Progress 08/01/22 to 12/31/24
Outputs
Target Audience:The target audiences for the project were the scientific communities in the field of dietary fiber and gut microbiome research, nutrition research, industry members in the area of dietary fiber production/product development, and the general public. These communities were reached through the following efforts: Presenting results in an oral presentation at the 2023 and 2024 USDA project directors' annual meetings (July 2023, May 2024) Presenting results in an oral presentation at a department seminar at Michigan State University in the Department of Biological and Agricultural Engineering (March 2024) Presenting results in a poster presentation at the Midwest Microbiome Symposium (May 2024) Attending the 2023 and 2024 Institute of Food Technologists (IFT) conference (July 2024) Presenting results in an oral presentation at the 2024 Conference of Food Engineering (CoFE) (August 2024) Presenting a poster presentation at three annual meetings of the Whistler Center for Carbohydrate Research at Purdue University (May 2023, May 2024, May 2025) Preparing two manuscripts for publication (in preparation). Submitting two additional manuscripts (both submitted in January 2025) Publishing one peer-reviewed manuscript (Published 04 February 2025) Creating a YouTube video about artificial intelligence-assisted microbiome data analysis with an accompanying open access dataset (January 2025) Undergraduate and graduate students in the fields of food science, microbiome science, and systems biology were also a target audience of the current project. To reach these groups, the project director has organized a journal club on the topic of "fiber and the microbiome", and thus far has facilitated four meetings attended by approximately 6-10 students and postdoctoral researchers per meeting to discuss relevant published research articles. The project director has helped to mentor 7 PhD students in the lab of the primary mentor, Dr. Bruce Hamaker, which has helped the project director develop skills in mentorship and reach out to the next generation of scientists. Changes/Problems:The original proposed modeling approach was to use deep learning on bacterial genomes to predict the endpoint community composition of a microbiota during in vitro fecal fermentation from training data consisting of bacterial Carbohydrate-Active enZYmes (CAZymes) genes obtained from the National Center for Biotechnology Information database, however, this "microbe focused" approach has been changed in favor of a "fiber focused" empirical approach. The new modeling method focuses on developing a pipeline that can identify fibers that strongly promote beneficial microbes or inhibit potentially pathogenic microbes by analyzing large empirical datasets from previous studies. So far, 11 different datasets from previous studies have been downloaded and analyzed. This new approach has several advantages. First, it represents an intermediate step that must be accomplished before a bacterial genome-level understanding of fiber-microbe specificity can be developed. Second, the identification of fibers that promote specific beneficial microbes consistently between different human subjects is needed for the improvement of health in consumers with dysbiosis of the lower gut environment. Another change that was made was applying a recently developed statistical technique called "Dissimilarity-Overlap Curve Analysis (DOCA)(Bashan et al., 2016, "Universality of human microbial dynamics", Nature 534: 259-262) to infer whether prebiotic fibers enforce shared resource utilization dynamics across different individuals.This was not anticipated to be a useful technique in the project proposal but was applied todata from 11 previous studies, encompassing 2,488 biological samples from 469 human participants. Within each study, each participant's before and after-intervention samples were referencedto determine the log change of each microbial taxa. Then, the average log change of each taxa that was found in at least three donors was calculated, as well as the Standard Deviation (SD) of each change. Finally, taxa-level randomization was conducted (as per Bashan et al 2016) to computationally remove any shared dynamics, and then the magnitude and SD of changes to all taxa were recalculated.Out of 2,429 taxa-level changes that were quantified across the 11 studies in the dataset, 5.0% of all taxa changed by >0.5 log, 0.3% changed by >1 log, and 0.1% changed by >1.5 log. DOCA showed that the samples in the entire dataset had shared dynamics (p< 0.05) that were successfully removed by taxa-level randomization (Fns = 0.93 vs 0.06). Comparing the real and randomized datasets demonstrated that the changes to microbial taxa had an average SD of 0.42 log in the real data with preserved, shared dynamics vs 0.55 log in the randomized data which lacked the shared dynamics. In short, this anlaysis showed that shared resource dyamics make responses to prebiotic interventions more consistent between individual study participants than if the resource dynamics were not shared. This work was accepted for publication at the 2025 American Society for Nutrition Conference, and will be pursued intently in the future as it has promising applications for the development of precision prebiotic fiber supplements. What opportunities for training and professional development has the project provided?This project has provided the project director with significant opportunities for training and professional development. The project director attended the Annual Meeting of the Whistler Center for Carbohydrate Research (May 2023, and 2024), presented a research poster at each conference as well as presented a poster as co-author in 2025, and received feedback from members of the food industry and academic community. The project director attended the Midwest Microbiome Symposium (May 2024), presented a research poster, and received feedback from members of the microbiome research community. The project director attended the Institute of Food Technologists (IFT) conference (July 2023 and July 2024) and interfaced with companies that produce dietary fiber products (ex. Interfiber, Tate and Lyle, Cargill). The project director presented an oral presentation and received constructive feedback at two USDA-NIFA annual project directors' meetings (July 2023 and May 2024). The project director also presented an oral presentation on the results of the project at the Conference of Food Engineering (August 2024). At these conferences and meetings the project director was able to meet and network with leading scientists in areas of research relevant to the project goals. The project director has attended sessions of Purdue Applied Microbiome Sciences group, as well as workshops and seminars through the Whistler Center for Carbohydrate Research at Purdue University. Being part of a laboratory affiliated with the Whistler Center for Carbohydrate Research has given the project director access to the mentorship of leading carbohydrate scientists and helped the project director to provide mentorship to 4 students in the Hamaker Laboratory. The project director served as a peer reviewer for 18 manuscripts submitted to scientific journals during the reporting period. The project director recently accepted an offer of employment as "Research Associate" at Oregon State University and plans to continue this research in collaboration with the primary mentor while starting to build his own research group at Oregon State University (starting in March 2025). This career opportunity is the direct result of the opportunities from this project. How have the results been disseminated to communities of interest?The communities of interest are the scientific community, members of the food industry, students, the public, and representatives from the USDA. Progress has been made to disseminate project findings to each of these communities. To disseminate results to the scientific community, one manuscript has been published, two are currently submitted (under review) and two more are in preparation to dissemenate the results of this project to communities of interest. Presentations at four conferences (presentations attended by ca. 125 researchers in total) and one department seminar (attended by ca. 20 researchers) were given.Open access to a fiber-microbe specificity analysis pipeline generated for the project was made available through the project director's GitHub. Communication of project results with industry members was carried out at the Whistler Center for Carbohydrate Research annual short course (where the project director developed and taught an educational module about artificial intelligence applications in microbiome research), poster presentations at three annual meetings of the Whistler Center, as well as by attending the Institute of Food Technologists (IFT) conference, Project results have been communicated with students as part of discussions during a new journal club (the "Fiber and the microbiome" journal club) which was founded by the project director. Communication of project results with the general public has been carried out by developing an AI-assited microbiome data analysis workflow with accompanying published YouTube video and publicaly available dataset. Lastly, project results were communicated with USDA personnel at the 2023 and 2024 Annual Project Directors meeting hosted by the United States Department of Agriculture-National Institute of Food and Agriculture (USDA-NIFA) in the form of oral presentations. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
Progress has been made under both of the scientific specific goals of the project. The first project goal was to determine the change in relative abundance of butyrogenic bacteria during in vitro fecal fermentation in the presence of arabinoxylans varying in their degree of structure. Arabinoxylans were extracted from corn bran and their monosaccharide composition and glycosidic linkage profiles were determined. These arabinoxylans were subsequently modified by debranching and cross-linking processes, and the resulting library of 6 fibers were analyzed according to their monosaccharide composition and glycosidic linkage profile. These fibers were then subjected to in vitro fecal fermentation with pooled fecal samples from three human donors. DNA was extracted and analyzed using 16s rRNA sequencing, and the relative abundance of butyrogenic bacteria was determined. Short chain fatty acids were also analyzed, allowing for a more in-depth analysis of the differences in microbial communities that developed on each of the 6 fibers in the library during in vitro fecal fermentation. Sequencing data has been fully analyzed along with short chain fatty acid production data, and the manuscript on these datasets is in preparation for submission to a scientific journal. Objective 2 of the study was to elucidate the biological basis for the relative abundance of butyrogenic bacteria in a fecal fermentation when growing on arabinoxylans differing in their degree of structure. To accomplish this objective, a mathematical model (linear consumer resource) was constructed to study the behavior of a bacterial community with access to multiple resources, with microbial taxa that vary in their ability to utilize specific dietary fiber structures. This linear consumer resource model is currently in use to determine the types of interactions between taxa (synergistic vs competitive) that drive microbial community dynamics in the colonic environment. In the current reporting period, an additional modeling approach was implemented called "Dissimilarity-Overlap Curve Analysis" which is based on a recent study (Bashan et al., 2016, "Universality of human microbial dynamics", Nature 534: 259-262). This model allows for quantification of the degree of universality of microbiomes in different contexts. In simple terms, this approach allows researchers to better understand which factors affect microbiome dynamics (specifically referring to the growth rates of individual taxa and the inter-taxa interaction coefficients). Preliminary results showed that fibers enforce more consistent dynamics in gut microbial communities than polyphenols, supporting the hypothesis that access to dietary fibers as a carbon source and thus as a substrate for growth is the driving factor for relative abundance changes in the gut microbiome. This approach has implications for the development of precision prebiotics, as it suggests that the consistent response in relative abundance profiles of bacteria from different donors observed in previous studies is due to differential utilization of these resources by taxa in the colon. This modeling workflow has been uploaded to repositories on the project director's Github, and is being used for a large-scale analysis of 11 publically available datasets with an abstract based on this work accepted for publication in the American Society of Nutrition Conference (2025), and accompanying manuscript currently in preparation.
Publications
- Type:
Peer Reviewed Journal Articles
Status:
Published
Year Published:
2025
Citation:
Hayes, A.M.R., Swackhamer, C., Quezada-Calvillo, R. et al. Moderating carbohydrate digestion rate in mice promotes fat oxidation and metabolic flexibility revealed through a new approach to assess metabolic substrate utilization. Eur J Nutr 64, 83 (2025). https://doi.org/10.1007/s00394-025-03585-1
- Type:
Peer Reviewed Journal Articles
Status:
Submitted
Year Published:
2025
Citation:
F. Cisse , C. Swackhamer , H. Diall, A. Rahmanifar, M. Sylla, A.R. Opekun, M.A. Grusak, A. H-M. Lin, E.A. Pletsch, A. M.R. Hayes, R. Quezado-Calvillo, B.L. Nichols, B. R. Hamaker, Stunted African toddlers digest and obtain energy from energy-dense thick sorghum porridge. 2025. Submitted to European Journal of Clinical Nutrition.
- Type:
Peer Reviewed Journal Articles
Status:
Submitted
Year Published:
2025
Citation:
C. Swackhamer , S. Jang , B.R. Park, B. R. Hamaker, S. K. Jung. Structure-based
standardization of prebiotic dietary fibers: monosaccharide composition, degree of polymerization, and linkage composition. 2025. Submitted to Carbohydrate Polymers.
- Type:
Peer Reviewed Journal Articles
Status:
Submitted
Year Published:
2025
Citation:
V. Igwe, C. Mensah, C. Swackhamer, D. Smith. Synergistic Enhancement of Corn Insoluble Dietary Fiber via Combined Radiofrequency Heating and Enzymatic Hydrolysis: Fermentability and Short Chain Fatty Acid (SCFA) Production. 2025. Submitted to Journal of Food Science.
|
Progress 08/01/23 to 07/31/24
Outputs
Target Audience:The target audiences for the project are the scientific communities in the field of dietary fiber and gut microbiome research, nutrition research, industry members in the area of dietary fiber production/product development, and the general public. These communities have been reached through the following efforts: Presenting results in an oral presentation at the 2024 USDA project directors' annual meeting (May 2024) Presenting results in an oral presentation at a department seminar at Michigan State University in the Department of Biological and Agricultural Engineering (March 2024) Presenting results in a poster presentation at the Midwest Microbiome Symposium (May 2024) Attending the 2024 Institute of Food Technologists (IFT) conference (July 2024) Presenting results in an oral presentation at the 2024 Conference of Food Engineering (CoFE) (August 2024) Presenting a poster presentation at the annual meeting of the Whistler Center for Carbohydrate Research at Purdue University (May 2024) Preparing two manuscripts for publication (in preparation). Undergraduate and graduate students in the fields of food science, microbiome science, and systems biology are also a target audience of the current project, particularly individuals from backgrounds or groups historically disadvantaged or underrepresented in the fields of carbohydrate science and microbiome science. To reach these groups, the project director has organized a journal club on the topic of "fiber and the microbiome", and thus far has facilitated four meetings attended by approximately 6-10 students and postdoctoral researchers per meeting to discuss relevant published research articles. The project director has helped to mentor 4 PhD students in the lab of the primary mentor, Dr. Bruce Hamaker, which has helped the project director develop skills in mentorship and reach out to the next generation of scientists. All four of the mentees are members of underrepresented groups. Changes/Problems:The original proposed modeling approach was to use deep learning on bacterial genomes to predict the endpoint community composition of a microbiota during in vitro fecal fermentation from training data consisting of bacterial Carbohydrate-Active enZYmes (CAZymes) genes obtained from the National Center for Biotechnology Information database, however, this "microbe focused" approach has been changed in favor of a "fiber focused" empirical approach. The new modeling method focuses on developing a pipeline that can identify fibers that strongly promote beneficial microbes or inhibit potentially pathogenic microbes by analyzing large empirical datasets from previous studies. So far, 11 different datasets from previous studies have been downloaded and analyzed. This new approach has several advantages. First, it represents an intermediate step that must be accomplished before a bacterial genome-level understanding of fiber-microbe specificity can be developed. Second, the identification of fibers that promote specific beneficial microbes consistently between different human subjects is needed for the improvement of health in consumers with dysbiosis of the lower gut environment. One problem that has been encountered is the difficulty in finding an appropriate venue for dissemination of project results to the general public. Despite widespread interest in relationships between gut health and diet, data from the National Health and Nutrition Examination Survey (NHANES) showed that only 1 in 20 Americans consume the recommended daily allowance of dietary fiber (14 g fiber per 1000 kCal), indicating that there is a need for outreach and education on the importance of dietary fiber. This project provides an opportunity to interface with consumers to help educate them about the gut microbiome, and particularly its interactions with dietary fiber, but also to determine how the needs of the general public with respect to gut health can be advanced by evidence-based research. The project director is currently seeking opportunities for this, and at the very least will try to produce a general interest article to be published either on LinkedIn or on the project director's personal website to facilitate this type of dissemination of results. What opportunities for training and professional development has the project provided?This project has provided the project director with diverse opportunities for training and professional development. The project director attended the Annual Meeting of the Whistler Center for Carbohydrate Research (May 2024), presented a research poster, and received feedback from members of the food industry. The project director attended the Midwest Microbiome Symposium (May 2024), presented a research poster, and received feedback from members of the microbiome research community. The project director attended the Institute of Food Technologists (IFT) conference (July 2024) and interfaced with companies that produce dietary fiber products (ex. Interfiber, Tate and Lyle, Cargill). The project director presented an oral presentation and received constructive feedback at the USDA-NIFA annual project directors' meeting (May 2024). The project director also presented an oral presentation on the results of the project at the Conference of Food Engineering (August 2024). At these conferences and meetings the project director was able to meet and network with leading scientists in areas of research relevant to the project goals. The project director has attended sessions of Purdue Applied Microbiome Sciences group, as well as workshops and seminars through the Whistler Center for Carbohydrate Research at Purdue University (91 seminars or workshops attended in 2024 thus far). Being part of a laboratory affiliated with the Whistler Center for Carbohydrate Research has given the project director access to the mentorship of leading carbohydrate scientists and helped the project director to provide mentorship to 4 students in the Hamaker Laboratory. The project director served as a peer reviewer for 12 manuscripts submitted to scientific journals during the reporting period. The project director recently accepted an offer of employment as "Research Associate" at Oregon State University and plans to continue this research in collaboration with the primary mentor while starting to build his own research group at Oregon State University (starting in March 2025). This career opportunity is the direct result of the opportunities from this project. How have the results been disseminated to communities of interest?The communities of interest are the scientific community, members of the food industry, students, the public, and representatives from the USDA. Progress has been made to disseminate project findings to each of these communities. To disseminate results to the scientific community, presentations at three conferences (presentations attended by ca. 100 researchers in total) and one department seminar (attended by ca. 20 researchers) were given. Two manuscripts are in preparation to disseminate results from the project: one empirical research article and one review article. Open access to a fiber-microbe specificity analysis pipeline generated for the project was made available through the project director's GitHub. Communication of project results with industry members was carried out at the Whistler Center for Carbohydrate Research annual short course, and annual meeting, as well as at the Institute of Food Technologists (IFT) conference, Project results have been communicated with students as part of discussions during a new journal club (the "Fiber and the microbiome" journal club) which was founded by the project director. Communication of project results with the general public has been an ongoing challenge. The project director is searching for a good venue where these results could be communicated in an effective way. Lastly, project results were communicated with USDA personnel at the 2024 Annual Project Directors meeting hosted by the United States Department of Agriculture-National Institute of Food and Agriculture (USDA-NIFA) in the form of an oral presentation. What do you plan to do during the next reporting period to accomplish the goals?In order to accomplish the project goals during the next reporting period, the remaining items in specific aim 1 of the project will be carried out. The main experimental steps on the project are complete, however, rheological analysis of the 6 fibers in the library, microscopy analysis of the fibers, and molecular weight analysis of the fibers will be conducted before the end of the project. Analysis of experimental data from in vitro fecal fermentation is nearly complete, but some additional analysis of the specific taxa that were differentially promoted by fibers in the library will be conducted. The remaining items in specific aim 2 of the project will be accomplished by refining the linear consumer resource model already developed by the project director and using it to analyze experimental results from the study. Additionally, Dissimilarity Overlap Curve Analysis will be used to determine which fibers in the library enforced the most consistent community dynamics. These results will help future researchers understand the mechanisms of how complex dietary fibers shape the relative abundance of different microbial taxa in the colonic environment, potentially leading to more precise prebiotics for an anti-inflammatory gut.
Impacts
What was accomplished under these goals?
Progress has been made under both of the specific goals of the project. The first project goal was to determine the change in relative abundance of butyrogenic bacteria during in vitro fecal fermentation in the presence of arabinoxylans varying in their degree of structure. In the last reporting period, arabinoxylans were extracted from corn bran and their monosaccharide composition was determined. In the current reporting period, these arabinoxylans were modified by debranching and cross-linking processes, and the resulting library of 6 fibers were analyzed according to their monosaccharide composition and glycosidic linkage profile. These fibers were then subjected to in vitro fecal fermentation with pooled fecal samples from three human donors. DNA was extracted and analyzed using 16s rRNA sequencing, and the relative abundance of butyrogenic bacteria was determined. Short chain fatty acids were also analyzed, allowing for a more in-depth analysis of the differences in microbial communities that developed on each of the 6 fibers in the library during in vitro fecal fermentation. Sequencing data is being analyzed and bioinformatics done in the current grant extension period. Objective 2 of the study is to elucidate the biological basis for the relative abundance of butyrogenic bacteria in a fecal fermentation when growing on arabinoxylans differing in their degree of structure. In the last reporting period, a mathematical model (linear consumer resource) was constructed to study the behavior of a bacterial community with access to multiple resources, with microbial taxa that vary in their ability to utilize specific dietary fiber structures. This linear consumer resource model is currently in use to determine the types of interactions between taxa (synergistic vs competitive) that drive microbial community dynamics in the colonic environment. In the current reporting period, an additional modeling approach was implemented called "Dissimilarity-Overlap Curve Analysis" which is based on a recent study (Bashan et al., 2016, "Universality of human microbial dynamics", Nature 534: 259-262). This model allows for quantification of the degree of universality of microbiomes in different contexts. In simple terms, this approach allows researchers to better understand which factors affect microbiome dynamics (specifically referring to the growth rates of individual taxa and the inter-taxa interaction coefficients). Preliminary results showed that fibers enforce more consistent dynamics in gut microbial communities than polyphenols, supporting the hypothesis that access to dietary fibers as a carbon source and thus as a substrate for growth is the driving factor for relative abundance changes in the gut microbiome. This approach has implications for the development of precision prebiotics, as it suggests that the consistent response in relative abundance profiles of bacteria from different donors observed in previous studies is due to differential utilization of these resources by taxa in the colon.
Publications
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2024
Citation:
Clay Swackhamer, Thaisa Cantu-Jungles, Bruce R. Hamaker. Three patterns in the gut microbial community during in vitro fecal fermentation of dietary fibers varying their level of complexity." Poster presentation. Midwest Microbiome Symposium.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2024
Citation:
Clay Swackhamer, Nuseybe Bulut, Thaisa Cantu-Jungles, Bruce R. Hamaker. Engineering the gut microbiome using designer prebiotics and consumer-resource modeling Oral Presentation. Conference of Food Engineering.
|
Progress 08/01/22 to 07/31/23
Outputs
Target Audience:The target audiences for the project include relevant scientific communities, industry members, and the general public. The first target audience consists of scientific researchers that focus on the development and characterization of prebiotic dietary fibers. Another scientific target audience consists of researchers developing mathematical models for the interactions between dietary fibers and the gut microbiome, which can be considered part of the field of systems biology. These communities of researchers have been reached by the project director attending the Institute of Food Technologists (IFT) conference, and Conference of Food Engineering (CoFE), by presenting a poster presentation at the annual meeting of the Whistler Center for Carbohydrate Research at Purdue University, and by preparing manuscripts for publication (in preparation). Another target audience of the project are members of the food industry, in particular individuals developing food products using dietary fibers for improved gut health through modification of the microbiome. Members of the food industry were reached by the project director by giving a seminar at the annual meeting of the Whistler Center for Carbohydrate Research, and by designing a new educational module for the annual short course of the center, attended by approximately 40 members of the food industry. Students at the undergraduate and graduate level in the fields of food science, microbiome science, and systems biology are also a target audience, particulary those individuals from backgrounds or groups historically disadvantaged or underrepreseted in food science and microbiome science. To reach these groups, the project director has organized a journal club, called the "Fiber and the microbiome" journal club, and has facilitated 12 meetings attended by approximately 6-10 students and postdoctoral researchers per meeting to discuss published studies on these topics. The project director has helped to mentor 4 PhD students in the lab of the primary mentor, Dr. Bruce Hamaker, which has helped the project director develop skills in mentorship and reach out to the next generation of scientists. Finally, scientists at the USDA are also part of the target audience for this project. Preliminary results from the project were presented at the 2023 Annual Project Directors meeting hosted by the United States Department of Agriculture-National Institute of Food and Agriculture (USDA-NIFA) in the form of an oral presentation. Changes/Problems:The original proposed modeling approach was to use deep learning on bacterial genomes to predict the endpoint community composition of a microbiota during in vitro fecal fermentation from training data consisting of bacterial Carbohydrate-Active enZYmes (CAZymes) genes extracted from the National Center for Biotechnology Information database. This approach has been modified as consumer-resource models can already efficiently determine community assembly from information about bacterial resource preference and growth rates. However, growth rates of relevant bacteria in community context from substrates (dietary fibers) with well-characterized physicochemical structure is not avaialble in the scientirfic literature. Obtaining this data for the 8 fibers generated in this project is part of the first specific aim of the project. In essence, the overall goal of linking dietary fiber structure to bacterial preference and resulting community composition is unchanged, but a different modeling methodology than the one originally planned has been identified as the most promising approach. Lastly, the general public is also a target audience of the project. There is widespread interest in relationships between gut health and diet, and this project provides an opportunity to interface with consumers to help educate them about the gut microbiome, and particularly its interactions with dietary fiber, but also to determine how the needs of the general public with respect to gut health can be advanced by evidence-based research. According to data from the National Health and Nutrition Examination Survey (NHANES) approximately 1 in 20 Americans consume the recommended daily allowance of dietary fiber (14 g fiber per 1000 kCal), indicating that there is a need for outreach and education on the importance of dietary fiber. There has not been any outreach to the public thus far, but the project director will seek opportunities to do so during the next reporting period. What opportunities for training and professional development has the project provided?This project has provided the project director with diverse opportunties for training and professional development. The project director attended the Conference of Food Engineering (COFE) in 2022 and the Institute of Food Technologists (IFT) conference in 2023. At these conferences the project director was able to meet and network with leading scientists in areas of research relevant to the project goals. The project director had the opportunity to present progress and receive constructive feedback at the USDA-NIFA annual project directors meeting in 2023. The project director completed two courses with through the Collaborative Institutional Training Initiative (CITI) program: Biosafety for Principal Investigators, Lab Personnel, and IBC Members, and Responsible Conduct of Research Training for Faculty, Postdoctoral, and Graduate Students. Trainings on equipment in the Hamaker laboratory were completed including an anaerobic chamber and gas chromatography - mass spectroscopy system. The project director has attended sessions of Purdue Applied Microbiome Sciences group, including seminars by several distinguished speakers, and audited a graduate-level bioinformatics class at Purdue University. This course was instrumental to develop skills navigating 16s sequencing data analysis piplines using QIIME2, and to be able to more critically consider 16s sequencing results from other research groups. Being in a research group affiliated with the Whistler Center for Carbohydrate Research at Purdue University has given the project director access to the mentorship of leading carbohydrate scientists and also helped the project director to help provide mentorship to 4 students in the Hamaker Laboratory. The project director founded a new journal club at Purdue, on the topic of "fiber and the microbiome" and hosted 12 sessions that were attended by students and faculty members of the Whistler Center for Carbohydrate Research to discuss scientific studies relevant to this research area. The project director attended 62 academic seminars in 2022 and 57 seminars in 2023 thus far. The project director has maintained a Github account to share computational resources, and profiles on ResearchGate and LinkedIn to share project updates and maintain a professional network. How have the results been disseminated to communities of interest?The communities of interest have been identified as the scientific community, members of the food industry, students, the general public, and representatives from the USDA. Progress has been made to dissemenate project findings to each of these communities. To disseminate results to the scientific community, publication of scientific manuscripts is of high importance, and thus a review article, perspective article, and original research article are being prepared for submission to peer-reviewed journals. Project results have been discussed through conversations with leading scientists at the Institute of Food Technologists (IFT) conference, the Conference of Food Engineering (CoFE), and by providing free and open access to certain project documents and code through the project director's Github. Scientific communication of project results was carried out at a poster presented by the project director for members of the Whistler Center for Carbohydrate Research, as well as through a seminar titled "Effect of fiber structure on the taxonomic composition of the colonic microbiome" given to the Department of Food Science at Purdue University. Communication of project results with industry members was carried out at the Whistler Center for Carbohydrate Research annual short course, where the project director co-developed and taught a module called "Computational Approaches to Big Data in Gut Microbiome Studies" which was attended by approximately 40 representatives (~25 in-person and ~15 on-line) from carbohydrate-utilizing food companies. Project results have been communicated with students as part of discussions during a new journal club (the "Fiber and the microbiome" journal club) which was founded by the project director. The project director has helped schedule and organize 12 discussions of publised studies on this topic, which is highly relevant to the project, and allows for free exchange of concepts and scientific ideas among students. Communication with the general public has been attempted by posting some project documents and code on the project director's GitHub. The project director is searching for opportunities to communicate results of the project with the general public, which will be discussed in the next section. Lastly, project results were communicated with USDA personnel during the 2023 Annual Project Directors meeting hosted by the United States Department of Agriculture-National Institute of Food and Agriculture (USDA-NIFA) in the form of an oral presentation. What do you plan to do during the next reporting period to accomplish the goals?In order to accomplish the project goals during the next reporting period, the remaining items in specific aim 1 of the project will be carried out. These goals consist of debranching and cross linking the fibers that have been extracted and characterized, and then subjecting them to in vitro fecal fermentation. To accelerate progress in the laboratory toward these goals, the project director has purchased additional materials such as sample preparation test tubes for chromatographic analysis to increase experimental throughput. To help increase resources for conducting laboratory experiments, an undergraduate researcher will be recruited, which will also provide opportunites for the project director to hone mentorship skills, as described in the project narrative. The remaining items in specific aim 2of the project will be accomplished by refining the mathematical model already prototyped by the project director, using it to analyze experimental results from the study, as well as attempting to design and then test mixtures of the 8 fibers generated in this project that can be used to shape an anti-inflammatory microbiome using in vitro fecal fermentation experiments. Accomplishing this goal will require the project director to refine the existing model, and then to gather additional experimental data for model training and validation.
Impacts
What was accomplished under these goals?
Progress has been made under both of the specific goals of the project. The first project goal is to determine the change in relative abundance of butyrogenic bacteria during in vitro fecal fermentation in the presence of arabinoxylans varying in their degree of structure. In the first specific goal, experimental progress has been the extraction of arabinoxylans from corn bran and the assessment of the monosaccharide composition of these fibers. The project director has been trained in the protocols for in vitro fecal fermentatation including sample collection and experimental methods. Learning to analyze data from 16s sequencing was carried out by auditing a graduate bioinformatics course, and these skills will be leveraged to analyze data from in vitro fecal fermentation on the fibers produced during this project. An experimental apparatus was designed and built to hold large volumes of liquid (ca. 4 L) with precise temperature control to carry out enzymatic reactions necessary for the hydrolysis of residual protein in dietary fibers (proteinase) and for cross-linking them (laccase). Objective 2 of the study is to elucidate the biological basis for the relative abundance of butyrogenic bacteria in the fecal fermentation when growing on arabinoxylans differing in their degree of structure. For this objective, a preliminary mathematical model was implemented to study the behavior of a bacterial community with access to multiple resources, and where taxonomical groups vary in their ability to utilize specific dietary fiber structures. Specifically, this mathematical model is classified as a consumer-resource model which consists of two, coupled, linear, ordinary differential equations, with one equation handling microbial growth kinetics as a function of substrate (dietary fiber) availability, and the second equation reconciling microbial growth with resource depletion. Both equations are solved simultaneously. This approach was developed based on recent studies that used a similar method to model bacterial communities in the gut. A Lotka-Volterra term was also included in the model development, which implements direct microbe-microbe interactions which can take the form of synergistic growth (for example, due to cross feeding) or antagonistic growth (for example, due to resource competition or secretion of inhibitory compounds). This model can be used to determine which classes of interactions are responsible for shaping the response of the gut microbiota, and crucially, can be solved in a forward-engineering approach to quantitatively determine a mixture of fibers to reshape an existing gut bacterial community with a specific goal, such as to promote anti-inflammatory, butyrate-producing bacteria. To our knowledge this is the first approach that has these capabilities. This model has thus far been used to reproduce findings from previous researchers, and to generalize relationships from small model systems (10 microbes growing on one fiber) to larger contexts (ex. 100 microbes growing on 10 fibers) but has not yet been tested using fibers developed in the current project and thus requires additional experimental validation.
Publications
|
|