Research Project: In Vitro Human Intestinal Microbial Ecosystem: Effects of Diet

Location: Dairy and Functional Foods Research

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

The impact of environmental pH on the gut microbiota community structure and short chain fatty acid production - (Peer Reviewed Journal)
Firrman, J., Liu, L.S., Mahalak, K.K., Tu, V., Tanes, C., Bittinger, K., Bobokalonov, J., Mattei, L., Zhang, H., Van Den Abeele, P. 2022. The impact of environmental pH on the gut microbiota community structure and short chain fatty acid production. FEMS Microbiology Ecology. 98(5). https://doi.org/10.1093/femsec/fiac038.

Analysis of the ability of capsaicin to modulate the human gut microbiota in vitro - (Peer Reviewed Journal)
Mahalak, K.K., Bobokalonov, J., Firrman, J., Williams, R., Evans, B., Fanelli, B., Soares, J., Liu, L.S., Kobori, M. 2022. Analysis of the ability of capsaicin to modulate the human gut microbiota in vitro. Nutrients. https://doi.org/10.3390/nu14061283.

Comparative analysis of the gut microbiota cultured in vitro using a single colon versus a 3-stage colon experimental design - (Peer Reviewed Journal)
Firrman, J., Liu, L.S., Mahalak, K.K., Tanes, C., Bittinger, K., Bobokalonov, J., Van Den Abbeele, P., Mattei, L., Zhang, H. 2021. Comparative analysis of the gut microbiota cultured in vitro using a single colon versus a 3-stage colon experimental design. Applied Microbiology and Biotechnology. volume 105, pages 3353–3367. https://link.springer.com/article/10.1007/s00253-021-11241-x.

Characterization of Bacterial Cellulose Nanocrystals: Effect of Acid Treatments and Neutralization - (Peer Reviewed Journal)
Arserim-Ucar, K., Korel, F., Liu, L.S., Yam, K.L. 2020. Characterization of bacterial cellulose nanocrystals: Effect of acid treatments and neutralization. Food Chemistry. 1-23. https://doi.org/10.1016/j.foodchem.2020.127597.

Effects of thermally induced configuration changes on rAAV genome’s enzymatic accessibility - (Peer Reviewed Journal)
Xu, Y., Guo, P., Chrzanowski, M., Chew, H., Firrman, J., Sang, N., Diao, Y., Xiao, W., Zhang, J. 2020. Effects of thermally induced configuration changes on rAAV genome’s enzymatic accessibility. Molecular Therapy. 18: 328-334. https://doi.org/10.1016/j.omtm.2020.06.005.

Triclosan has a robust, yet reversible impact on human gut microbial composition in vitro. - (Peer Reviewed Journal)
Mahalak, K.K., Firrman, J., Lee, J., Bittinger, K., Nunez, A., Bobokalonov, J., Arango-Argoty, G., Zhang, L., Zhang, G., Liu, L.S. 2020. Triclosan has a robust, yet reversible impact on human gut microbial composition in vitro. PLoS One. 15(6): 1-22. https://doi.org/10.1371/journal.pone.0234046.

Characterization of two types of polysaccharides from Eremurus hissaricus roots growing in Tajikistan - (Peer Reviewed Journal)
Muhidinov, Z.K., Bobokalonov, J.T., Ismoilov, I.B., Strahan, G.D., Chau, H.K., Hotchkiss, A.T., Liu, L.S. 2020. Characterization of two types of polysaccharides from Eremurus hissaricus roots growing in Tajikistan. Food Hydrocolloids. 205. https://doi.org/10.1016/j.foodhyd.2020.105768.

Impact of steviol glycosides and erythritol on the human and Cebus apella gut microbiome - (Peer Reviewed Journal)
Mahalak, K.K., Firrman, J., Tomasula, M.M., Nunez, A., Lee, J., Bittinger, K., Rinaldi, W., Liu, L.S. 2019. Impact of steviol glycosides and erythritol on the human and Cebus apella gut microbiome. Journal of Agricultural and Food Chemistry. Pages A-I. https://doi.org/10.1021/acs.jafc.9b06181.

Metabolic analysis of the regionally distinct gut microbial communities using an in vitro platform - (Peer Reviewed Journal)
Firrman, J., Liu, L.S., Tanes, C., Friedman, E., Bittinger, K., Daniel, S., Van Den Abbeele, P., Evans, B. 2019. Metabolic analysis of the regionally distinct gut microbial communities using an in vitro platform. Journal of Agriculture and Food Sciences. Pages A-L. https://doi.org/10.1021/acs.jafc.9b05202.

Metagenomic assessment of the Cebus Apella gut microbiota - (Peer Reviewed Journal)
Firrman, J., Tanes, C., Bittinger, K., Mahalak, K.K., Rinaldi, W., Liu, L.S. 2019. Metagenomic assessment of the Cebus Apella gut microbiota. American Journal of Primatology. https://doi.org/10.1002/ajp.23023.

Incorporation of tannic acid in food-grade guar gum fibrous mats by electrospinning technique - (Peer Reviewed Journal)
Yang, W., Zhang, M., Li, X., Jiang, J., Sousa, A., Zhao, Q., Pontious, S., Liu, L.S. 2019. Incorporation of tannic acid in food-grade guar gum fibrous mats by electrospinning technique. Polymers. 11:141. https://doi.org/10.3390/polym11010141.

Rapid AAV neutralizing antibody determination with a cell-binding assay - (Peer Reviewed Journal)
Guo, P., Zhang, J., Huang, J., Chew, H., Firrman, J., Sang, N., Diao, Y., Xiao, W. 2018. Rapid AAV neutralizing antibody determination with a cell-binding assay. Molecular Therapy. 13:40-46. https://doi.org/10.1016/j.omtm.2018.11.007.

Applying in vitro culturing technology to establish and evaluate the human gut microbiota - (Peer Reviewed Journal)
Firrman, J., Liu, L.S., Van Den Abbeele, P., Tanes, C., Bittinger, K., Tomasula, P.M. 2019. Applying in vitro culturing technology to establish and evaluate the human gut microbiota. Journal of Visualized Experiments. 144:1-12. https://doi.org/10.3791/59054.

Processable conductive and mechanically reinforced polylactide/graphene bionanocomposites through interfacial compatibilizer - (Peer Reviewed Journal)
Cai, C., Liu, L.S., Fu, Y. 2017. Processable conductive and mechanically reinforced polylactide/graphene bionanocomposites through interfacial compatibilizer. Polymer Composites. https://doi.org/10.1002/pc.24663.

A deficiency in cathelicidin reduces lung tumor growth in NNK/NTHi-induced A/J mice - (Peer Reviewed Journal)
Yao, Y., Wu, J., Zhou, H., Firrman, J., Xiao, W., Sun, Z., Li, D. 2018. A deficiency in cathelicidin reduces lung tumor growth in NNK/NTHi-induced A/J mice. American Journal of Cancer Research. 8(7):1190-1199.

Novel generation systems of gaseous chlorine dioxide for salmonella inactivation on fresh tomato - (Peer Reviewed Journal)
Zhou, S., Hu, C., Zhao, G., Jin, Z.T., Sheen, S., Liu, L.S., Yam, K.L. 2018. Novel generation systems of gaseous chlorine dioxide for salmonella inactivation on fresh tomato. Food Control. 92:479-487. https://doi.org/10.1016/j.foodcont.2018.05.025.

Establishing a mucosal gut microbial community in vitro using an an artificial simulator - (Peer Reviewed Journal)
Liu, L.S., Firrman, J., Tanes, C., Bittinger, K., Thomas-Gahring, A.E., Wu, G.D., Van Den Abbeel, P., Tomasula, P.M. 2018. Establishing a mucosal gut microbial community in vitro using an an artificial simulator. PLoS One. 13(7):1-20. https://doi.org/10.1371/journal.pone.0197692.

Transcriptomics analysis on the regulation of tomato ripening by the ethylene inhibitor 1-methylcyclopropene - (Peer Reviewed Journal)
Bobokalonov, J., Liu, Y., Shahrin, T., Liu, L.S. 2018. Transcriptomics analysis on the regulation of tomato ripening by the ethylene inhibitor 1-methylcyclopropene. Journal of Plant Studies. 7(2):49-60. https://doi.org/10.5539/jps.v7n2p49.

Analysis of temporal changes in growth and gene expression for commensal gut microbes in response to the polyphenol naringenin - (Peer Reviewed Journal)
Firrman, J., Liu, L.S., Arango Argoty, G., Zhang, L., Tomasula, P.M., Wang, M., Pontious, S., Kobori, M., Xiao, W. 2018. Analysis of temporal changes in growth and gene expression for commensal gut microbes in response to the polyphenol naringenin. Microbial Insights. 11:1-12. https://doi.org/10.1177/1178636118775100.

A novel gaseous chlorine dioxide generating method utilizing carbon dioxide and moisture respired from tomato for Salmonella inactivation - (Peer Reviewed Journal)
Zhou, S., Hu, C., Liu, L.S., Sheen, S., Zhao, G., Yam, K.L. 2018. A novel gaseous chlorine dioxide generating method utilizing carbon dioxide and moisture respired from tomato for Salmonella inactivation. Food Control. 89:54-61. https://doi.org/10.1016/j.foodcont.2018.01.009.

A robust system for production of superabundant VP1 recombinant AAV vectors - (Peer Reviewed Journal)
Wang, Q., Wu, Z., Zhang, J., Firrman, J., Wei, H., Zhuang, Z., Liu, L.S., Miao, L., Hu, Y., Diao, Y., Xiao, W. 2017. A robust system for production of superabundant VP1 recombinant AAV vectors. Molecular Therapy. 7:146-156. https://doi.org/10.1016/j.omtm.2017.11.002.