all pigs were euthanized to collect intestinal lumen and tissue samples. Data were analyzed for the main effects of LA and FP and their interaction using the MIXED procedure of SAS. Lactose improved average daily feed intake (ADFI; P = 0.017), the ATTD of DM (P = 0.014), the ATTD of GE (P = 0.028), and N retention (P = 0.043) and tended to increase the butyric acid concentration in the colon (P = 0.062). The FP tended to increase the digestibility of N (P = 0.090). Neither LA nor the FP affected intestinal barrier function or inflammation markers. The interaction between LA and FP affected intestinal morphology: in the jejunum, pigs fed LA+FP− had increased villus height compared with those fed LA+FP+ and LA−FP−, whereas LA+FP+ was intermediate (interaction P = 0.034). At the terminal ileum, pigs fed LA−FP+ and LA+FP− had increased villus height and villus: crypt compared with those fed LA−FP−, whereas LA+FP+ was intermediate (interaction P = 0.007 and P = 0.007, respectively). In conclusion, the addition of LA brings important nutritional attributes to nursery diets by improving feed intake, digestibility of DM and GE, and the N retention of weaned pigs; however, the functional capacity of LA to improve markers of intestinal function is limited. On the other hand, the FP showed only a mild increase in the digestibility of N but a limited capacity to improve markers of intestinal function.