Research Project: Molecular Approaches to Control Intestinal Parasites that Affect the Microbiome in Swine and Small Ruminants

Location: Animal Parasitic Diseases Laboratory

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

Rumen microbial predictors for short-chain fatty acid levels and the grass-fed regimen in angus cattle - (Peer Reviewed Journal)
Liu, J., Bai, Y., Liu, F., Kohn, R.A., Tadesse, D.A., Sarria, S., Li, R.W., Song, J. 2022. Rumen microbial predictors for short-chain fatty acid levels and the grass-fed regimen in angus cattle. Animals. 12(21). Article 2995. https://doi.org/10.3390/ani12212995.

Microbial composition and co-occurrence patterns in the gut microbial community of healthy and obese mice in response to astaxanthin in its native and lipid emulsion forms - (Peer Reviewed Journal)
Gao, Y., Liu, F., Li, R.W., Xue, C., Tang, Q. 2022. Microbial composition and co-occurrence patterns in the gut microbial community of healthy and obese mice in response to astaxanthin in its native and lipid emulsion forms. Frontiers in Microbiology. https://doi.org/10.3389/fmicb.2021.671271.

Large-scale meta-longitudinal microbiome data with a known batch factor - (Peer Reviewed Journal)
Oh, S., Li, R.W. 2022. Large-scale meta-longitudinal microbiome data with a known batch factor. Nature Methods. https://doi.org/10.3390/genes13030392.

Tools and resources enabling marker gene-based microbiome studies - (Book / Chapter)
Liu, J., Li, R.W. 2022. Tools and resources enabling marker gene-based microbiome studies. In: Wu, V.C.H., editor. The Gut Microbiome: Bench to Table. 1st edition. Boca Raton, FL: CRC Press. p. 3-44. https://doi.org/10.1201/b22970.

Transcriptome analysis unravels that triacylglycerol bound docosahexaenoic acid regulates appetite via the mediation of leptin and intestinal epithelial function in animal models - (Peer Reviewed Journal)
Cao, W., Liu, F., Li, R.W., Wang, Y. 2022. Transcriptome analysis unravels that triacylglycerol bound docosahexaenoic acid regulates appetite via the mediation of leptin and intestinal epithelial function in animal models. Journal of Nutritional Biochemistry. https://doi.org/10.1016/j.jnutbio.2021.108856.

Docosahexaenoic acid prevented insulin resistance by modulating gut microbiome and promoting colonic peptide YY expression in diet-induced obesity mice - (Peer Reviewed Journal)
Cao, W., Li, R.W., Chin, Y., Wang, Y., Xue, C., Tang, Q. 2021. Docosahexaenoic acid prevented insulin resistance by modulating gut microbiome and promoting colonic peptide YY expression in diet-induced obesity mice. Food Science and Human Wellness. https://doi.org/10.1016/j.fshw.2021.07.018.

Molecular methods for identifying and diagnosing Trichinella; from historical perspectives to the ‘-omics’ revolution - (Book / Chapter)
Zarlenga, D.S. 2021. Molecular methods for identifying and diagnosing Trichinella; from historical perspectives to the ‘-omics’ revolution. In: Bruschi, Fabrizio, editor. Trichinella and Trichinellosis. London, UK: Elsevier Academic Press. 35-76.

Taxonomy of the Trichinella genus - (Book / Chapter)
Pozio, E., Zarlenga, D.S. 2021. Taxonomy of the Trichinella genus. In: Bruschi, Fabrizio, editor. Trichinella and Trichinellosis. London, UK: Elsevier Academic Press. 395-415.

Yeast particle encapsulation of scaffolded terpene compounds for controlled terpene release - (Peer Reviewed Journal)
Soto, E., Rus, F., Li, H., Garceau, C., Chicca, J., Elfawal, M., Gazzola, D., Nielsen, M., Urban Jr., J.F., Aroian, R., Ostroff, G. 2021. Yeast particle encapsulation of scaffolded terpene compounds for controlled terpene release. Foods. https://doi.org/10.3390/foods10061207.

Transcriptome analysis reveals the protective role of fructo-oligosaccharide in colonic mucosal barriers in exercise-induced stressed mice - (Peer Reviewed Journal)
Cao, W., Chin, Y., Li, R.W., Xue, C., Wang, Y., Tang, Q. 2021. Transcriptome analysis reveals the protective role of fructo-oligosaccharide in colonic mucosal barriers in exercise-induced stressed mice. Food and Function. https://doi.org/10.1039/D0FO02556A.

Enteric helminth coinfection enhances host susceptibility to West Nile virus in the brain via a tuft cell-IL-4Ra signaling axis in gut epithelium - (Peer Reviewed Journal)
Desai, P., Janova, H., White, J.P., Reynoso, G.V., Hickman, H.D., Baldridge, M.T., Urban Jr, J.F., Stappenbeck, T.S., Thackray, L.B., Diamond, M.S. 2021. Enteric helminth coinfection enhances host susceptibility to West Nile virus in the brain via a tuft cell-IL-4Ra signaling axis in gut epithelium . Cell. https://doi.org/10.1016/j.cell.2021.01.051.

Temporal dynamic methods for bulk RNA-Seq time series data - (Peer Reviewed Journal)
Oh, S., Li, R.W. 2021. Temporal dynamic methods for bulk RNA-Seq time series data. Genes. 12(3):352. https://doi.org/10.3390/genes12030352.

Whipworm-associated intestinal microbiome members consistent across both human and mouse hosts - (Peer Reviewed Journal)
Rosa, B.A., Snowden, C., Martin, J., Fisher, K., Kupritz, J., Beshah, E., Supali, T., Gankpala, L., Fisher, P.U., Urban Jr, J.F., Mitreva, M. 2021. Whipworm-associated intestinal microbiome members consistent across both human and mouse hosts. Frontiers in Cellular and Infection Microbiology. https://doi.org/10.3389/fcimb.2021.637570.

Genistein reduces the risk of local mammary cancer recurrence and ameliorates alterations in the gut microbiota in the offspring of obese dams - (Peer Reviewed Journal)
Oliveira De Andrade, F., Liu, F., Zhang, X., Mariana, R., Dani, C., Cruz, I., Wang, T.T., Helferiche, W., Li, R.W., Hilakivi-Clarke, L. 2021. Genistein reduces the risk of local mammary cancer recurrence and ameliorates alterations in the gut microbiota in the offspring of obese dams. Nutrients. 12(1):201. https://doi.org/10.3390/nu13010201.

New paraprobiotic-based treatment for control of the barber pole worm Haemonchus contortus in sheep - (Peer Reviewed Journal)
Sanders, J., Xie, Y., Gazzola, D., Li, H., Abraham, A., Flanagan, K., Rus, F., Miller, M., Hu, Y., Zarlenga, D.S., Li, R.W., Urban Jr, J.F., Ostroff, G., Zajac, A., Aroian, R.V. 2020. New paraprobiotic-based treatment for control of the barber pole worm Haemonchus contortus in sheep. International Journal for Parasitology: Drug and Drug Resistance. 14(230-236). https://doi.org/10.1016/j.ijpddr.2020.11.004.

Diet-induced changes in bacterial communities in the jejunum and their associations with bile acids in Angus beef cattle - (Peer Reviewed Journal)
Liu, J., Liu, F., Cai, W., Jia, C., Ying, B., Yanghua, H., Weiyun, Z., Li, R.W., Song, J. 2020. Diet-induced changes in bacterial communities in the jejunum and their associations with bile acids in Angus beef cattle. Microbiome. 2:33. https://doi.org/10.1186/s42523-020-00051-7.

Polymannuronic acid prevents dopaminergic neuronal loss via brain-gut-microbiota axis in Parkinson’s disease model - (Peer Reviewed Journal)
Dong, X., Wang, X., Liu, F., Li, R.W., Xue, C., Wong, K., Wong, W., Tang, Q. 2020. Polymannuronic acid prevents dopaminergic neuronal loss via brain-gut-microbiota axis in Parkinson’s disease model. International Journal of Biological Macromolecules. 164:994-1005. https://doi.org/10.1016/j.ijbiomac.2020.07.180.

Molecular and metabolomic changes in the proximal colon of pigs infected with Trichuris suis - (Peer Reviewed Journal)
Dawson, H.D., Chen, C.T., Li, R.W., Bell, N., Shea-Donohue, T., Kringel, H., Beshah, E., Hill, D.E., Urban Jr, J.F. 2020. Molecular and metabolomic changes in the proximal colon of pigs infected with Trichuris suis. Scientific Reports. 10, 12853. https://doi.org/10.1038/s41598-020-69462-5.

Molecular and microbial signatures predictive of prebiotic action of neoagarotetraose in a dextran sulfate sodium-induced murine colitis model - (Peer Reviewed Journal)
Liu, F., Liu, J., Wang, T.T., Changhu, X., Ziangzhao, M., Qingjuan, T., Li, R.W. 2020. Molecular and microbial signatures predictive of prebiotic action of neoagarotetraose in a dextran sulfate sodium-induced murine colitis model. Microorganisms. 8(7):995. https://doi.org/10.3390/microorganisms8070995.

Mechanistic insights into the attenuation of intestinal inflammation and modulation of the gut microbiome by krill oil using in vitro and in vivo models - (Peer Reviewed Journal)
Liu, F., Smith, A.D., Solano Aguilar, G., Wang, T.T., Pham, Q., Tang, Q., Urban Jr, J.F., Xue, C., Li, R.W. 2020. Mechanistic insights into the attenuation of intestinal inflammation and modulation of the gut microbiome by krill oil using in vitro and in vivo models. Microbiome. 8:83. https://doi.org/10.1186/s40168-020-00843-8.

An inactivated bacterium (paraprobiotic) expressing Bacillus thuringiensis Cry5B as a therapeutic for Ascaris and Parascaris spp. infections in large animals - (Peer Reviewed Journal)
Urban Jr, J.F., Nielsen, M., Gazzola, D., Xie, Y., Beshah, E., Hu, Y., Rus, F., Flanagan, K., Draper, A., Vakalapudi, S., Li, R.W., Ostroff, G.R., Aroian, R.V. 2020. An inactivated bacterium (paraprobiotic) expressing Bacillus thuringiensis Cry5B as a therapeutic for Ascaris and Parascaris spp. infections in large animals. Elsevier. 164:994-1005. https://doi.org/10.1016/j.onehlt.2021.100241.

Astaxanthin n-octanoic acid diester ameliorated insulin resistance in high-fat and high-sucrose diet-fed mice by modulating the gut microbiome - (Peer Reviewed Journal)
Gao, Y., Yang, L., Chin, Y., Liu, F., Li, R.W., Cao, W., Yuan, S., Xue, C., Xu, J., Tang, Q. 2020. Astaxanthin n-octanoic acid diester ameliorated insulin resistance in high-fat and high-sucrose diet-fed mice by modulating the gut microbiome. Scientific Reports. 21:2149. https://doi.org/10.3390/ijms21062149.

Gut microbial signatures with predictive power for moxidectin treatment outcomes in - (Peer Reviewed Journal)
Liu, F., Xie, Y., Zajaz, A.M., Hu, Y., Aroian, R.V., Urban Jr, J.F., Li, R.W. 2020. Gut microbial signatures with predictive power for moxidectin treatment outcomes in. Journal of Parasitology. 242(2020):108607. https://doi.org/10.1016/j.vetmic.2020.108607.

BBhlhe40 promotes TH2 cell-mediated anti-helminth immunity and reveals cooperative Csf2rb family cytokines - (Peer Reviewed Journal)
Jarjour, N.N., Bradstreet, T.R., Schwarzkopf, E.A., Cook, M.E., Lai, C., Huang, S., Taneja, R., Stappenbeck, T.S., Urban Jr, J.F., Edelson, B.T. 2020. BBhlhe40 promotes TH2 cell-mediated anti-helminth immunity and reveals cooperative Csf2rb family cytokines. Journal of Immunology. 204(4):923-932. https://doi.org/10.4049/jimmunol.1900978.

An integrated computational and evidence-based approach identifies small molecule inhibitors detrimental to intestinal cells and tissue of parasitic nematodes - (Peer Reviewed Journal)
Jasmer, D.P., Rosa, B.A., Tyagi, R., Bulman, C.A., Beernsten, B., Urban Jr, J.F., Sakanari, J., Mitreva, M. 2020. An integrated computational and evidence-based approach identifies small molecule inhibitors detrimental to intestinal cells and tissue of parasitic nematodes. PLOS Neglected Tropical Diseases. 14(5):e0007942. https://doi.org/10.1371/journal.pntd.0007942.

Bhlhe40 mediates tissue-specific control of macrophage proliferation in homeostasis and type 2 immunity - (Peer Reviewed Journal)
Jarjour, N.N., Schwarzkopf, E.A., Bradstreet, T.R., Shchukina, I., Lin, C., Huang, S., Lai, C., Cook, M.E., Taneja, R., Stappenbeck, T., Randolph, G.J., Artyomov, M.N., Urban Jr, J.F., Edelson, B.T. 2019. Bhlhe40 mediates tissue-specific control of macrophage proliferation in homeostasis and type 2 immunity. Nature Immunology. 20:687-700. https://doi.org/10.1038/s41590-019-0382-5.

Network analysis detected microbial co-occurrence patterns and identified keystone species in the gut microbial community of mice in response to stress and chondroitin sulfate disaccharide dietary supplement - (Peer Reviewed Journal)
Liu, F., Li, Z., Wang, Z., Xue, C., Tang, Q., Li, R.W. 2019. Network analysis detected microbial co-occurrence patterns and identified keystone species in the gut microbial community of mice in response to stress and chondroitin sulfate disaccharide dietary supplement. International Journal of Molecular Sciences. 20(9):2130. https://doi.org/10.3390/ijms20092130

The caprine abomasal microbiome - (Abstract Only)

Chronic helminth infection does not impair immune response to malaria transmission blocking vaccine Pfs230D1M-EPA/Alhydrogel® in mice - (Peer Reviewed Journal)
Coelho, C.H., Gazzinelli-Guimaraes, P.H., Howard, J., Barnafo, E., Alani, N.A., Muratova, O., Mccormack, A., Kelnhofer, E., Urban Jr, J.F., Narum, D., Anderson, C., Langhorne, J., Nutman, T.B., Duffy, P.E. 2019. Chronic helminth infection does not impair immune response to malaria transmission blocking vaccine Pfs230D1M-EPA/Alhydrogel® in mice. Scientific Reports. 37(8):1038-1045. https://doi.org/10.1016/j.vaccine.2019.01.027.

Transcriptome analysis unraveled potential mechanisms of resistance to Haemonchus contortus infection in Merino sheep populations bred for parasite resistance - (Peer Reviewed Journal)
Zhang, R., Liu, F., Hunt, P., Li, C., Zhang, L., Ingham, A., Li, R.W. 2019. Transcriptome analysis unraveled potential mechanisms of resistance to Haemonchus contortus infection in Merino sheep populations bred for parasite resistance. Veterinary Research. 50:7. https://doi.org/10.1186/s13567-019-0622-6.

Temporal dynamics in meta longitudinal RNA-Seq data - (Peer Reviewed Journal)
Oh, S., Li, C., Baldwin, R.L., Song, S., Liu, F., Li, R.W. 2019. Temporal dynamics in meta longitudinal RNA-Seq data. Scientific Reports. 9(1):763. https://doi.org/10.1038/s41598-018-37397-7.

The valproic acid rat model of autism present with gut bacterial dysbiosis similar to that in human autism - (Peer Reviewed Journal)
Liu, F., Horton-Sparks, K., Hull, V., Li, R.W., Martinez-Cerdeno, V. 2018. The valproic acid rat model of autism present with gut bacterial dysbiosis similar to that in human autism. Molecular Autism. 9:61. https://doi.org/10.1186/s13229-018-0251-3.

The effect of dietary Agaricus bisporus mushroom on intestinal microbiota composition and host immunological function - (Peer Reviewed Journal)
Solano Aguilar, G., Jang, S., Lakshman, S., Gupta, R., Beshah, E., Sikaroodi, M., Vinyard, B.T., Molokin, A., Gillevet, P., Urban Jr, J.F. 2018. The effect of dietary Agaricus bisporus mushroom on intestinal microbiota composition and host immunological function. Nutrients. 10(11):1721. https://doi.org/10.3390/nu10111721.

Ascaris suum infection was associated with a worm-independent reduction in microbial diversity and altered metabolic potential in the porcine gut microbiome - (Peer Reviewed Journal)
Wang, Y., Liu, F., Urban Jr, J.F., Paerewijck, O., Geldhof, P., Li, R.W. 2019. Ascaris suum infection was associated with a worm-independent reduction in microbial diversity and altered metabolic potential in the porcine gut microbiome. International Journal for Parasitology. 49(3-4):247-256. https://doi.org/10.1016/j.ijpara.2018.10.007.

Analysis of the Trichuris suis excretory/secretory proteins as a function of life cycle stage and their immunomodulatory properties - (Peer Reviewed Journal)
Leroux, L., Nasr, M., Valanparamabil, R., Tam, M., Rosa, B.A., Siciliani, E., Hill, D.E., Zarlenga, D.S., Jaramillo, M., Weinstock, J.V., Geary, T.G., Stevenson, M.M., Urban Jr, J.F., Makedonka, M., Jardim, A. 2018. Analysis of the Trichuris suis excretory/secretory proteins as a function of life cycle stage and their immunomodulatory properties. Scientific Reports. 8:15921. https://doi.org/10.1038/s41598-018-34174-4.

Comparative genomics of the major parasitic worms - (Peer Reviewed Journal)
Beasely, H., Bennett, H.M., Coghlan, A., Cotton, J., Doyle, S.R., Gordon, D., Harsha, B., Huckvale, T., Lomax, J., Holroyd, N., Reid, A.J., Ribeiro, D., Rinaldi, G., Shafie, M., Stanley, E., Tracey, A., Berriman, M., Hallsworth-Pepin, K., Martin, J., Ozersky, P., Rosa, B.A., Tyagi, R., Zhang, X., Mitreva, M., Laetsch, D.R., Koutsovoulos, G., Kumar, S., Kaur, G., Blaxter, M., Howe, K.L., Leach, A.R., Mutowo, P., Rawlings, N., Kuo, T., Lee, T.J., Ke, H., Tsai, I.J., Wheeler, N.J., Day, T.A., Zamanian, M., Beech, R.N., Parkinson, J., Seshadri, S.L., Kikuchi, T., Maizels, R.M., Partono, F., Babayan, S., Allen, J.E., O'Boyle, N., Wang, L., Osuna, A., Cruz-Bustos, T., Samblas, M.G., Cuellar, C., Cooper, P.J., Devaney, E., Harcus, Y., Hodgkinson, J., Bah, G., Tanya, V.N., Eberhard, M.L., Asano, K., Rodriguez, P.F., Sato, H., Gilleard, J.S., Matthews, J.B., Cook, J., Toldeo, R., Scholz, T., Schnyder, M., Allan, F., Emery, A., Olson, P.D., Rollinson, D., Castillo, E., Kalbe, M., Eom, K.S., Horak, P., Mitreva, M., Hawdon, J.M., Urban Jr, J.F., Hill, D.E., Zarlenga, D.S., Bisset, S.A., Pfarr, K., Makepeace, B., Taylor, D.W. 2018. Comparative genomics of the major parasitic worms. Nature Genetics. 5:163-174. https://doi.org/10.1038/s41588-018-0262-1.

Transcriptomic analysis reveals effects of fucoxanthin on intestinal glucose transport - (Peer Reviewed Journal)
Cao, W., Li, J., Chin, Y., Xue, C., Li, R.W., Tang, Q. 2018. Transcriptomic analysis reveals effects of fucoxanthin on intestinal glucose transport. Journal of Functional Foods. 49:205-213. 10.1016/j.jff.2018.08.018.

Bifidobacterium animalis subspecies lactis modulates the local immune response and glucose uptake in the small intestine of juvenile pigs infected with the parasitic nematode Ascaris suum - (Peer Reviewed Journal)
Solano Aguilar, G., Shea-Donohue, T., Madden, K., Quinones, A., Beshah, E., Lakshman, S., Xie, Y., Dawson, H.D., Urban Jr, J.F. 2018. Bifidobacterium animalis subspecies lactis modulates the local immune response and glucose uptake in the small intestine of juvenile pigs infected with the parasitic nematode Ascaris suum. Gut Microbes. 19:1-15. https://doi.org/10.1080/19490976.2018.1460014.

Bacillus thuringiensis Cry5B protein as a new pan-hookworm cure - (Peer Reviewed Journal)
Hu, Y., Nguyen, T., Lee, A.C., Urban Jr, J.F., Miller, M.M., Zhan, B., Koch, D.J., Noon, J., Abraham, A., Fujiwara, T. 2018. Bacillus thuringiensis Cry5B protein as a new pan-hookworm cure. International Journal for Parasitology: Drug and Drug Resistance. 8:287-294. https://doi.org/10.1016/j.ijpddr.2018.05.001

Transcriptome analysis revealed anti-obesity effects of the alginate polysaccharide in high-fat diet-induced obese mice - (Peer Reviewed Journal)
Wang, X., Liu, F., Yuan, G., Xue, C., Li, R.W., Tang, Q. 2018. Transcriptome analysis revealed anti-obesity effects of the alginate polysaccharide in high-fat diet-induced obese mice. International Journal of Biological Macromolecules. 115:861-870.

Bcl11b is essential for licensing Th2 differentiation during helminth infection and allergic asthma - (Peer Reviewed Journal)
Lorentsen, K., Cho, J., Luo, X., Zuniga, A., Urban Jr, J.F., Zhou, L., Gharaibeh, R., Jobin, C., Kladde, M., Avram, D. 2018. Bcl11b is essential for licensing Th2 differentiation during helminth infection and allergic asthma. Nature Communications. 9(1)1679. https://doi.org/10.1038/s41467-018-04111-0.

S1P dependent inter organ trafficking of group 2 innate lymphoid cells supports host defense - (Peer Reviewed Journal)
Huang, Y., Mao, K., Chen, X., Sun, M., Kawabe, T., Li, W., Usher, N., Zhu, J., Urban Jr, J.F., Paul, W.E., Germain, R.N. 2018. S1P dependent inter organ trafficking of group 2 innate lymphoid cells supports host defense. Science. 359:114–119. https://doi.org/10.1126/science.aam5809.