Progress 10/01/19 to 09/30/20
Outputs
Target Audience:Other researchers in the field and also ingredient producers and food manufacturers interested in microbiome andhealth impacts of their products Changes/Problems:The biggest problem was a halt to our research during the height of the pandemic in Pennsylvania along with continuing restrictions on research, particularly human research. We have altered our research protocols to satisfy increased safety demands, but this has also had a negative impact on the pace of research. To some extent we expect this to continue through the following reporting period, but sill expect to make strong progress. The Covid-19 pandemic severely hampered dissemination of our research during this reporting period. Several planned talks and poster presentations needed to be cancelled. What opportunities for training and professional development has the project provided?Finding training and professional development opportunities has been challenging during the pandemic. Two of my graduate students and two of my undergraduate students were able to attend a conference this past fall. The PI, along with several other members of the Penn State Microbiome Center, were also able to develop a week long bootcamp focused on developing microbiome analysis skills. This was primarily targeted at incoming studentsbut was made available to other students interested in developing these skills. The entire workshop was delivered remotely and received lots of positive feedback. How have the results been disseminated to communities of interest?The results have been disseminated through fouroral presentations by the PI, fourstudent poster presentations and onejournal article publication. Two graduate students and two undergraduate students were able to attend and present their research at the Allegheny Branch of the American Society for Microbiology meeting, a regional, student-focused meeting. Unfortunately, additional dissemination opportunities were lost due to the pandemic.The PI was able to present research at three invited seminars within Penn State for the Microbiome Center, the Biomedical Engineering department and the Penn State One Health initiative. The PI also presented an invited research talk at Laurier University in Canada. The PI was also able to publish an invited review in Current Opinion in Biotechnology, highlighting some of the lab's work on this project. What do you plan to do during the next reporting period to accomplish the goals?Goal 1: We will be receiving the initial isolates from our collaboration with GALT in the coming weeks. We will then begin characterizing these strains and genome sequencing any that seem particularly promising. Upon receipt of our new culturing instrument we will begin exploring additional ways to cultivate/characterize these organisms and utilize additional microbiomes as our starting material. Goal 2: We plan on initiating our high-throughput methods for enzyme reconstruction and screening the hybrid constructs for differing activity against insoluble starches, resistant or otherwise. Goal 3: We will be particularly focused on exploring fermentations using microbiomes from people who either consume large amounts of pulses or those who consume very little. While we are exploring a variety of substrates, pulses processed in various ways will be the main subject of investigation. We hope to learn how much adaptations of microbiomes to a given dietary component impacts the health benefits that are derived from it. Goal 4: We will complete data collection for our cross-over clinical trial.
Impacts
What was accomplished under these goals?
Goal 1: We have initiated a collaboration with Gut Associated Lymphoid Tissue(GALT), a company specializing in high-throughput culturing. We are working with them to develop ways to isolate bacteria with certain functional characteristics. For this we are developing ways of detecting resistant starch degrading bacteria, starch degradation products using bacteria and butyrate producing bacteria. We will be able to continue this work longer term via an instrument we and a group of other researchers are purchasing from the company through a National Institute of Food and Agriculture (NIFA) equipment grant. Goal 2: The pandemic has somewhat disrupted this goal for this reporting period as part of our collaboration for this was to involve travel to Europe to develop techniques for randomly recombining starch degrading enzymes. However, we have continued to make progress on characterizing starch degrading enzymes from both resistant starch utilizing and non-resistant starch utilizing gut bacteria, particularly Eubacterium rectale, Ruminococcus bromii and Bifidobacterium adolescentis. We are also exploring how the starches from various grains and pulses behave during enzymatic or microbial degradation. Goal 3: We have continued to develop our in vitro fermentation approaches and have multiple collaborations underway to explore how individual microbiomes differ in their responses to various forms of resistant starch and dietary fibers. We are also exploring co-cultures that bring together various starch degrading organisms to see if collectively they can degrade resistant starches where individually they cannot. This is providing valuable information about community interactions in starch digestion in the gut. Goal 4: Unfortunately, the pandemic has impeded the progress of our human clinical trials. We have recently been able to modify our protocols to satisfy Penn State of their safety and are currently resuming human trials. However, this has delayed the completion of our cross-over clinical trial with participants sequentially consuming multiple resistant starches until the next reporting period. Initial data are quite promising in demonstrating personalized responses to various forms of resistant starch.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
DeMartino P, Cockburn DW. Resistant starch: impact on the gut microbiome and health. Curr Opin Biotechnol. 2020 Feb;61:66-71. doi: 10.1016/j.copbio.2019.10.008. Epub 2019 Nov 22. Review. PubMed PMID: 31765963.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2019
Citation:
Teichmann J, DeMartino P, Cockburn DW. Resistant starch and the gut microbiome: the path from fiber to butyrate. Invited lecture presented at Laurier University, Canada, Nov 2019.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2019
Citation:
Teichmann J, Cockburn DW. Individual differences in gut microbiome responses to resistant starch supplementation. Invited lecture presented at Penn State University, Dec 2019.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2020
Citation:
DeMartino P, Pickens T, Teichmann J, Cockburn DW. Resistant starch and the Gut Microbiome: the Path from Fiber to Butyrate. Invited presentation at the Penn State Microbiome Center Apr 2020.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2020
Citation:
Teichmann J, Cockburn DW, Using in vitro fermentations to predict human gut microbiome responses to resistant starch supplementation. Accepted presentation at ASM Microbe, Jul 2020.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2020
Citation:
DeMartino P, Teichmann J, Pickens T, Cockburn DW. Using Resistant Starch to Tailor Diets to the Human Gut Microbiome. Invited presentation to the Department of Biomedical Engineering, Penn State University, Sept 2020.
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Progress 10/01/18 to 09/30/19
Outputs
Target Audience:During this reporting period there were numerous conference presentations by the PI and students. There were three graduate student poster presentations at the Penn State Life Sciences Symposium, a local event that communicates with life science researchers at Penn State. One of the posters was awarded the best poster of the competition. There were also three graduate student poster presentations at the Penn State Microbiome Center Networking event, a local event connecting with microbiome researchers at Penn State.There were 3 graduate student and one undergraduate presented poster at the Alleghany Branch of the American Society for Microbiology meeting, a regional meeting that highlights student microbiology work in the region. There was also a graduate student poster presentation and two invited oral presentations by the PI at the National American Society for Microbiology (Microbe) meeting. There was a poster presentation and a selected oral talk by the PIat the national Institute for Food Technologists meeting. There were poster presentations by a graduate student and the PI at the Gordon research conference on Carbohydrate Active Enzymes. There was also an invited talk given by the PI at the Pulse Innovation Summit hosted by the American Pulse Association. Finally the PI gave a selected oral lecture at the international alpha-amylase conference. Overall, knowledge from the project was able to be widely disseminated in the reported project year. Changes/Problems:The only major change will come in our recombinant enzyme construction. During the past year we have initiated a collaboration with a lab that has developed a system for recombining multi-modular enzymes. This will offer a more efficient approach to producing these enzymes and will allow us to screen a much larger library of recombinant enzymes without much additional effort. This will increase the probablility of success for this goal and will likely open up additional research opportunities in the future once we have an extensive library of enzymes with differing properties to work with. What opportunities for training and professional development has the project provided?All three graduate students attended at least two conferences over the course of the reporting period, leading to the development of communication and networking skills. The graduate students all had opportunities to supervise undergraduate students in the lab including through an underrepresented minority program at Penn State and through a USDA sponsored REEU program in food microbiology at Penn State. There have also been several workshops attended by the graduate students offered through the Microbiome Center at Penn State, offering training in a variety of microbiome related techniques. Students have also received additional training in preparing fellowship applications. How have the results been disseminated to communities of interest?The results have mostly been disseminated through conference poster and oral presentations. This project has in this reporting period has led to 12 poster presentations and 7 oral presentations to regional, national and international audiences. Publications of the work are also in preparation or have been submitted. What do you plan to do during the next reporting period to accomplish the goals?Goal 1: We will continue to analyze our resistant starch degrading isolates and experiment with media compositions that will allow us to isolate non-Bifidobacterium resistant starch degrading organisms that we believe are playing an important role. Goal 2: We will complete our analysis of wild-type enzymes and begin to assemble our chimeric constructs. Additonall we will begin to transfer these constructs into a new host organism to test impact on ability to grow on resistant starch. Goal 3: Now that we have completed the first phase of this line of inquiry we will expand into investigating other starch types and combinations of starches. In the immediate future we will be investigating starches isolated from pulses under different processing conditions and using microbiomes isolated from both habitual and rare consumers of pulses to test the impact of dietary history on microbiome outcomes. Goal 4: We will continue conductiong the clinical trial and continue analyzing samples as they become available. We plan on completing sample collection in this coming reporting period, however, data analysis will likely continue longer.
Impacts
What was accomplished under these goals?
Goal 1: We have continued to refine our methodology for isolating novel resistant starch degrading organisms. We have good strategies for identifying Bifidobacterium species members with this capability, but we are still not satisfied with our ability to detect non-Bifidobacterium members that are more difficult to culture, particularly on solid media. We are excited to try out some of our new ideas in this direction in the coming year. Goal 2: We are beginning to pursue a novel approach whereby we can randomly assort together domains from a large number of starch degrading enzymes. This approach should definitively allow us to answer the necessary minimal components for degrading resistant starch and if they differ between starches. We have mostly completed our characterization of the wild-type enzymes and will soon be beginning our experiments with recombinant combinations of enzymes and binding domains. Goal 3: We have completed a study examining in vitro fermentations using fecal samples from 12 individuals and testing their ability to ferment 8 different starches. We have found substantial interindividual variability in responses to resistant starch and for each individual there were a range of resistant starches for which they experienced increases in butyrate levels. 16S sequencing has revealed that which resistant starch degraders and which butyrate producers are present play a large role in determining these outcomes. Goal 4: We have now enrolled 40 individuals into our study and have had 19 complete the full protocol. We have begun to analyze the samples coming in and have intriguingly seen similar results to our in vitro studies in terms of the distribution of butyrate responses to the different resistant starches, suggesting that our in vitro model is capturing the key information needed to predict the results of human trials.
Publications
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Progress 07/01/18 to 09/30/18
Outputs
Target Audience:During this reporting period, we had one conference presentation of the work at the Penn State Life Sciences Symposium. A student on the project, June Teichmann presented a poster of her work on developing in vitro fermentations for investigating resistant starch digestion. the presentation was well received and provided some interesting feedback for moving forward on the project. During this period we have also had contact with 20 participants in our clinical trial, providing them with information about the trial and our general study of the gut microbiome, helping to educate these participants about the microbiome while also enrolling them in the trial. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?In this period we have had one graduate student give a conference poster presentation and two incoming PhD students have received training in fellowship applications, which they plan to pursue in the coming year. All three graduate students in the lab have received trianing in relation to their specific roles in the project, particularly with regards to anaerobic microbiology and data analysis. How have the results been disseminated to communities of interest?At this early stage there has been limited opportunity to disseminate results and the results are relatively preliminary. We have had one conference poster presentation and an oral presentation at an internal group meeting (all food microbiologists within our department). We anticipate much more of this activity in the next period. What do you plan to do during the next reporting period to accomplish the goals?1. We will fully characterize the existing resistant starch degrading organisms (about two dozen) that we have currently isolated and anticipate isolating another two dozen or so in the next period. 2. We will complete characterization of the Bifidobacterium adolescentis enzyme and will begin experiments to create chimeric enzymes with parts from resistant starch degrading and non-resistant starch degrading enzymes to determine the necessary pieces. 3. We will complete development of our in vitro fecal fermentation model and expand out analysis to integrate results from multiple starting microbiomes and incorporate 16S rDNA analysis into the pipeline. 4. We will complete recruiting for our clinical trial, with the majority finishing by the end of the next reporting period. We will also begin analyzing our samples from the trial.
Impacts
What was accomplished under these goals?
1. We have isolated two dozen resistant starch degrading bacteria and have begun characterizing the range of resistant starch that they are able to efficiently degrade and use as a growth substrate. 2. We have cloned out the key resistant starch degrading enzyme from Bifidobacterium adolescentis and have begun its characterization. 3. We have conducted a number of in vitro fermentation experiments looking at the effects of different types of resistant starch, whether the resistant starch is isolated or in a whole food context or if the fermentation is supplemented with resistant starch degrading organisms. We have found intriguing differences between resistant starch types, whole foods vs isolated starch and supplementation with different bacteria. These data all stem from analysis of fermentation products and we are now moving to investigate how the communities have changed to produce these differences through 16S sequencing. 4. We have continued to recruit volunteers for our clinical trial and now have 21 participants. The furthest along participants are over halfway through the protocol, so data will start to come in soon.
Publications
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