Opportunities for undergraduates to discover the microbial communities in the New York City environment

The increasing accessibility and affordability of next-generation sequencing, in combination with metagenomic or tag sequencing strategies, has opened the door to an exciting range of hands-on research projects for undergraduates. The Authentic Research Experience in Microbiology (AREM) is a program that builds on this opportunity to engage college students in microbial community analysis and next-generation sequencing projects around their campuses. AREM strives to broaden the horizons of students by introducing them to another perspective of their environment and how microbiology research relates to their daily activities. AREM started at Brooklyn College of the City University of New York (CUNY) with a novel urban microbiome project in a single undergraduate microbiology lab of 18 students. It has developed into a scalable microbiome research module, which is currently incorporated into courses at over 10 campuses across the CUNY system. Students participating have broad backgrounds: science and non-science majors, taking introductory biology and upper-level capstone courses, attend four-year and community colleges. AREM has grown to reach over 200 students in a semester. Data gathered by the students has expanded from a handful of environmental samples to several dozen and data sets of a few thousand 16S rRNA gene sequences to data sets of a few million sequences.

The near-future goal for AREM is to expand to most CUNY colleges and introduce similar projects into their introductory biology laboratory courses. Basic protocols are established for sampling the urban environment (i.e., subway platforms, sidewalks, soil, water, etc.). PCR amplification and sequencing of the 16S rRNA gene are currently completed by Dr. Scot Dowd of MrDNA.

For students, the bioinformatics will be summarized with reporting how the samples are related and community diversity for each sample. An assessment plan has been developed by outside evaluators to measure the efficacy of the research experiences as a way to improve critical thinking and problem solving skills. For faculty incorporating the AREM project into a course there are minimal commitments.

AREM ran a workshop introducing course-based microbiome research to over 30 educators.  As part of the workshop, we went through how AREM grew to the network it is now, how it can be integrated into a variety of courses, then how the instructors can lead students in interpreting the microbiome data.

This project is funded jointly by the National Science Foundation Directorate for Biological Sciences, the Directorate of Education and Human Resources, and Division of Undergraduate Education as part of their efforts to support Vision and Change in Undergraduate Biology Education.

NSF grant 


Theodore Muth

Theodore Muth is an associate professor of biology and heads the microbiology curriculum. Muth did postdoctoral training with Dr. Shimon Schuldiner at the Hebrew University of Jerusalem and with Dr. Patricia Zambryski at the University of California – Berkeley. He joined Brooklyn College in 2000.

Avrom Caplan

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Avrom Caplan received his PhD in biochemistry from King’s College, at the University of London in 1987, where he studied chromosome structure.  After completing postdoctoral work at Southwestern Medical Center in Dallas, TX, and the University of North Carolina at Chapel Hill, Dr. Caplan began his independent research career at Mount Sinai School of Medicine in 1993, where he studied cellular quality control processes.  Dr. Caplan moved to The City College of New York in 2008 and currently serves as the CUNY Associate University Dean for Research where he focuses on broadening participation in undergraduate research. Dr. Caplan is currently the co-principal investigator on an NSF grant to integrate authentic genomics research into the undergraduate curriculum.

Jessica Joyner


Jessica earned her doctorate degree in Ecology in 2014 from the Odum School of Ecology at the University of Georgia. Her Biology bachelor’s degree is from the Florida State University. Her dissertation was focused on coastal water quality and coral disease in the Florida Keys. Jessica designed a sensitive molecular detection method for a common coral pathogen that causes White Pox Disease in Elkhorn coral, which was also applied to detect introduction of the bacterium through coastal sewage pollution. Applying this method revealed greater intricacies to the disease, such as the potential for additional bacteria contributing to the disease process. Through integrating public health and coral reef health, Jessica navigated the process of communicating science to diverse audiences. Recognizing the importance of undergraduate education in furthering the field of oceans and human health as well as environmental stewardship, she moved from the South to New York City for her a City University of New York Postdoctoral Fellow at Brooklyn College. Currently she manages the Authentic Research Experience in Microbiology, facilitating undergraduates to broaden their perspective of their urban environment to include the microbiota. Just as molecular techniques were essential to uncovering more about coral disease, these techniques are serving as a way to engage students in innovative research. Jessica’s goal is to continue researching and teaching in the field of environmental microbiology.