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Microbiome Metabolic Engineering

To view the full list of publications across IGB's research portfolio, please visit our Illinois Experts page

2023

McLeod, A., Wolf, P., Chapkin, R. S., Davidson, L. A., Ivanov, I., Berbaum, M., Williams, L. R., Gaskins, H. R., Ridlon, J., Sanchez-Flack, J., Blumstein, L., Schiffer, L., Hamm, A., Cares, K., Antonic, M., Bernabe, B. P., Fitzgibbon, M., & Tussing-Humphreys, L. (2023). Design of the Building Research in CRC prevention (BRIDGE-CRC) trial: a 6-month, parallel group Mediterranean diet and weight loss randomized controlled lifestyle intervention targeting the bile acid-gut microbiome axis to reduce colorectal cancer risk among African American/Black adults with obesity. Trials, 24(1), Article 113. https://doi.org/10.1186/s13063-023-07115-4

Guo, B., Holscher, H. D., Auvil, L. S., Welge, M. E., Bushell, C. B., Novotny, J. A., Baer, D. J., Burd, N. A., Khan, N. A., & Zhu, R. (2023). Estimating Heterogeneous Treatment Effect on Multivariate Responses Using Random Forests. Statistics in Biosciences, 15(3), 545-561. https://doi.org/10.1007/s12561-021-09310-w

Yun, E. J., Yu, S., Kim, D. H., Park, N. J., Liu, J. J., Jin, Y. S., & Kim, K. H. (2023). Identification of the enantiomeric nature of 2-keto-3-deoxy-galactonate in the catabolic pathway of 3,6-anhydro-l-galactose. Applied Microbiology and Biotechnology, 107(24), 7427-7438. https://doi.org/10.1007/s00253-023-12807-7

Brukner Havelková, P., Crevecoeur, I., Varadzin, L., Ambrose, S. H., Tartar, E., Thibeault, A., Buckley, M., Villotte, S., & Varadzinová, L. (2023). Patterns of Violence in the Pre-Neolithic Nile Valley. African Archaeological Review, 40(4), 597-619. https://doi.org/10.1007/s10437-023-09533-w

Wu, J., Gathman, R. J., Quintanilla Portillo, J., Gaulke, C., Kim, M., & Stasiewicz, M. J. (2023). Aggregative Soil Sampling Using Boot Covers Compared to Soil Grabs From Commercial Romaine Fields Shows Similar Indicator Organism and Microbial Community Recoveries. Journal of Food Protection, 86(11), Article 100177. https://doi.org/10.1016/j.jfp.2023.100177

Kang, Y., Oba, P. M., Gaulke, C. A., Sánchez-Sánchez, L., & Swanson, K. S. (2023). Dietary Inclusion of Yellow Mealworms (T. molitor) and Lesser Mealworms (A. diaperinus) Modifies Intestinal Microbiota Populations of Diet-Induced Obesity Mice. Journal of Nutrition, 153(11), 3220-3236. https://doi.org/10.1016/j.tjnut.2023.09.007

Park, S., Park, B. R., Jeong, D., Park, J., Ko, J. K., Kim, S. J., Kim, J. S., Jin, Y. S., & Kim, S. R. (2023). Functional expression of RuBisCO reduces CO2 emission during fermentation by engineered Saccharomyces cerevisiae. Process Biochemistry, 134, 286-293. https://doi.org/10.1016/j.procbio.2023.10.013

Resendiz-Moctezuma, C., Fonville, A. P. L., Harsh, B. N., Stasiewicz, M. J., & Miller, M. J. (2023). Use of Doehlert Matrix as a Tool for High-Throughput Screening of Organic Acids and Essential Oils on Miniaturized Pork Loins, Followed by Lab-Scale Validation That Confirmed Tested Compounds Do Not Show Synergistic Effects against Salmonella Typhimurium. Foods, 12(21), Article 4034. https://doi.org/10.3390/foods12214034

Cannavale, C. N., Keye, S. A., Rosok, L. M., Martell, S. G., Holthaus, T. A., Raine, L. R., Mullen, S. P., Holscher, H. D., Hillman, C. H., Kramer, A. F., Cohen, N. J., Hammond, B. R., Renzi-Hammond, L., & Khan, N. A. (2023). Macular Pigment Optical Density and Skin Carotenoids in a Childhood Sample. Journal of Nutrition, 153(10), 3144-3151. https://doi.org/10.1016/j.tjnut.2023.06.006

Xu, G., Pan, Y-X., Mei, W., & Chen, H. (2023). Single-Cell RNA Sequencing (scRNA-seq) Identifies L1CAM as a Key Mediator between Epithelial Tuft Cell and Innate Lymphoid Cell in the Colon of Hnrnp I Knockout Mice. Biomedicines, 11(10), Article 2734. https://doi.org/10.3390/biomedicines11102734

Nguyen, M. T., Kim, S. A., Cheng, Y. Y., Hong, S. H., Jin, Y. S., & Han, N. S. (2023). A qPCR Method to Assay Endonuclease Activity of Cas9-sgRNA Ribonucleoprotein Complexes. Journal of Microbiology and Biotechnology, 33(9), 1228-1237. https://doi.org/10.4014/jmb.2305.05010

Sarker, K., Zhu, R., Holscher, H. D., & Zhai, C. X. (2023). Augmenting nutritional metabolomics with a genome-scale metabolic model for assessment of diet intake. In ACM-BCB 2023 - 14th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics Article 4 (ACM-BCB 2023 - 14th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics). Association for Computing Machinery. https://doi.org/10.1145/3584371.3612958

Grosicki, G. J., Pugh, J., Wosinska, L., Quilter, K., Mattimoe, D., Allen, J., Joyce, S. A., O’Sullivan, O., & Close, G. L. (2023). Ultra-Endurance triathlon competition shifts fecal metabolome independent of changes to microbiome composition. Journal of Applied Physiology, 135(3), 549-558. https://doi.org/10.1152/japplphysiol.00024.2023

Kim, J., Cheong, Y. E., Yu, S., Yun, E. J., Jin, Y. S., & Kim, K. H. (2023). Biosynthesis of L-fucose and L-fuculose using engineered Saccharomyces cerevisiae. Process Biochemistry, 132, 152-156. https://doi.org/10.1016/j.procbio.2023.07.010

Caicedo, K. Y. O., Fernandez-Materan, F. V., Hernandez, A. G., Daniel, S. L., Alves, J. M. P., & Ridlon, J. M. (2023). Complete genome sequence of the archetype bile acid 7α-dehydroxylating bacterium, Clostridium scindens VPI12708, isolated from human feces, circa 1980. Microbiology Resource Announcements, 12(9). https://doi.org/10.1128/MRA.00029-23

Xu, G. B., Cai, M., Kadayifci, F. Z., Dong, J., Zheng, S., Mei, W., Zhao, W., Pan, Y. X., & Chen, H. (2023). Increasing dietary nutrient levels modulates colon immune adaptation and alleviates inflammation in the epithelial heterogeneous nuclear ribonucleoprotein I (Hnrnp I) knockout mice. Journal of Nutritional Biochemistry, 119, Article 109406. https://doi.org/10.1016/j.jnutbio.2023.109406

Fan, Y., McMath, A. L., & Donovan, S. M. (2023). Review on the Impact of Milk Oligosaccharides on the Brain and Neurocognitive Development in Early Life. Nutrients, 15(17), Article 3743. https://doi.org/10.3390/nu15173743

Cai, T., Sutter, C., Donovan, S. M., & Fiese, B. H. (2023). The Relationship Between Maternal and Infant Sleep Duration Across the First Two Years. Journal of Developmental and Behavioral Pediatrics, 44(6), E421-E428. https://doi.org/10.1097/DBP.0000000000001195

Ragunathan, P. T., Lim, E. N. K., Ma, X., Massé, E., & Vanderpool, C. K. (2023). Mechanisms of Regulation of Cryptic Prophage-Encoded Gene Products in Escherichia coli. Journal of bacteriology, 205(8). https://doi.org/10.1128/jb.00129-23

Kim, J., Atkinson, C., Miller, M. J., Kim, K. H., & Jina, Y. S. (2023). Microbiome Engineering Using Probiotic Yeast: Saccharomyces boulardii and the Secreted Human Lysozyme Lead to Changes in the Gut Microbiome and Metabolome of Mice. Microbiology Spectrum, 11(4). https://doi.org/10.1128/spectrum.00780-23

Holthaus, T. A., Sethi, S., Cannavale, C. N., Aguiñaga, S., Burd, N. A., Holscher, H. D., & Khan, N. A. (2023). MIND dietary pattern adherence is inversely associated with visceral adiposity and features of metabolic syndrome. Nutrition Research, 116, 69-79. https://doi.org/10.1016/j.nutres.2023.06.001

Ridlon, J. M., Daniel, S. L., & Gaskins, H. R. (2023). The Hylemon-Björkhem pathway of bile acid 7-dehydroxylation: history, biochemistry, and microbiology. Journal of Lipid Research, 64(8), Article 100392. https://doi.org/10.1016/j.jlr.2023.100392

Basso, T. P., Procópio, D. P., Petrin, T. H. C., Giacon, T. G., Jin, Y. S., Basso, T. O., & Basso, L. C. (2023). Engineering xylose fermentation in an industrial yeast: continuous cultivation as a tool for selecting improved strains. Letters in Applied Microbiology, 76(7). https://doi.org/10.1093/lambio/ovad077

Shi, Q., Abdel-Hamid, A. M., Sun, Z., Cheng, Y., Tu, T., Cann, I., Yao, B., & Zhu, W. (2023). Carbohydrate-binding modules facilitate the enzymatic hydrolysis of lignocellulosic biomass: Releasing reducing sugars and dissociative lignin available for producing biofuels and chemicals. Biotechnology Advances, 65, Article 108126. https://doi.org/10.1016/j.biotechadv.2023.108126

Baldeon, A. D., McDonald, D., Gonzalez, A., Knight, R., & Holscher, H. D. (2023). Diet Quality and the Fecal Microbiota in Adults in the American Gut Project. Journal of Nutrition, 153(7), 2004-2015. https://doi.org/10.1016/j.tjnut.2023.02.018

Unger, A. L., Astrup, A., Feeney, E. L., Holscher, H. D., Gerstein, D. E., Torres-Gonzalez, M., & Brown, K. (2023). Harnessing the Magic of the Dairy Matrix for Next-Level Health Solutions: A Summary of a Symposium Presented at Nutrition 2022. Current Developments in Nutrition, 7(7), Article 100105. https://doi.org/10.1016/j.cdnut.2023.100105

Morton, J. T., Jin, D. M., Mills, R. H., Shao, Y., Rahman, G., McDonald, D., Zhu, Q., Balaban, M., Jiang, Y., Cantrell, K., Gonzalez, A., Carmel, J., Frankiensztajn, L. M., Martin-Brevet, S., Berding, K., Needham, B. D., Zurita, M. F., David, M., Averina, O. V., ... Taroncher-Oldenburg, G. (2023). Multi-level analysis of the gut–brain axis shows autism spectrum disorder-associated molecular and microbial profiles. Nature Neuroscience, 26(7), 1208-1217. https://doi.org/10.1038/s41593-023-01361-0

Hutchinson, N. T., Wang, S. S., Rund, L. A., Caetano-Silva, M. E., Allen, J. M., Johnson, R. W., & Woods, J. A. (2023). Effects of an inulin fiber diet on the gut microbiome, colon, and inflammatory biomarkers in aged mice. Experimental Gerontology, 176, Article 112164. https://doi.org/10.1016/j.exger.2023.112164

Fridman D'Alessandro, V., D'Alessandro-Gabazza, C. N., Yasuma, T., Toda, M., Takeshita, A., Tomaru, A., Tharavecharak, S., Lasisi, I. O., Hess, R. Y., Nishihama, K., Fujimoto, H., Kobayashi, T., Cann, I., & Gabazza, E. C. (2023). Inhibition of a Microbiota-Derived Peptide Ameliorates Established Acute Lung Injury. American Journal of Pathology, 193(6), 740-754. https://doi.org/10.1016/j.ajpath.2023.03.003

Kim, J., Jin, Y. S., & Kim, K. H. (2023). L-Fucose is involved in human–gut microbiome interactions. Applied Microbiology and Biotechnology, 107(12), 3869-3875. https://doi.org/10.1007/s00253-023-12527-y

Cannavale, C. N., Edwards, C. G., Liu, R., Keye, S. A., Iwinski, S. J., Holscher, H. D., Renzi-Hammond, L., & Khan, N. A. (2023). Macular pigment is inversely related to circulating C-reactive protein concentrations in school-aged children. Nutrition Research, 114, 13-19. https://doi.org/10.1016/j.nutres.2023.03.003

Lee, S. H., Yun, E. J., Han, N. R., Jung, I., Pelton, J. G., Lee, J-E., Kang, N. J., Jin, Y-S., & Kim, K. H. (2023). Production of Ethyl-agarobioside, a Novel Skin Moisturizer, by Mimicking the Alcoholysis from the Japanese Sake-Brewing Process. Marine Drugs, 21(6), Article 341. https://doi.org/10.3390/md21060341

Bailey, M. A., Thompson, S. V., Mysonhimer, A. R., Bennett, J. N., Vanhie, J. J., De Lisio, M., Burd, N. A., Khan, N. A., & Holscher, H. D. (2023). Dietary fiber intake and fecal short chain fatty acid concentrations are associated with lower plasma lipopolysaccharide-binding protein and inflammation. American Journal of Physiology - Gastrointestinal and Liver Physiology, 324(5), G369-G377. https://doi.org/10.1152/ajpgi.00176.2021

Mysonhimer, A. R., & Holscher, H. D. (2023). Nondigestible Carbohydrate Consumption: Balancing Therapeutics With Gastrointestinal Effects and Tolerance. Nutrition Today, 58(3), 100-104. https://doi.org/10.1097/NT.0000000000000605

Finet, S., He, F., Utterback, P. L., Parsons, C. M., & de Godoy, M. R. C. (2023). Nutrient profile, amino acid digestibility, true metabolizable energy and indispensable amino acid scoring of whole hemp seeds for use in canine and feline diets. Journal of animal science, Article skad106. https://doi.org/10.1093/jas/skad106

Hughes, R. L., Pindus, D. M., Khan, N. A., Burd, N. A., & Holscher, H. D. (2023). Associations between Accelerometer-Measured Physical Activity and Fecal Microbiota in Adults with Overweight and Obesity. Medicine and Science in Sports and Exercise, 55(4), 680-689. https://doi.org/10.1249/MSS.0000000000003096

Watson, K. M., Gardner, I. H., Anand, S., Siemens, K. N., Sharpton, T. J., Kasschau, K. D., Dewey, E. N., Martindale, R., Gaulke, C. A., & Tsikitis, V. L. (2023). Colonic Microbial Abundances Predict Adenoma Formers. Annals of Surgery, 277(4), E817-E824. https://doi.org/10.1097/SLA.0000000000005261

Donovan, S. M., Aghaeepour, N., Andres, A., Azad, M. B., Becker, M., Carlson, S. E., Järvinen, K. M., Lin, W., Lönnerdal, B., Slupsky, C. M., Steiber, A. L., & Raiten, D. J. (2023). Evidence for human milk as a biological system and recommendations for study design—a report from “Breastmilk Ecology: Genesis of Infant Nutrition (BEGIN)” Working Group 4. American Journal of Clinical Nutrition, 117, S61-S86. https://doi.org/10.1016/j.ajcnut.2022.12.021

Lane, S., Turner, T. L., & Jin, Y. S. (2023). Glucose assimilation rate determines the partition of flux at pyruvate between lactic acid and ethanol in Saccharomyces cerevisiae. Biotechnology Journal, 18(4), Article 2200535. https://doi.org/10.1002/biot.202200535

Mysonhimer, A. R., Cannavale, C. N., Bailey, M. A., Khan, N. A., & Holscher, H. D. (2023). Prebiotic Consumption Alters Microbiota but Not Biological Markers of Stress and Inflammation or Mental Health Symptoms in Healthy Adults: A Randomized, Controlled, Crossover Trial. Journal of Nutrition, 153(4), 1283-1296. https://doi.org/10.1016/j.tjnut.2023.02.015

Donovan, S. M., Abrams, S. A., Azad, M. B., Belfort, M. B., Bode, L., Carlson, S. E., Dallas, D. C., Hettinga, K., Järvinen, K., Kim, J. H., Lebrilla, C. B., McGuire, M. K., Sela, D. A., & Neu, J. (2023). Summary of the Joint National Institutes of Health and the Food and Drug Administration Workshop Titled “Exploring the Science Surrounding the Safe Use of Bioactive Ingredients in Infant Formula: Considerations for an Assessment Framework”. Journal of Pediatrics, 255, 30-41.e1. https://doi.org/10.1016/j.jpeds.2022.11.027

Chembazhi, U. V., Tung, W. S., Hwang, H., Wang, Y., Lalwani, A., Nguyen, K. L., Bangru, S., Yee, D., Chin, K., Yang, J., Kalsotra, A., & Mei, W. (2023). PTBP1 controls intestinal epithelial regeneration through post-transcriptional regulation of gene expression. Nucleic acids research, 51(5), 2397-2414. Article gkad042. https://doi.org/10.1093/nar/gkad042

Varadzinová, L., Varadzin, L., & Ambrose, S. H. (2023). New radiocarbon dates for postglacial reoccupation of the Sudanese Nile. Quaternary Science Reviews, 303, Article 107953. https://doi.org/10.1016/j.quascirev.2023.107953

Kasperek, M. C., Mailing, L., Piccolo, B. D., Moody, B., Lan, R., Gao, X., Hernandez-Saavedra, D., Woods, J. A., Adams, S. H., & Allen, J. M. (2023). Exercise training modifies xenometabolites in gut and circulation of lean and obese adults. Physiological Reports, 11(6), Article e15638. https://doi.org/10.14814/phy2.15638

Hutchinson, N. T., Wang, S. S., Dokhanchi, J., Johnson, R. W., Buford, T. W., Allen, J. M., & Woods, J. A. (2023). Effects of Broad-spectrum Antibiotic Treatment or Germ-free Status on Endurance Performance and Exercise Adaptations in Mice. Medicine and Science in Sports and Exercise, 55(2), 225-234. https://doi.org/10.1249/MSS.0000000000003051

Yukawa, T., Bamba, T., Matsuda, M., Yoshida, T., Inokuma, K., Kim, J., Won Lee, J., Jin, Y. S., Kondo, A., & Hasunuma, T. (2023). Enhanced production of 3,4-dihydroxybutyrate from xylose by engineered yeast via xylonate re-assimilation under alkaline condition. Biotechnology and bioengineering, 120(2), 511-523. https://doi.org/10.1002/bit.28278

Holscher, H. D. (2023). Let's do the math: embracing mathematical modeling to advance nutrition research. American Journal of Clinical Nutrition, 117(2), 220-221. https://doi.org/10.1016/j.ajcnut.2022.12.011

Splichal, I., Donovan, S. M., Kindlova, Z., Stranak, Z., Neuzil Bunesova, V., Sinkora, M., Polakova, K., Valaskova, B., & Splichalova, A. (2023). Release of HMGB1 and Toll-like Receptors 2, 4, and 9 Signaling Are Modulated by Bifidobacterium animalis subsp. lactis BB-12 and Salmonella Typhimurium in a Gnotobiotic Piglet Model of Preterm Infants. International journal of molecular sciences, 24(3), Article 2329. https://doi.org/10.3390/ijms24032329

Varadzin, L., Varadzinová, L., Abdallah, A., Abdallah, B. A., Abdalla Mohammed, M., Ambrose, S. H., Burgert, P., Černý, M., DˊErcole, G., Fuller, D. Q., Garcea, E. A. A., Hošek, J., Hošková, K., Jones, M. B., Kapustka, K., Madani Ahmed, I., McCool, J-P., Mohamed Hamdeen, H., Novák, J., ... Unger, J. (2023). The Shaqadud Archaeological Project (Sudan): exploring prehistoric cultural adaptations in the Sahelian hinterlands. Antiquity, 97(391), Article e2. https://doi.org/10.15184/aqy.2022.148

Zhou, Y., Mirts, E. N., Yook, S., Waugh, M., Martini, R., Jin, Y. S., & Lu, Y. (2023). Reshaping the 2-Pyrone Synthase Active Site for Chemoselective Biosynthesis of Polyketides. Angewandte Chemie - International Edition, 62(5), Article e202212440. https://doi.org/10.1002/anie.202212440

Shinn, L. M., Mansharamani, A., Baer, D. J., Novotny, J. A., Charron, C. S., Khan, N. A., Zhu, R., & Holscher, H. D. (2023). Fecal Metabolites as Biomarkers for Predicting Food Intake by Healthy Adults. The Journal of nutrition, 152(12), 2956-2965. Article nxac195. https://doi.org/10.1093/jn/nxac195

Holthaus, T. A., Kashi, M., Cannavale, C. N., Edwards, C. G., Aguiñaga, S., Walk, A. D. M., Burd, N. A., Holscher, H. D., & Khan, N. A. (2023). MIND Dietary Pattern Adherence Is Selectively Associated with Cognitive Processing Speed in Middle-Aged Adults. The Journal of nutrition, 152(12), 2941-2949. Article nxac203. https://doi.org/10.1093/jn/nxac203

Rigaud, S., Queffelec, A., Le Bourdonnec, F. X., Alisher Kyzy, S., Ambrose, S. H., Ledevin, R., Kurbanov, R., Buzhilova, A., Berezina, N., Ziganshin, R. H., & Shnaider, S. (2023). Exploring Hypotheses on Early Holocene Caspian Seafaring Through Personal Ornaments: A Study of Changing Styles and Symbols in Western Central Asia. Open Archaeology, 9(1), Article 20220289. https://doi.org/10.1515/opar-2022-0289

Su, D. F., Ambrose, S. H., & Degusta, D. (2023). Paleoenvironment. In Ardipithecus Kadabba: Late Miocene Evidence from the Middle Awash, Ethiopia (pp. 521-547). University of California Press.

Lee, J. W., Bhagwat, S. S., Kuanyshev, N., Cho, Y. B., Sun, L., Lee, Y. G., Cortés-Peña, Y. R., Li, Y., Rao, C. V., Guest, J. S., & Jin, Y. S. (2023). Rewiring yeast metabolism for producing 2,3-butanediol and two downstream applications: Techno-economic analysis and life cycle assessment of methyl ethyl ketone (MEK) and agricultural biostimulant production. Chemical Engineering Journal, 451, Article 138886. https://doi.org/10.1016/j.cej.2022.138886

Deshavath, N. N., Dien, B. S., Slininger, P. J., Jin, Y-S., & Singh, V. (2023). A Chemical-Free Pretreatment for Biosynthesis of Bioethanol and Lipids from Lignocellulosic Biomass: An Industrially Relevant 2G Biorefinery Approach. Fermentation, 9(1), Article 5. https://doi.org/10.3390/fermentation9010005

McMath, A. L., Iwinski, S., Shen, S., Bost, K. F., Donovan, S. M., & Khan, N. A. (2023). Adherence to screen time and physical activity guidelines is associated with executive function in US toddlers participating in the STRONG Kids 2 birth cohort study. The Journal of Pediatrics, 252, 22-30.e6. https://doi.org/10.1016/j.jpeds.2022.08.026

Abdulla, S. Z., Kim, K., Azam, M. S., Golubeva, Y. A., Cakar, F., Slauch, J. M., & Vanderpool, C. K. (2023). Small RNAs Activate Salmonella Pathogenicity Island 1 by Modulating mRNA Stability through the hilD mRNA 39 Untranslated Region. Journal of bacteriology, 205(1). https://doi.org/10.1128/jb.00333-22

McMath, A. L., Aguilar-Lopez, M., Cannavale, C. N., Khan, N. A., & Donovan, S. M. (2023). A systematic review on the impact of gastrointestinal microbiota composition and function on cognition in healthy infants and children. Frontiers in Neuroscience, 17, Article 1171970. https://doi.org/10.3389/fnins.2023.1171970

Cannavale, C. N., Mysonhimer, A. R., Bailey, M. A., Cohen, N. J., Holscher, H. D., & Khan, N. A. (2023). Consumption of a fermented dairy beverage improves hippocampal-dependent relational memory in a randomized, controlled cross-over trial. Nutritional Neuroscience, 26(3), 265-274. https://doi.org/10.1080/1028415X.2022.2046963

Fan, Y., Vinjamuri, A., Tu, D., Lebrilla, C. B., & Donovan, S. M. (2023). Determinants of human milk oligosaccharides profiles of participants in the STRONG kids 2 cohort. Frontiers in Nutrition, 10, Article 1105668. https://doi.org/10.3389/fnut.2023.1105668

Golden, R. K., Sutkus, L. T., Bauer, L. L., Donovan, S. M., & Dilger, R. N. (2023). Determining the safety and efficacy of dietary supplementation with 3ˊ-sialyllactose or 6ˊ-sialyllactose on growth, tolerance, and brain sialic acid concentrations. Frontiers in Nutrition, 10, Article 1278804. https://doi.org/10.3389/fnut.2023.1278804

Metras, B. N., Oba, P. M., Miller, M. J., & Swanson, K. S. (2023). Effects of Commercial and Traditional Kefir Supplementation on Apparent Total Tract Macronutrient Digestibility and the Fecal Characteristics, Metabolites, and Microbiota of Healthy Adult Dogs. Journal of animal science, 101, Article skad316. https://doi.org/10.1093/jas/skad316

Kim, H. W., Kim, N. K., Thompson, J., de Jesus, M., Rehberger, J., Rehberger, T., Smith, A. H., & Mackie, R. I. (2023). Effects of dosing non-toxigenic Clostridia on the bacterial populations and immunological responses in the intestinal tract of lactating dairy cows. Frontiers in Microbiology, 14, Article 1107964. https://doi.org/10.3389/fmicb.2023.1107964

Shinn, L. M., Mansharamani, A., Baer, D. J., Novotny, J. A., Charron, C. S., Khan, N. A., Zhu, R., & Holscher, H. D. (in press). Fecal Metagenomics to Identify Biomarkers of Food Intake in Healthy Adults: Findings from Randomized, Controlled, Nutrition Trials. Journal of Nutrition. https://doi.org/10.1016/j.tjnut.2023.11.001

Vinderola, G., Cotter, P. D., Freitas, M., Gueimonde, M., Holscher, H. D., Ruas-Madiedo, P., Salminen, S., Swanson, K. S., Sanders, M. E., & Cifelli, C. J. (2023). Fermented foods: a perspective on their role in delivering biotics. Frontiers in Microbiology, 14, Article 1196239. https://doi.org/10.3389/fmicb.2023.1196239

Kim, H. W., Kim, N. K., Phillips, A. P. R., Parker, D. A., Liu, P., Whitaker, R. J., Rao, C. V., & Mackie, R. I. (2023). Genomic insight and physiological characterization of thermoacidophilic Alicyclobacillus isolated from Yellowstone National Park. Frontiers in Microbiology, 14, Article 1232587. https://doi.org/10.3389/fmicb.2023.1232587

Jagtap, S. S., Liu, J-J., Walukiewicz, H. E., Pangilinan, J., Lipzen, A., Ahrendt, S., Koriabine, M., Cobaugh, K., Salamov, A., Yoshinaga, Y., Ng, V., Daum, C., Grigoriev, I. V., Slininger, P. J., Dien, B. S., Jin, Y-S., & Rao, C. V. (2023). Near-complete genome sequence of Lipomyces tetrasporous NRRL Y-64009, an oleaginous yeast capable of growing on lignocellulosic hydrolysates. Microbiology Resource Announcements, 12(11). https://doi.org/10.1128/MRA.00426-23

Tondini, S. M., Mackie, R. I., & McCann, J. C. (2023). Polyclonal antibodies inhibit growth of key cellulolytic rumen bacterial species. Frontiers in Microbiology, 14, Article 1196492. https://doi.org/10.3389/fmicb.2023.1196492

Sommer, K. M., Lee, Y., Donovan, S. M., & Dilger, R. N. (2023). Purification methods to reduce interference by dextran sodium sulfate with quantification of gene expression in intestinal tissue samples from a piglet model of colitis. Journal of animal science, 101, Article skad202. https://doi.org/10.1093/jas/skad202

Hsu, C., Utterback, P. L., Parsons, C. M., Marx, F., Guldenpfennig, R., & de Godoy, M. R. C. (2023). Standardized amino acid digestibility and protein quality in extruded canine diets containing hydrolyzed protein using a precision fed rooster assay. Journal of animal science, 101, Article skad289. https://doi.org/10.1093/jas/skad289

Clark, S. D., Hsu, C., McCauley, S. R., De Godoy, M. R. C., He, F., Streeter, R. M., Taylor, E. G., & Quest, B. W. (2023). The impact of protein source and grain inclusion on digestibility, fecal metabolites, and fecal microbiome in adult canines. Journal of animal science, 101, Article skad268. https://doi.org/10.1093/jas/skad268

 

2022

Mysonhimer, A. R., & Holscher, H. D. (2022). Gastrointestinal Effects and Tolerance of Nondigestible Carbohydrate Consumption. Advances in Nutrition, 13(6), 2237-2276. [nmac094]. https://doi.org/10.1093/advances/nmac094

Holscher, H. D., Chumpitazi, B. P., Dahl, W. J., Fahey, G. C., Liska, D. J., Slavin, J. L., & Verbeke, K. (2022). Perspective: Assessing Tolerance to Nondigestible Carbohydrate Consumption. Advances in Nutrition, 13(6), 2084-2097. [nmac091]. https://doi.org/10.1093/advances/nmac091

Hwang, H., Yun, S., Arcanjo, R. B., Divyanshi, Chen, S., Mei, W., Nowak, R. A., Kwon, T., & Yang, J. (2022). Regulation of RNA localization during oocyte maturation by dynamic RNA-ER association and remodeling of the ER. Cell Reports, 41(11), [111802]. https://doi.org/10.1016/j.celrep.2022.111802

Cheong, Y. E., Kim, J., Jin, Y. S., & Kim, K. H. (2022). Elucidation of the fucose metabolism of probiotic Lactobacillus rhamnosus GG by metabolomic and flux balance analyses. Journal of Biotechnology, 360, 110-116. https://doi.org/10.1016/j.jbiotec.2022.11.002

Lee, Y. G., Ju, Y., Sun, L., Park, S., Jin, Y. S., & Kim, S. R. (2022). Acetate-rich Cellulosic Hydrolysates and Their Bioconversion Using Yeasts. Biotechnology and Bioprocess Engineering, 27(6), 890-899. https://doi.org/10.1007/s12257-022-0217-3

Davis, E. W., Wong, C. P., Arnold, H. K., Kasschau, K., Gaulke, C. A., Sharpton, T. J., & Ho, E. (2022). Age and micronutrient effects on the microbiome in a mouse model of zinc depletion and supplementation. PloS one, 17(12 December), [e0275352]. https://doi.org/10.1371/journal.pone.0275352

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Kim, J., Cheong, Y. E., Yu, S., Jin, Y. S., & Kim, K. H. (2022). Strain engineering and metabolic flux analysis of a probiotic yeast Saccharomyces boulardii for metabolizing l-fucose, a mammalian mucin component. Microbial cell factories, 21(1), [204]. https://doi.org/10.1186/s12934-022-01926-x

Pei, S., Liu, P., Parker, D. A., Mackie, R. I., & Rao, C. V. (2022). Systems analysis of the effect of hydrogen sulfide on the growth of Methylococcus capsulatus Bath. Applied Microbiology and Biotechnology, 106(23), 7879-7890. https://doi.org/10.1007/s00253-022-12236-y

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Dodd, D., & Cann, I. (2022). Tutorial: Microbiome studies in drug metabolism. Clinical and Translational Science, 15(12), 2812-2837. https://doi.org/10.1111/cts.13416

Sommer, K. M., Jespersen, J. C., Sutkus, L. T., Lee, Y., Donovan, S. M., & Dilger, R. N. (2022). Oral gamma-cyclodextrin-encapsulated tributyrin supplementation in young pigs with experimentally induced colitis. Journal of animal science, 100(11), [skac314]. https://doi.org/10.1093/jas/skac314

Kim, M., Miller, M. J., & Stasiewicz, M. J. (2022). Perspective: Challenges with product testing in powdered infant formula. Journal of Dairy Science, 105(11), 8591-8593. https://doi.org/10.3168/jds.2022-22374

Han, N. R., Yu, S., Yun, E. J., Jin, Y. S., & Kim, K. H. (2022). Production of colanic acid hydrolysate and its use in the production of fucosylated oligosaccharides by engineered Saccharomyces cerevisiae. Process Biochemistry, 122, 332-340. https://doi.org/10.1016/j.procbio.2022.10.025

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Kuehn, D., Zeisel, S. H., Orenstein, D. F., German, J. B., Field, C. J., Teerdhala, S., Knezevic, A., Patil, S., Donovan, S. M., & Lönnerdal, B. (2022). Effects of a Novel High-Quality Protein Infant Formula on Energetic Efficiency and Tolerance: A Randomized Trial. Journal of Pediatric Gastroenterology and Nutrition, 75(4), 521-528. https://doi.org/10.1097/MPG.0000000000003490

Lee, Y. G., Kim, C., Kuanyshev, N., Kang, N. K., Fatma, Z., Wu, Z. Y., Cheng, M. H., Singh, V., Yoshikuni, Y., Zhao, H., & Jin, Y. S. (2022). Cas9-Based Metabolic Engineering of Issatchenkia orientalis for Enhanced Utilization of Cellulosic Hydrolysates. Journal of Agricultural and Food Chemistry, 70(38), 12085-12094. https://doi.org/10.1021/acs.jafc.2c04251

Subramanian, S., Geng, H., Du, C., Chou, P. M., Bu, H. F., Wang, X., Swaminathan, S., Tan, S. C., Ridlon, J. M., De Plaen, I. G., & Tan, X. D. (2022). Feeding mode influences dynamic gut microbiota signatures and affects susceptibility to anti-CD3 mAb-induced intestinal injury in neonatal mice. American Journal of Physiology - Gastrointestinal and Liver Physiology, 323(3), G205-G218. https://doi.org/10.1152/ajpgi.00337.2021

Deewan, A., Liu, J. J., Jagtap, S. S., Yun, E. J., Walukiewicz, H., Jin, Y. S., & Rao, C. V. (2022). System analysis of Lipomyces starkeyi during growth on various plant-based sugars. Applied Microbiology and Biotechnology, 106(17), 5629-5642. https://doi.org/10.1007/s00253-022-12084-w

Aguilar-Lopez, M., Wetzel, C., MacDonald, A., Ho, T. T. B., & Donovan, S. M. (2022). Metagenomic profile of the fecal microbiome of preterm infants consuming mother’s own milk with bovine milk–based fortifier or infant formula: a cross-sectional study. American Journal of Clinical Nutrition, 116(2), 435-445. https://doi.org/10.1093/ajcn/nqac081

Liechty, J. M., Keck, A. S., Sloane, S., Donovan, S. M., & Fiese, B. H. (2022). Assessing Transdisciplinary Scholarly Development: A Longitudinal Mixed Method Graduate Program Evaluation. Innovative Higher Education, 47(4), 661-681. https://doi.org/10.1007/s10755-022-09593-x

Ishaq, S. L., Wissel, E. F., Wolf, P. G., Grieneisen, L., Eggleston, E. M., Mhuireach, G., Friedman, M., Lichtenwalner, A., Otero Machuca, J., Weatherford Darling, K., Pearson, A. L., Wertheim, F. S., Johnson, A. J., Hodges, L., Young, S. K., Nielsen, C. C., Kozyrskyj, A. L., MacRae, J. D., Myers, E. M., ... Hosler, S. (2022). Designing the Microbes and Social Equity Symposium: A Novel Interdisciplinary Virtual Research Conference Based on Achieving Group-Directed Outputs. Challenges, 13(2). https://doi.org/10.3390/challe13020030

VanderHoek, Z. K., Browning, A. M., Washburn, Q., Kent, M. L., Sharpton, T. J., & Gaulke, C. A. (2022). Draft Genome Sequence of Plesiomonas shigelloides Strain zfcc0051 (Phylum Proteobacteria). Microbiology Resource Announcements, 11(7). https://doi.org/10.1128/mra.00074-22

Luo, Y., Ren, W., Smidt, H., Wright, A. D. G., Yu, B., Schyns, G., McCormack, U. M., Cowieson, A. J., Yu, J., He, J., Yan, H., Wu, J., Mackie, R. I., & Chen, D. (2022). Dynamic Distribution of Gut Microbiota in Pigs at Different Growth Stages: Composition and Contribution. Microbiology Spectrum, 10(3). https://doi.org/10.1128/spectrum.00688-21

Lee, Y. G., Kim, B. Y., Bae, J. M., Wang, Y., & Jin, Y. S. (2022). Genome-edited Saccharomyces cerevisiae strains for improving quality, safety, and flavor of fermented foods. Food Microbiology, 104, [103971]. https://doi.org/10.1016/j.fm.2021.103971

Davis, E. C., Wang, M., & Donovan, S. M. (2022). Microbial Interrelationships across Sites of Breastfeeding Mothers and Infants at 6 Weeks Postpartum. Microorganisms, 10(6). https://doi.org/10.3390/microorganisms10061155

Bode, L., & Donovan, S. M. (2022). Fructooligosaccharides are not the same as Fucosylated Human Milk Oligosaccharides. Advances in Nutrition, 13(3), 972-973. https://doi.org/10.1093/advances/nmac033

Cerqueira, F. M., Photenhauer, A. L., Doden, H. L., Brown, A. N., Abdel-Hamid, A. M., Moraïs, S., Bayer, E. A., Wawrzak, Z., Cann, I., Ridlon, J. M., Hopkins, J. B., & Koropatkin, N. M. (2022). Sas20 is a highly flexible starch-binding protein in the Ruminococcus bromii cell-surface amylosome. Journal of Biological Chemistry, 298(5), [101896]. https://doi.org/10.1016/j.jbc.2022.101896

Yuan, F., Sharma, J., Nanjappa, S. G., Gaulke, C. A., & Fang, Y. (2022). Effect of Killed PRRSV Vaccine on Gut Microbiota Diversity in Pigs. Viruses, 14(5), [1081]. https://doi.org/10.3390/v14051081

Agrawal, R. M., Miller, M. J., Singh, V., Stein, H. H., & Takhar, P. S. (2022). Enzymatic hydrolysis and fermentation of soy flour to produce ethanol and soy protein concentrate with increased polyphenols. JAOCS, Journal of the American Oil Chemists' Society, 99(5), 379-391. https://doi.org/10.1002/aocs.12573

Jagtap, S. S., Liu, J. J., Walukiewicz, H. E., Pangilinan, J., Lipzen, A., Ahrendt, S., Koriabine, M., Cobaugh, K., Salamov, A., Yoshinaga, Y., Ng, V., Daum, C., Grigoriev, I. V., Slininger, P. J., Dien, B. S., Jin, Y. S., & Rao, C. V. (2022). Near-Complete Genome Sequence of Zygosaccharomyces rouxii NRRL Y-64007, a Yeast Capable of Growing on Lignocellulosic Hydrolysates. Microbiology Resource Announcements, 11(5). https://doi.org/10.1128/mra.00050-22

Shin, J., Miller, M., & Wang, Y. C. (2022). Recent advances in CRISPR-based systems for the detection of foodborne pathogens. Comprehensive Reviews in Food Science and Food Safety, 21(3), 3010-3029. https://doi.org/10.1111/1541-4337.12956

Sutkus, L. T., Joung, S., Hirvonen, J., Jensen, H. M., Ouwehand, A. C., Mukherjea, R., Donovan, S. M., & Dilger, R. N. (2022). Influence of 2′-Fucosyllactose and Bifidobacterium longum Subspecies infantis Supplementation on Cognitive and Structural Brain Development in Young Pigs. Frontiers in Neuroscience, 16, [860368]. https://doi.org/10.3389/fnins.2022.860368

Iwazaki, E., Lee, A. H., Kruis, A. M., Phungviwatnikul, T., Valentine, H., Arend, L. S., Knox, R. V., De Godoy, M. R. C., & Swanson, K. S. (2022). Effects of a high-protein, high-fiber diet rich in antioxidants and l-carnitine on body weight, body composition, metabolic status, and physical activity levels of cats after spay surgery. Journal of animal science, 100(4), [skac104]. https://doi.org/10.1093/jas/skac104

Finet, S., He, F., Clark, L. V., & De Godoy, M. R. C. (2022). Functional properties of miscanthus fiber and prebiotic blends in extruded canine diets. Journal of animal science, 100(4), [skac078]. https://doi.org/10.1093/jas/skac078

Spencer, T. E., Wells, K. D., Lee, K., Telugu, B. P., Hansen, P. J., Bartol, F. F., Blomberg, L., Schook, L. B., Dawson, H., Lunney, J. K., Driver, J. P., Davis, T. A., Donovan, S. M., Dilger, R. N., Saif, L. J., Moeser, A., McGill, J. L., Smith, G., & Ireland, J. J. (2022). Future of biomedical, agricultural, and biological systems research using domesticated animals. Biology of reproduction, 106(4), 629-638. https://doi.org/10.1093/biolre/ioac019

Zhao, A., Jeffery, E. H., & Miller, M. J. (2022). Is Bitterness Only a Taste? The Expanding Area of Health Benefits of Brassica Vegetables and Potential for Bitter Taste Receptors to Support Health Benefits. Nutrients, 14(7), [1434]. https://doi.org/10.3390/nu14071434

Do, S., Koutsos, E. A., Mccomb, A., Phungviwatnikul, T., De Godoy, M. R. C., & Swanson, K. S. (2022). Palatability and apparent total tract macronutrient digestibility of retorted black soldier fly larvae-containing diets and their effects on the fecal characteristics of cats consuming them. Journal of animal science, 100(4), [skac068]. https://doi.org/10.1093/jas/skac068

Kang, N. K., Kim, M., Baek, K., Chang, Y. K., Ort, D. R., & Jin, Y. S. (2022). Photoautotrophic organic acid production: Glycolic acid production by microalgal cultivation. Chemical Engineering Journal, 433, [133636]. https://doi.org/10.1016/j.cej.2021.133636

Abdel-Hamid, A. M., D'Alessandro-Gabazza, C. N., Yasuma, T., Walden, K. K. O., Fields, C. J., Gabazza, E. C., & Cann, I. (2022). Complete Genome Sequences of Three Staphylococcus haemolyticus Strains Isolated from the Lung of a TGFb1 Transgenic Mouse with Lung Fibrosis. Microbiology Resource Announcements, 11(4). https://doi.org/10.1128/mra.01176-21

Ibarra-Sánchez, L. A., Miller, M. J., & Holle, M. J. (2022). Recent Advances in Listeria Mitigation for Queso Fresco. ACS Food Science and Technology, 2(3), 425-434. https://doi.org/10.1021/acsfoodscitech.1c00343

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Ellis, J. L., Wang, M., Fu, X., Fields, C. J., Donovan, S. M., & Booth, S. L. (2022). Feeding Practice and Delivery Mode Are Determinants of Vitamin K in the Infant Gut: An Exploratory Analysis. Current Developments in Nutrition, 6(3), [nzac019]. https://doi.org/10.1093/cdn/nzac019

Moreno, L. A., Meyer, R., Donovan, S. M., Goulet, O., Haines, J., Kok, F. J., & Van't Veer, P. (2022). Perspective: Striking a Balance between Planetary and Human Health-Is There a Path Forward? Advances in Nutrition, 13(2), 355-375. https://doi.org/10.1093/advances/nmab139

Hughes, R. L., Alvarado, D. A., Swanson, K. S., & Holscher, H. D. (2022). The Prebiotic Potential of Inulin-Type Fructans: A Systematic Review. Advances in Nutrition, 13(2), 492-529. https://doi.org/10.1093/advances/nmab119

Kwak, S., Robinson, S. J., Lee, J. W., Lim, H., Wallace, C. L., & Jin, Y. S. (2022). Dissection and enhancement of prebiotic properties of yeast cell wall oligosaccharides through metabolic engineering. Biomaterials, 282, [121379]. https://doi.org/10.1016/j.biomaterials.2022.121379

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Kelly, V. W., & Sirk, S. J. (2022). Short FcRn-Binding Peptides Enable Salvage and Transcytosis of scFv Antibody Fragments. ACS chemical biology, 17(2), 404-413. https://doi.org/10.1021/acschembio.1c00862

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Choi, H. J., Jin, Y. S., & Lee, W. H. (2022). Effects of Engineered Saccharomyces cerevisiae Fermenting Cellobiose through Low-Energy-Consuming Phosphorolytic Pathway in Simultaneous Saccharification and Fermentation. Journal of Microbiology and Biotechnology, 32(1), 117-125. https://doi.org/10.4014/jmb.2111.11047

Daniels, V. C., Monaco, M. H., Wang, M., Hirvonen, J., Jensen, H. M., Ouwehand, A. C., Mukherjea, R., Dilger, R. N., & Donovan, S. M. (2022). Evaluation of 2’-fucosyllactose and bifidobacterium longum subspecies infantis on growth, organ weights, and intestinal development of piglets. Nutrients, 14(1), [199]. https://doi.org/10.3390/nu14010199

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