Evaluation of the Effects of Flushing Feed Manufacturing Equipment with Chemically- Treated Rice Hulls on Porcine Epidemic Diarrhea Virus Cross Contamination During Feed Manufacturing

Various strategies have been proposed to mitigate potential risk of porcine epidemic diarrhea virus (PEDV) transmission via feed and feed ingredients. Wet decontamination has been found to be the most effective decontamination of feed mill surfaces; however, this is not practical on a commercial feed production-scale. Another potential mitigation strategy, easier to implement, would be using chemically-treated rice hulls flushed through the feed manufacturing equipment. The objective of this experiment was to determine the impact of MCFA- or formaldehyde-treated rice hull flush batches as potential PEDV mitigation strategies during feed manufacturing. Feed without evidence of PEDV RNA contamination was inoculated with PEDV. Based on PCR analysis, this feed had a Ct = 30.2 and was confirmed infective in bioassay. After manufacture of PEDV positive feed, untreated rice hulls, or rice hulls treated with Sal CURB, 2%, or 10% medium chain fatty acid blend (MCFA; 1:1:1 ratio of caproic, caprylic, and capric acid) were flushed through laboratory-scale mixers. For the untreated rice hulls, 3 of 6 samples had detectable PEDV RNA (avg. Ct = 41.4) while 1 of 6 Sal CURB treated rice hull flush samples and 2 of 6 of the 2% MCFA rice hull flush samples had detectable PEDV RNA. However, PEDV RNA was not detected in any of the 10% MCFA rice hull flush samples. Additionally, rice hulls treated with 10% MCFA were mixed and discharged through a production-scale mixer and bucket elevator following manufacturing of PEDV positive feed. In the production-scale system, no rice hull flush or feed samples from the mixer following chemically-treated rice hull flush had detectable PEDV RNA. However, one 10% MCFA rice hull sample collected from the bucket elevator discharge spout had detectable PEDV RNA. Dust collected following mixing of PEDV-contaminated feed had a large quantity of PEDV RNA (avg. Ct = 29.4). Dust collected immediately after the 10% MCFA rice hull flush batch had a reduced quantity of PEDV RNA (Ct = 33.7), and the subsequent feed following the 10% rice hull flush had no detectable PEDV RNA. Pigs inoculated with dust collected after manufacturing PEDV-positive feed were shedding PEDV RNA by 2 dpi and continued to have detectable RNA until necropsy. Dust collected from the 10% MCFA rice hull flush batch or the subsequent batch was not infective. Overall, the use of rice hull flushes effectively reduced the quantity of detectable RNA present after mixing a batch of PEDV-positive feed. Chemical treatment of rice hulls with Sal CURB and 10% MCFA provided additional reduction in detectable RNA present in the rice hull flush samples. Finally, dust collected after manufacturing PEDVinoculated feed contains a very high quantity of viral RNA and was found infective, demonstrating it has the potential to serve as a vector for PEDV transmission

Evaluating Medium Chain Fatty Acids as an Alternative to Chlortetracycline in Nursery Pig Diets

An experiment was conducted to evaluate medium chain fatty acids (MCFA) as a potential alternative to chlortetracycline (CTC) in nursery pigs. One hundred entire male pigs (initially 14.1 ± 1.6 lb body weight (BW) and weaned at 22 d of age) were used in a 29-d disease challenge study. Pigs were allowed 5 acclimation days after weaning, followed by 2 d of disease challenge with Enterotoxigenic β-hemolytic Escherichia coli (ETEC), serotype O149:K91: K88. After the challenge, pigs were allotted to a diet with 1 of 5 treatments: 1) control with no additives; 2) 400 g/ton CTC (Chlortet 200G, Eco Animal Health, London, United Kingdom); 3) 1.08% of a 1:1:1 blend of C6:0, C8:0, and C10:0 (Nuscience Group, Drongen, Belgium); 4) 3.93% developmental Product A (Nuscience Group, Drongen, Belgium); and 5) 1.04% developmental Product B (Kemin Industries, Des Moines, IA, USA). Treatments 3, 4, and 5 were included at rates to derive a 1% MCFA concentration in finished feed. Pigs were fed treatment diets for 14 days following the disease challenge to mimic a therapeutic dose of CTC and fed a common diet from d 14 to 21. There was no evidence of difference (P \u3e 0.10) of dietary treatment on growth performance from d 0 to 7 or d 14 to 21. From d 7 to 14, pigs fed diets with added CTC, 1:1:1 blend, or Product B had improved (P \u3c 0.05) F:G compared to those fed the control diet, with pigs fed diets with Product A intermediate. A treatment × day interaction for the ETEC fecal shedding was observed (P \u3c 0.05), which was driven by pigs fed diets with CTC having decreased (P \u3c 0.05) fecal shedding on d 7 than d 14, while those fed diets with Product B having greater (P \u3c 0.05) fecal ETEC shedding on d 1 than d 14. While other disease markers, such as fecal score, plasma urea nitrogen, and haptoglobin, decreased (P \u3c 0.05) with time, they were not affected (P \u3e 0.05) by dietary treatment. In conclusion, supplementing ETECchallenged nursery pigs with MCFA-based dietary treatments led to similar growth performance as a therapeutic dose of 400 g/ton of CTC. Further research is needed to confirm the mode of action, most effective MCFA or combination, and effective dose of medium chain fatty acids in ETEC-challenged pigs

Effects of Oceanfeed Swine Feed Additive on Performance of Sows and Their Offspring

The objective of this study was to evaluate the effects of the Oceanfeed SwineTM feed additive on sows and their offspring performance. Oceanfeed Swine is a product created by drying and blending a selected mix of brown, red, and green seaweeds (Ocean Harvest Technology, Galway, Ireland). A total of 28 sows (DNA 241, DNA Genetics, Columbus, NE) and litters were used from d 30 of gestation until weaning (d 20 of lactation). Treatments consisted of providing a control diet (n = 14 sows) or the Oceanfeed Swine diet (n = 14 sows) added at 0.5% of complete diet in gestation and 0.66% in lactation diets. Then offspring of these sows were used for the nursery and grow-finish portions of the study. In the nursery, a total of 360 weanling pigs (DNA 241 × 600), were used in a 56-d trial. There were 5 pigs per pen and 18 replications per treatment. Treatments were arranged in a split-plot design with sow treatment (control vs. Oceanfeed Swine diet) as a whole-plot and nursery treatment (control vs. Oceanfeed Swine diet) as the sub-plot. In the nursery phase, the Oceanfeed Swine was added at 0.75% of the diet. During the nursery phase, fecal scoring was used to categorize fecal consistency and fecal samples were collected for microbial analysis. At the end of the nursery portion, pigs from two nursery pens within weight block and treatment were combined and moved to the finishing barn with approximately 10 pigs per pen and 9 replications per treatment. Pigs were weighed weekly (nursery) or every two weeks (finisher) to determine growth performance. At the conclusion of the finishing phase, all pigs were marketed for carcass data collection. The addition of the Oceanfeed Swine in sow diets during gestation and lactation did not influence (P \u3e 0.10) sow body weight (BW) at the end of gestation or at weaning. Also, there were no differences in colostrum yield, colostrum and milk composition, or litter performance between the two treatments during the lactation period. In the nursery, there was no evidence for the effect of sow by nursery treatment, interactions (P \u3e 0.10) observed. For the overall nursery period (weaning to day 56), no sow or nursery effects were observed for growth performance. For fecal scores, there was a sow × nursery treatment interaction (P \u3c 0.062) observed. In general, pigs weaned from control sows then fed the control diet, or pigs weaned from Oceanfeed Swine sows and fed Oceanfeed Swine had firmer fecal scores than the other two combinations. There was also a sow treatment by day interaction (P \u3c 0.007) observed with pigs weaned from control sows initially (day 7) having firmer feces than those weaned from sows fed Oceanfeed Swine in the nursery. However, by day 21, there appeared to be no differences in fecal consistency among pigs weaned from either sow treatment group. For microbial analysis, there was a marginally significant increase in the proportion of pigs with the families Peptostreptococcaceae and Veillonellaceae detected in the pigs from sows fed Oceanfeed Swine diets and fed Oceanfeed Swine compared with the control group (P = 0.085). Moreover, pigs from sows that were fed Oceanfeed Swine diet and then fed Oceanfeed Swine had an increased (P = 0.048) mean number of species detected within the family Ruminococcaceae and had a marginally significant increased (P = 0.076) mean number of species detected within the family Lachnospiraceae, two families that are generally considered beneficial. Finally, pigs from sows that were fed Oceanfeed Swine diets, then fed Oceanfeed Swine had marginally significant lower (P = 0.069) mean number of species detected within the family Fusobacteriaceae, a family that is generally considered pathogenic. In the finishing period, a sow by finishing treatment interaction (P = 0.061) was observed for F/G from d 0 to 55 after weaning. Pigs weaned from sows fed control diets and switched to Oceanfeed Swine in the nursery or pigs weaned from sows fed Oceanfeed Swine then fed control diets in the finishing phase had improved F/G compared with the two other treatment combinations. No evidence for any main effect differences (P \u3e 0.10) was observed on overall growth performance. However, sow by finishing treatment interaction (P = 0.059) was observed for backfat depth. This inter- action was similar to the day 0 to 55 F/G response. Pigs weaned from sows fed control diets and then fed control diets in the nursery/finishing period had greater backfat depth and decreased percentage lean compared with other treatment combinations (sow treatment × nursery/finishing treatment interaction (P \u3c 0.073)). In summary, the addition of Oceanfeed Swine in gestation, lactation, and the nursery/finishing phases had no consistent effect on sow or litter performance. However, a shift in the microbiota was observed in the pigs from sows fed Oceanfeed Swine diet, then fed Oceanfeed Swine with higher number of species detected within Ruminoccocaceae and Lachnospiraceae families that are generally considered beneficial and lower number of species within the family Fusobacteriaceae that is normally considered pathogenic

Effect of Medium Chain Fatty Acid Supplementation on Nursery Pig Fecal Microbial Populations

A total of 360 pigs [DNA (Columbus, NE) 400 × 200; initially = 14.8 ± 0.15 lb] were used to evaluate the effects of dietary medium chain fatty acid (MCFA) addition on fecal microbial populations. Upon arrival at the nursery, pigs were randomized to pens (5 pigs per pen) and allowed a 6-d acclimation period, at which point pens of pigs were blocked by body weight (BW) and randomized to dietary treatment (9 pens per treatment). Medium chain fatty acids (Sigma Aldrich, St. Louis, MO) included hexanoic (C6), octanoic (C8), and decanoic (C10), and were guaranteed ≥ 98% purity. Treatment diets were formulated to meet or exceed NRC requirements for 15- to 25-lb pigs. Fecal samples were collected from pigs fed control and 1.5% MCFA blend (1:1:1 ratio C6, C8, and C10) diets on d 0 and d 14 and analyzed using 16s rDNA sequencing. A total of 6 phyla were identified with ≥ 1% relative abundance for at least one of the treatment × day analysis combinations. The largest proportion of relative abundance on a phyla level on d 14 consisted of Firmicutes (54% control, 44% MCFA) and Bacteroidetes (32% control, 43% MCFA). A marginally significant treatment × day interaction was observed in the Proteobacteria phylum (P = 0.080), where relative abundance did not change over time in pigs fed the control diet (P = 0.848), whereas a marginally significant decrease over time was observed in pigs fed the MCFA diet (P = 0.092). There was no evidence of an effect of MCFA addition over time for the relative abundance of the remaining phyla (treatment × day, P ≥ 0.359). The main effect of day indicated a significant increase over time in the Tenericutes phylum (P = 0.008) and a significant decrease over time in the Proteobacteria (P = 0.017) and Spirochaetes phyla (P = 0.020). A Firmicutes:Bacteroidetes ratio was calculated, and there was no evidence of a treatment × day interaction (P = 0.338) or day effect (P = 0.211). A total of 23 microbial families were detected at ≥ 1% relative abundance for at least one of the treatment × day analysis combinations. The families with the greatest relative abundance were Prevotellaceae, Ruminococcaceae, and S24-7 families, which had ≥ 10% relative abundance for at least one of the treatment × day analysis combinations. There was no evidence of an effect of MCFA addition over time on the relative abundance for any family (treatment × day, P ≥ 0.123). For both treatments, a reduction over time was observed for Ruminococcaceae (P = 0.048), Lachnospiraceae (P = 0.004), Christensenellaceae (P = 0.004), Spirochaetaceae (P = 0.029), Bacteroidaceae (P = 0.010), and Succinivibrionaceae (P = 0.029) families. An increase in relative abundance over time was observed for the unclassified Clostridiales (P = 0.019), Clostridiaceae (P \u3c 0.001), unclassified RF39 (P = 0.008), and Clostridiales; and other (P \u3c 0.001) families. No evidence of a difference in alpha diversity was observed for either Chao1 (estimate of species richness) or observed operational taxonomic units (OTUs). In summary, adding 1.5% MCFA blend in swine nursery diets did not appear to significantly alter the composition of fecal microbial populations compared to a control diet using 16s rDNA sequencing analysis. Changes in microbial populations were observed over time with both treatments. Further investigation into the mechanism by which MCFA addition benefits growth performance is necessary. Moreover, additional studies into understanding the interactions between MCFA and the gastrointestinal microbiome are warranted due to its well-known inactivation effects on selected microbes

Determining the Minimum Inhibitory Concentration of Medium Chain Fatty Acids for Generic Escherichia coli, Enterotoxigenic Escherichia coli, Salmonella Typhimurium, and Campylobacter coli

Research has demonstrated that medium chain fatty acids (MCFA) can serve as reduction strategies for bacterial and viral pathogens in animal feed and ingredients. However, it is unknown how the type or level of MCFA impact bacteria growth. This can be tested through a minimum inhibitory concentration (MIC) benchtop assay, which identifies the lowest concentration of a chemical that prevents visible growth of a bacterium. The objective of this study was to 1) determine the MCFA MIC of C6:0, C8:0, C10:0, and C12:0 for generic Escherichia coli, Enterotoxigenic Escherichia coli, Salmonella Typhimurium, Campylobacter coli, and Clostridium perfringens; 2) determine the MIC of commercial based MCFA products against the same bacteria; and 3) determine the effect of 2 commercial based MCFA products on the quantification of Enterotoxigenic Escherichia coli. For Exp. 1 and 2, MIC were determined by modified microbroth dilution method using a 96 well microtiter plate with a concentration of 105 CFU/mL for each bacterial strain. For Exp. 3, the two products selected for quantification were mixed with a complete swine diet and inoculated with two concentrations (106 or 102 CFU/g of feed) of a NalR strain of Enterotoxigenic Escherichia coli (ETEC) for bacterial enumeration. From Exp. 1, the MIC of MCFA varied among bacteria species. The lowest MIC of the MCFA was 0.43% of a 1:1:1 blend of C6:0, C8:0, and C10:0 for Campylobacter coli, 0.25% C12:0 for Clostridium perfringens, 0.60% 1:1:1 blend for generic Escherichia coli, 0.53% C6:0 for ETEC, and 0.40% C6:0 for Salmonella Typhimurium. In Exp. 2, products containing high concentrations of C6:0 or C8:0 had lower MIC in gram negative bacteria. In Exp. 3, feed containing either of the commercial based MCFA products reduced (linear, P \u3c 0.05) quantifiable ETEC. Overall, the inhibitory efficacy of MCFA varies among bacteria species. This suggests that MCFA mixtures may provide a wider spectrum of bacterial control. As commercial products containing MCFA become available for livestock, it is important to consider the interaction between MCFA chain length and concentration on the potential to effectively mitigate various feed-based bacteria

Further host-genomic characterization of total antibody response to PRRSV vaccination and its relationship with reproductive performance in commercial sows: genome-wide haplotype and zygosity analyses

Background The possibility of using antibody response (S/P ratio) to PRRSV vaccination measured in crossbred commercial gilts as a genetic indicator for reproductive performance in vaccinated crossbred sows has motivated further studies of the genomic basis of this trait. In this study, we investigated the association of haplotypes and runs of homozygosity (ROH) and heterozygosity (ROHet) with S/P ratio and their impact on reproductive performance. Results There was no association (P-value ≥ 0.18) of S/P ratio with the percentage of ROH or ROHet, or with the percentage of heterozygosity across the whole genome or in the major histocompatibility complex (MHC) region. However, specific ROH and ROHet regions were significantly associated (P-value ≤ 0.01) with S/P ratio on chromosomes 1, 4, 5, 7, 10, 11, 13, and 17 but not (P-value ≥ 0.10) with reproductive performance. With the haplotype-based genome-wide association study (GWAS), additional genomic regions associated with S/P ratio were identified on chromosomes 4, 7, and 9. These regions harbor immune-related genes, such as SLA-DOB, TAP2, TAPBP, TMIGD3, and ADORA. Four haplotypes at the identified region on chromosome 7 were also associated with multiple reproductive traits. A haplotype significantly associated with S/P ratio that is located in the MHC region may be in stronger linkage disequilibrium (LD) with the quantitative trait loci (QTL) than the previously identified single nucleotide polymorphism (SNP) (H3GA0020505) given the larger estimate of genetic variance explained by the haplotype than by the SNP. Conclusions Specific ROH and ROHet regions were significantly associated with S/P ratio. The haplotype-based GWAS identified novel QTL for S/P ratio on chromosomes 4, 7, and 9 and confirmed the presence of at least one QTL in the MHC region. The chromosome 7 region was also associated with reproductive performance. These results narrow the search for causal genes in this region and suggest SLA-DOB and TAP2 as potential candidate genes associated with S/P ratio on chromosome 7. These results provide additional opportunities for marker-assisted selection and genomic selection for S/P ratio as genetic indicator for litter size in commercial pig populations.This article is published in Sanglard, Leticia P., Yijian Huang, Kent A. Gray, Daniel CL Linhares, Jack Dekkers, Megan C. Niederwerder, Rohan L. Fernando, and Nick VL Serão. "Further host-genomic characterization of total antibody response to PRRSV vaccination and its relationship with reproductive performance in commercial sows: genome-wide haplotype and zygosity analyses." Genetics Selection Evolution 53, no. 1 (2021): 1-17. DOI: 10.1186/s12711-021-00676-5. Copyright 2021 The Author(s). Attribution 4.0 International (CC BY 4.0). Posted with permission

Novel complete methanogenic pathways in longitudinal genomic study of monogastric age-associated archaea

Abstract Background Archaea perform critical roles in the microbiome system, including utilizing hydrogen to allow for enhanced microbiome member growth and influencing overall host health. With the majority of microbiome research focusing on bacteria, the functions of archaea are largely still under investigation. Understanding methanogenic functions during the host lifetime will add to the limited knowledge on archaeal influence on gut and host health. In our study, we determined lifelong archaea dynamics, including detection and methanogenic functions, while assessing global, temporal and host distribution of our novel archaeal metagenome-assembled genomes (MAGs). We followed 7 monogastric swine throughout their life, from birth to adult (1–156 days of age), and collected feces at 22 time points. The samples underwent gDNA extraction, Illumina sequencing, bioinformatic quality and assembly processes, MAG taxonomic assignment and functional annotation. MAGs were utilized in downstream phylogenetic analysis for global, temporal and host distribution in addition to methanogenic functional potential determination. Results We generated 1130 non-redundant MAGs, representing 588 unique taxa at the species level, with 8 classified as methanogenic archaea. The taxonomic classifications were as follows: orders Methanomassiliicoccales (5) and Methanobacteriales (3); genera UBA71 (3), Methanomethylophilus (1), MX-02 (1), and Methanobrevibacter (3). We recovered the first US swine Methanobrevibacter UBA71 sp006954425 and Methanobrevibacter gottschalkii MAGs. The Methanobacteriales MAGs were identified primarily during the young, preweaned host whereas Methanomassiliicoccales primarily in the adult host. Moreover, we identified our methanogens in metagenomic sequences from Chinese swine, US adult humans, Mexican adult humans, Swedish adult humans, and paleontological humans, indicating that methanogens span different hosts, geography and time. We determined complete metabolic pathways for all three methanogenic pathways: hydrogenotrophic, methylotrophic, and acetoclastic. This study provided the first evidence of acetoclastic methanogenesis in archaea of monogastric hosts which indicated a previously unknown capability for acetate utilization in methanogenesis for monogastric methanogens. Overall, we hypothesized that the age-associated detection patterns were due to differential substrate availability via the host diet and microbial metabolism, and that these methanogenic functions are likely crucial to methanogens across hosts. This study provided a comprehensive, genome-centric investigation of monogastric-associated methanogens which will further improve our understanding of microbiome development and functions