{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,13]],"date-time":"2025-10-13T07:11:25Z","timestamp":1760339485857,"version":"build-2065373602"},"reference-count":62,"publisher":"Walter de Gruyter GmbH","funder":[{"name":"NA","award":["NA"],"award-info":[{"award-number":["NA"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Benef. Microbes"],"published-print":{"date-parts":[[2025,3,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n<jats:p>Prebiotics or fermentable dietary fibres are known for their potential to shape the gut microbial community and could be used as a tool in treating gut dysbiotic states found in a wide range of diseases. However, it remains unclear whether the microbiota of individuals with distinct diseases respond to fibre treatments in the same way as healthy individuals do. In this study, a mechanistic understanding of fibre responses across health conditions was performed through <jats:italic>in vitro<\/jats:italic> faecal fermentations with various dietary fibres and faecal microbial communities from healthy individuals (HC) as well as Crohn\u2019s disease (CD), ulcerative colitis (UC), and Parkinson\u2019s disease (PD). Production of short chain fatty acids (SCFAs) was measured, and microbial community structure shifts were assessed using 16S rRNA gene amplicon sequencing. All tested dietary fibres increased short chain fatty acid production upon fermentation, with variations based on both, disease state and fibre type. The magnitude of shifts in microbial community structure resulting from <jats:italic>in vitro<\/jats:italic> fermentation varied by condition; for example, samples from individuals with UC responded weakly to fibre fermentation, while those from individuals with PD underwent dramatic changes. Still, each health condition had distinct fibre types that were more effective in shifting the community structure and increasing SCFAs. Overall, these results suggest that the response to fibres on gut microbiota varies by disease. The selection of disease-specific prebiotics could be tailored according to health conditions for optimal desired gut microbiota responses.<\/jats:p>","DOI":"10.1163\/18762891-bja00067","type":"journal-article","created":{"date-parts":[[2025,4,1]],"date-time":"2025-04-01T04:56:48Z","timestamp":1743483408000},"page":"1-24","source":"Crossref","is-referenced-by-count":0,"title":["Dietary fibre responses in microbiota reveal opportunity for disease-specific prebiotic approaches"],"prefix":"10.1163","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5191-8784","authenticated-orcid":true,"given":"T.","family":"Chen","sequence":"first","affiliation":[{"name":"State Key Laboratory of Food Science & Technology, School of Food Science & Technology, Nanchang University, 235 East Nanjing Road, Nanchang 330047, P.R. China"},{"name":"Whistler Center for Carbohydrate Research, Department of Food Science, https:\/\/dx.doi.org\/311308Purdue University, West Lafayette, IN 47907, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8928-9717","authenticated-orcid":true,"given":"T.M.","family":"Cantu-Jungles","sequence":"additional","affiliation":[{"name":"Whistler Center for Carbohydrate Research, Department of Food Science, https:\/\/dx.doi.org\/311308Purdue University, West Lafayette, IN 47907, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4465-4826","authenticated-orcid":true,"given":"B.","family":"Zhang","sequence":"additional","affiliation":[{"name":"Whistler Center for Carbohydrate Research, Department of Food Science, https:\/\/dx.doi.org\/311308Purdue University, West Lafayette, IN 47907, USA"},{"name":"School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, P.R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"T.","family":"Yao","sequence":"additional","affiliation":[{"name":"Whistler Center for Carbohydrate Research, Department of Food Science, https:\/\/dx.doi.org\/311308Purdue University, West Lafayette, IN 47907, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5270-1875","authenticated-orcid":true,"given":"L.","family":"Lamothe","sequence":"additional","affiliation":[{"name":"Whistler Center for Carbohydrate Research, Department of Food Science, https:\/\/dx.doi.org\/311308Purdue University, West Lafayette, IN 47907, USA"},{"name":"Department of Food Science and Technology, Nestle\u0301 Research Center, PO Box 44, Vers-chez-les-blanc, Lausanne 26, 1000 Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"M.","family":"Shaikh","sequence":"additional","affiliation":[{"name":"Department of Internal Medicine, Division of Gastroenterology, Rush University Medical Center, Chicago, IL 60612, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5276-5174","authenticated-orcid":true,"given":"P.A.","family":"Engen","sequence":"additional","affiliation":[{"name":"Department of Internal Medicine, Division of Gastroenterology, Rush University Medical Center, Chicago, IL 60612, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2781-359X","authenticated-orcid":true,"given":"S.J.","family":"Green","sequence":"additional","affiliation":[{"name":"Genomics and Microbiome Core Facility, Rush University Medical Center, Chicago, IL, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7969-3369","authenticated-orcid":true,"given":"A.","family":"Keshavarzian","sequence":"additional","affiliation":[{"name":"Department of Internal Medicine, Division of Gastroenterology, Rush University Medical Center, Chicago, IL 60612, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6591-942X","authenticated-orcid":true,"given":"B.R.","family":"Hamaker","sequence":"additional","affiliation":[{"name":"Whistler Center for Carbohydrate Research, Department of Food Science, https:\/\/dx.doi.org\/311308Purdue University, West Lafayette, IN 47907, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"374","reference":[{"author":"Abdel-Haq, R.","key":"R000001","unstructured":"Abdel-Haq, R., Schlachetzki, J.C.M., Boktor, J.C., Cantu-Jungles, T.M., Thron, T., Zhang, M., Bostick, J.W., Khazaei, T., Chilakala, S., Morais, L.H., Humphrey, G., Keshavarzian, A., Katz, J.E., Thomson, M., Knight, R., Gradinaru, V., Hamaker, B.R., Glass, C.K. and Mazmanian, S.K., 2022a. A prebiotic diet modulates microglial states and motor deficits in \u03b1-synuclein overexpressing mice. bioRxiv: 2022.06.27.497828."},{"author":"Abdel-Haq, R.","key":"R000002","unstructured":"Abdel-Haq, R., Schlachetzki, J.C.M., Boktor, J.C., Cantu-Jungles, T.M., Thron, T., Zhang, M., Bostick, J.W., Khazaei, T., Chilakala, S., Morais, L.H., Humphrey, G., Keshavarzian, A., Katz, J.E., Thomson, M., Knight, R., Gradinaru, V., Hamaker, B.R., Glass, C.K. and Mazmanian, S.K., 2022b. A prebiotic diet modulates microglial states and motor deficits in \u03b1-synuclein overexpressing mice. bioRxiv: 2022.06.27.497828."},{"key":"R000003","series-title":"EBioMedicine","first-page":"691","article-title":"Gut microbiota in Parkinson\u2019s disease: Temporal stability and relations to disease progression","volume":"44","author":"Aho, V.T.E.","unstructured":"Aho, V.T.E., Pereira, P.A.B., Voutilainen, S., Paulin, L., Pekkonen, E., Auvinen, P. and Scheperjans, F., 2019. Gut microbiota in Parkinson\u2019s disease: Temporal stability and relations to disease progression. EBioMedicine 44: 691-707."},{"key":"R000004","series-title":"Gastroenterology","first-page":"573","article-title":"Metabolism and metabolic disorders and the microbiome: the intestinal microbiota associated with obesity, lipid metabolism, and metabolic health\u00a0\u2013 pathophysiology and therapeutic strategies","volume":"160","author":"Aron-Wisnewsky, J.","unstructured":"Aron-Wisnewsky, J., Warmbrunn, M.V., Nieuwdorp, M. and Cle\u0301ment, K., 2021. Metabolism and metabolic disorders and the microbiome: the intestinal microbiota associated with obesity, lipid metabolism, and metabolic health\u00a0\u2013 pathophysiology and therapeutic strategies. Gastroenterology 160: 573-599."},{"key":"R000005","series-title":"NPJ Parkinson\u2019s Disease","first-page":"1","article-title":"Parkinson\u2019s disease patients\u2019 short chain fatty acids production capacity after in vitro faecal fiber fermentation","volume":"7","author":"Baert, F.","unstructured":"Baert, F., Matthys, C., Maselyne, J., Van Poucke, C., Van Coillie, E., Bergmans, B. and Vlaemynck, G., 2021. Parkinson\u2019s disease patients\u2019 short chain fatty acids production capacity after in vitro faecal fiber fermentation. 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Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-na\u00efve Parkinson\u2019s disease patients. Genome Medicine 9: 1-13."},{"key":"R000008","series-title":"Foods","article-title":"An update on prebiotics and on their health effects","volume":"13","author":"Bevilacqua, A.","unstructured":"Bevilacqua, A., Campaniello, D., Speranza, B., Racioppo, A., Sinigaglia, M. and Corbo, M.R., 2024. An update on prebiotics and on their health effects. Foods 13: 446."},{"author":"Bokulich, N.A.","key":"R000009","unstructured":"Bokulich, N.A., Zhang, Y., Dillon, M., Rideout, J.R., Bolyen, E., Li, H., Albert, P.S. and Caporaso, J.G., 2017. 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Dietary fiber hierarchical specificity: the missing link for predictable and strong shifts in gut bacterial communities. mBio 12: e0102821. https:\/\/doi.org\/10.1128\/MBIO.01028-21"},{"key":"R000012","series-title":"mBio","article-title":"New view on dietary fiber selection for predictable shifts in gut microbiota","volume":"11","author":"Cantu-Jungles, T.","unstructured":"Cantu-Jungles, T. and Hamaker, B., 2020. New view on dietary fiber selection for predictable shifts in gut microbiota. mBio 11: e02179-19."},{"key":"R000013","series-title":"Bioactive Carbohydrates and Dietary Fibre","first-page":"1","article-title":"A pectic polysaccharide from peach palm fruits (Bactris gasipaes) and its fermentation profile by the human gut microbiota in vitro","volume":"9","author":"Cantu-Jungles, T.M.","unstructured":"Cantu-Jungles, T.M., Cipriani, T.R., Iacomini, M., Hamaker, B.R. and Cordeiro, L.M.C., 2017. A pectic polysaccharide from peach palm fruits (Bactris gasipaes) and its fermentation profile by the human gut microbiota in vitro. Bioactive Carbohydrates and Dietary Fibre 9: 1-6."},{"key":"R000014","series-title":"Carbohydrate Polymers","first-page":"219","article-title":"In vitro fermentation of Cookeina speciosa glucans stimulates the growth of the butyrogenic Clostridium cluster XIVa in a targeted way","volume":"183","author":"Cantu-Jungles, T.M.","unstructured":"Cantu-Jungles, T.M., Ruthes, A.C., El-Hindawy, M., Moreno, R.B., Zhang, X., Cordeiro, L.M.C., Hamaker, B.R. and Iacomini, M., 2018. In vitro fermentation of Cookeina speciosa glucans stimulates the growth of the butyrogenic Clostridium cluster XIVa in a targeted way. Carbohydrate Polymers 183: 219-229."},{"key":"R000015","series-title":"Neurology","first-page":"e848","article-title":"Association of fecal and plasma levels of short-chain fatty acids with gut microbiota and clinical severity in patients with Parkinson Disease","volume":"98","author":"Chen, S.J.S.","unstructured":"Chen, S.J.S., Chen, C.C.C., Liao, H.Y.H., Lin, Y.T.Y., Wu, Y.Y.W., Liou, J.M., Wu, M.S., Kuo, C.H. and Lin, C.H., 2022. Association of fecal and plasma levels of short-chain fatty acids with gut microbiota and clinical severity in patients with Parkinson Disease. Neurology 98: e848-e858."},{"key":"R000016","series-title":"Scientific Reports","article-title":"Fiber-utilizing capacity varies in Prevotella\u00a0\u2013 versus Bacteroides-dominated gut microbiota","volume":"7","author":"Chen, T.","unstructured":"Chen, T., Long, W., Zhang, C., Liu, S., Zhao, L. and Hamaker, B.R., 2017. Fiber-utilizing capacity varies in Prevotella\u00a0\u2013 versus Bacteroides-dominated gut microbiota. Scientific Reports 7: 2594."},{"key":"R000017","series-title":"Nature Protocols","first-page":"799","article-title":"Using MicrobiomeAnalyst for comprehensive statistical, functional, and meta-analysis of microbiome data","volume":"15","author":"Chong, J.","unstructured":"Chong, J., Liu, P., Zhou, G. and Xia, J., 2020. Using MicrobiomeAnalyst for comprehensive statistical, functional, and meta-analysis of microbiome data. Nature Protocols 15: 799-821."},{"key":"R000018","series-title":"Movement Disorders","first-page":"1208","article-title":"Microbiota composition and metabolism are associated with gut function in Parkinson\u2019s disease","volume":"35","author":"Cirstea, M.S.","unstructured":"Cirstea, M.S., Yu, A.C., Golz, E., Sundvick, K., Kliger, D., Radisavljevic, N., Foulger, L.H., Mackenzie, M., Huan, T., Finlay, B.B. and Appel-Cresswell, S., 2020. Microbiota composition and metabolism are associated with gut function in Parkinson\u2019s disease. Movement Disorders 35: 1208-1217."},{"key":"R000019","series-title":"Frontiers in Microbiology","article-title":"Insight into gut dysbiosis of patients with inflammatory bowel disease and ischemic colitis","volume":"14","author":"Dahal, R.H.","unstructured":"Dahal, R.H., Kim, S., Kim, Y.K., Kim, E.S. and Kim, J., 2023. Insight into gut dysbiosis of patients with inflammatory bowel disease and ischemic colitis. Frontiers in Microbiology 14: 1174832. https:\/\/doi.org\/10.3389\/FMICB.2023.1174832"},{"key":"R000020","series-title":"Nucleic Acids Research","first-page":"W180","article-title":"MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data","volume":"45","author":"Dhariwal, A.","unstructured":"Dhariwal, A., Chong, J., Habib, S., King, I.L., Agellon, L.B. and Xia, J., 2017. 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Gut Microbes 3: 289-306. https:\/\/doi.org\/10.4161\/gmic.19897"},{"key":"R000022","series-title":"Nature Reviews Gastroenterology & Hepatology","first-page":"491","article-title":"Expert consensus document: The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of prebiotics","volume":"14","author":"Gibson, G.R.","unstructured":"Gibson, G.R., Hutkins, R., Sanders, M.E., Prescott, S.L., Reimer, R.A., Salminen, S.J., Scott, K., Stanton, C., Swanson, K.S., Cani, P.D., Verbeke, K. and Reid, G., 2017. Expert consensus document: The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of prebiotics. Nature Reviews Gastroenterology & Hepatology 14: 491."},{"key":"R000023","series-title":"Neurology","article-title":"Proof of concept study of prebiotics to modulate gut microbiome in Parkinson\u2019s disease (P13-11.002)","volume":"98","author":"Hall, D.","unstructured":"Hall, D., Voight, R., Cantu-Jungles, T., Hamaker, B., Raeisi, S., Shaikh, M., Green, S., Engen, P., Ouyang, B., Naqib, A., Forsyth, C., Rasmussen, H., Sedghi, S., Goetz, C. and Keshavarzian, A., 2022. Proof of concept study of prebiotics to modulate gut microbiome in Parkinson\u2019s disease (P13-11.002). Neurology 98 (Suppl.): 18. https:\/\/doi.org\/10.1212\/WNL.98.18_supplement.946"},{"key":"R000024","series-title":"Nature Communications","article-title":"An open label, non-randomized study assessing a prebiotic fiber intervention in a small cohort of Parkinson\u2019s disease participants","volume":"14","author":"Hall, D.A.","unstructured":"Hall, D.A., Voigt, R.M., Cantu-Jungles, T.M., Hamaker, B., Engen, P.A., Shaikh, M., Raeisi, S., Green, S.J., Naqib, A., Christopher, B.F., Manfready, R., Chen, T., Ouyang, B., Rasmussen, H.E., Sedghi, S., Goetz, C.G. and Keshavarzian, A., 2023. An open label, non-randomized study assessing a prebiotic fiber intervention in a small cohort of Parkinson\u2019s disease participants. Nature Communications 14: 926."},{"key":"R000025","series-title":"PLoS ONE","article-title":"Intestinal dysbiosis and lowered serum lipopolysaccharide-binding protein in Parkinson\u2019s disease","volume":"10","author":"Hasegawa, S.","unstructured":"Hasegawa, S., Goto, S., Tsuji, H., Okuno, T., Asahara, T., Nomoto, K., Shibata, A., Fujisawa, Y., Minato, T., Okamoto, A., Ohno, K. and Hirayama, M., 2015. Intestinal dysbiosis and lowered serum lipopolysaccharide-binding protein in Parkinson\u2019s disease. PLoS ONE 10: e0142164."},{"key":"R000026","series-title":"Nutrition Reviews","first-page":"1059","article-title":"Interindividual variability in gut microbiota and host response to dietary interventions","volume":"1","author":"Healey, G.R.","unstructured":"Healey, G.R., Murphy, R., Brough, L., Butts, C.A. and Coad, J., 2017. Interindividual variability in gut microbiota and host response to dietary interventions. 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The gut microbiota metabolite propionate ameliorates intestinal epithelial barrier dysfunction-mediated Parkinson\u2019s disease via the AKT signaling pathway. NeuroReport 32: 244-251."},{"key":"R000029","series-title":"Advances in Nutrition","first-page":"979","article-title":"The Role of the Gut Microbiome in Predicting Response to Diet and the Development of Precision Nutrition Models. Part II: Results","volume":"10","author":"Hughes, R.L.","unstructured":"Hughes, R.L., Kable, M.E., Marco, M. and Keim, N.L., 2019. The Role of the Gut Microbiome in Predicting Response to Diet and the Development of Precision Nutrition Models. Part II: Results. 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Movement Disorders 30: 1351-1360."},{"key":"R000034","series-title":"Microorganisms","article-title":"Unraveling the role of the human gut microbiome in health and diseases","volume":"12","author":"Khalil, M.","unstructured":"Khalil, M., Di Ciaula, A., Mahdi, L., Jaber, N., Di Palo, D.M., Graziani, A., Baffy, G. and Portincasa, P., 2024. Unraveling the role of the human gut microbiome in health and diseases. Microorganisms 12: 2333."},{"key":"R000035","series-title":"European Journal of Neurology","first-page":"3581","article-title":"Gut microbiota dysbiosis in Parkinson disease: a systematic review and pooled analysis","volume":"30","author":"Kleine Bardenhorst, S.","unstructured":"Kleine Bardenhorst, S., Cereda, E., Severgnini, M., Barichella, M., Pezzoli, G., Keshavarzian, A., Desideri, A., Pietrucci, D., Aho, V.T.E., Scheperjans, F., Hildebrand, F., Weis, S., Egert, M., Karch, A., Vital, M. and R\u00fcbsamen, N., 2023. Gut microbiota dysbiosis in Parkinson disease: a systematic review and pooled analysis. European Journal of Neurology 30: 3581-3594."},{"key":"R000036","series-title":"PLoS ONE","article-title":"Gut microbiota signatures predict host and microbiota responses to dietary interventions in obese individuals","volume":"9","author":"Korpela, K.","unstructured":"Korpela, K., Flint, H.J., Johnstone, A.M., Lappi, J., Poutanen, K., Dewulf, E., Delzenne, N., de Vos, W.M. and Salonen, A., 2014. Gut microbiota signatures predict host and microbiota responses to dietary interventions in obese individuals. PLoS ONE 9: e90702."},{"key":"R000037","series-title":"Science China Life Sciences","first-page":"1223","article-title":"Structural changes of gut microbiota in Parkinson\u2019s disease and its correlation with clinical features","volume":"60","author":"Li, W.","unstructured":"Li, W., Wu, X., Hu, X., Wang, T., Liang, S., Duan, Y., Jin, F. and Qin, B., 2017. 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