Travis J. De Wolfe


I am a Postdoctoral Scholar studying spatial structuring of the microbiome. The goal of my research is to use advanced technologies to test theories about the role of 3D structuring in shaping the ecology of microbial communities in biological and environmental samples. In addition, I am working to optimize high-throughput workflows for microbiome data collection and bioinformatic analysis. Please feel free to contact me with any questions.



Academic Appointments


2018 – Postdoctoral Scholar
University of Pittsburgh, Department of Biomedical Informatics
Mentor: Erik Wright

Education


Ph.D. University of Wisconsin – Madison
Department of Food Science, 2018
Dissertation: Probiotics for the prevention of Clostridium difficile infection
Committee: James L. Steele, Nasia Safdar, Benjamin J. Darien, and Jan-Peter van Pijkeren

M.S. University of Wisconsin – Madison
Department of Comparative Biomedical Sciences, 2012
Thesis: Prophylactic efficacy of an engineered biotherapeutic fusion protein against Cryptosporidium parvum in dairy calves

B.S. University of Wisconsin – Madison
Department of Dairy Science, 2010
Natural sciences degree track

Publications

Refereed Journal Articles*


2018 De Wolfe TJ, Eggers S, Barker AK, Kates AE, Dill-McFarland KA, Suen G, Safdar N. Oral probiotic combination of Lactobacillus and Bifidobacterium alters the gastrointestinal microbiota during antibiotic treatment for Clostridium difficile infection. PLoS One. 2018 Sept 28

2017 Wyche TP, Ramos-Alvarenga RF, Piotrowski JS, Duster MN, Warrack S, Cornilescu G, De Wolfe TJ, Hou Y, Braun D, Ellis GA, Simpkins SW, Nelson J, Meyers CL, Mori H, Safdar N, Markley JL, Rajski SR, Bugni TS. Chemical genomics, structure elucidation, and in vivo studies of the marine-derived anticlostridial ecteinamycin. ACS Chem. Biol. 2017 Jul 14

2016 Julliard W, De Wolfe TJ, Fechner JH, Safdar N, Agni R, Mezrich JD. Amelioration of Clostridium difficile infection in mice by dietary supplementation with indole-3-carbinol. Ann Surg. 2016 Jun 8

Aktas B, De Wolfe TJ, Safdar N, Darien BJ, Steele JL. The impact of Lactobacillus casei on the composition of the cecal microbiota and innate immune system is strain specific. PLoS One. 2016 May 31

Zellmer C, De Wolfe TJ, Van Hoof S, Blakney R, Safdar N. Patient perspectives on fecal microbiota transplantation for Clostridium difficile infection. Infect Dis Ther. 2016 Apr 5

2015 Aktas B, De Wolfe TJ, Tandee K, Safdar N, Darien BJ, Steele JL. The effect of Lactobacillus casei 32G on the mouse cecum microbiota and innate immune response is dose and time dependent. PLoS One. 2015 Dec 29

Sawin EA, De Wolfe TJ, Aktas B, Stroup BM, Murali SG, Steele JL, Ney DM. Glycomacropeptide is a prebiotic that reduces Desulfovibrio bacteria, increases cecal short-chain fatty acids, and is anti-inflammatory in mice. Am J Physiol Gastrointest Liver Physiol. 2015 Oct 1

2012 Brooks VJ, De Wolfe TJ, Paulus TJ, Xu J, Cai J, Keuler NS, Godbee RG, Peek SF, McGuirk SM, Darien BJ. Ethnoveterinary application of Morinda citrifolia fruit puree on a commercial heifer rearing facility with endemic salmonellosis. Afr J Tradit Complement Altern Med. 2012 Oct 1

*A full collection of my peer-reviewed articles can be viewed at “My Bibliography” from NCBI. Feel free to request a copy by email.


Public Scholarship


2016 The risks of antibiotic overuse: a neglected public priority, Edge Effects Digital Magazine

2015 Review: Martin Blaser’s Missing Microbes, Edge Effects Digital Magazine

Research appointments


2017 – 2018 Research Assistant, Examining the potential of the microbiome in children to reduce antibiotic resistance: the EPIC study

2016 – 2017 Research Assistant, Optimizing recovery of pathogenic organisms from duodenoscopes

2011 – 2012 Research Intern, Anticryptosporidial efficacy of pre-colostrally delivered Directed Biocide: an immunopathogenic investigation

Grants


2017 National Institutes of Health, Agency for Healthcare Research and Quality, Small Research Grant Program (R03), The GRAFT Study: Gut RecolonizAtion by Fecal Transplantation, University of Wisconsin – Madison
Role: Grant writer
Total: $100,000

2015 Office of the Vice Chancellor for Research and Graduate Education, Biological Sciences Fall Research Competition Award, Prebiotics and probiotics to mitigate Clostridium difficile infection, University of Wisconsin – Madison
Role: Grant writer
Total: $48,823

Conference participation

Poster Presentations


2017 Eggers S, De Wolfe TJ, Barker A, Duster MN, Dill-McFarland K, Suen G, Safdar N, Changes to the composition of the gastrointestinal microbiome after probiotics for Clostridium difficile infection in adults, October 4-8, Infectious Disease Week, San Diego, CA

Aktas B, De Wolfe TJ, Safdar N, Darien BJ, Steele JL, Lactobacillus casei cell-surface components and their impact on immunomodulation and cecal microbiota composition, August 27-31, 12th International Symposium on Lactic Acid Bacteria, Egmond aan Zee, Netherlands

Gopal DV, Meller ME, Marx J, Pfau P, Benson M, De Wolfe TJ, Nelsen EM, Soni A, Reichelderfer M, Safdar N, Optimizing recovery of pathogenic organisms from duodenoscopes – a prospective randomized comparison of CDC vs. UWHC sampling and culture methods, May 6-9, Digestive Disease Week, Chicago, IL

Aktas B, De Wolfe TJ, Safdar N, Darien BJ, Steele JL, Lactobacillus casei cell-surface components and their impact on immunomodulation and cecal microbiota composition, Lactobacillus casei cell-surface components and their impact on immunomodulation and cecal microbiota composition, April 22-26, Experimental Biology, Chicago, IL

Eggers S, De Wolfe TJ, Barker A, Duster MN, Dill-McFarland K, Suen G, Safdar N, Changes to the composition of the gastrointestinal microbiota after probiotics for Clostridium difficile infection in adults, March 15, Population Health Sciences Annual Poster Session, Madison, WI

2016 De Wolfe TJ, Duster MN, Hasegawa Y, Aktas B, Darien BJ, Steele JL, Safdar N, Translational mouse model of Clostridium difficile infection, June 16-20, ASM Microbe, Boston, MA

Ramos-Alvarenga RF, Cornilescu G, Schwieters CD, Gil RR, Wyche TP, De Wolfe TJ, Piotrowski JS, Markley JL, Bugni TS, Residual dipolar couplings for the configurational analysis of bioactive marine invertebrate-associated microbial natural products, March 6-11, Gordon Research Conference, Ventura, CA

2015 De Wolfe TJ, McGuirk SM, Keuler NS, Bremel RD, Homan J, Imboden M, Schaefer DA, Darien BJ, Prophylactic efficacy of an engineered biotherapeutic fusion protein against Cryptosporidium parvum in experimentally challenged neonatal calves, July 9-12, Joint Annual Meeting, Orlando, FL

Checura CM, McGreevey N, De Wolfe TJ, Peek SF, Barrett-Wilt GA, Godbee RG, Darien BJ, Valerenic acid detection in equine urine after administration of calming supplement, July 9-12, Joint Annual Meeting, Orlando, FL

Sawin E, Aktas B, De Wolfe TJ, Stroup B, Murali S, Steel JL, Ney D, Glycomacropeptide shows prebiotic and immune modulating properties for phenylketonuria in wild type mice, March 28-April 1, Experimental Biology, Boston, MA

Julliard WA, Fechner J, De Wolfe TJ, Safdar N, Mezrich J, Dietary supplementation of the AHR ligand indole-3-carbonyl reduces Clostridium difficile disease in mice, February 3-5, 10th Annual Academic Surgical Congress, Las Vegas, NV

2014 Julliard WA, Fechner J, De Wolfe TJ, Safdar N, Mezrich J, Dietary supplementation of the aryl hydrocarbon receptor ligand indole-3-carbonyl prevents Clostridium difficile disease in mice, November 14-15, The Wisconsin Chapter of the American College of Surgeons Annual Conference, Kohler, WI

Aktas B, De Wolfe TJ, Tandee K, Steele JL, The effect of Lactobacillus casei 32G on the mouse cecum microbiota and innate immune response is dose and time dependent, August 31-September 4, 11th International Symposium on Lactic Acid Bacteria, Egmond aan Zee, Netherlands

Duster MN, Warrack, SR, De Wolfe TJ, Aktas B, Steele JL, Safdar N, Establishing a murine model of Clostridium difficile infection: trials and tribulations, June 28-July 1, Anaerobe Society of the Americas, Chicago, IL

2008 Brooks VJ, Paulus TJ, De Wolfe TJ, Godbee RG, Peek SF, McGuirk SM, Darien BJ, A clinical trial evaluating MorindaMax calf immune supplement on health and performance of preweaned, holstein, heifer calves, July 7-11, Joint Annual Meeting, Indianapolis, IN


Oral Presentations


2018 De Wolfe TJ and Arefin MR, What is a healthy microbiome? The politics of microbial baselines, June 21-22, Max Planck Institute for the History of Science, Berlin, Germany

2017 De Wolfe TJ, Anderman N, Arefin MR, Geographies of the microbiome, April 5-9, American Association of Geographers, Boston, MA

Departmental talks


2017 Probiotics for the prevention of Clostridium difficile infection, December 4, Department of Food Science, University of Wisconsin – Madison

2015 Lactobacillus casei probiotics for the prevention of Clostridium difficile infection, September 21, Department of Food Science, University of Wisconsin – Madison

Teaching


2015 Food Microbiology Laboratory, University of Wisconsin – Madison, Fall semester

2014 Fermented Foods and Beverages, University of Wisconsin – Madison, Fall semester

Introduction to the Science and Technology of Food, University of Wisconsin – Madison, Fall semester

2013 – 2014 Introduction to the Science and Technology of Food, University of Wisconsin – Madison, Fall and Spring semesters

Workshops


2018 Shifting baselines, altered horizons: politics, practice, and knowledge in environmental science and policy workshop, June 21-22, Max Planck Institute for the History of Science

Software Carpentry, Jan 10-11, University of Wisconsin – Madison

Data Carpentry, Jan 8-9, University of Wisconsin – Madison

2017 Danube: Environments, Histories, and Cultures, June 4-11, Rachel Carson Center Place-Based Workshop, Ludwig-Maximilian University of Munich

Quantifying biotic and abiotic ecosystem novelty, March 16, Novel Ecosystems Integrative Graduate Education and Research Traineeship, University of Wisconsin – Madison

2016 Disclosing/Enclosing Knowledge in the Life Sciences, July 11-16, Holtz Center for Science & Technology Studies Summer School, University of Wisconsin – Madison

2015 RNA Sequencing Data Analysis, November 6, UW Bioinformatics Resource Center, University of Wisconsin – Madison

Introduction to Next-Generation Sequencing Analysis, October 30, UW Bioinformatics Resource Center, University of Wisconsin – Madison

Linux Essentials for Next-Generation Sequencing Data Analysis, October 23, UW Bioinformatics Resource Center, University of Wisconsin – Madison

Service


2017 Panel organizer, Microbial Matters: Towards a geography of the microbiome, AAG annual meeting, April 5-9, Boston, MA

Co-organizer, 10th Annual Center for Culture, History, and Environment Graduate Student Symposium, February 11, Nelson Institute for Environmental Studies, University of Wisconsin – Madison

Computational skills


Bash programming, R, Python, UNIX/Linux, Microbiome processing (QIIME, mothur, and USEARCH), Metagenomic processing (PICRUSt, HUMAnN, LEfSe, etc.), SAS, HTML/CSS, MATLAB, JMP


Awards


2018 National Library of Medicine Traineeship (T15) for research in biomedical informatics and data science

Culture, History, and Environment Research and Travel Grant, $1000

2017 Cyagen Animal Model Award, $7,500

Holtz Center for Science and Technology Studies Travel Award, $1,000

University of Wisconsin – Madison Student Conference Travel Award, $600

Culture, History, and Environment Research and Travel Grant, $500

2016 University of Wisconsin – Madison Student Conference Travel Award, $1,200

Culture, History, and Environment Research and Travel Grant, $500

2015 Culture, History, and Environment Research and Travel Grant, $500

2014 Daryl B. Lund Graduate Fellowship, $500

W.D. Hoard Memorial Graduate Scholarship, $750

Website updated: October 6, 2018