Research Project: Intestinal Microbial Ecology and Metagenomic Strategies to Reduce Antibiotic Resistance and Foodborne Pathogens

Location: Food Safety and Enteric Pathogens Research

Publications (Clicking on the reprint icon will take you to the publication reprint.)

The acute host-response of turkeys colonized with Campylobacter coli - (Peer Reviewed Journal)
Sylte, M.J., Sivasankaran, S.K., Trachsel, J.M., Sato, Y., Wu, Z., Johnson, T.A., Chandra, L.C., Zhang, Q., Looft, T.P. 2021. The acute host-response of turkeys colonized with Campylobacter coli. Frontiers in Veterinary Science. 8. Article 613203. https://doi.org/10.3389/fvets.2021.613203.

Differential impact of OTC regimen on growth and gut microbiota of pigs co-infected with respiratory pathogens - (Abstract Only)

Complete genome sequence and annotation for turicibacter sanguinis MOL361T (DSM 14220) - (Peer Reviewed Journal)
Maki, J., Nielsen, D.W., Looft, T.P. 2020. Complete genome sequence and annotation for turicibacter sanguinis MOL361T (DSM 14220). Microbiology Resource Announcements. 9(25):e00475-20. https://doi.org/10.1128/MRA.00475-20.

Single cell and deep transcriptomic analysis identify common and cell type specific genes in porcine immune cell - (Abstract Only)

A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity - (Peer Reviewed Journal)
Wylensek, D., Hitch, T.C., Riedel, T., Afrizal, A., Kumar, N., Wortmann, E., Liu, T., Devendran, S., Lesker, T.R., Cumbo, F., Wyschkon, M., Looft, T.P., Parreira, V.R., Abt, B., Agostino, P.D., Doden, H.L., Ly, L., Alves, J.M., Reichlin, M., Flisikowski, K., Navarro Suarez, L., Neumann, A.P., Suen, G., Wells, J., Wouters, T., Rohn, S., Lagkouvardos, I., Allen-Vercoe, E., Neuhaus, K., Schnieke, A., Segata, N., Strowig, T., Ridlon, J.M., Gulder, T.A., Overmann, J., Clavel, T. 2020. A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity. Nature Communications. 11. Article 6389. https://doi.org/10.1038/s41467-020-19929-w.

Differential induction of innate memory in porcine monocytes by B-glucan or bacillus Calmette-Guerin - (Peer Reviewed Journal)
Byrne, K.A., Tuggle, C., Loving, C.L. 2020. Differential induction of innate memory in porcine monocytes by B-glucan or bacillus Calmette-Guerin. Innate Immunity. https://doi.org/10.1177/1753425920951607.

Changes in H3K27ac at gene regulatory regions in porcine alveolar macrophages following LPS or PolyIC exposure - (Peer Reviewed Journal)
Uribe, J.H., Liu, H., Byrne, K.A., Bond, Z.F., Loving, C.L., Tuggle, C. 2020. Changes in H3K27ac at gene regulatory regions in porcine alveolar macrophages following LPS or PolyIC exposure. Frontiers in Genetics. 11. https://doi.org/10.3389/fgene.2020.00817.

Complete genome sequence and annotation for romboutsia sp. CE17 - (Peer Reviewed Journal)
Maki, J.J., Nielsen, D.W., Looft, T.P. 2020. Complete genome sequence and annotation for romboutsia sp. strain CE17. Microbiology Resource Announcements. 9(23):e00382-20. https://doi.org/10.1128/MRA.00382-20.

Intraepithelial T cells diverge by intestinal location as pigs age - (Peer Reviewed Journal)
Wiarda, J.E., Trachsel, J.M., Bond, Z.F., Byrne, K.A., Gabler, N.K., Loving, C.L. 2020. Intraepithelial T cells diverge by intestinal location as pigs age. Frontiers in Immunology. 11:1139. https://doi.org/10.3389/fimmu.2020.01139.

Innate immunomodulation in food animals: evidence for trained immunity? - (Peer Reviewed Journal)
Byrne, K.A., Loving, C.L., McGill, J.L. 2020. Innate immunomodulation in food animals: evidence for trained immunity? Frontiers in Immunology. 11:1099. https://doi.org/10.3389/fimmu.2020.01099.

Toward antibiotic stewardship: Route of antibiotic administration impacts the microbiota and resistance gene diversity in swine feces - (Peer Reviewed Journal)
Ricker, N., Trachsel, J.M., Colgan, P., Jones, J., Choi, J., Lee, J., Coetzee, J., Howe, A., Brockmeier, S., Loving, C.L., Allen, H.K. 2020. Toward antibiotic stewardship: Route of antibiotic administration impacts the microbiota and resistance gene diversity in swine feces. Frontiers in Veterinary Science. 7:255. https://doi.org/10.3389/fvets.2020.00255.

Detection of Campylobacter jejuni liver dissemination in experimentally colonized turkey poults - (Peer Reviewed Journal)
Sylte, M.J., Shippy, D.C., Bearson, B.L., Bearson, S.M. 2020. Detection of Campylobacter jejuni liver dissemination in experimentally colonized turkey poults. Poultry Science. 99(8):4028-4033. https://doi.org/10.1016/j.psj.2020.03.042.

Eggshell and environmental bacteria contribute to the intestinal microbiota of growing chickens - (Peer Reviewed Journal)
Maki, J.J., Bobeck, E.A., Sylte, M.J., Looft, T.P. 2020. Eggshell and environmental bacteria contribute to the intestinal microbiota of growing chickens. Journal of Animal Science and Biotechnology. 11:60. https://doi.org/10.1186/s40104-020-00459-w.

Outer membrane protein A (OmpA) of extraintestinal pathogenic Escherichia coli - (Peer Reviewed Journal)
Nielsen, D., Ricker, N., Barbieri, N.L., Allen, H.K., Nolan, L.K., Logue, C.M. 2020. Outer membrane protein A (OmpA) of extraintestinal pathogenic Escherichia coli. BMC Research Notes. 13. Article 51. https://doi.org/10.1186/s13104-020-4917-5.

Novel engraftment and T cell differentiation of human hematopoietic cells in Art-/- IL2RG-/SCID pigs - (Peer Reviewed Journal)
Boettcher, A.N., Li, Y., Ahrens, A.P., Kiupel, M., Byrne, K.A., Loving, C.L., Cino-Ozuna, A., Wiarda, J.E., Adur, M., Schultz, B., Swanson, J.J., Snella, E.M., Ho, C., Charley, S.E., Kiefer, Z.E., Cunnick, J.E., Putz, E.J., Giuseppe, Dell A., Jens, J., Sathe, S., Goldman, F., Westin, E.R., Dekkers, J.C.M., Ross, J.W., Tuggle, C.K. 2020. Novel engraftment and T cell differentiation of human hematopoietic cells in Art-I- IL2RG-IY SCID pigs. Frontiers in Immunology. 11:100. https://doi.org/10.3389/fimmu.2020.00100.

Complete genome sequence of Campylobacter jejuni strain NADC 20827 isolated from commercial turkeys - (Peer Reviewed Journal)
Nielsen, D.W., Maki, J.J., Looft, T.P., Ricker, N., Sylte, M.J. 2020. Complete genome sequence of Campylobacter jejuni strain NADC 20827 isolated from commercial turkeys. Microbiology Resource Announcements. 9(1):e01403-19. https://doi.org/10.1128/MRA.01403-19.

Successful development of methodology for detection of hapten-specific contact hypersensitivity (CHS) memory in swine - (Peer Reviewed Journal)
Putz, E.J., Putz, A.M., Boettcher, A., Charley, S., Sauer, M., Palmer, M.V., Phillips, R., Hostetter, J.M., Loving, C.L., Cunnick, J.E., Tuggle, C.K. 2019. Successful development of methodology for detection of hapten-specific contact hypersensitivity (CHS) memory in swine. PLoS One. 14(10):e0223483. https://doi.org/10.1371/journal.pone.0223483.

Acute systemic inflammatory response to lipopolysaccharide stimulation in pigs divergently selected for residual feed intake - (Peer Reviewed Journal)
Liu, H., Feye, K.M., Nguyen, Y.T., Rakhshandeh, A., Loving, C.L., Dekkers, J.C., Gabler, N.K., Tuggle, C.K. 2019. Acute systemic inflammatory response to lipopolysaccharide stimulation in pigs divergently selected for residual feed intake. BMC Genomics. 20(728). https://doi.org/10.1186/s12864-019-6127-x.

The microbial pecking order: utilization of intestinal microbiota for poultry health - (Review Article)
Maki, J.J., Klima, C.L., Sylte, M.J., Looft, T.P. 2019. The microbial pecking order: utilization of intestinal microbiota for poultry health. Microorganisms. 7(10):376. https://doi.org/10.3390/microorganisms7100376.

Dietary resistant potato starch alters intestinal microbial communities and metabolites and markers of immune regulation and barrier function - (Peer Reviewed Journal)
Trachsel, J., Briggs, C., Gabler, N.K., Allen, H.K., Loving, C.L. 2019. Dietary resistant potato starch alters intestinal microbial communities and their metabolites and markers of immune regulation and barrier function in swine. Frontiers in Immunology. 10:1381. https://doi.org/10.3389/fimmu.2019.01381.

In-feed bacitracin methylene disalicylate modulates the turkey microbiota and metabolome in a dose-dependent manner - (Peer Reviewed Journal)
Johnson, T., Sylte, M.J., Looft, T.P. 2019. In-feed bacitracin methylene disalicylate modulates the turkey microbiota and metabolome in a dose-dependent manner. Scientific Reports. 9:8212. https://doi.org/10.1038/s41598-019-44338-5.

Intestinal colonization and acute immune response in commercial turkeys following inoculation with Campylobacter jejuni constructs encoding antibiotic-resistance markers - (Peer Reviewed Journal)
Sylte, M.J., Johnson, T.A., Meyer, E.L., Inbody, M.H., Trachsel, J., Looft, T., Leonardo, S., Wu, Z., Zhang, Q. 2019. Intestinal colonization and acute immune response in commercial turkeys following inoculation with Campylobacter jejuni constructs encoding antibiotic-resistance markers. Veterinary Immunology and Immunopathology. 210:6-14. https://doi.org/10.1016/j.vetimm.2019.02.003.

Exogenous carbohydrase reduced markers of intestinal and systemic immune activation and decreased Lactobacillus in weaned pigs - (Peer Reviewed Journal)
Li, Q., Schmitz-Esser, S., Loving, C.L., Gabler, N.K., Gould, S.A., Patience, J.F. 2018. Exogenous carbohydrase added to a starter diet reduced markers of systemic immune activation and decreased Lactobacillus in weaned pigs. Journal of Animal Science. 97(3):1242-1253. https://doi.org/10.1093/jas/sky481.

Avian intestinal mucus modulates Campylobacter jejuni gene expression in a host-specific manner - (Peer Reviewed Journal)
Looft, T.P., Cai, G., Choudhury, B., Lai, L.X., Lippolis, J.D., Reinhardt, T.A., Sylte, M.J., Casey, T.A. 2019. Avian intestinal mucus modulates Campylobacter jejuni gene expression in a host-specific manner. Frontiers in Microbiology. 9:3215. https://doi.org/10.3389/fmicb.2018.03215.

Development of severe combined immunodeficient (SCID) pig models for translational cancer modeling: future insights on how humanized SCID pigs can improve preclinical cancer research - (Peer Reviewed Journal)
Boettcher, A., Loving, C.L., Cunnick, J., Tuggle, C. 2018. Development of severe combined immunodeficient (SCID) pig models for translational cancer modeling: future insights on how humanized SCID pigs can improve preclinical cancer research. Frontiers in Oncology. 8:559. https://doi.org/10.3389/fonc.2018.00559.

Nanoparticle microarray for high-throughput microbiome metabolomics using matrix-assisted laser desorption Ionization mass spectrometry - (Peer Reviewed Journal)
Hansen, R.L., Duenas, M.E., Looft, T., Lee, Y.J. 2018. Nanoparticle microarray for high-throughput microbiome metabolomics using matrix-assisted laser desorption ionization mass spectrometry. Analytical and Bioanalytical Chemistry. 411(1):147-156. https://doi.org/10.1007/s00216-018-1436-5.

Complete genome sequence of Megasphaera stantonii AJH120T, isolated from a chicken cecum - (Peer Reviewed Journal)
Maki, J.J., Looft, T. 2018. Complete genome sequence of Megasphaera stantonii AJH120T, isolated from a chicken cecum. Microbiology Resource Announcements. 7:e01148-18. https://doi.org/10.1128/MRA.01148-18.

A dietary carbohydrase blend improved intestinal barrier function and growth rate in nursery pigs fed higher fiber diets - (Peer Reviewed Journal)
Li, Q., Gabler, N.K., Loving, C.L., Gould, S.A., Patience, J.F. 2018. A dietary carbohydrase blend improved intestinal barrier function and growth rate in weaned pigs fed higher fiber diets. Journal of Animal Science. 96(12):5233-5243. https://doi.org/10.1093/jas/sky383.

Porcine SIRPA binds to human CD47 to inhibit phagocytosis: Implications for human hematopoietic stem cell transplantation into severe combined immunodeficient (SCID) pigs - (Peer Reviewed Journal)
Boettcher, A.N., Cunnick, J.E., Powell, E., Egner, T.K., Charley, S.E., Loving, C.L., Tuggle, C.K. 2018. Porcine signal regulatory protein alpha binds to human CD47 to inhibit phagocytosis: Implications for human hematopoietic stem cell transplantation into severe combined immunodeficient pigs. Xenotransplantation. 26(2):e12466. https://doi.org/10.1111/xen.12466.

Bordetella bronchiseptica colonization limits efficacy, but not immunogenicity, of live-attenuated influenza virus vaccine and enhances pathogenesis after influenza challenge - (Peer Reviewed Journal)
Hughes, H.R., Brockmeier, S., Loving, C.L. 2018. Bordetella bronchiseptica colonization limits efficacy, but not immunogenicity, of live-attenuated influenza virus vaccine and enhances pathogenesis after influenza challenge. Frontiers in Immunology. 9:2255. https://doi.org/10.3389/fimmu.2018.02255.

Megasphaera stantonii sp. nov., a butyrate-producing bacterium isolated from the cecum of a healthy chicken - (Peer Reviewed Journal)
Maki, J.J., Looft, T., 2018. Megasphaera stantonii sp. nov., a butyrate-producing bacterium isolated from the cecum of a healthy chicken. International Journal of Systematic and Evolutionary Microbiology. 68:3409-3415. https://doi.org/10.1099/ijsem.0.002991.

Complete genome sequence of the multi-drug resistant neonatal meningitis Escherichia coli serotype O75:H5:K1 strain mcjchv-1 (NMEC-O75) - (Peer Reviewed Journal)
Nielsen, D.W., Ricker, N., Barbieri, N.L., Wynn, J., Gomez-Duarte, O.G., Iqbal, J., Nolan, L.K., Allen, H.K., Logue, C.M. 2018. Complete genome sequence of the multi-drug resistant neonatal meningitis Escherichia coli serotype O75:H5:K1 strain mcjchv-1 (NMEC-O75). Genome Announcements. 7(10):e01043-18. https://doi.org/10.1128/MRA.01043-18.

Segmented filamentous bacteria - metabolism meets immunity - (Peer Reviewed Journal)
Hedblom, G.A., Reiland, H.A., Sylte, M.J., Johnson, T.J., Baumler, D.J. 2018. Segmented filamentous bacteria - metabolism meets immunity. Frontiers in Microbiology. 9:1991. https://doi.org/10.3389/fmicb.2018.01991.

Butyricicoccus porcorum sp. nov. a butyrate-producing bacterium from swine intestinal tract - (Peer Reviewed Journal)
Trachsel, J., Humphrey, S.B., Allen, H.K. 2018. Butyricicoccus porcorum sp. nov. a butyrate-producing bacterium from swine intestinal tract. International Journal of Systematic and Evolutionary Microbiology. 68:1737-1742. https://doi.org/10.1099/ijsem.0.002738.

A soluble and highly fermentable dietary fiber with carbohydrases improved gut barrier integrity markers and growth performance in ETEC challenged pigs - (Peer Reviewed Journal)
Li, Q., Burrough, E.R., Gabler, N.K., Loving, C.L., Sahin, O.A., Gould, S.A., Patience, J.F. 2019. A soluble and highly fermentable dietary fiber with carbohydrases improved gut barrier integrity markers and growth performance in F18 ETEC challenged pigs. Journal of Animal Science. 97(5):2139-2153. https://doi.org/10.1093/jas/skz093.

Practical implications of erythromycin resistance gene diversity on surveillance and monitoring of resistance - (Peer Reviewed Journal)
Choi, J., Rieke, E.L., Moorman, T.B., Soupir, M.L., Allen, H.K., Smith, S., Howe, A. 2018. Practical implications of erythromycin resistance gene diversity on surveillance and monitoring of resistance. FEMS Microbiology Ecology. 94(4). https://doi.org/10.1093/femsec/fiy006.

Evaluation of different Campylobacter jejuni isolates to colonize the intestinal tract of commercial turkey poults and selective media for enumeration - (Peer Reviewed Journal)
Sylte, M.J., Inbody, M.H., Johnson, T., Looft, T.P., Line, J.E. 2018. Evaluation of different Campylobacter jejuni isolates to colonize the intestinal tract of commercial turkey poults and selective media for enumeration. Poultry Science. 97(5):1689-1698. https://doi.org/10.3382/ps/pex384.

T cell epitope content comparison (EpiCC) of swine H1 influenza A virus hemagglutinin - (Peer Reviewed Journal)
Gutierrez, A.H., Rapp-Gabrielson, V., Loving, C.L., Terry, F.E., Moise, L., Martin, W.D., De Groot, A.S. 2017. T cell epitope content comparison (EpiCC) of swine H1 influenza A virus hemagglutinin. Influenza and Other Respiratory Viruses. 11(6):531-542. https://doi.org/10.1111/irv.12513.

The in-feed antibiotic carbadox induces phage gene transcription in the swine gut microbiome - (Peer Reviewed Journal)
Johnson, T.A., Looft, T.P., Severin, A.J., Bayles, D.O., Nasko, D.J., Wommack, E., Howe, A., Allen, H.K. 2017. The in-feed antibiotic carbadox induces phage gene transcription in the swine gut microbiome. mBio. 8(4):e00709-17. https://doi.org/10.1128/mBio.00709-17.

Alternatives to antibiotics: why and how - (Proceedings)
Allen, H.K. 2017. Alternatives to antibiotics: why and how. In: Proceedings of the National Academy of Medicine Perspectives. Institute of Medicine's Food Forum Meeting, April 27, 2016, Washington, DC. Available: https://nam.edu/alternatives-to-antibiotics-why-and-how.

Factors affecting induction of peripheral IFN-gamma recall response to influenza A virus vaccination in pigs - (Peer Reviewed Journal)
Olson, Z.F., Sandbulte, M.R., Kunzler Souza, C., Perez, D.R., Vincent, A.L., Loving, C.L. 2017. Factors affecting induction of peripheral IFN-gamma recall response to influenza A virus vaccination in pigs. Veterinary Immunology and Immunopathology. 185:57-65. doi: 10.1016/j.vetimm.2017.01.009.

Evaluation of disinfectants and antiseptics to eliminate bacteria from the surface of turkey eggs and hatch gnotobiotic poults - (Peer Reviewed Journal)
Sylte, M.J., Chandra, L.C., Looft, T.P. 2017. Evaluation of disinfectants and antiseptics to eliminate bacteria from the surface of turkey eggs and hatch gnotobiotic poults. Poultry Science. 96(7):2412-2420. doi: 10.3382/ps/pex022.

Interrogating the plasmidome to determine antibiotic resistance gene mobility within the swine fecal microbiota - (Abstract Only)

NK cells are intrinsically functional in pigs with Severe Combined Immunodeficiency (SCID) caused by spontaneous mutations in the Artemis gene - (Peer Reviewed Journal)
Powell, E.J., Cunnick, J.E., Knetter, S.M., Loving, C.L., Waide, E.H., Dekkers, J.C., Tuggle, C. 2016. NK cells are intrinsically functional in pigs with Severe Combined Immunodeficiency (SCID) caused by spontaneous mutations in the Artemis gene. Veterinary Immunology and Immunopathology. 175:1-6. doi: 10.1016/j.vetimm.2016.04.008.