From Snoot to Tail: A Brief Review of Influenza Virus Infection and Immunity in Pigs

Pigs play an important role in influenza A virus (IAV) epidemiology because they support replication of human, avian, and swine origin viruses and act as an IAV reservoir for pigs and other species, including humans. Moreover, novel IAVs with human pandemic potential may be generated in pigs. To minimize the threat of IAVs to human and swine health, it is crucial to understand host defense mechanisms that restrict viral replication and pathology in pigs. In this article, we review IAV strains circulating in the North American swine population, as well as porcine innate and acquired immune responses to IAV, including recent advances achieved through immunological tools developed specifically for swine. Furthermore, we highlight unique aspects of the porcine pulmonary immune system, which warrant consideration when developing vaccines and therapeutics to limit IAV in swine or when using pigs to model human IAV infections.

Integrative profiling of gene expression and chromatin accessibility elucidates specific transcriptional networks in porcine neutrophils

Neutrophils are vital components of the immune system for limiting the invasion and proliferation of pathogens in the body. Surprisingly, the functional annotation of porcine neutrophils is still limited. The transcriptomic and epigenetic assessment of porcine neutrophils from healthy pigs was performed by bulk RNA sequencing and transposase accessible chromatin sequencing (ATAC-seq). First, we sequenced and compared the transcriptome of porcine neutrophils with eight other immune cell transcriptomes to identify a neutrophil-enriched gene list within a detected neutrophil co-expression module. Second, we used ATAC-seq analysis to report for the first time the genome-wide chromatin accessible regions of porcine neutrophils. A combined analysis using both transcriptomic and chromatin accessibility data further defined the neutrophil co-expression network controlled by transcription factors likely important for neutrophil lineage commitment and function. We identified chromatin accessible regions around promoters of neutrophil-specific genes that were predicted to be bound by neutrophil-specific transcription factors. Additionally, published DNA methylation data from porcine immune cells including neutrophils were used to link low DNA methylation patterns to accessible chromatin regions and genes with highly enriched expression in porcine neutrophils. In summary, our data provides the first integrative analysis of the accessible chromatin regions and transcriptional status of porcine neutrophils, contributing to the Functional Annotation of Animal Genomes (FAANG) project, and demonstrates the utility of chromatin accessible regions to identify and enrich our understanding of transcriptional networks in a cell type such as neutrophils.

Effect of dietary β-glucan on intestinal microbial diversity and Salmonella vaccine immunogenicity and efficacy in pigs

Alternatives to antibiotics to improve animal performance, limit the negative impact of infectious disease, and/or reduce colonization with foodborne pathogens is a major focus of animal agricultural research. β-glucans, a generally-recognized-as-safe (GRAS) product derived from various sources, are used in swine and can serve as both a prebiotic and/or stimulant of the immune system given the expression of β-glucan receptors on immune cells. When supplied in the diet of nursery pigs, it is unclear how dietary additives, particularly those known to modulate immune status, impact immunogenicity and efficacy of mucosal-delivered vaccines. Salmonellosis is one of the most common bacterial foodborne infections in the United States, and consumption of contaminated pork is a major source of human infection. Reduction of foodborne Salmonella in pigs via vaccination is one strategy to reduce contamination risk and subsequently reduce human disease. We examined the ability of dietary β-glucan to modulate fecal microbial diversity, and immunogenicity and efficacy of a mucosally-delivered, live-attenuated Salmonella vaccine during the nursery period. While dietaryβ-glucan did modulate fecal alpha diversity, it did not alter the induction of peripheral Salmonella-specific IFN-γ secreting Tcells or Salmonella-specific IgA in oral fluids. In addition, vaccination reduced Salmonella enterica serovar Typhimurium fecal shedding and tissue colonization. Overall, addition of β-glucan to the nursery diet of pigs impacted the microbiota but did not alter mucosal vaccine immunogenicity and efficacy.

Effects of β-glucan on Salmonella enterica serovar Typhimurium swine colonization and microbiota alterations

BACKGROUND

The 2017 Veterinary Feed Directive eliminated the use of medically important antibiotics for growth promotion of food animals; thus, alternative growth promoters are highly desirable by food animal producers to enhance animal health and reduce pathogen colonization, including the human foodborne pathogen Salmonella. β(1-3)(1-6)-D-glucan (β-glucan) is a soluble fiber with prebiotic characteristics; it has been shown to modulate immune and intestinal functions that strengthen swine resistance to health challenges such as bacterial infections when supplemented in the diets of growing pigs. The current study evaluated the effects of a β-glucan product on gut microbial community structure as well as Salmonella shedding and intestinal colonization.

RESULTS

Five-week-old pigs were fed a β-glucan amended diet at 500 g/ton (n = 13) or a non-amended control diet (n = 14) for three weeks, followed by inoculation of the 27 pigs with 1 × 10⁹ colony forming units of Salmonella enterica serovar Typhimurium strain UK1. While remaining on the respective diets, fecal samples collected at 2, 4, 7, and 16 days post-inoculation (dpi) were similar for Salmonella shedding counts between the two diets. At 16 dpi, Salmonella counts were significantly lower in the cecal contents of the β-glucan-fed pigs (P = 0.0339) and a trend towards a reduction was observed in the Peyer's patches region of the ileum (P = 0.0790) compared to the control pigs. Pigs fed β-glucan for three weeks exhibited an increase in members of the Clostridia class in their fecal microbial communities, and after inoculation with Salmonella, several potentially beneficial microorganisms were enriched in the microbiota of β-glucan-fed pigs (Lactobacillus, Ruminococcaceae, Prevotellaceae, Veillonellaceae, Bifidobacterium and Olsenella).

CONCLUSION

Administration of β-glucan altered the swine gut microbiome and reduced Salmonella colonization in the cecal contents.

Intestinal location- and age-specific variation of intraepithelial T lymphocytes and mucosal microbiota in pigs

Intraepithelial T lymphocytes (T-IELs) are T cells located within the epithelium that provide a critical line of immune defense in the intestinal tract. In pigs, T-IEL abundances and phenotypes are used to infer putative T-IEL functions and vary by intestinal location and age, though investigations regarding porcine T-IELs are relatively limited. In this study, we expand on analyses of porcine intestinal T-IELs to include additional phenotypic designations not previously recognized in pigs. We describe non-conventional CD8α⁺CD8β^- αβ T-IELs that were most prevalent in the distal intestinal tract and primarily CD16⁺CD27^-, a phenotype suggestive of innate-like activation and an activated cell state. Additional T-IEL populations included CD8α⁺CD8β⁺ αβ, CD2⁺CD8α⁺ γδ, and CD2⁺CD8α^- γδ T-IELs, with increasing proportions of CD16⁺CD27^- phenotype in the distal intestine. Thus, putative non-conventional, activated T-IELs were most abundant in the distal intestine within multiple γδ and αβ T-IEL populations. A comparison of T-IEL and respective mucosal microbial community structures across jejunum, ileum, and cecum of 5- and 7-week-old pigs revealed largest community differences were tissue-dependent for both T-IELs and the microbiota. Between 5 and 7 weeks of age, the largest shifts in microbial community compositions occurred in the large intestine, while the largest shifts in T-IEL communities were in the small intestine. Therefore, results indicate different rates of community maturation and stabilization for porcine T-IELs and the mucosal microbiota for proximal versus distal intestinal locations between 5 and 7 weeks of age. Collectively, data emphasize the intestinal tract as a site of location- and age-specific T-IEL and microbial communities that have important implications for understanding intestinal health in pigs.

Regional epithelial cell diversity in the small intestine of pigs

Understanding regional distribution and specialization of small intestinal epithelial cells is crucial for developing methods to control appetite, stress, and nutrient uptake in swine. To establish a better understanding of specific epithelial cells found across different regions of the small intestine in pigs, we utilized single-cell RNA sequencing (scRNA-seq) to recover and analyze epithelial cells from duodenum, jejunum, and ileum. Cells identified included crypt cells, enterocytes, BEST4 enterocytes, goblet cells, and enteroendocrine (EE) cells. EE cells were divided into two subsets based on the level of expression of the EE lineage commitment gene, NEUROD1. NEUROD1hi EE cells had minimal expression of hormone-encoding genes and were dissimilar to EE cells in humans and mice, indicating a subset of EE cells unique to pigs. Recently discovered BEST4 enterocytes were detected in both crypts and villi throughout the small intestine via in situ staining, unlike in humans, where BEST4 enterocytes are found only in small intestinal villi. Proximal-to-distal gradients of expression were noted for hormone-encoding genes in EE cells and nutrient transport genes in enterocytes via scRNA-seq, demonstrating regional specialization. Regional gene expression in EE cells and enterocytes was validated via quantitative PCR (qPCR) analysis of RNA isolated from epithelial cells of different small intestinal locations. Though many genes had similar patterns of regional expression when assessed by qPCR of total epithelial cells, some regional expression was only detected via scRNA-seq, highlighting advantages of scRNA-seq to deconvolute cell type-specific regional gene expression when compared to analysis of bulk samples. Overall, results provide new information on regional localization and transcriptional profiles of epithelial cells in the pig small intestine.

Intraepithelial lymphocytes in the pig intestine: T cell and innate lymphoid cell contributions to intestinal barrier immunity

Intraepithelial lymphocytes (IELs) include T cells and innate lymphoid cells that are important mediators of intestinal immunity and barrier defense, yet most knowledge of IELs is derived from the study of humans and rodent models. Pigs are an important global food source and promising biomedical model, yet relatively little is known about IELs in the porcine intestine, especially during formative ages of intestinal development. Due to the biological significance of IELs, global importance of pig health, and potential of early life events to influence IELs, we collate current knowledge of porcine IEL functional and phenotypic maturation in the context of the developing intestinal tract and outline areas where further research is needed. Based on available findings, we formulate probable implications of IELs on intestinal and overall health outcomes and highlight key findings in relation to human IELs to emphasize potential applicability of pigs as a biomedical model for intestinal IEL research. Review of current literature suggests the study of porcine intestinal IELs as an exciting research frontier with dual application for betterment of animal and human health.

Evaluation of digestively resistant or soluble fibers, short- and medium-chain fatty acids, trace minerals, and antibiotics in nonchallenged nursery pigs on performance, digestibility, and intestinal integrity

Three experiments (EXP) were conducted to determine the effect of feed additives on performance, intestinal integrity, gastrointestinal volatile fatty acids (VFA), and energy and nutrient digestion in nonchallenged nursery pigs. In EXP 1, 480 pigs (6.36-kg body weight, BW) were placed into 96 pens with 5 pigs/pen, and allotted to 1 of 10 dietary treatments: 1) negative control containing no feed additive (NC), 2) NC + 44 mg chlortetracycline and 38.5 mg tiamulin/kg diet (CTsb), 3) NC + 5% resistant potato starch (RSpo), 4) NC + 5% soluble corn fiber (SCF), 5) NC + 5% sugar beet pulp (SBP), 6) NC + 0.30% fatty acid mix (FAM), 7) NC + 0.10% phytogenic blend of essential oils and flavoring compounds (PHY), 8) NC + 50 mg Cu and 1,600 mg zinc oxide/kg diet (CuZn), 9) NC + 5% resistant corn starch (RScn), and 10) NC + 0.05% β-glucan (BG) for 28 d. There was no impact of dietary treatment on BW gain or feed intake (P ≥ 0.22). Pigs fed diets containing SCF, CTsb, and RSpo resulted in microbial community differences compared to pigs fed the NC (P < 0.05). In EXP 2, 48 barrows (12.8 kg BW) were selected at the end of EXP 1 and fed the same dietary treatments they had previously received: 1) NC, 2) NC + 5% RScn, 3) NC + 5% SCF, and 4) NC + FAM for 8 d. There was no effect of feeding diets containing RScn, SCF, or FAM on in vivo intestinal permeability (P ≤ 0.21). Ileal or colon pH, concentrations of VFA did not differ due to dietary treatment (P ≥ 0.36), but pigs fed diets containing FAM resulted in a greater butyric acid concentration in the cecum compared to pigs fed the NC (P ≤ 0.05). In EXP 3, 156 pigs (6.11 kg BW) were placed into 52 pens with 3 pigs/pen and allotted to 1 of 4 dietary treatments arranged in a factorial manner: 1) NC, 2) NC + 5% RSpo, 3) NC + 0.30% FAM, and 4) NC + 5% RSpo + 0.30% FAM for 24 d. Feeding pigs diets containing RSpo did not affect BW gain (P = 0.91) while pigs fed diets containing FAM grew improved BW gain (P = 0.09). Colonic butyric acid concentrations were greater in pigs fed diets containing RSpo (P = 0.03), while pigs fed diets containing FAM exhibited reduced total VFA concentrations (P = 0.11). The results indicate that supplementing diets with digestively resistant but fermentable fibers, short- and medium-chain fatty acids, or antibiotics do not have a consistent effect, positive or negative, on markers of intestinal integrity or barrier function, intestinal VFA patterns, ATTD of energy and nutrients, or on pig performance.

Intestinal single-cell atlas reveals novel lymphocytes in pigs with similarities to human cells

Single-cell RNA sequencing of porcine ileal lymphocytes reveals similarities to human cells and discovery of porcine intestinal innate lymphoid cells.

Lymphocytes can heavily influence intestinal health, but resolving intestinal lymphocyte function is challenging as the intestine contains a vastly heterogeneous mixture of cells. Pigs are an advantageous biomedical model, but deeper understanding of intestinal lymphocytes is warranted to improve model utility. Twenty-six cell types were identified in the porcine ileum by single-cell RNA sequencing and further compared with cells in human and murine ileum. Though general consensus of cell subsets across species was revealed, some porcine-specific lymphocyte subsets were identified. Differential tissue dissection and in situ analyses conferred spatial context, revealing similar locations of lymphocyte subsets in Peyer’s patches and epithelium in pig-to-human comparisons. Like humans, activated and effector lymphocytes were abundant in the ileum but not periphery of pigs, suggesting tissue-specific and/or activation-associated gene expression. Gene signatures for peripheral and ileal innate lymphoid cells newly discovered in pigs were defined and highlighted similarities to human innate lymphoid cells. Overall, we reveal novel lymphocyte subsets in pigs and highlight utility of pigs for intestinal research applications.

Assessment of DNA methylation in porcine immune cells reveals novel regulatory elements associated with cell-specific gene expression and immune capacity traits

Background

Genetics studies in the porcine immune system have enhanced selection practices for disease resistance phenotypes and increased the efficacy of porcine models in biomedical research; however limited functional annotation of the porcine immunome has hindered progress on both fronts. Among epigenetic mechanisms that regulate gene expression, DNA methylation is the most ubiquitous modification made to the DNA molecule and influences transcription factor binding as well as gene and phenotype expression. Human and mouse DNA methylation studies have improved mapping of regulatory elements in these species, but comparable studies in the pig have been limited in scope.

Results

We performed whole-genome bisulfite sequencing to assess DNA methylation patterns in nine pig immune cell populations: CD21⁺ and CD21⁻ B cells, four T cell fractions (CD4⁺, CD8⁺, CD8⁺CD4⁺, and SWC6γδ⁺), natural killer and myeloid cells, and neutrophils. We identified 54,391 cell differentially methylated regions (cDMRs), and clustering by cDMR methylation rate grouped samples by cell lineage. 32,737 cDMRs were classified as cell lowly methylated regions (cLMRs) in at least one cell type, and cLMRs were broadly enriched in genes and regions of intermediate CpG density. We observed strong correlations between differential methylation and expression across immune cell populations, with cell-specific low methylation disproportionately impacting genes exhibiting enriched gene expression in the same cell type. Motif analysis of cLMRs revealed cell type-specific enrichment of transcription factor binding motifs, indicating that cell-specific methylation patterns may influence accessibility by trans-acting factors. Lastly, cDMRs were enriched for immune capacity GWAS SNPs, and many such overlaps occurred within genes known to influence immune cell development and function (CD8B, NDRG1).

Conclusion

Our DNA methylation data improve functional annotation of the porcine genome through characterization of epigenomic regulatory patterns that contribute to immune cell identity and function, and increase the potential for identifying mechanistic links between genotype and phenotype.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08773-5.

Short Chain Fatty Acids and Bacterial Taxa Associated with Reduced Salmonella enterica serovar I 4,[5],12:i:- Shedding in Swine Fed a Diet Supplemented with Resistant Potato Starch

Salmonella enterica serovar I 4,[5],12:i:- is a foodborne pathogen of concern because many isolates are multidrug-resistant (resistant to ≥3 antimicrobial classes) and metal tolerant. In this study, three in-feed additives were individually tested for their ability to reduce Salmonella I 4,[5],12:i:- shedding in swine: resistant potato starch (RPS), high amylose corn starch, and a fatty acid blend, compared with a standard control diet over 21 days. Only RPS-fed pigs exhibited a reduction in Salmonella fecal shedding, different bacterial community compositions, and different cecal short chain fatty acid (SCFA) profiles relative to control animals. Within the RPS treatment group, pigs shedding the least Salmonella tended to have greater cecal concentrations of butyrate, valerate, caproate, and succinate. Additionally, among RPS-fed pigs, several bacterial taxa (Prevotella_7, Olsenella, and Bifidobacterium, and others) exhibited negative relationships between their abundances of and the amount of Salmonella in the feces of their hosts. Many of these same taxa also had significant positive associations with cecal concentrations of butyrate, valerate, caproate, even though they are not known to produce these SCFAs. Together, these data suggest the RPS-associated reduction in Salmonella shedding may be dependent on the establishment of bacterial cross feeding interactions that result in the production of certain SCFAs. However, directly feeding a fatty acid mix did not replicate the effect. RPS supplementation could be an effective means to reduce multidrug-resistant (MDR) S. enterica serovar I 4,[5],12:i:- in swine, provided appropriate bacterial communities are present in the gut. IMPORTANCE Prebiotics, such as resistant potato starch (RPS), are types of food that help to support beneficial bacteria and their activities in the intestines. Salmonella enterica serovar I 4,[5],12:i:- is a foodborne pathogen that commonly resides in the intestines of pigs without disease, but can make humans sick if unintentionally consumed. Here we show that in Salmonella inoculated pigs, feeding them a diet containing RPS altered the colonization and activity of certain beneficial bacteria in a way that reduced the amount of Salmonella in their feces. Additionally, within those fed RPS, swine with higher abundance of these types of beneficial bacteria had less Salmonella I 4,[5],12:i:- in their feces. This work illustrates likely synergy between the prebiotic RPS and the presence of certain gut microorganisms to reduce the amount of Salmonella in the feces of pigs and therefore reduce the risk that humans will become ill with MDR Salmonella serovar I 4,[5],12:i:-.

Gene signatures for intestinal and peripheral innate lymphoid cells in pigs reveal tissue-specific imprinting and similarities to human cells via single-cell RNA sequencing

Intestinal innate lymphoid cells (iILCs) impact intestinal health outcomes, but study of iILCs in humans is limited. Human peripheral ILCs (pILCs) are easily obtained but may vary substantially from iILCs, thus requiring comparison of iILCs and pILCs to determine applicability of pILCs as surrogates to study iILC function. Pigs have anatomic, physiological, nutritional, and immune similarities to humans that are lacking in rodent models, making pigs a relevant biomedical model; however, ILCs are poorly defined in pigs. Single-cell RNA sequencing was performed to compare porcine iILCs to pILCs and determine potential similarities of porcine to human ILCs. Porcine pILCs matched porcine natural killer (NK) cell descriptions, while iILCs were annotated as group 1 and group 3 ILCs. Gene modules obtained independent of cell annotations were distilled to core signatures of genes most highly specific to pILCs, pan-iILCs, group 1 iILCs, and group 3 iILCs. The pILC signature included conventional NK cell genes, while the group 3 iILC signature included genes associated with type 3 immunity. Pan-iILC and group 1 iILC signatures included genes associated with tissue residency, cell activation, and metabolism, indicating tissue-specific, activation-associated imprinting. Gene profiles were used to develop in situ iILC detection methods, establishing group 1 iILCs were intraepithelial, while group 3 iILCs resided in lamina propria/gut-associated lymphoid tissue. Findings indicated iILCs were ILC subsets distinct from pILCs, thus opposing pILCs as surrogates to study iILC dynamics. Moreover, gene profiles and in situ locations of iILCs drew close parallels to human iILCs functions, supporting pigs as a biomedical model for iILC research.

Research was supported by appropriated funds from USDA-ARS CRIS 5030-31320-004-00D, an appointment to the Agricultural Research Service (ARS) Research Participation Program administered by the Oak Ridge Institute for Science and Education (ORISE) through an interagency agreement between the U.S. Department of Energy (DOE) and the U.S. Department of Agriculture (USDA). ORISE is managed by ORAU under DOE contract number DE-SC0014664. All opinions expressed in this paper are the authors’ and do not necessarily reflect the policies and views of USDA, ARS, DOE, or ORAU/ORISE. This research used resources provided by the SCINet project of the USDA ARS project number 0500-00093-001-00-D.

Innate Memory Following Intravenous BCG in Neonatal Pigs

In adults and rodents, Bacillus Calmette-Guerin (BCG) inoculation alters innate immune cells via epigenetic and metabolic modifications resulting in heightened responses to subsequent microbial exposure (innate memory). Neonatal BCG vaccination can correlate to improved disease resistance in some human populations, but studies with human infants are extremely limited. Pigs are a relevant biomedical model for human disease and offer a path to directly asses neonatal innate memory to improve disease resilience. BCG administration in a weaned (3 week old) pig model elicited monocyte memory only with intravenous (IV) but not subcutaneous administration. Therefore, to evaluate induction of innate memory in neonates, 3–5 day old piglets received intravenous (IV) BCG or mock and ex vivo monocyte memory was assessed. At 3 and 6 weeks post-BCG, monocytes from the IV-BCG group had elevated TNF but not IL-1β production in response to LPS stimulation ex vivo, indicating neonatal BCG exposure induced innate memory. Interestingly, broncho-alveolar lavage cells from IV-BCG group had minimal differences compared to mock group in response to LPS, suggesting IV-BCG alters responses in peripheral monocytes differently than tissue resident myeloid-lineage cells. Overall, IV-BCG administration induced monocyte memory in neonatal pigs, highlighting piglets as a valuable model for continued study on the utility of BCG induced innate memory to improve disease resilience.

This work was funded by USDA-NIFA AFRI grant # 2019-07511 as part of the joint USDA-NIFA-NIH Dual Purpose with Dual Benefit: Research in Biomedicine and Agriculture Using Agriculturally Important Domestic Animal Species Program and USDA-ARS CRIS project 5030-32000-225-000D

Reference Transcriptomes of Porcine Peripheral Immune Cells Created Through Bulk and Single-Cell RNA Sequencing

Pigs are a valuable human biomedical model and an important protein source supporting global food security. The transcriptomes of peripheral blood immune cells in pigs were defined at the bulk cell-type and single cell levels. First, eight cell types were isolated in bulk from peripheral blood mononuclear cells (PBMCs) by cell sorting, representing Myeloid, NK cells and specific populations of T and B-cells. Transcriptomes for each bulk population of cells were generated by RNA-seq with 10,974 expressed genes detected. Pairwise comparisons between cell types revealed specific expression, while enrichment analysis identified 1,885 to 3,591 significantly enriched genes across all 8 cell types. Gene Ontology analysis for the top 25% of significantly enriched genes (SEG) showed high enrichment of biological processes related to the nature of each cell type. Comparison of gene expression indicated highly significant correlations between pig cells and corresponding human PBMC bulk RNA-seq data available in Haemopedia. Second, higher resolution of distinct cell populations was obtained by single-cell RNA-sequencing (scRNA-seq) of PBMC. Seven PBMC samples were partitioned and sequenced that produced 28,810 single cell transcriptomes distributed across 36 clusters and classified into 13 general cell types including plasmacytoid dendritic cells (DC), conventional DCs, monocytes, B-cell, conventional CD4 and CD8 αβ T-cells, NK cells, and γδ T-cells. Signature gene sets from the human Haemopedia data were assessed for relative enrichment in genes expressed in pig cells and integration of pig scRNA-seq with a public human scRNA-seq dataset provided further validation for similarity between human and pig data. The sorted porcine bulk RNAseq dataset informed classification of scRNA-seq PBMC populations; specifically, an integration of the datasets showed that the pig bulk RNAseq data helped define the CD4CD8 double-positive T-cell populations in the scRNA-seq data. Overall, the data provides deep and well-validated transcriptomic data from sorted PBMC populations and the first single-cell transcriptomic data for porcine PBMCs. This resource will be invaluable for annotation of pig genes controlling immunogenetic traits as part of the porcine Functional Annotation of Animal Genomes (FAANG) project, as well as further study of, and development of new reagents for, porcine immunology.

Characterization of circulating porcine immune cells using single-cell RNA-sequencing and comparison to human datasets

Pigs are part of global food security and serve as a valuable human biomedical model. Immunoreagent unavailability limits resolution of pig leukocyte populations by protein markers; thus, single-cell RNA-sequencing (scRNA) was used to characterize pig peripheral blood mononuclear cell (PBMC) populations and infer function based on transcriptional profiles and comparison to human datasets. Across seven PBMC samples partitioned and sequenced, 28,810 cells distributed across 36 clusters were classified into 13 general cell types including plasmacytoid dendritic cells (DC), conventional DCs, monocytes, more than ten B cell clusters including plasmablasts, conventional CD4 and CD8 αβ T cells, NK cells, and four clusters of γδ T cells. Signature gene sets for a publicly available human bulk RNA-seq dataset were assessed for relative enrichment in genes expressed in pig cells and substantial overlap in gene expression between specific pig and human PBMC populations was detected. Integration of pig scRNA with a public human scRNA dataset provided further validation for similarity between human and pig. Of four pig γδ T cell clusters, two had high prediction and mapping scores with human γδ T cells. The other two pig γδ T cell clusters had gene expression profiles predictive of human γδ T cells, but also human CD4 T central memory (Tcm) and innate lymphoid cells, suggesting innate and adaptive function of some pig γδ T cells. Pigs have a population of circulating double-positive (DP) CD4+CD8αα+ αβ T cells, and putative DP clusters had high prediction scores to human CD4 Tcm cells, supporting their classification in literature as memory cells. Overall, the data provided the first single-cell atlas for porcine PBMCs and comparison to human datasets.

Development and characterization of new swine immune reagents to understand immune correlates for vaccines, infection, and biomedical research outcomes

The USDA-NIFA Swine Immune Toolkit Initiative has a goal to generate priority immune reagents, based on inputs from veterinary immunology researchers worldwide, and pipeline them for marketing. Our efforts are aimed at expression of soluble proteins and production of panels of monoclonal antibodies (mAbs) using collaborations with commercial partners for protein expression and mAb production. Generation of new panels of mAbs reactive with porcine IL-5 and IL-21 have been initiated. Panels of mAbs to IL-6, IL-13, IL-17A, IL-28B, CXCL10, and BAFF are being screened for their reactivity in multiple immune assays. Reactivity tests of labeled anti-IL-6, -IL-17A, -IL-13 and -CXCL10 mAbs for intracellular staining of porcine myeloid and T cells using flow cytometry-based assays are in progress. Sensitive sandwich ELISA assays are now available for IL-17A, IL-13 and CXCL10; other targets are being screened for best mAb pairs for such assays. Planning for the generation of SLA-I & -II tetramers to identify swine CD4 and CD8 T cells specific for influenza virus peptides has been initiated. For each target, our goal is to provide the veterinary community with new commercial reagents and standardized techniques using these reagents for their research efforts. Tools and reagents generated by this project will undoubtedly advance swine immune, disease, vaccine, and biomedical research efforts.

Identification of porcine ileal innate lymphoid cells using single-cell RNA sequencing

Innate lymphoid cells (ILCs) are integral in maintaining intestinal defense and homeostasis, but intestinal ILCs have not been identified in pigs. Pigs are an important global food source and human biomedical model, thus identifying and characterizing porcine intestinal ILCs can have broad implications. Single-cell RNA sequencing of porcine ileal lymphocytes yielded 31,983 cells distributed across 54 clusters. Five clusters were closely related to T cell clusters yet lacked expression of the pan-T cell marker, CD3E. One cluster had high expression of genes related to type 3 immunity, including IL22, RORC, and CXCL8, indicating identification of putative ILC3s. The other four clusters expressed genes encoding for NK receptors (KLRK1, KLRC1, KLRD1) and effector molecules (CCL5, PRF1), yet they lacked expression of genes traditionally expressed by porcine NK cells (CD8A, KLRB1, HCST). Thus, we putatively identified the four clusters as ILC1s. Profiles of putative porcine ILC clusters were further compared to transcriptomic signatures of murine intestinal ILC subsets. Results indicated a relative enrichment of murine ILC3 gene signatures in the porcine ILC3 cluster, while relative enrichment of murine ILC1 gene signatures was observed for the other four clusters of porcine ILC1s. We further utilized single-cell gene expression profiles to develop a gating strategy to identify porcine intestinal ILCs as CD45+CD2+CD3ɛ−CD79α− lymphocytes at the protein level by flow cytometry. Altogether, the data allowed us to create the first transcriptomic descriptions of porcine intestinal ILCs and develop approaches to identify ILCs at the protein level, which will be applicable for future research.

Comparative annotation of porcine bone marrow cell types using scRNAseq

Pigs are important as a biomedical model and for worldwide meat production. Therefore, a better understanding of porcine hematopoiesis and immune system development could have a wide impact on human disease research and food production. The bone marrow represents a unique environment that is the major site of differentiation of stem cells and progenitors into mature blood cells. We performed scRNA-seq on bone marrow from healthy adult pigs and sequenced a total of 3,576 cells. After QC, 2,707 cells and 16,432 genes were used for downstream analysis. The porcine bone marrow cells were grouped into 15 distinct clusters and these relationships were mapped using non-linear dimensional reduction. To find markers that defined each cluster, we found a total of 3,335 differentially expressed genes using the non-parameteric Wilcoxon rank sum test. Further, pairwise differential expression testing and random forest models were used to evaluate the similarity between clusters and further define the unique features of each cluster. Using these defined markers, we were able to annotate the cell types for each cluster. The clusters represented a diverse set of cell types including myeloid and lymphoid cells, myeloid and lymphoid cell progenitors, and platelet and red blood cell progenitors. We validated these annotations using publicly available datasets including the CITE-seq database of human bone marrow mononuclear cells (Stuart et al., 2019). We also compared the expression profiles between similarly annotated cell types between human and pig. Our novel annotation of porcine bone marrow cells will be a resource for the study of porcine hematopoiesis and immune system development and help inform human translational biomedical research.

Innate and Adaptive Responses to Bacillus Calmette-Guerin in Young Pigs

Development of novel antibiotic alternatives is a critical One Health priority impacting both human and animal wellbeing. While the attenuated strain of M. bovis (Bacillus Calmette-Guerin, BCG) was developed as a vaccine against tuberculosis; recently, BCG has been observed to alter circulating monocytes leading to enhanced inflammatory immune responses to heterologous agonists. These changes can persist for months after the initial BCG exposure, and may serve to enhance innate immune health and reduce disease without the use of antibiotics. Following in vitro observation of innate training in pig monocytes, we wanted to study in vivo BCG responses in pigs as a potential path to enhance innate immunity. Young pigs were inoculated with BCG and weeks later ex vivo cytokine responses to innate TLR agonists and IFNγ response to M. bovis purified protein derivates (PPDb) were measured. PPDb stimulated PBMCs from pigs inoculated subcutaneous with 107 CFU of BCG produced the highest amount of IFNγ as compared to intramuscular inoculated or 106 CFU inoculated pigs. No differences were observed in PBMCs or monocytes stimulated ex vivo with TLR agonists between control and BCG inoculated pigs regardless of route or dose administered. Unlike cattle and humans, in pigs BCG does not seem to readily disseminate from the inoculation site, which may explain the lack of altered innate immune responses observed. Differences in adaptive immune responses indicated alterations to dose or route of BCG administration impacted immunogenicity. Future studies will employ intravenous BCG administration to understand if peripheral exposure to BCG is required to alter innate responses in circulating pig monocytes.

Butyrate alters lipopolysaccharide-induced inflammatory response by porcine monocytes

Continuous, low-level inflammation can have a negative impact on intestinal health. Butyrate is a short-chain fatty acid produced in the lower intestinal tract by microbial fermentation of dietary fibers and modulates immune cell responses through various mechanisms. Blood monocytes migrate into the intestine and respond to signals, including potential modulation by butyrate or in response to microbial components, such as lipopolysaccharide (LPS). To investigate the impact of butyrate on inflammatory response to LPS, porcine monocytes were either cultured with a combination of LPS and varying butyrate concentrations or pre-treated with butyrate before LPS exposure. Independent of butyrate, LPS stimulation of monocytes induced IL-1β and TNF production. Monocytes cultured just three hours (h) prior to LPS stimulation had reduced overall cytokine production, suggesting rapid phenotypic changes in monocytes. Butyrate had varying effects on the amount of cytokine produced in response to LPS. Specifically, low butyrate concentrations (0.25 mM) limited IL-1β production, but did not impact TNF production. Higher butyrate concentrations (&gt; 4 mM) limited TNF production to LPS stimulation. Pre-treatment of monocytes with butyrate for 3 h prior to LPS stimulation altered IL-1β production. Pre-treatment with 0.25 mM butyrate did not limit IL-1β production, but concentrations &gt; 4 mM did. In conclusion, reduction of LPS-induced cytokine production by porcine monocytes was dependent on butyrate concentration and exposure time relative to LPS exposure. Further work is ongoing to understand the mechanism of butyrate modulation of pig monocytes and inflammatory response to LPS for potential application in vivo.

The Role of Salmonella Genomic Island 4 in Metal Tolerance of Salmonella enterica Serovar I 4,[5],12:i:- Pork Outbreak Isolate USDA15WA-1

Multidrug-resistant (MDR; resistance to >3 antimicrobial classes) Salmonella enterica serovar I 4,[5],12:i:- strains were linked to a 2015 foodborne outbreak from pork. Strain USDA15WA-1, associated with the outbreak, harbors an MDR module and the metal tolerance element Salmonella Genomic Island 4 (SGI-4). Characterization of SGI-4 revealed that conjugational transfer of SGI-4 resulted in the mobile genetic element (MGE) replicating as a plasmid or integrating into the chromosome. Tolerance to copper, arsenic, and antimony compounds was increased in Salmonella strains containing SGI-4 compared to strains lacking the MGE. Following Salmonella exposure to copper, RNA-seq transcriptional analysis demonstrated significant differential expression of diverse genes and pathways, including induction of at least 38 metal tolerance genes (copper, arsenic, silver, and mercury). Evaluation of swine administered elevated concentrations of zinc oxide (2000 mg/kg) and copper sulfate (200 mg/kg) as an antimicrobial feed additive (Zn+Cu) in their diet for four weeks prior to and three weeks post-inoculation with serovar I 4,[5],12:i:- indicated that Salmonella shedding levels declined at a slower rate in pigs receiving in-feed Zn+Cu compared to control pigs (no Zn+Cu). The presence of metal tolerance genes in MDR Salmonella serovar I 4,[5],12:i:- may provide benefits for environmental survival or swine colonization in metal-containing settings.

Differential induction of innate memory in porcine monocytes by -glucan or bacillus Calmette-Guerin

Innate immunomodulation via induction of innate memory is one mechanism to alter the host’s innate immune response to reduce or prevent disease. Microbial products modulate innate responses with immediate and lasting effects. Innate memory is characterized by enhanced (training) or depressed (tolerance) innate immune responses, including pro-inflammatory cytokine production, to secondary exposure following a priming event. To investigate the ability of β-glucans and bacillus Calmette-Guerin to induce innate training or tolerance in pig cells, porcine monocytes were cultured with priming agonist (β-glucans or bacillus Calmette-Guerin) then re-stimulated 5 d later with a heterologous microbial agonist to determine induction of innate memory. Priming with β-glucan from Saccharomyces cerevisiae depressed IL-1β and TNF-α cytokine responses to re-stimulation with LPS, indicative of a tolerized state. However, bacillus Calmette-Guerin priming induced a trained state in porcine monocytes, as LPS re-stimulation enhanced IL-1β and TNF-α gene expression and protein production. We present the first evidence of innate memory in pig monocytes, with bacillus Calmette-Guerin (training) or Saccharomyces cerevisiae β-glucan (tolerance). Induction of a trained or tolerized state in vitro is a first step to identify agonists to alter the innate immune system at the animal level with the intent of enhancing disease resistance.

Changes in H3K27ac at Gene Regulatory Regions in Porcine Alveolar Macrophages Following LPS or PolyIC Exposure

Changes in chromatin structure, especially in histone modifications (HMs), linked with chromatin accessibility for transcription machinery, are considered to play significant roles in transcriptional regulation. Alveolar macrophages (AM) are important immune cells for protection against pulmonary pathogens, and must readily respond to bacteria and viruses that enter the airways. Mechanism(s) controlling AM innate response to different pathogen-associated molecular patterns (PAMPs) are not well defined in pigs. By combining RNA sequencing (RNA-seq) with chromatin immunoprecipitation and sequencing (ChIP-seq) for four histone marks (H3K4me3, H3K4me1, H3K27ac and H3K27me3), we established a chromatin state map for AM stimulated with two different PAMPs, lipopolysaccharide (LPS) and Poly(I:C), and investigated the potential effect of identified histone modifications on transcription factor binding motif (TFBM) prediction and RNA abundance changes in these AM. The integrative analysis suggests that the differential gene expression between non-stimulated and stimulated AM is significantly associated with changes in the H3K27ac level at active regulatory regions. Although global changes in chromatin states were minor after stimulation, we detected chromatin state changes for differentially expressed genes involved in the TLR4, TLR3 and RIG-I signaling pathways. We found that regions marked by H3K27ac genome-wide were enriched for TFBMs of TF that are involved in the inflammatory response. We further documented that TF whose expression was induced by these stimuli had TFBMs enriched within H3K27ac-marked regions whose chromatin state changed by these same stimuli. Given that the dramatic transcriptomic changes and minor chromatin state changes occurred in response to both stimuli, we conclude that regulatory elements (i.e. active promoters) that contain transcription factor binding motifs were already active/poised in AM for immediate inflammatory response to PAMPs. In summary, our data provides the first chromatin state map of porcine AM in response to bacterial and viral PAMPs, contributing to the Functional Annotation of Animal Genomes (FAANG) project, and demonstrates the role of HMs, especially H3K27ac, in regulating transcription in AM in response to LPS and Poly(I:C).

Intraepithelial T Cells Diverge by Intestinal Location as Pigs Age

T cells resident within the intestinal epithelium play a central role in barrier integrity and provide a first line of immune defense. Intraepithelial T cells (IETs) are among the earliest immune cells to populate and protect intestinal tissues, thereby giving them an important role in shaping gut health early in life. In pigs, IETs are poorly defined, and their maturation in young pigs has not been well-studied. Given the importance of IETs in contributing to early life and long-term intestinal health through interactions with epithelial cells, the microbiota, and additional environmental factors, a deeper characterization of IETs in pigs is warranted. The objective of this study was to analyze age- and intestinal location-dependent changes in IETs across multiple sites of the small and large intestine in pigs between 4- and 8-weeks of age. IETs increased in abundance over time and belonged to both γδ and αβ T cell lineages. Similar compositions of IETs were identified across intestinal sites in 4-week-old pigs, but compositions diverged between intestinal sites as pigs aged. CD2⁺CD8α⁺ γδ T cells and CD4^-CD8α⁺ αβ T cells comprised >78% of total IETs at all intestinal locations and ages examined. Greater percentages of γδ IETs were present in large intestine compared to small intestine in older pigs. Small intestinal tissues had greater percentages of CD2⁺CD8α^- γδ IETs, while CD2⁺CD8α⁺ γδ IET percentages were greater in the large intestine. Percentages of CD4^-CD8α⁺ αβ IETs increased over time across all intestinal sites. Moreover, percentages of CD27⁺ cells decreased in ileum and large intestine over time, indicating increased IET activation as pigs aged. Percentages of CD27⁺ cells were also higher in small intestine compared to large intestine at later timepoints. Results herein emphasize 4- to 8-weeks of age as a critical window of IET maturation and suggest strong associations between intestinal location and age with IET heterogeneity in pigs.

Innate Immunomodulation in Food Animals: Evidence for Trained Immunity?

Antimicrobial resistance (AMR) is a significant problem in health care, animal health, and food safety. To limit AMR, there is a need for alternatives to antibiotics to enhance disease resistance and support judicious antibiotic usage in animals and humans. Immunomodulation is a promising strategy to enhance disease resistance without antibiotics in food animals. One rapidly evolving field of immunomodulation is innate memory in which innate immune cells undergo epigenetic changes of chromatin remodeling and metabolic reprogramming upon a priming event that results in either enhanced or suppressed responsiveness to secondary stimuli (training or tolerance, respectively). Exposure to live agents such as bacille Calmette-Guerin (BCG) or microbe-derived products such as LPS or yeast cell wall ß-glucans can reprogram or "train" the innate immune system. Over the last decade, significant advancements increased our understanding of innate training in humans and rodent models, and strategies are being developed to specifically target or regulate innate memory. In veterinary species, the concept of enhancing the innate immune system is not new; however, there are few available studies which have purposefully investigated innate training as it has been defined in human literature. The development of targeted approaches to engage innate training in food animals, with the practical goal of enhancing the capacity to limit disease without the use of antibiotics, is an area which deserves attention. In this review, we provide an overview of innate immunomodulation and memory, and the mechanisms which regulate this long-term functional reprogramming in other animals (e.g., humans, rodents). We focus on studies describing innate training, or similar phenomenon (often referred to as heterologous or non-specific protection), in cattle, sheep, goats, swine, poultry, and fish species; and discuss the potential benefits and shortcomings of engaging innate training for enhancing disease resistance.

Dietary Soluble and Insoluble Fiber With or Without Enzymes Altered the Intestinal Microbiota in Weaned Pigs Challenged With Enterotoxigenic E. coli F18

Post-weaning diarrhea caused by enterotoxigenic E. coli (ETEC) causes significant economic losses for pig producers. This study was to test the hypotheses that an ETEC challenge disrupts intestinal microbial homeostasis and the inclusion of dietary soluble (10% sugar beet pulp) or insoluble fiber (15% corn distillers dried grains with solubles) with or without exogenous carbohydrases will protect or restore the gut microbial homeostasis in weaned pigs. Sixty crossbred piglets (6.9 ± 0.1 kg) were blocked by body weight and randomly assigned to one of six treatments (n = 10), including a non-challenged control (NC), ETEC F18-challenged positive control (PC), ETEC-challenged soluble fiber without (SF-) or with carbohydrases (SF+), and ETEC-challenged insoluble fiber without (IF-) or with carbohydrases (IF+). Pigs were housed individually and orally received either ETEC inoculum or PBS-sham inoculum on day 7 post-weaning. Intestinal contents were collected on day 14 or 15. The V4 region of the bacterial 16S rRNA was amplified and sequenced. High-quality reads (total 6,671,739) were selected and clustered into 3,330 OTUs. No differences were observed in α-diversity among treatments. The ileal microbiota in NC and PC had modest separation in the weighted PCoA plot; the microbial structures were slightly altered by SF+ and IF- compared with PC. The PC increased ileal Escherichia-Shigella (P < 0.01) and numerically decreased Lactobacillus compared to NC. Predicted functional pathways enriched in the ileal microbiota of PC pigs indicated enhanced activity of Gram-negative bacteria, in agreement with increased Escherichia-Shigella. The SF+ tended to decrease (P < 0.10) ileal Escherichia-Shigella compared to PC. Greater abundance of ileal Streptococcus, Turicibacter, and Roseburia and colonic Prevotella were observed in SF- and SF+ than PC (P < 0.05). Pigs fed IF + had greater Lactobacillus and Roseburia than PC pigs (P < 0.05). The ETEC challenge reduced total volatile fatty acid (VFA) compared with NC (P < 0.05). The SF+ tended to increase (P < 0.10) and SF- significantly increased (P < 0.05) colonic total VFA compared with PC. Collectively, ETEC challenge disrupted gut microbial homeostasis and impaired microbial fermentation capacity. Soluble fiber improved VFA production. Dietary fiber and carbohydrases altered microbiota composition to maintain or restore microbial homeostasis.

Evaluation of the recombinant proteins RlpB and VacJ as a vaccine for protection against Glaesserella parasuis in pigs

BACKGROUND

Glaesserella parasuis, the causative agent of Glӓsser's disease, is widespread in swine globally resulting in significant economic losses to the swine industry. Prevention of Glӓsser's disease in pigs has been plagued with an inability to design broadly protective vaccines, as many bacterin based platforms generate serovar or strain specific immunity. Subunit vaccines are of interest to provide protective immunity to multiple strains of G. parasuis. Selected proteins for subunit vaccination should be widespread, highly conserved, and surface exposed.

RESULTS

Two candidate proteins for subunit vaccination (RlpB and VacJ) against G. parasuis were identified using random mutagenesis and an in vitro organ culture system. Pigs were vaccinated with recombinant RlpB and VacJ, outer membrane proteins with important contributions to cellular function and viability. Though high antibody titers to the recombinant proteins and increased interferon-γ producing cells were found in subunit vaccinated animals, the pigs were not protected from developing systemic disease.

CONCLUSIONS

It appears there may be insufficient RlpB and VacJ exposed on the bacterial surface for antibody to bind, preventing high RlpB and VacJ specific antibody titers from protecting animals from G. parasuis. Additionally, this work confirms the importance of utilizing the natural host species when assessing the efficacy of vaccine candidates.

Toward Antibiotic Stewardship: Route of Antibiotic Administration Impacts the Microbiota and Resistance Gene Diversity in Swine Feces

Oral antibiotics are a critical tool for fighting bacterial infections, yet their use can have negative consequences, such as the disturbance of healthy gut bacterial communities and the dissemination of antibiotic residues in feces. Altering antibiotic administration route may limit negative impacts on intestinal microbiota and reduce selective pressure for antimicrobial resistance genes (ARG) persistence and mobility. Thus, a study was performed in pigs to evaluate route of therapeutic oxytetracycline (oxytet) administration, an antibiotic commonly used in the U.S. swine industry, on intestinal microbial diversity and ARG abundance. Given that oral antibiotics would be in direct contact with intestinal bacteria, we hypothesized that oral administration would cause a major shift in intestinal bacterial community structure when compared to injected antibiotic. We further postulated that the impact would extend to the diversity and abundance of ARG in swine feces. At approximately 3 weeks-of-age, piglets were separated into three groups (n = 21–22 per group) with two groups receiving oxytet (one via injection and the second via feed) and a third non-medicated group. Oxytet levels in the plasma indicated injected antibiotic resulted in a spike 1 day after administration, which decreased over time, though oxytet was still detected in plasma 14 days after injection. Conversely, in-feed oxytet delivery resulted in lower but less variable oxytet levels in circulation and high concentrations in feces. Similar trends were observed in microbial community changes regardless of route of oxytet administration; however, the impact on the microbial community was more pronounced at all time points and in all samples with in-feed administration. Fecal ARG abundance was increased with in-feed administration over injected, with genes for tetracycline and aminoglycoside resistance enriched specifically in the feces of the in-feed group. Sequencing of plasmid-enriched samples revealed multiple genetic contexts for the resistance genes detected and highlighted the potential role of small plasmids in the movement of antibiotic resistance genes. The findings are informative for disease management in food animals, but also manure management and antibiotic therapy in human medicine for improved antibiotic stewardship.

Intraepithelial T cell phenotype and function diverge by intestinal location with age

Intestinal intraepithelial T cells (IETs) provide a first line of defense against intestinal pathogens and play an important role in immune tolerance versus activation. In pigs, intestinal T cell populations stabilize at ~8 weeks of age, but IET phenotypes and function are poorly understood during the early postnatal period. Better understanding age- and location-dependent characteristics of porcine IETs may be useful in developing strategies to maintain intestinal integrity and improve health. To assess impacts of age and intestinal location on abundance and composition of IETs, sections of jejunum, ileum, cecum, and colon from 4-, 6-, and 8-week-old pigs were analyzed by histologic staining and flow cytometric analyses. IET abundance increased with age, and CD2+CD8α+γδ and CD4−CD8α+αβ T cells were the primary IET populationsin all samples (&gt;78%). Compositions of IETs were similar at all locations in 4-week-old pigs. As pigs aged, cecal and colonic IET compositions remained similar to each other but diverged from small intestinal IETs, while jejunal and ileal IET compositions diverged from both large intestinal IETs and each other. These findings indicate both intestinal location and age are drivers of IET heterogeneity. Small intestinal IETs had lower percentages of γδ IETs in 6- and 8-week-old pigs, and CD4−CD8α+αβ IETs increased in abundance at all intestinal locations as pigs aged. Percentages of CD27+IETs in ileum and large intestine decreased over time, but decreases were more drastic in large intestine, suggesting IETs in the distal but not proximal intestinal tract were activated as pigs aged. Small intestinal IET compositions closely resembled human IET populations, highlighting pigs as a biomedical model for IET research.

The transcriptional landscape of porcine peripheral blood immune cells

Blood consists of different immune cells with essential functions given by distinct molecular signatures including transcriptomic profiles. The porcine immune system shares many similarities with that in human; however, the porcine immune cell transcriptome has not been as comprehensively studied. To identify distinct transcriptomic profiles of major porcine peripheral blood immune cells, we employed magnetic separation and fluorescence activated cell sorting methods to isolate 9 different cell types from blood PBMCs from two healthy pigs, representing monocytes, neutrophils, NK cells and specific populations of T and B cells. We obtained deep individual cell type transcriptomes using RNA-seq, detecting up to 10,974 genes. Principal component analysis revealed appropriate clustering of replicate samples and the separation of T, B, NK and myeloid cell groups. Pairwise comparisons revealed significant expression of a large number of genes specific for monocytes, neutrophils and NK cells only, while enrichment analysis identified highly differentially expressed genes for all cell types. Gene Ontology term analysis showed high enrichment of biological processes related to the nature of each cell type (i.e., B cell antigen presentation enriched in B cell transcriptome). The gene enrichment and specific genes of porcine immune cells is being further validated in silico to human datasets using gene set enrichment analysis (GSEA), and in vitro using qRT-PCR analysis. Taken together, the gene expression profiles reported here is the first comprehensive transcriptomic study of circulating porcine immune cell types and provides a valuable resource to elucidate molecular markers for porcine immune cell identity and function.

Glucose is required for IFN-γ secretion but not IFN-γ mRNA expression by peripheral T cells

T cells play a key role in adaptive immunity, proliferating and producing effector molecules upon activation. T cell effector function is regulated by changes in their metabolism, which is necessary for ensuring availability of biosynthetic precursors for expansion, gene transcription, and protein translation. Impaired or altered immune T cell function often coincides with cellular metabolic impairment or shifts, and may be a cause for defective immune responses. For example, peripheral porcine T cells have increased glycolytic capacity following Arterivirus infection, but fail to produce IFN-γ protein in response to antigen stimulation. To understand the mechanism by which porcine T cell effector function is controlled by metabolic substrate availability a series of in vitro studies with varying culture conditions were performed. Specifically, peripheral blood mononuclear cells were stimulated with phorbol 12-myristate 13-acetate plus ionomycin in the presence or absence of glucose for varying amounts of time, and IFN-γ mRNA expression and IFN-γ protein secretion assessed. Glucose was required at the time of stimulation for both IFN-γ mRNA expression and translation/secretion. If glucose was removed 24h after stimulation, IFN-γ mRNA and protein were still produced, though protein levels were reduced. However, if glucose was not readily available upon stimulation, IFN-γ mRNA was transcribed, but not secreted. L-glutamine was supplied in all assays. Collectively, glucose availability to T cells can impact effector function and may be a factor in impaired responses during infection.

Dietary β-glucan reduced Salmonella shedding, shifted intestinal microbiome, and altered intestinal integrity

β-glucan is a prebiotic dietary fiber with immune and microbiota modulating properties. Dietary β-glucan can shift intestinal microbial populations and concentrations of short chain fatty acids (notably, butyrate and propionate), which may alter local populations of regulatory T-cells. Additionally, epigenetic reprograming of monocytes by β-glucan impacts subsequent monocyte responses to heterologous agonists, a form of innate training. Here, β-glucan from Saccharomyces cerevisiae was evaluated as a non-antibiotic dietary additive to limit shedding of the foodborne pathogen, Salmonella enterica server Typhimurium, via changes to the intestinal microbiota, intestinal integrity, and/or the local and peripheral immune system in pigs. Overall Salmonella shedding and cecal mucosa burden was significantly reduced in pigs fed dietary β-glucan compared to Salmonella challenged pigs on control diet. Shifts in microbial communities were associated with reduced Salmonella burden, as pigs fed β-glucan exhibited enhanced cecal epithelial barrier function, altered fecal bacterial communities, and increased short chain fatty acid concentrations. However, no significant differences in regulatory T cell population nor ex vivo monocyte responses were found between groups. Collectively, the non-antibiotic dietary additive β-glucan altered microbial communities and host epithelial cell function in conjunction with reduced Salmonella shedding in pigs.

CD3ε+ Cells in Pigs With Severe Combined Immunodeficiency Due to Defects in ARTEMIS

Severe combined immunodeficiency (SCID) is described as the lack of functional T and B cells. In some cases, mutant genes encoding proteins involved in the process of VDJ recombination retain partial activity and are classified as hypomorphs. Hypomorphic activity in the products from these genes can function in the development of T and B cells and is referred to as a leaky phenotype in patients and animals diagnosed with SCID. We previously described two natural, single nucleotide variants in ARTEMIS (DCLR1EC) in a line of Yorkshire pigs that resulted in SCID. One allele contains a splice site mutation within intron 8 of the ARTEMIS gene (ART16), while the other mutation is within exon 10 that results in a premature stop codon (ART12). While initially characterized as SCID and lacking normal levels of circulating lymphoid cells, low levels of CD3ε⁺ cells can be detected in most SCID animals. Upon further assessment, we found that ART16/16, and ART12/12 SCID pigs had abnormally small populations of CD3ε⁺ cells, but not CD79α⁺ cells, in circulation and lymph nodes. Newborn pigs (0 days of age) had CD3ε⁺ cells within lymph nodes prior to any environmental exposure. CD3ε⁺ cells in SCID pigs appeared to have a skewed CD4α⁺CD8α⁺CD8β⁻ T helper memory phenotype. Additionally, in some pigs, rearranged VDJ joints were detected in lymph node cells as probed by PCR amplification of TCRδ V5 and J1 genomic loci, as well as TCRβ V20 and J1.1, providing molecular evidence of residual Artemis activity. We additionally confirmed that TCRα and TCRδ constant region transcripts were expressed in the thymic and lymph node tissues of SCID pigs; although the expression pattern was abnormal compared to carrier animals. The leaky phenotype is important to characterize, as SCID pigs are an important tool for biomedical research and this additional phenotype may need to be considered. The pig model also provides a relevant model for hypomorphic human SCID patients.

Novel Engraftment and T Cell Differentiation of Human Hematopoietic Cells in ART-/-IL2RG-/Y SCID Pigs

Pigs with severe combined immunodeficiency (SCID) are an emerging biomedical animal model. Swine are anatomically and physiologically more similar to humans than mice, making them an invaluable tool for preclinical regenerative medicine and cancer research. One essential step in further developing this model is the immunological humanization of SCID pigs. In this work we have generated T- B- NK- SCID pigs through site directed CRISPR/Cas9 mutagenesis of IL2RG within a naturally occurring DCLRE1C (ARTEMIS)-/- genetic background. We confirmed ART-/-IL2RG-/Y pigs lacked T, B, and NK cells in both peripheral blood and lymphoid tissues. Additionally, we successfully performed a bone marrow transplant on one ART-/-IL2RG-/Y male SCID pig with bone marrow from a complete swine leukocyte antigen (SLA) matched donor without conditioning to reconstitute porcine T and NK cells. Next, we performed in utero injections of cultured human CD34+ selected cord blood cells into the fetal ART-/-IL2RG-/Y SCID pigs. At birth, human CD45+ CD3ε+ cells were detected in cord and peripheral blood of in utero injected SCID piglets. Human leukocytes were also detected within the bone marrow, spleen, liver, thymus, and mesenteric lymph nodes of these animals. Taken together, we describe critical steps forwards the development of an immunologically humanized SCID pig model.

Detection of Salmonella-specific antibody in swine oral fluids

Salmonella is a leading cause of bacterial foodborne-related illness and pork products are a food-associated source. With > 50% of U.S. swine herds testing positive for Salmonella, asymptomatic carrier pigs that shed Salmonella in their feces are a food safety and environmental contamination issue. Herd level surveillance of Salmonella shedding status is useful, but collection of feces and culture methods for Salmonella detection are laborious and time-consuming. Surveillance for Salmonella-exposure through detection of Salmonella-specific serum antibody is a reliable method, but presents labor and animal-welfare issues. Oral fluids are a reliable, antemortem sample with proven utility for surveillance in the swine industry. We tested oral fluid samples as a potential non-invasive, repeatable sample type for the presence of Salmonella-specific antibodies. An indirect enzyme-linked immunosorbent assay (ELISA) detected anti-Salmonella IgG, IgM, and predominantly IgA in oral fluids from Salmonella enterica serovar Typhimurium-exposed pigs. Furthermore, with minor modifications, a commercial ELISA-based kit also detected Salmonella-specific antibodies in oral fluids. Collectively, oral fluids may serve as a prospective surveillance tool for herd level monitoring of Salmonella exposure.

Cattle intestinal microbiota shifts following Escherichia coli O157:H7 vaccination and colonization

Vaccination-induced Escherichia coli O157:H7-specific immune responses have been shown to reduce E. coli O157:H7 shedding in cattle. Although E. coli O157:H7 colonization is correlated with perturbations in intestinal microbial diversity, it is not yet known whether vaccination against E. coli O157:H7 could cause shifts in bovine intestinal microbiota. To understand the impact of E. coli O157:H7 vaccination and colonization on intestinal microbial diversity, cattle were vaccinated with two doses of different E. coli O157:H7 vaccine formulations. Six weeks post-vaccination, the two vaccinated groups (Vx-Ch) and one non-vaccinated group (NonVx-Ch) were orally challenged with E. coli O157:H7. Another group was neither vaccinated nor challenged (NonVx-NonCh). Fecal microbiota analysis over a 30-day period indicated a significant (FDR corrected, p <0.05) association of bacterial community structure with vaccination until E. coli O157:H7 challenge. Shannon diversity index and species richness were significantly lower in vaccinated compared to non-vaccinated groups after E. coli O157:H7 challenge (p < 0.05). The Firmicutes:Bacteroidetes ratio (p > 0.05) was not associated with vaccination but the relative abundance of Proteobacteria was significantly lower (p < 0.05) in vaccinated calves after E. coli O157:H7 challenge. Similarly, Vx-Ch calves had higher relative abundance of Paeniclostridium spp. and Christenellaceae R7 group while Campylobacter spp., and Sutterella spp. were more abundant in NonVx-Ch group post-E. coli O157:H7 challenge. Only Vx-Ch calves had significantly higher (p < 0.001) E. coli O157:H7-specific serum IgG but no detectable E. coli O157:H7-specific IgA. However, E. coli O157:H7-specific IL-10-producing T cells were detected in vaccinated animals prior to challenge, but IFN-γ-producing T cells were not detected. Neither E. coli O157:H7-specific IgG nor IgA were detected in blood or feces, respectively, of NonVx-Ch and NonVx-NonCh groups prior to or post vaccinations. Both Vx-Ch and NonVx-Ch animals shed detectable levels of challenge strain during the course of the study. Despite the lack of protection with the vaccine formulations there were detectable shifts in the microbiota of vaccinated animals before and after challenge with E. coli O157:H7.

Acute systemic inflammatory response to lipopolysaccharide stimulation in pigs divergently selected for residual feed intake

Background

It is unclear whether improving feed efficiency by selection for low residual feed intake (RFI) compromises pigs’ immunocompetence. Here, we aimed at investigating whether pig lines divergently selected for RFI had different inflammatory responses to lipopolysaccharide (LPS) exposure, regarding to clinical presentations and transcriptomic changes in peripheral blood cells.

Results

LPS injection induced acute systemic inflammation in both the low-RFI and high-RFI line (n = 8 per line). At 4 h post injection (hpi), the low-RFI line had a significantly lower (p = 0.0075) mean rectal temperature compared to the high-RFI line. However, no significant differences in complete blood count or levels of several plasma cytokines were detected between the two lines. Profiling blood transcriptomes at 0, 2, 6, and 24 hpi by RNA-sequencing revealed that LPS induced dramatic transcriptional changes, with 6296 genes differentially expressed at at least one time point post injection relative to baseline in at least one line (n = 4 per line) (|log₂(fold change)| ≥ log₂(1.2); q < 0.05). Furthermore, applying the same cutoffs, we detected 334 genes differentially expressed between the two lines at at least one time point, including 33 genes differentially expressed between the two lines at baseline. But no significant line-by-time interaction effects were detected. Genes involved in protein translation, defense response, immune response, and signaling were enriched in different co-expression clusters of genes responsive to LPS stimulation. The two lines were largely similar in their peripheral blood transcriptomic responses to LPS stimulation at the pathway level, although the low-RFI line had a slightly lower level of inflammatory response than the high-RFI line from 2 to 6 hpi and a slightly higher level of inflammatory response than the high-RFI line at 24 hpi.

Conclusions

The pig lines divergently selected for RFI had a largely similar response to LPS stimulation. However, the low-RFI line had a relatively lower-level, but longer-lasting, inflammatory response compared to the high-RFI line. Our results suggest selection for feed efficient pigs does not significantly compromise a pig’s acute systemic inflammatory response to LPS, although slight differences in intensity and duration may occur.

Shifts in the nasal microbiota of swine in response to different dosing regimens of oxytetracycline administration

The impacts of antibiotic treatment and dosing regimen of an antibiotic on the swine respiratory microbiota are poorly defined. To begin to address this, this study characterized the impact of oxytetracycline administration, given either parenterally or in feed, on the diversity of the nasal and tonsil microbiotas of post-weaned pigs over a two-week period. One group received a single intramuscular injection (IM) of oxytetracycline, the second was treated with oxytetracycline mixed in feed (IF), and the control group received non-medicated (NON) feed. Nasal samples were collected on days 0 (before start of treatment), 4, 7, 11, and 14. Tonsil tissue samples were collected from a subset of pigs selected for necropsy on days 4, 7, and 14. The results showed that the tonsil microbiota was stable regardless of antibiotic treatment. In contrast, the nasal bacterial diversity decreased for both oxytetracycline-treated groups compared to NON. The IF group also exhibited decreased diversity on more days than the IM group. The nasal bacterial community structures of the antibiotic treatment groups were significantly different from the NON group that persisted from day 4 until day 7 for the IM group, and up until day 11 for the IF group. This included relative increased abundances of Actinobacillus and Streptococcus, and relative decreased abundances of multiple commensal genera. The microbiota of the IF group was also more disturbed than the microbiota of the IM group, relative to NON. This study revealed that short-term exposure to broad-spectrum antibiotics like oxytetracycline can disturb the upper respiratory microbiota, and the dosing regimen has differential effects on the microbiota.

159 Impact of dietary fiber and carbohydrases on intestinal gene transcription in enterotoxigenic E. coli challenged pigs

This study aimed to evaluate if soluble (10% sugar beet pulp) or insoluble dietary fiber (15% corn DDGS) with or without exogenous carbohydrases protect piglets against enterotoxigenic E. coli (ETEC)-induced changes in gene transcription of markers of intestinal inflammation and barrier integrity. Sixty newly-weaned piglets (BW=6.9 ± 0.1 kg; L337 X Camborough, PIC, Hendersonville, TN) were blocked by initial BW, preselected for F18 ETEC sensitivity and placed in individual pens. Pens were randomly assigned to 1 of 6 treatments (n = 10/trt): non-challenged (NC), ETEC-challenged (PC), PC-fed a soluble fiber diet without (SF-) or with (SF+) carbohydrases (xylanase, β-glucanase, and pectinase), or PC fed an insoluble fiber diet without (IF-) or with carbohydrases (IF+). Pigs were orally inoculated with ETEC or PBS on d 7 post-weaning. Intestinal tissues were collected on d 14 or 15. Data were analyzed using PROC GLIMMIX (SAS 9.4); treatment was a fixed effect and block a random effect. The NC decreased interleukin (IL)-8 and increased claudin-1 (CLDN1; 2.32 vs. 0.96) mRNA abundance in the ileum compared to PC (P < 0.05). The SF- increased ileal CLDN1 mRNA compared to PC (P < 0.05). A trend (P < 0.10) for lower levels of tumor necrosis factor alpha (TNFα) and greater occludin (OCLN) mRNA in the ileum was observed in SF+ compared with PC. The IF+ decreased ileal cluster of differentiation 14 (CD14) mRNA abundance compared to PC (P < 0.05). Greater colonic abundance of zonula occludens (ZO-1) mRNA was observed in NC than PC (P < 0.05). Pigs fed SF+ tended (P = 0.051) to have greater ZO-1 and greater OCLN mRNA abundance than pigs on PC (P < 0.05). Collectively, these data suggest that an ETEC challenge increased markers of gut inflammation and reduced mRNA levels of tight junction proteins. Soluble fiber, regardless of enzyme supplementation, may help improve gut barrier integrity during such a challenge.

130 Young Scholar Presentation: Can exogenous carbohydrase supplementation to higher-fiber diets improve gut function, microbiota, and growth performance of weaned pigs?

There is increasing interest in feeding higher-fiber coproducts to weaned pigs due to their potential benefits on gut function and microbiota. However, young pigs are not efficient at utilizing fibrous coproducts. Exogenous carbohydrases can be used to improve nutrient utilization and growth of pigs fed higher levels of coproducts. Previous results regarding the impact of carbohydrases on performance in pigs have been inconsistent, thus a better understanding of associated mechanisms is needed. Using 460 weaned pigs (6.4 ± 0.1 kg), our first study showed that a carbohydrase enzyme blend (EB) improved ADG of weaned pigs fed higher-fiber diets (with added DDGS and wheat middlings) over a 28-d experimental period (P < 0.05). Pigs fed EB-supplemented diets had lower urinary lactulose:mannitol ratio, decreased plasma IL-8 concentration, and greater ileal CLDN3 (claudin 3) mRNA abundance, compared with those fed diets without EB (P < 0.05). These changes may partly explain the improved growth, providing mode of action evidence for carbohydrase in improving performance of weaned pigs. Carbohydrases may also exert prebiotic effects through release of oligosaccharides from fiber degradation. Thus, carbohydrases and dietary fiber may improve disease resilience of young pigs against bacterial infections, for example, enterotoxigenic Escherichia coli (ETEC) induced post-weaning diarrhea. Our second study evaluated the impact of soluble versus insoluble fiber with or without carbohydrases in newly weaned pigs (n = 60; 6.9 ± 0.07 kg) challenged with F18 ETEC. A diet containing a soluble and highly fermentable fiber from sugar beet pulp with added carbohydrases improved (P < 0.05) ADG, tended to increase (P < 0.10) ileal OCLN (occludin) mRNA, increased (P < 0.05) colonic OCLN mRNA, and tended to decrease (P < 0.10) ileal Escherichia-Shigella compared with ETEC-challenged control. Collectively, appropriate use of exogenous carbohydrases in higher-fiber diets (with the right type and amount of enzyme substrate) is promising in improving gut health and growth performance in weaned pigs.

PSIV-18 Effect of sub-therapeutic antibiotics and pharmacological zinc oxide on nursery pig performance and intestinal integrity and function

The objective of this study was to evaluate the impact of sub-therapeutic chlortetracycline (CTC) and pharmacological zinc oxide on nursery pig performance and intestinal integrity and function. Twenty-four newly weaned pigs (4.51 ± 0.21 kg BW) were randomly assigned to one of three dietary treatments for 21 d (n = 8/treatment): 1) Control diet (NC), 2) NC + Zinc oxide at 3000 ppm for 7 d followed by 2000 ppm for 14 d (ZnO), and 3) NC + 40 ppm CTC for 21 d (sCTC). Pig ADG, ADFI, and G:F were determined for the overall 21 d test period. At d 21, all pigs were euthanized for tissue collection. Jejunum and ileum ex vivo transepithelial resistance (TER), macromolecule (FD4) flux, and active glucose and glutamine transport were assessed in modified Ussing Chambers. Additionally, jejunum brush border enzyme and Na+/K+ ATPase activities were determined. Morphology and T-cell abundance were determined in all ileum sections by H&E staining and immunohistochemistry, respectively. Compared to the NC, sCTC and ZnO increased ADG (0.14, 0.20 and 0.23 kg/d, respectively, P = 0.020). Overall ADFI was increased by 150% due to sCTC compared to the NC and ZnO pigs (P < 0.05). G:F was increased due to ZnO and sCTC compared to the NC (0.82, 0.63 and 0.47, respectively, P < 0.01). Jejunum and ileum ex vivo function and integrity did not differ. Ileal villus height was increased in the NC compared to sCTC treatment (P < 0.01), but not different from the ZnO treatment. In the ileum, total T-cell number per unit area was significantly lower in the ZnO segments compared to sCTC and NC (0.95, 2.29 and 2.59 count per μm2, respectively, P = 0.05). These data indicate that ZnO and sCTC improved pig performance but did not directly alter small intestinal integrity and function. However, mucosal T cell abundance was altered.

Dietary Resistant Potato Starch Alters Intestinal Microbial Communities and Their Metabolites, and Markers of Immune Regulation and Barrier Function in Swine

Interactions between diet, the microbiota, and the host set the ecological conditions in the gut and have broad implications for health. Prebiotics are dietary compounds that may shift conditions toward health by promoting the growth of beneficial microbes that produce metabolites capable of modulating host cells. This study's objective was to assess how a dietary prebiotic could impact host tissues via modulation of the intestinal microbiota. Pigs fed a diet amended with 5% resistant potato starch (RPS) exhibited alterations associated with gut health relative to swine fed an unamended control diet (CON). RPS intake increased abundances of anaerobic Clostridia in feces and several tissues, as well as intestinal concentrations of butyrate. Functional gene amplicons suggested bacteria similar to Anaerostipes hadrus were stimulated by RPS intake. The CON treatment exhibited increased abundances of several genera of Proteobacteria (which utilize respiratory metabolisms) in several intestinal locations. RPS intake increased the abundance of regulatory T cells in the cecum, but not periphery, and cecal immune status alterations were indicative of enhanced mucosal defenses. A network analysis of host and microbial changes in the cecum revealed that regulatory T cells positively correlated with butyrate concentration, luminal IgA concentration, expression of IL-6 and DEF1B, and several mucosa-associated bacterial taxa. Thus, the administration of RPS modulated the microbiota and host immune status, altering markers of cecal barrier function and immunological tolerance, and suggesting a reduced niche for bacterial respiration.

A soluble and highly fermentable dietary fiber with carbohydrases improved gut barrier integrity markers and growth performance in F18 ETEC challenged pigs1

This study aimed to evaluate the effects of a source of dietary soluble (SF) and insoluble fiber (IF) without or with exogenous carbohydrases (xylanase, β-glucanase, and pectinase) on diarrhea incidence, selected immune responses, and growth performance in enterotoxigenic Escherichia coli (ETEC)-challenged pigs. Sixty weaned pigs (6.9 ± 0.1 kg BW, ~23 d of age) were blocked by initial BW and placed in individual pens. Pens were randomly assigned to one of six treatments (n = 10 per treatment), including a nonchallenged control (NC), a positive challenge control (PC), the PC + a soluble fiber diet (10% sugar beet pulp) without (SF-) or with carbohydrases (SF+), and PC + an IF diet (15% corn distillers dried grains with solubles) without (IF-) or with carbohydrases (IF+). The control diet was primarily based on corn and soybean meal with 13.5% whey powder. The two sources of fiber were added at the expense of cornstarch in the control diet. Pigs were orally inoculated with 6 mL hemolytic F18 ETEC (~3.5 × 109 cfu/mL) or sham infected with 6 mL phosphate-buffered saline on day 7 (0 d postinoculation, dpi) postweaning. All ETEC challenged pigs were confirmed to be genetically susceptible to F18 ETEC. Pigs had free access to feed and water throughout the 14-d trial. Pig BW and feed intake were recorded on dpi -7, 0, and 7 or 8. Fecal swabs were collected on dpi -7, 0, 1, 2, 3, 5, and 7 or 8 to evaluate hemolytic E. coli shedding. Fecal score was visually ranked daily postchallenge to evaluate diarrhea incidence. Blood samples were collected on dpi -1, 3, and 7 or 8 at necropsy and intestinal tissues were collected at necropsy. Pigs on PC had lower dpi 1 to 7 ADG and ADFI than those on NC (P < 0.05). Compared with PC pigs, SF+ pigs had greater ADG during both pre- and postchallenge period (P < 0.05). The IF- increased postchallenge diarrhea incidence compared with PC (P < 0.05). Pigs on SF- had lower ileal E. coli attachment than PC (P < 0.05). The SF+ reduced haptoglobin and IF+ reduced C-reactive protein on dpi 3 compared with PC (P < 0.05). Compared with PC pigs, SF+ pigs tended to have lower ileal tumor necrosis factor alpha and greater ileal occludin (OCLN) mRNA (P < 0.10) and had greater (P < 0.05) colonic OCLN mRNA levels. Collectively, IF- increased incidence of diarrhea and fecal E. coli shedding compared with PC. The SF+ pigs had improved growth compared with PC pigs, likely due in part to a reduction in inflammatory intermediates.

Cellular and Mucosal Immune Responses Following Vaccination with Inactivated Mutant of Escherichia coli O157:H7

Shiga toxin-producing Escherichia coli O157:H7 (O157) can cause mild to severe gastrointestinal disease in humans. Cattle are the primary reservoir for O157, which colonizes the intestinal tract without inducing any overt clinical symptoms. Parenteral vaccination can reduce O157 shedding in cattle after challenge and limit zoonotic transmission to humans, although the impact of vaccination and vaccine formulation on cellular and mucosal immune responses are undetermined. To better characterize the cattle immune response to O157 vaccination, cattle were vaccinated with either water-in-oil-adjuvanted, formalin-inactivated hha deletion mutant of Shiga toxin 2 negative (stx2^-) O157 (Adj-Vac); non-adjuvanted (NoAdj-Vac); or non-vaccinated (NoAdj-NoVac) and peripheral T cell and mucosal antibody responses assessed. Cattle in Adj-Vac group had a higher percentage of O157-specific IFNγ producing CD4⁺ and γδ⁺ T cells in recall assays compared to the NoAdj-Vac group. Furthermore, O157-specific IgA levels detected in feces of the Adj-Vac group were significantly lower in NoAdj-Vac group. Extracts prepared only from Adj-Vac group feces blocked O157 adherence to epithelial cells. Taken together, these data suggest parenteral administration of adjuvanted, inactivated whole-cell vaccines for O157 can induce O157-specific cellular and mucosal immune responses that may be an important consideration for a successful vaccination scheme.

Exogenous carbohydrases added to a starter diet reduced markers of systemic immune activation and decreased Lactobacillus in weaned pigs1

Although the impact of carbohydrases on performance and nutrient utilization has been well studied, their effects on immune status and intestinal microbiota are less known in pigs. This study aimed to evaluate the impact of xylanase (X) and a carbohydrase enzyme blend (EB; cellulase, ß-glucanase, and xylanase) on the immune profile of the intestine and peripheral system as well as intestinal microbes and microbial metabolites of weaned pigs fed higher fiber diets. Pigs (n = 460; 6.43 ± 0.06 kg BW; F25 × 6.0 Genetiporc) were blocked by initial BW. Pens (n = 48; 12 per treatment; 9 or 10 pigs per pen) were randomly assigned to 1 of 4 dietary treatments, including a higher fiber control diet (CON) and the CON supplemented with 0.01% X, 0.01% EB, or both enzymes (X + EB), arranged in a 2 × 2 factorial. The diets were based on corn, soybean meal, corn distillers dried grains with solubles, and wheat middlings. After 7-d adaptation to the environment, pigs were fed experimental diets ad libitum for 28 d. Blood samples were collected from the same pig within each pen on days 0, 7, 14, and 28. Intestinal tissues and digesta were collected on day 28. Bacteria 16S rRNA gene copy numbers were quantified using qPCR. The mRNA levels of colonic IL-17, occludin (OCLN), and claudin 3 (CLDN3) were greater in pigs fed diets with X + EB, but not X or EB, compared with those fed CON (P < 0.05). The EB in the diet reduced plasma IL-8 over the 28-d trial compared with diets without EB (P < 0.05). There was an X × EB interaction on plasma tumor necrosis factor α and IL-1ß (P < 0.05); their levels were decreased when X and EB were added together, but not individually, compared with CON. The EB decreased cecal propionate, butyrate, and total volatile fatty acids (P < 0.05). Pigs fed X had lower ileal Lactobacillus and greater ileal and cecal Enterobacteriaceae compared with those fed unsupplemented diets (P < 0.05). The EB decreased Lactobacillus (P < 0.05) and tended to decrease (P = 0.065) Enterobacteriaceae in the colon compared with diets without EB. In conclusion, the addition of X and EB together decreased systemic markers of immune activation, potentially diverting energy and nutrients towards growth. The EB reduced colonic Lactobacillus and cecal total volatile fatty acids, probably due to improved prececal fiber and starch degradation and thus reduced substrate availability in the large intestine. These data corroborated previously observed enhanced growth in pigs fed EB-supplemented diets.

A dietary carbohydrase blend improved intestinal barrier function and growth rate in weaned pigs fed higher fiber diets

The objective of this study was to evaluate the effects of dietary xylanase (X) and a carbohydrase enzyme blend (EB: cellulase, β-glucanase, and xylanase) on nutrient digestibility, intestinal barrier integrity, inflammatory status, and growth performance in weaned piglets fed higher fiber diets. A total of 460 pigs (6.43 ± 0.06 kg BW; F25 × 6.0 Genetiporc) were blocked by initial BW and pens (n = 12 per treatment) were randomly assigned to 1 of 4 dietary treatments. The diets included a higher fiber unsupplemented control diet (CON) and the CON supplemented with 0.01% X, 0.01% EB, or both enzymes, arranged in a 2 × 2 factorial. The diets were based on corn, soybean meal, corn distillers dried grains with solubles (DDGS), and wheat middlings. Pigs had 7 d to adapt to the environment and consumed the same commercial diet. Pigs were fed the experimental diets for 28 d with free access to feed and water. Body weight and feed disappearance were recorded weekly. One pig with BW closest to the pen average from each pen was selected and moved to metabolism crates on day 16 and intragastric gavaged a solution of lactulose and mannitol on day 22 followed by 12-h urine collection. Feces were collected from day 23 to 25. Intestinal tissues and mucosal scrapings were collected on day 28. Data were analyzed using PROC MIXED of SAS (9.4). Xylanase, EB, and their interaction were fixed effects and block was a random effect. The EB, but not X, increased pig BW and improved ADG over 28 d (P < 0.05). Neither carbohydrase impacted ADFI, G:F, or apparent total tract digestibility (ATTD) of DM, GE, or CP. The EB improved ATTD of ADF (32.45 vs. 26.57%; P < 0.01), but had no effect on NDF. Unexpectedly, X reduced ATTD of NDF and ADF (P < 0.01). The EB reduced urinary lactulose:mannitol and increased ileal claudin-3 mRNA abundance (P < 0.05), indicating improved small intestinal barrier integrity. There was a X × EB interaction on ileal secretory immunoglobulin A (sIgA) concentration (P < 0.05); in the absence of X, EB decreased sIgA compared to CON, but this effect disappeared in the presence of X. The EB also reduced ileal IL-22 mRNA abundance (P < 0.05), probably indicating decreased immune activation. In conclusion, EB but not X enhanced growth rate of weaned pigs fed higher fiber diets, which may be partly explained by the improved small intestinal barrier integrity and reduced immune activation, rather than improvement in nutrient digestibility.

Development of Severe Combined Immunodeficient (SCID) Pig Models for Translational Cancer Modeling: Future Insights on How Humanized SCID Pigs Can Improve Preclinical Cancer Research

Within the last decade there have been several severe combined immunodeficient (SCID) pig models discovered or genetically engineered. The animals have mutations in ARTEMIS, IL2RG, or RAG1/2 genes, or combinations thereof, providing SCID pigs with NK cells, but deficient in T and B cells, or deficient in NK, T, and B cells for research studies. Biocontainment facilities and positive pressure isolators are developed to limit pathogen exposure and prolong the life of SCID pigs. Raising SCID pigs in such facilities allows for completion of long-term studies such as xenotransplantation of human cells. Ectopically injected human cancer cell lines develop into tumors in SCID pigs, thus providing a human-sized in vivo model for evaluating imaging methods to improve cancer detection and therapeutic research and development. Immunocompromised pigs have the potential to be immunologically humanized by xenotransplantation with human hematopoietic stem cells, peripheral blood leukocytes, or fetal tissue. These cells can be introduced through various routes including injection into fetal liver or the intraperitoneal (IP) space, or into piglets by intravenous, IP, and intraosseous administration. The development and maintenance of transplanted human immune cells would be initially (at least) dependent on immune signaling from swine cells. Compared to mice, swine share higher homology in immune related genes with humans. We hypothesize that the SCID pig may be able to support improved engraftment and differentiation of a wide range of human immune cells as compared to equivalent mouse models. Humanization of SCID pigs would thus provide a valuable model system for researchers to study interactions between human tumor and human immune cells. Additionally, as the SCID pig model is further developed, it may be possible to develop patient-derived xenograft models for individualized therapy and drug testing. We thus theorize that the individualized therapeutic approach would be significantly improved with a humanized SCID pig due to similarities in size, metabolism, and physiology. In all, porcine SCID models have significant potential as an excellent preclinical animal model for therapeutic testing.

Porcine signal regulatory protein alpha binds to human CD47 to inhibit phagocytosis: Implications for human hematopoietic stem cell transplantation into severe combined immunodeficient pigs

BACKGROUND

Severe combined immunodeficient (SCID) pigs are an emerging animal model being developed for biomedical and regenerative medicine research. SCID pigs can successfully engraft human-induced pluripotent stem cells and cancer cell lines. The development of a humanized SCID pig through xenotransplantation of human hematopoietic stem cells (HSCs) would be a further demonstration of the value of such a large animal SCID model. Xenotransplantation success with HSCs into non-obese diabetic (NOD)-derived SCID mice is dependent on the ability of NOD mouse signal regulatory protein alpha (SIRPA) to bind human CD47, inducing higher phagocytic tolerance than other mouse strains. Therefore, we investigated whether porcine SIRPA binds human CD47 in the context of developing a humanized SCID pig.

METHODS

Peripheral blood mononuclear cells (PBMCs) were collected from SCID and non-SCID pigs. Flow cytometry was used to assess whether porcine monocytes could bind to human CD47. Porcine monocytes were isolated from PBMCs and were subjected to phagocytosis assays with pig, human, and mouse red blood cell (RBC) targets. Blocking phagocytosis assays were performed by incubating human RBCs with anti-human CD47 blocking antibody B6H12, non-blocking antibody 2D3, and nonspecific IgG1 antibody and exposing to human or porcine monocytes.

RESULTS

We found that porcine SIRPA binds to human CD47 in vitro by flow cytometric assays. Additionally, phagocytosis assays were performed, and we found that porcine monocytes phagocytose human and porcine RBCs at significantly lower levels than mouse RBCs. When human RBCs were preincubated with CD47 antibodies B6H12 or 2D3, phagocytosis was induced only after B6H12 incubation, indicating the lower phagocytic activity of porcine monocytes with human cells requires interaction between porcine SIRPA and human CD47.

CONCLUSIONS

We have shown the first evidence that porcine monocytes can bind to human CD47 and are phagocytically tolerant to human cells, suggesting that porcine SCID models have the potential to support engraftment of human HSCs.

Bordetella bronchiseptica Colonization Limits Efficacy, but Not Immunogenicity, of Live-Attenuated Influenza Virus Vaccine and Enhances Pathogenesis After Influenza Challenge

Intranasally administered live-attenuated influenza virus (LAIV) vaccines provide significant protection against heterologous influenza A virus (IAV) challenge. However, LAIV administration can modify the bacterial microbiota in the upper respiratory tract, including alterations in species that cause pneumonia. We sought to evaluate the effect of Bordetella bronchiseptica colonization on LAIV immunogenicity and efficacy in swine, and the impact of LAIV and IAV challenge on B. bronchiseptica colonization and disease. LAIV immunogenicity was not significantly impacted by B. bronchiseptica colonization, but protective efficacy against heterologous IAV challenge in the upper respiratory tract was impaired. Titers of IAV in the nose and trachea of pigs that received LAIV were significantly reduced when compared to non-vaccinated, challenged controls, regardless of B. bronchiseptica infection. Pneumonia scores were higher in pigs colonized with B. bronchiseptica and challenged with IAV, but this was regardless of LAIV vaccination status. While LAIV vaccination provided significant protection against heterologous IAV challenge, the protection was not sterilizing and IAV replicated in the respiratory tract of all LAIV vaccinated pig. The interaction between IAV, B. bronchiseptica, and host led to development of acute-type B. bronchiseptica lesions in the lung. Thus, the data presented do not negate the efficacy of LAIV vaccination, but instead indicate that controlling B. bronchiseptica colonization in swine could limit the negative interaction between IAV and Bordetella on swine health.