APPLICATION OF MACHINE LEARNING FOR THE CREATION OF GUT MICROBIAL BIOMARKER PANEL ENABLING PERSONALIZED NUTRITION RECOMMENDATIONS

• Sponsoring Institution: National Institute of Food and Agriculture
• Project Status: COMPLETE
• Funding Source: AFRI COMPETITIVE GRANT
• Reporting Frequency: Annual
• Accession No.: 1026383
• Grant No.: 2021-67034-35114
• Cumulative Award Amt.: $120,000.00
• Proposal No.: 2020-10015
• Project Start Date: Jun 15, 2021
• Project End Date: Jun 14, 2023
• Grant Year: 2021
• Program Code: [A7101]- AFRI Predoctoral Fellowships

Recipient Organization
UNIVERSITY OF ILLINOIS
2001 S. Lincoln Ave.
URBANA,IL 61801

Performing Department
Nutritional Scinces

Non Technical Summary
Diet affects thebacteria within our guts, their genes (metagenome), and the byproducts they create (metabolome). Currently, researchers use self-reported measures (e.g. 24-hour food recalls and food frequency questionnaires) to survey research subjects and determine what they normally eat. However, these current tools aren't the most accurate as they are subjective.The goal of this pre-doctoral fellowship project is to identify objective biomarkers of food intake. In other words, we intend to measure bacteria, their genes, and their byproducts in fecal samples to objectively measure what foods research subjects ate. Therefore, this proposal strengthens our previous findings by adding fecal samples from five completed clinical trials where we fed participants almonds, avocados, broccoli, whole grains, and walnuts intake to achieve our objectives of: 1) Using frozen fecal samples from these studies to complete metagenomic (genes) and metabolomic (byproducts) analyses to confirm that methods we currently use with post-intervention-only (no baseline) data are valid; and 2) Creating a panel of biomarkers of food intake made up of the bacteria, their genes, and metabolites. Our previous research efforts revealed our ability to predict if research subjects consumed a specific food with 86% accuracy using fifteenunique fecal bacteria. Our ongoing efforts show promise in using post-intervention-only (no baseline) measures of bacterial genes and byproducts to predict food intake. Hence, our plans to accomplish our goal used storedfecal samples and ongoing collaborations to continue to pursue these efforts and add baseline data to confirm that our post-intervention-only methods are sound. This proposal will provide the groundwork for non-invasive, objective, fecal biomarkers of food intake, which can be used in future research studies to compare to self-reported measures and increase the accuracy of diet reporting. In the future, this research could help us to develop diet recommendations specific to individuals based on their microbiota for disease treatment and prevention. Furthermore, this project will help my professional development by strengthening my research, leadership, communication, and collaboration skills. Overall, this project will benefit the field of nutrition and microbiome research and my professional development into an independent nutrition scientist with essential skills.

Animal Health Component

50%

Research Effort Categories

Basic

50%

Applied

50%

Developmental

(N/A)

Classification

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
701	6010	1010	100%

Knowledge Area
701 - Nutrient Composition of Food;

Subject Of Investigation
6010 - Individuals;

Field Of Science
1010 - Nutrition and metabolism;

Keywords

[other key words to research]

predoctoral fellowship

Goals / Objectives
Training objectives are tobroadenresearch skills,enhance leadership skills,strengthen science communication to a variety of audiences, andcontinue to deepen my collaborative abilities.The overall research objective is toidentify microbial biomarkers of specific, whole food intake using advanced analytic techniques.Objective One: Validate the use of post-intervention microbial genes and metabolites through the addition of pre-intervention measures of the same outcomes.Objective Two: Create a biomarker panel of each of the sixindividual foodscomprised of microbes, their genes, and metabolites.

Project Methods
TrainingI will continue to work towards Objective 1: Becoming an independent researcher with expertise in nutrition-focused microbiome research to develop biomarkers of food intake using fecal microbes, genes, and metabolites. While my strong nutrition foundation is being strengthened through my PhD program, microbiome research requires proficiency in molecular biology and bioinformatics. However, not many nutritionists are trained in bioinformatics and vice versa. I am fortunate to have mentors and collaborators who support my development of these skills. This fellowship will allow me to continue developing proficiency in new techniques and methods with the guidance of my mentors and to attend workshops like Strategies and Techniques for Analyzing Microbial Population Structures (STAMPs) and the University of Maryland's Institute for Genome Sciences (IGS) Omics courses. Weekly meetings with Drs. Holscher and Zhu, and annual meetings with my dissertation committee comprised of nutrition scientists, computer scientists, and statisticians, will allow me to continue to develop my expertise in melding these areas.For Objective 2, I aim to further develop leadership skills through participation in the Academy of Nutrition and Dietetics' Leadership Institute, and continued involvement in leadership roles on campus and with national organizations, such as Chair for the Nutritional Sciences Graduate Student Association (NSGSA), President-Elect for the Eastern Illinois Academy of Nutrition and Dietetics, Membership Liaison of the Research Dietetic Practice Group (RDPG), and the Advisory Board of the American Society for Nutrition's Nutrition Translation Research Interest Section. My mentorship skills will be strengthened through continued supervision of undergraduate research assistants, participation in the NSGSA's Mentorship Program, and leading a scientific translation assignment for Dr. Radlowski's students.This fellowship will also allow me to strengthen skills essential for the attainment of Objective 3 by communicating scientific findings to diverse audiences through manuscripts, press releases, conference presentations, and webinars/seminars. During my PhD, I have participated in graduate student writing groups, presented at conferences, and authored a manuscript (in peer review). I will write a press release translating our findings on the use of fecal microbes as biomarkers of food intake pending manuscript acceptance. Furthermore, I plan to submit at least one article to RDPG's peer-reviewed newsletter.I completedUI's NUTR510 Translating andCommunicating Science course in Fall 2020. I have given three invited webinars, oneon my research (>300 attendees) and twoon more general nutrition topics. I plan to continue engaging in speakingopportunities. I utilize social media platforms (Instagram andTwitter) to further engage with the public about nutrition topics. Recently, I accepted an internship with PepsiCo where I will create scientific materials for internal and external use. Finally, I plan to further enhance my communication skills by serving as a discussion leader for UI's Principles of Nutrition course,giving a guest lecture in Dr. Holscher's Diet and the GI Microbiome course, and engaging in instruction opportunities with Dr. Radlowski. In maintaining relationships with colleagues with varied backgrounds, clear communication is essential.Maintaining relationships also requires interdisciplinary collaboration (Objective 4). My PhD research relies on collaboration with various scientists (nutrition, statistics, computer scientists) to reach our goals. I also have regular communication with past mentors and colleagues, which helps to maintain our past collaborative relationships and facilitate the opportunity for future partnerships. Volunteering as NSGSA Chair and continuing Grads Understanding Wellness IN Discussions (UNWIND), a series organized by graduate students covering wellness and mental health across UI, gives me the opportunity to collaborate with peers. From a social networking aspect, I maintain a LinkedIn profile (>500 connections) and regularly update career milestones.Attainment of these objectives will be assessed at bi-annual meetings with career/training mentors and weekly meetings with my primary mentor. SMART goals established for identified milestones will ensure outputs and impact are appropriate.Research:Metagenomic Sequencing:Fecal DNA from each of the fivestudies will be used to construct and sequence the shotgun libraries for characterization of metagenomic communities, including taxonomy and functional genes. The library construction will be done in the Carver Biotechnology Center with the Kapa Hyper kit (Roche, CA), using unique dual indexed (UDI) adaptors to prevent index switching. DNA libraries will be combined in equimolar ratios to create a DNA pool that is used for sequencing. The final libraries will be quantitated with Qubit (ThermoFisher, MA) and the average size will be determined on a Fragment Analyzer (Agilent Technologies, CA). Sequencing will be performed on a NovaSeq6000 (Illumina Inc.) using an S4 flowcell, which allows for 2 x 150 base paired-read sequencing and generates a deep sequencing depth of ~5-6 billion high accuracy (typical error rate of 0.1-1%) pair-end reads (~800 gigabases of data). Sequence data will be analyzed using the Biocluster in the HPCBio Center of the Carver Biotechnolgoy Center. Briefly, sequences will be separated into forward and reverse reads and merged into paired-end reads using VSEARCH. The merged sequences will then undergo removal of contaminant host (human) DNA using the kneadData tool against the GRCh37/hg19 human reference genome. DIAMOND will then be used to align the sequences against the NCBI non-redundant (NR) protein reference databaseand the UniRef90 protein reference database.The alignment process will utilize an e-value (significance score) cutoff of 1e-5 and report only the top 20 alignments per query. The MEGANtool will provide taxonomic and KEGG pathway annotationsfor the resulting DIAMOND alignments. Data are quantitatively expressed as gene counts. In parallel to DIAMOND, HUMAnN2 will be run on the merged and cleaned metagenome with the default search parameters to produce gene family abundances, pathway abundances, and pathway coverage stratified by organism.Metabolomic Sequencing:Fecal extractions will be performed at the Carver Biotechnology Center Metabolomics Unit using previously published protocols . Briefly, two one ml fractions will be taken from each sample and dried. One fraction will be derivatized for 90 minutes at 500° C with 80 μl of methoxyamine hydrochloride in pyridine (20 mg/ml) followed by a 60 minute treatment at 500° C with 80μl MSTFA. A 5μl aliquot of a C31 fatty acid internal standard will be added to each, in the derivatized samples this will occur prior to trimethylsilylation. Sample volumes of onemL will be injected with a split ratio of 7:1 into a GC-MS system consisting of an Agilent 7890A (Agilent Inc, Palo Alto) gas chromatograph, an Agilent 5975C mass selective detector and Agilent 7683B autosampler. The spectra of all chromatogram peaks will be compared with electron impact mass spectrum libraries NIST08 (NIST, Gaithersburg), WILEY08 (Palisade Corporation), and to a custom library of the University of Illinois metabolomics center. To allow direct comparisons between samples all data will be normalized to the internal standard in each chromatogram. The chromatograms and mass spectra will be evaluated using the MSD ChemStation (Agilent, Palo Alto) and AMDIS (NIST, Gaithersburg).Machine Learning:Methods previously utilized (as detailed in Shinn et al.'s 2020 Journal of Nutrition publication) on fecal bacterial species will be used with fecal bacterial genes and metabolites to achieve the proposed specific aims.

Progress 06/15/21 to 11/10/22

Outputs
Target Audience:Bioinformatics workshops (Nature's Reshaping the Microbiome through Nutrition) provided knowledge that was shared with our lab group. Leadership and mentorship involvement (NSGSA and undergraduate) directly benefitted graduate and undergraduate students, respectively. I have also continued to mentor Aditya Mansharamani, now a full-time computer scientist ,with his BS and MS in Computer Science, through the publication process for the results related to this proposal. Community webinars and social media presence have reached a broad public audience from middle-schoolers through older adults. Formal classroom experiences (Teaching Assistantship with Dr. Radlowski) have imparted knowledge upon undergraduate students and graduate students. Specific to my research, committee and co-mentor meetings have propelled research progress forward resulting in conference presentations (scientific audience) and manuscript publications (scientific audience). Changes/Problems:Project was terminated early due to early completion and PD starting a full-time Senior Scientist role with PepsiCo, Inc. on 8/22/2022. What opportunities for training and professional development has the project provided? Bi-annual meetings with mentors, Drs. Emily Radlowski, Chris Cifelli, and Mickey Rubin Guest lectures in Dr. Emily Radlowski's Medical Nutrition Therapy courses Weekly meetings with mentors, Dr. Hannah Holscher and Dr. Ruoqing Zhu, and mentee, Aditya Mansharamani to continue progressing project aims Secured full-time roll as a Senior Scientist with PepsiCo, Inc. starting August 2022 How have the results been disseminated to communities of interest?Publications: Leila M Shinn, Aditya Mansharamani, David J Baer, Janet A Novotny, Craig S Charron, Naiman A Khan, Ruoqing Zhu, Hannah D Holscher, Fecal Metabolites as Biomarkers for Predicting Food Intake By Healthy Adults, The Journal of Nutrition, 2022;, nxac195. Shinn LM, Holscher HD. Personalized nutrition and multi-omics analyses: A guide for nutritionists. Nutrition Today. 2021;56(6):270-278. Shinn LM, Li Y, Mansharamani A, Auvil L, Welge M, Bushell C, Khan NA, Charron CS, Novotny J, Baer D, Zhu R, Holscher HD. Fecal bacteria as biomarkers for predicting food intake in healthy adults. Journal of Nutrition. 2020;nxaa285. Conferences: Shinn LM, Mansharamani A, Zhu R, Holscher, HD. Machine learning identifies fecal metabolites predictive of whole food consumption. Personalized Nutrition Initiative Symposium, Oral Presentation. November 2021. Guest Lectures/Presentations: Shinn, LM. Path to Science Translation. NUTR 401: MNT 1, Dominican University. Webinar. 10 live attendees. February 2022. Shinn, LM. Registered Dietitians in Research. NUTR 430: MNT Seminar, Dominican University. Webinar. 18 live attendees. February 2022. Shinn LM, Toney AM, Ortiz S, Zhang X. How to Write an Award-Winning Abstract. American Society for Nutrition Student Interest Group, Webinar. February 2022. Shinn LM. The Impact of Diet on the Gastrointestinal Microbiome. Educational Webinar for Ayatana Artists' Research Program. October 2021. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? Enhance leadership skills Elected as the Illinois Academy of Nutrition and Dietetics' (AND) Nominating Chair-Elect Served as the AND's Research Dietetic Practice Group (RDPG) Membership Chair (June 2021-May 2022) Served as a mentor to one early career Registered Dietitian Nutritionist through the RDPG's mentorship program Currently serving as a mentor to an undergraduate senior in dietetics interested in graudate school through AND's Mentorship program Served as AND's Eastern Illinois District President (June 2021-May 2022) Precepted five dietetic interns and provided learning opportunities to meet competencies in order for them to become eligible to sit for the Registered Dietitian exam Obtained Mentorship Certification from the University of Illinois at Urbana-Champaign (UIUC)'s Graduate College in April 2022 Received Illinois AND's Emerging Dietetic Leader Award (2021) Received AND's RDPG Emerging Researcher Author Award (2021) Received UIUC's Graduate Student Leadership Award Special Recognition (2021) Nominated as Emerging Clinical Leader nomination for American Society for Nutrition (2021) Served as Chair for Department's Nutritional Sciences Graduate Student Association (NSGSA) from 2021-22 Completed AND's Leadership Institute (LI) from 2020-21 Strengthen science communication to a variety of audiences Delivered two lectures to Dr. Emily Radlowski's undergraduate and graduate students: Shinn, LM. Path to Science Translation. NUTR 401: MNT 1, Dominican University. Webinar. 10 live attendees. February 2022. Shinn, LM. Registered Dietitians in Research. NUTR 430: MNT Seminar, Dominican University. Webinar. 18 live attendees. February 2022. Work from this project has resulted in award-winning abstracts and an invitation to speak: Shinn LM, Toney AM, Ortiz S, Zhang X. How to Write an Award-Winning Abstract. American Society for Nutrition Student Interest Group, Webinar. February 2022. AND's LI resulted in poster presentations and publication in progress: McKinley EM, Shinn LM, Hinck S, Jones L, Paczosa AB, Goldberg K. Skills, Satisfaction, and Future Recommendations for Salary and Benefit Negotiation Success Among Nutrition and Dietetics Professionals in the United States. American Society for Nutrition. Poster Presentation (PO10-11-22). June 2022 (Presenting Author) Goldberg K, Hinck S, Jones L, McKinley EM, Paczosa AB, Shinn LM. Evaluation of Negotiation Success and Skill Sets Among Nutrition and Dietetics Professionals in the United States. Food and Nutrition Conference and Expo. Poster Presentation. October 2021. Published Shinn LM, Holscher HD. Personalized nutrition and multi-omics analyses: A guide for nutritionists. Nutrition Today. 2021;56(6):270-278. Presented at UIUC's Personalized Nutrition Initiative virtual conference: Shinn LM, Mansharamani A, Zhu R, Holscher, HD. Machine learning identifies fecal metabolites predictive of whole food consumption. Personalized Nutrition Initiative Symposium, Oral Presentation. November 2021. Discussed the gastrointestinal microbiome in general with artists: Shinn LM. The Impact of Diet on the Gastrointestinal Microbiome. Educational Webinar for Ayatana Artists' Research Program. October 2021. Completed a three-month internship with PepsiCo Inc.'s Global Research andDevelopment team reviewing and summarizing substantive research to complete a project on the gastrointestinal microbiome while also compiling recommendations for improvement of the healthcare professional website based on first quarter performance (May-August 2021) Placed first in NSGSA's 2021 oral presentation competition (2021) Continue to deepen collaborative abilities Worked with NSGSA steering committee as 2020-21 Chair to organize annual Nutrition symposium Served on symposium organizing committee to assist 2021-22 Chair Completed UIUC's Carl R. Woese Institute for Genomic Biology's Professional Skills for Careers in Biosciences (2021) Continued weekly meetings with mentors, Dr. Hannah Holscher and Dr. Ruoqing Zhu, and mentee, Aditya Mansharamani 1. Validate the use of post-intervention microbial genes and metabolites through the addition of pre-intervention measures of the same outcomes Paper utilizing microbial genes is currently in progress - manuscript is being drafted for publication once published this objective is complete Paper utilizing metabolites is accepted in The Journal of Nutrition - objective regarding microbial metabolites is complete 2. Create a biomarker panel of each of the six individual foods comprised of microbes, their genes, and metabolites. Multi-omics analyses is currently in progresswith goal of publication by late 2022/early 2023

Publications

• Type: Journal Articles Status: Published Year Published: 2021 Citation: Leila M Shinn, Yutong Li, Aditya Mansharamani, Loretta S Auvil, Michael E Welge, Colleen Bushell, Naiman A Khan, Craig S Charron, Janet A Novotny, David J Baer, Ruoqing Zhu and Hannah D Holscher. 2021. Fecal Bacteria as Biomarkers for Predicting Food Intake in Healthy Adults. The Journal of Nutrition, Volume 151, Issue 2, February 2021, Pages 423433, https://doi.org/10.1093/jn/nxaa285.
• Type: Journal Articles Status: Published Year Published: 2021 Citation: Shinn, Leila M. and Holscher, Hannah D. 2021. Personalized Nutrition and Multiomics Analyses. Nutrition Today: 11/12/2021 - Volume 56 - Issue 6 - p 270-278 doi: 10.1097/NT.0000000000000513.
• Type: Journal Articles Status: Accepted Year Published: 2022 Citation: Leila M Shinn, Aditya Mansharamani, David J Baer, Janet A Novotny, Craig S Charron, Naiman A Khan, Ruoqing Zhu and Hannah D Holscher. Fecal Metabolites as Biomarkers for Predicting Food Intake By Healthy Adults, The Journal of Nutrition, 2022;, nxac195.

Progress 06/15/21 to 06/14/22

Outputs
Target Audience:Bioinformatics workshops (Nature'sReshaping the Microbiome through Nutrition) provided knowledge that wasshared with our lab group. Leadership and mentorship involvement (NSGSA and undergraduate) directly benefitted graduate and undergraduate students, respectively. I have also continued to mentor Aditya Mansharamani, a now-graduate research assistant with his BS and MS in Computer Science. Community webinars and social media presence have reached abroad public audience from middle-schoolers through older adults. Formal classroom experiences (Teaching Assistantshipwith Dr. Radlowski) have imparted knowledge upon undergraduate students and graduate students. Specific to my research, committee and co-mentor meetings have propelledresearch progress forward resulting in conference presentations (scientific audience) and manuscript publications (scientific audience). Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Bi-annual meetings with mentors, Drs. Emily Radlowski, Chris Cifelli, and Mickey Rubin Guest lectures in Dr. Emily Radlowski's Medical Nutrition Therapy courses Weekly meetings with mentors, Dr. Hannah Holscher and Dr. Ruoqing Zhu, and mentee, Aditya Mansharamani to continue progressing project aims How have the results been disseminated to communities of interest?Publications: Shinn LM, Mansharamani A, Baer D, Novotny J, Charron CS, Khan NA, Zhu R, Holscher HD. Fecal metabolites as biomarkers for predicting food intake in healthy adults.Under review. Shinn LM, Holscher HD. Personalized nutrition and multi-omics analyses: A guide for nutritionists. Nutrition Today. 2021;56(6):270-278. Shinn LM, Li Y, Mansharamani A, Auvil L, Welge M, Bushell C, Khan NA, Charron CS, Novotny J, Baer D, Zhu R, Holscher HD. Fecal bacteria as biomarkers for predicting food intake in healthy adults. Journal of Nutrition. 2020;nxaa285. Conferences: Shinn LM, Mansharamani A, Zhu R, Holscher, HD. Machine learning identifies fecal metabolites predictive of whole food consumption. Personalized Nutrition Initiative Symposium, Oral Presentation. November 2021. Guest Lectures/Presentations: Shinn, LM. Path to Science Translation. NUTR 401: MNT 1, Dominican University. Webinar. 10 live attendees. February 2022. Shinn, LM. Registered Dietitians in Research. NUTR 430: MNT Seminar, Dominican University. Webinar. 18 live attendees. February 2022. Shinn LM, Toney AM, Ortiz S, Zhang X. How to Write an Award-Winning Abstract. American Society for Nutrition Student Interest Group, Webinar. February 2022. Shinn LM. The Impact of Diet on the Gastrointestinal Microbiome. Educational Webinar for Ayatana Artists' Research Program. October 2021. What do you plan to do during the next reporting period to accomplish the goals? Continue to enhance leadership skills through: Role as the Illinois Academy of Nutrition and Dietetics' (AND)Nominating Chair-Elect Role as AND's Eastern Illinois district Past-President Continued mentorship to incoming and current graduate student peers in lab Continued application to relevant awards Strengthen science communication to a variety of audiences Continued progress on publications related to this project and complementary press releases Continue to deepen collaborative abilities Continuedweekly meetings with mentors, Dr. Hannah Holscher and Dr. Ruoqing Zhu, and mentee, Aditya Mansharamani 1. Validate the use of post-intervention microbial genes and metabolites through the addition of pre-intervention measures of the same outcomes Publication of paper utilizing microbial genes Publication of paperutilizing metabolites 2. Create a biomarker panel of each of the six individual foods comprised of microbes, their genes, and metabolites. Decide on an appropriate multi-omics tool for this project's data based on completion of a literature review and exploration Publication of paper integrating microbes, their genes, and metabolites

Impacts
What was accomplished under these goals? Enhance leadership skills Elected as the Illinois Academy of Nutrition and Dietetics' (AND)Nominating Chair-Elect Served as the AND's Research Dietetic Practice Group (RDPG) Membership Chair (June 2021-May 2022) Served as a mentor to one early career Registered Dietitian Nutritionist through the RDPG's mentorship program Served as AND's Eastern Illinois district President (June 2021-May 2022) Precepted fivedietetic interns and provided learning opportunities to meet competencies in order for them to become eligible to sit for the Registered Dietitian exam Obtained Mentorship Certification from the University of Illinois at Urbana-Champaign (UIUC)'sGraduate College in April 2022 Received Illinois AND's Emerging Dietetic Leader Award (2021) Received AND's RDPGEmerging Researcher Author Award (2021) Received UIUC'sGraduate Student Leadership Award Special Recognition (2021) Nominated asEmerging Clinical Leader nomination for American Society for Nutrition (2021) Served as Chair for Department's Nutritional Sciences Graduate Student Association (NSGSA) from 2021-22 Completed AND's Leadership Institute (LI) from 2020-21 Strengthen science communication to a variety of audiences Delivered two lectures to Dr. Emily Radlowski's undergraduate and graduate students: Shinn, LM. Path to Science Translation. NUTR 401: MNT 1, Dominican University. Webinar. 10 live attendees. February 2022. Shinn, LM. Registered Dietitians in Research. NUTR 430: MNT Seminar, Dominican University. Webinar. 18 live attendees. February 2022. Work from this project has resulted in award-winning abstracts and an invitation to speak: Shinn LM, Toney AM, Ortiz S, Zhang X. How to Write an Award-Winning Abstract. American Society for Nutrition Student Interest Group, Webinar. February 2022. AND's LI resulted in poster presentations and publication in progress: McKinley EM,Shinn LM, Hinck S, Jones L, Paczosa AB, Goldberg K. Skills, Satisfaction, and Future Recommendations for Salary and Benefit Negotiation Success Among Nutrition and Dietetics Professionals in the United States. American Society for Nutrition. Poster Presentation (PO10-11-22). June 2022. (Presenting author)Goldberg K, Hinck S, Jones L, McKinley EM, Paczosa AB,Shinn LM. Evaluation of Negotiation Success and Skill Sets Among Nutrition and Dietetics Professionals in the United States. Food and Nutrition Conference and Expo. Poster Presentation. October 2021. PublishedShinn LM, Holscher HD. Personalized nutrition and multi-omics analyses: A guide for nutritionists. Nutrition Today. 2021;56(6):270-278. Presented at UIUC's Personalized Nutrition Initiative virtual conference:Shinn LM, Mansharamani A, Zhu R, Holscher, HD. Machine learning identifies fecal metabolites predictive of whole food consumption. Personalized Nutrition Initiative Symposium, Oral Presentation. November 2021. Discussed the gastrointestinal microbiome in general with artists:Shinn LM. The Impact of Diet on the Gastrointestinal Microbiome. Educational Webinar for Ayatana Artists' Research Program. October 2021. Completed a 3-month internship with PepsiCo Inc.'s Global Research & Development team reviewingand summarizing substantive research to complete a project on the gastrointestinal microbiome while also compiling recommendations for improvement of the healthcare professional website based on first quarter performance (May-August 2021) Placed first in NSGSA's 2021 oral presentation competition (2021) Continue to deepen collaborative abilities Worked with NSGSA steering committee as 2020-21 Chair to organize annual Nutrition symposium Served on symposium organizing committee to assist 2021-22 Chair Completed UIUC'sCarl R. Woese Institute for Genomic Biology'sProfessional Skills for Careers in Biosciences (2021) Continued weekly meetings with mentors, Dr. Hannah Holscher and Dr. Ruoqing Zhu, and mentee, Aditya Mansharamani 1. Validate the use of post-intervention microbial genes and metabolites through the addition of pre-intervention measures of the same outcomes Paper utilizing microbial genes is currently in progress - results are in process of being finalized;once published this progress is complete Paper utilizing metabolites is currently under review - once published this progress is complete 2. Create a biomarker panel of each of the six individual foods comprised of microbes, their genes, and metabolites. Currently exploring multi-omics tools and completing a literature review to complete this aim

Publications

• Type: Journal Articles Status: Published Year Published: 2021 Citation: Leila M Shinn, Yutong Li, Aditya Mansharamani, Loretta S Auvil, Michael E Welge, Colleen Bushell, Naiman A Khan, Craig S Charron, Janet A Novotny, David J Baer, Ruoqing Zhu and Hannah D Holscher. 2021. Fecal Bacteria as Biomarkers for Predicting Food Intake in Healthy Adults. The Journal of Nutrition, Volume 151, Issue 2, February 2021, Pages 423433, https://doi.org/10.1093/jn/nxaa285.
• Type: Journal Articles Status: Published Year Published: 2021 Citation: Shinn, Leila M. and Holscher, Hannah D. 2021. Personalized Nutrition and Multiomics Analyses, Nutrition Today: 11/12 2021 - Volume 56 - Issue 6 - p 270-278 doi: 10.1097/NT.0000000000000513.
• Type: Journal Articles Status: Under Review Year Published: 2022 Citation: Shinn, L.M., Mansharamani, A., Baer, D., Novotny, J., Charron, C.S., Khan, N.A., Zhu, R. and Holscher, H.D. 2022. Fecal Metabolites as Biomarkers for Predicting Food Intake in Healthy Adults. Journal of Nutrition (Under review).