Active projects

These are the things I’ve been thinking about lately


A System for Reproducible Research

This series of blog posts will address my efforts to tackle reproducibility in my own work by producing better and more accessible documentation of methods and maximum transparency in data analysis

Modeling Neonatal Microbial Colonization in Human Intestinal Organoids

Understanding the mechanisms guiding the establishment of host-microbial symbiosis using stem-cell derived intestinal tissues

Real-time measurement of epithelial barrier permeability in human intestinal organoids

This protocol describes the measurement of epithelial barrier permeability in real-time following pharmacologic treatment in human intestinal organoids using fluorescent microscopy and live cell microscopy

Selected Publications

Advances in 3D culture of intestinal tissues obtained through biopsy or generated from pluripotent stem cells via directed differentiation, have resulted in sophisticated in vitro models of the intestinal mucosa. Leveraging these emerging model systems will require adaptation of tools and techniques developed for 2D culture systems and animals. Here, we describe a technique for measuring epithelial barrier permeability in human intestinal organoids in real-time. This is accomplished by microinjection of fluorescently-labeled dextran and imaging on an inverted microscope fitted with epifluorescent filters. Real-time measurement of the barrier permeability in intestinal organoids facilitates the generation of high-resolution temporal data in human intestinal epithelial tissue, although this technique can also be applied to fixed timepoint imaging approaches. This protocol is readily adaptable for the measurement of epithelial barrier permeability following exposure to pharmacologic agents, bacterial products or toxins, or live microorganisms. With minor modifications, this protocol can also serve as a general primer on microinjection of intestinal organoids and users may choose to supplement this protocol with additional or alternative downstream applications following microinjection.
JoVE, 2017

The human gastrointestinal tract is immature at birth, yet must adapt to dramatic changes such as oral nutrition and microbial colonization. The confluence of these factors can lead to severe inflammatory disease in premature infants; however, investigating complex environment-host interactions is difficult due to limited access to immature human tissue. Here, we demonstrate that the epithelium of human pluripotent stem-cell-derived human intestinal organoids is globally similar to the immature human epithelium and we utilize HIOs to investigate complex host-microbe interactions in this naive epithelium. Our findings demonstrate that the immature epithelium is intrinsically capable of establishing a stable host-microbe symbiosis. Microbial colonization leads to complex contact and hypoxia driven responses resulting in increased antimicrobial peptide production, maturation of the mucus layer, and improved barrier function. These studies lay the groundwork for an improved mechanistic understanding of how colonization influences development of the immature human intestine.
eLife, 2017

In recent years, increasing attention has been devoted to the concept that microorganisms play an integral role in human physiology and pathophysiology. Despite this, the molecular basis of host–pathogen and host–symbiont interactions in the human intestine remains poorly understood owing to the limited availability of human tissue, and the biological complexity of host–microbe interactions. Over the past decade, technological advances have enabled long-term culture of organotypic intestinal tissue derived from human subjects and from human pluripotent stem cells, and these in vitro culture systems already have shown the potential to inform our understanding significantly of host-microbe interactions. Gastrointestinal organoids represent a substantial advance in structural and functional complexity over traditional in vitro cell culture models of the human gastrointestinal epithelium while retaining much of the genetic and molecular tractability that makes in vitro experimentation so appealing. The opportunity to model epithelial barrier dynamics, cellular differentiation, and proliferation more accurately in specific intestinal segments and in tissue containing a proportional representation of the diverse epithelial subtypes found in the native gut greatly enhances the translational potential of organotypic gastrointestinal culture systems. By using these tools, researchers have uncovered novel aspects of host–pathogen and host–symbiont interactions with the intestinal epithelium. Application of these tools promises to reveal new insights into the pathogenesis of infectious disease, inflammation, cancer, and the role of microorganisms in intestinal development. This review summarizes research on the use of gastrointestinal organoids as a model of the host–microbe interface.
CMGH, 2017

Complete Publications

More Publications

. Generation of lung organoids from human pluripotent stem cells in vitro.. In: Nat Protoc,, 2019.

. Identification, isolation and characterization of human LGR5-positive colon adenoma cells.. In: Development, (145), 6,, 2018.

. In Vitro Induction and In Vivo Engraftment of Lung Bud Tip Progenitor Cells Derived from Human Pluripotent Stem Cells.. In: Stem Cell Reports, (10), 1, pp. 101-119,, 2018.

. Bacterial colonization stimulates a complex physiological response in the immature human intestinal epithelium. eLife, 2017.

Preprint Code Dataset Project DOI Custom Link

Recent & Upcoming Talks

Modeling neonatal microbial colonization in human intestinal organoids
Apr 2, 2019 3:30 PM

Academic Experience

July 2018 – Present
Ann Arbor MI

Research Assistant Professor

University of Michigan

Application of human pluripotent stem cell derived intestinal organoids to study microbial colonization of the neonatal digestive tract
January 2018 – May 2018
Ypsilanti MI

Part-time Lecturer

Eastern Michigan University

Course Director for Clinical Immunology, an upper level undergraduate course for students in the board certified Medical Technology program.
September 2014 – June 2018
Ann Arbor MI

Research Fellow

University of Michigan

Host-microbe interactions at the intestinal epithelial interface in human development using human pluripotent stem cell derived intestinal organoids.
June 2013 – August 2014
Chestnut Hill MA

Research Fellow

Boston College

Anti-inflammatory and prebiotic activity of human milk oligosaccharides and glycosaminoglycans in infant health and development.
July 2008 – May 2013
Cleveland OH

Graduate Student

Cleveland Clinic Lerner College of Medicine

Characterized size-dependent induction of innate antimicrobial defense of the intestinal epithelium by hyaluronan and demonstrated that hyaluronan is a natural component of the human milk glycome that enhances protection from enteric disease.
June 2006 – May 2008
Kent OH

Research Assistant

Kent State University

Worked with Dr. Helen Piontkivska investigating mechanisms of adaptive evolution in host-pathogen interactions using in silico molecular phylogenetic analysis.
June 2005 – May 2008
Cleveland OH

Research Assistant

Cleveland Clinic

Researched the role of extracellular matrix in inflammatory cell recruitment and activation in inflammatory bowel disease in the laboratory of Dr. Carol A de la Motte.


University of Michigan:

  • PIBS 503: Research Responsibility & Ethics (Instructor, Fall 2018)

Eastern Michigan University

  • CLSC 335: Clinical Immunology (Course Director, Winter 2018)

Case Western Reserve University

  • Graduate Biostatistics (Teaching Assistant, Summer 2010)

Kent State University

  • Introductory Biology (Supplemental Instructor, Fall 2007)
  • Evolutionary Biology (Supplemental Instructor, Winter 2008)

Recent Posts

Last winter I served as course director for Clinical Immunology at Eastern Michigan University’s School of Health Sciences. …

Albert and Mary Lasker Foundation Essay Contest Entry