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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


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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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).

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.

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.

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.

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).

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).

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.

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.

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).

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

Varadzinová, L., Varadzin, L., & Ambrose, S. H. (2023). New radiocarbon dates for postglacial reoccupation of the Sudanese Nile. Quaternary Science Reviews, 303, Article 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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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).

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.

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.

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.

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.

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.

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.

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.

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.

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.

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).

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.

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.

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.

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.



Mysonhimer, A. R., & Holscher, H. D. (2022). Gastrointestinal Effects and Tolerance of Nondigestible Carbohydrate Consumption. Advances in Nutrition, 13(6), 2237-2276. [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].

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].

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.

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.

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].

Bailey, R. L., Stang, J. S., Davis, T. A., Naimi, T. S., Schneeman, B. O., Dewey, K. G., Donovan, S. M., Novotny, R., Kleinman, R. E., Taveras, E. M., Bazzano, L., Snetselaar, L. G., de Jesus, J., Casavale, K. O., Stoody, E. E., Goldman, J. D., Moshfegh, A. J., Rhodes, D. G., Herrick, K. A., ... Pannucci, T. R. (2022). Dietary and Complementary Feeding Practices of US Infants, 6 to 12 Months: A Narrative Review of the Federal Nutrition Monitoring Data. Journal of the Academy of Nutrition and Dietetics, 122(12), 2337-2345.e1.

Watson, K. M., Siemens, K. N., Anand, S., Gardner, I. H., Sharpton, T. J., Dewey, E. N., Martindale, R., Gaulke, C. A., & Tsikitis, V. L. (2022). Dietary and lifestyle associations with microbiome diversity. Gut Pathogens, 14(1), [49].

Wolf, P. G., Cowley, E. S., Breister, A., Matatov, S., Lucio, L., Polak, P., Ridlon, J. M., Gaskins, H. R., & Anantharaman, K. (2022). Diversity and distribution of sulfur metabolic genes in the human gut microbiome and their association with colorectal cancer. Microbiome, 10(1), [64].

Brown, M. D., Shinn, L. M., Reeser, G., Browning, M., Schwingel, A., Khan, N. A., & Holscher, H. D. (2022). Fecal and soil microbiota composition of gardening and non-gardening families. Scientific reports, 12(1), [1595].

D’Alessandro-Gabazza, C. N., Yasuma, T., Kobayashi, T., Toda, M., Abdel-Hamid, A. M., Fujimoto, H., Hataji, O., Nakahara, H., Takeshita, A., Nishihama, K., Okano, T., Saiki, H., Okano, Y., Tomaru, A., Fridman D’Alessandro, V., Shiraishi, M., Mizoguchi, A., Ono, R., Ohtsuka, J., ... Gabazza, E. C. (2022). Inhibition of lung microbiota-derived proapoptotic peptides ameliorates acute exacerbation of pulmonary fibrosis. Nature communications, 13(1), [1558].

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