Research Project: In vitro Human Gut System: Interactions Between Diet, Food Processing, and Microbiota

Location: Dairy and Functional Foods Research

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

Supplementation with soluble or insoluble rice-bran fibers increases short-chain fatty acid producing bacteria in the gut microbiota in vitro - (Peer Reviewed Journal)
Mahalak, K.K., Liu, L.S., Bobokalonov, J., Narrowe, A.B., Firrman, J., Bittinger, K., Hu, W., Jones, S.M., Mustafa, A.M. 2024. Supplementation with soluble or insoluble rice-bran fibers increases short-chain fatty acid producing bacteria in the gut microbiota in vitro. Frontiers in Nutrition. https://doi.org/10.3389/fnut.2024.1304045.

Preservation of conjugated primary bile acids by oxygenation of the small intestinal microbiota in vitro - (Peer Reviewed Journal)
Firrman, J., Friedman, E.S., Hecht, A., Strange, W.C., Narrowe, A.B., Mahalak, K.K., Wu, G.D., Liu, L.S. 2024. Preservation of conjugated primary bile acids by oxygenation of the small intestinal microbiota in vitro. mBio. 15(6). https://doi.org/10.1128/mbio.00943-24.

Targeted remodeling of the human gut microbiome using Juemingzi (Senna seed extracts) - (Peer Reviewed Journal)
Narrowe, A.B., Scarino Lemons, J.M., Mahalak, K.K., Firrman, J., Van Den Abbeele, P., Baudot, A., Deyaert, S., Li, Y., Yu, L., Liu, L.S. 2024. Targeted remodeling of the human gut microbiome using Juemingzi (Senna seed extracts). Frontiers in Cellular and Infection Microbiology. 14. https://doi.org/10.3389/fcimb.2024.1296619.

Tomato seed extract promotes health of the gut microbiota and demonstrates a potential new way to valorize tomato waste - (Peer Reviewed Journal)
Firrman, J., Narrowe, A.B., Liu, L.S., Mahalak, K.K., Scarino Lemons, J.M., Van Den Abbeele, P., Baudot, A., Deyaert, S., Li, Y., Yao, Y., Yu, L. 2024. Tomato seed extract promotes health of the gut microbiota and demonstrates a potential new way to valorize tomato waste. PLOS ONE. 19(4):e0301381. https://doi.org/10.1371/journal.pone.0301381.

Dietary carbohydrates regulate intestinal colonization and dissemination of Klebsiella pneumoniae - (Peer Reviewed Journal)
Hetch, A., Harling, L., Friedman, E., Tanes, C., Lee, J., Firrman, J., Hao, F., Tu, V., Liu, L.S., Patterson, A.D., Bittinger, K., Goulian, M., Wu, G. 2024. Dietary carbohydrates regulate intestinal colonization and dissemination of Klebsiella pneumoniae. Journal of Clinical Investigation. 134(9):e174726. https://doi.org/10.1172/JCI174726.

Metagenomes and metagenome-assembled genomes from ex vivo fecal incubations of six unique donors - (Peer Reviewed Journal)
Narrowe, A.B., Liu, L.S., Scarino Lemons, J.M., Firrman, J., Mahalak, K.K., Deyaert, S., Baudot, A., Van Den Abbeele, P. 2024. Metagenomes and metagenome-assembled genomes from ex vivo fecal incubations of six unique donors. Microbiology Resource Announcements. https://doi.org/10.1128/mra.00862-23.

Impact of Baizhu, Daqingye, and Hehuan extracts on the human gut microbiome - (Peer Reviewed Journal)
Scarino Lemons, J.M., Narrowe, A.B., Liu, L.S., Firrman, J., Mahalak, K.K., Van Den Abbeele, P., Baudot, A., Deyaert, S., Li, Y., Yu, L. 2023. Impact of Baizhu, Daqingye, and Hehuan extracts on the human gut microbiome. Frontiers in Cellular and Infection Microbiology. 13:1298392. https://doi.org/10.3389/fcimb.2023.1298392.

Too much of a good thing: Imposing an upper limit to a high fiber diet - (Other)
Scarino Lemons, J.M. 2024. Too much of a good thing: Imposing an upper limit to a high fiber diet. Gastroenterology. 166(2): 250-51. https://doi.org/10.1053/j.gastro.2023.11.290.

Impact of ivermectin on gut microbial ecosystem - (Peer Reviewed Journal)
Liu, L.S., Mahalak, K.K., Bobokalonov, J.D., Narrowe, A.B., Firrman, J., Scarino Lemons, J.M., Bittinger, K., Hu, W., Jones, S.M., Mustafa, A.M. 2023. Impact of ivermectin on gut microbial ecosystem. International Journal of Molecular Sciences. 24:16125. https://doi.org/10.3390/ijms242216125.

Enterobacteriaceae growth promotion by intestinal acylcarnitines, a biomarker of dysbiosis in inflammatory bowel disease - (Peer Reviewed Journal)
Scarino Lemons, J.M., Conrad, M., Tanes, C., Chen, J., Friedman, E.S., Roggiana, M., Curry, D., Chau, L., Hecht, A.L., Harling, L., Vales, J., Kachelries, K.E., Baldassano, R.N., Goulian, M., Bittinger, K., Master, S.R., Liu, L.S., Wu, G.D. 2023. Enterobacteriaceae growth promotion by intestinal acylcarnitines, a biomarker of dysbiosis in inflammatory bowel disease. Cellular and Molecular Gastoenterology and Hepatology. 17(1):131-148. https://doi.org/10.1016/j.jcmgh.2023.09.005.

A new approach to the treatment of acute infection diseases with antibiotic-pectin formulae - (Peer Reviewed Journal)
Muhidinov, Z., Bobokalonov, J., Kimatov, R., Rahmonov, E., Komilova, G., Sherova, Z., Liu, L.S. 2024. A new approach to the treatment of acute infection diseases with antibiotic-pectin formulae. The Journal of Infection in Developing Countries. 18(3):407-419.

Transcriptomic analysis on the regulation of tomato ripening by carbon dioxide - (Peer Reviewed Journal)
Bobokalonov, J., Liu, Y., Mahalak, K.K., Firrman, J., Sheen, S., Zhou, S., Liu, L.S. 2023. Transcriptomic analysis on the regulation of tomato ripening by carbon dioxide. Sci. 5(3):26. https://doi.org/10.3390/sci5030026.

Lacticaseibacillus rhamnosus strain GG (LGG) regulate gut microbial metabolites, an in vitro study using three mature human gut microbial cultures in a simulator of human intestinal microbial ecosystem (SHIME) - (Peer Reviewed Journal)
Liu, L.S., Narrowe, A.B., Firrman, J., Mahalak, K.K., Bobokalonov, J., Scarino Lemons, J.M., Bittinger, K., Daniel, S., Tanes, C., Mattei, L., Friendman, E., Soares, J.W., Masuko, K., Zeng, W., Tomasula, M.M. 2023. Lacticaseibacillus rhamnosus strain GG (LGG) regulate gut microbial metabolites, an in vitro study using three mature human gut microbial cultures in a simulator of human intestinal microbial ecosystem (SHIME). Foods. https://doi.org/10.3390/foods12112105.

An in-vitro analysis of how lactose modifies the gut microbiota structure and function of adults in a donor-independent manner - (Peer Reviewed Journal)
Firrman, J., Liu, L.S., Mahalak, K.K., Hu, W., Bittinger, K., Moustafa, A., Jones, S.M., Narrowe, A.B., Tomasula, M.M. 2023. An in-vitro analysis of how lactose modifies the gut microbiota structure and function of adults in a donor-independent manner. Frontiers in Nutrition. https://doi.org/10.3389/fnut.2022.1040744.

Fructooligosaccharides (FOS) differentially modifies the in vitro gut microbiota in an age-dependent manner. - (Peer Reviewed Journal)
Mahalak, K.K., Firrman, J., Narrowe, A.B., Hu, W., Bittinger, K., Moustafa, A., Liu, L.S. 2023. Fructooligosaccharides (FOS) differentially modifies the in vitro gut microbiota in an age-dependent manner. Frontiers in Nutrition. https://doi.org/10.3389/fnut.2022.1058910.

Modulation of the Gut Microbiota Structure and Function by Two Structurally Different Lemon Pectins - (Peer Reviewed Journal)
Firrman, J., Mahalak, K.K., Bobokalonov, J., Liu, L.S., Lee, J., Bittinger, K., Mattei, L., Gadaingan, R.T., Narrowe, A.B., Scarino Lemons, J.M. 2022. Modulation of the Gut Microbiota Structure and Function by Two Structurally Different Lemon Pectins. Foods. https://doi.org/10.3390/foods11233877.

Chewing the fat with microbes: lipid crosstalk in the gut - (Review Article)
Scarino Lemons, J.M., Liu, L.S. 2022. Chewing the fat with microbes: lipid crosstalk in the gut. Nutrients. 14(3):573. https://doi.org/10.3390/nu14030573.

Microbial enzymes induce colitis by reactivating triclosan in the mouse gastrointestinal tract - (Peer Reviewed Journal)
Zhang, G., Redinbo, M., Cai, Z., Xiao, H., Liu, L.S., Gibbons, J., Kim, D., Minter, L., Panigrahy, A., Yang, J. 2022. Microbial enzymes induce colitis by reactivating triclosan in the mouse gastrointestinal tract. Nature. https://doi.org/10.1038/s41467-021-27762-y.

Probiotic effects of Lactobacillus fermentum I631 and Lactobacillus plantarum ZY08 on hypercholesteremic golden hamsters - (Peer Reviewed Journal)
Yang, D., Hu, Z., Gao, J., Zheng, Z., Wang, W., Liu, J., Firrman, J., Ren, D. 2021. Probiotic effects of Lactobacillus fermentum I631 and Lactobacillus plantarum ZY08 on hypercholesteremic golden hamsters. Frontiers in Nutrition. 8:705763. https://doi.org/10.3389/fnut.2021.705763.

Changes to environmental pH alters the colon microbial community in terms of both structure and function: An in vitro analysis - (Abstract Only)

Environmental pH is a determinant of the gut microbiota community composition and production of short chain fatty acids - (Abstract Only)

Characterization of pectin obtained by conventional and innovative methods - (Peer Reviewed Journal)
Muhidinov, Z., Ikromi, K., Jonmurodov, A., Nasriddinov, A., Usmanova, S.R.,Bobokalonov, J., Strahan, G.D., Liu, L.S. 2021. Characterization of pectin obtained by conventional and innovative methods. International Journal of Biological Macromolecules. 183:2227-2237. https://doi.org/10.1016/j.ijbiomac.2021.05.094.

Establishment of a Stable Human Small Intestinal and Colonic Microbiota in an In Vitro Cultivar: Form vs. Function and Response to Oxygen - (Abstract Only)

Enhancing therapeutic efficacy of in vivo platelet-targeted gene therapy in hemophilia A - (Peer Reviewed Journal)
Xuefeng, W., Fu, R., Chen, C., Firrman, J., Konkle, B., Zhang, J., Li, L., Xiao, W., Poncz, M., Miao, C. 2020. Enhancing therapeutic efficacy of in vivo platelet-targeted gene therapy in hemophilia A. Blood Advances. Volume 4, Issue 22, Pages 5722–5734.