PPEM 497 Studying and Shaping Microbiomes of the Environment

PPEM 497 Studying and Shaping Microbiomes of the Environment (3 credits) Fall Semester Course
Image: Terrence Bell, Penn State University

Image: Terrence Bell, Penn State University


Instructor: Terrence H. Bell, Ph.D.
Time: Tuesdays/Thursdays | 9:05-10:20 a.m. | Fall semester
Location: 216 Osmond Lab
No. of Credits: 3
Prerequisites: A solid background in ecology, microbiology, or both. If you have not taken BIOL 220W or MICRB 201, enrollment requires permission of the instructor.


The development of next-generation sequencing (NGS) technologies was initially spurred by the desire for a human genome sequence, but these tools are now essential to all areas of biology. The amount of data produced by NGS allows us to ask questions about processes that occur across genomes, communities, and even landscapes. In particular, NGS has revolutionized the study of environmental microbiology, allowing us to investigate the thousands of microbial “species” that co-occur in a given environment, even though most of these microorganisms have not been captured or observed in culture. The entire complement of microorganisms (and their genes) that occur in a particular environment is frequently referred to as the “microbiome” of that environment.

The field of microbiome research is evolving rapidly, which means that there are many opportunities to contribute to exciting new discoveries. However, this fast pace of change has made it difficult to properly prepare students for microbiome-focused graduate work. In this course, you will learn about the development of NGS techniques, as well as recent applications of NGS to natural and agricultural soil systems, including how these tools can be used to understand both targeted and unintentional human-induced changes to microbiomes. You will also develop the ability to interpret microbiome-related literature and to work with NGS data using freely available software. In your second assignment, you will explore additional software not used in class, in order to learn how to learn to use unfamiliar bioinformatics tools.

This course is intended for students with very little background in programming or bioinformatics, but with a strong understanding of microbiology, molecular biology, and/or ecology (if you have not taken BIOL 220W or MICRB 201, enrollment requires permission of the instructor).


As a student in this course you will:

  1. Become familiar with the use of computing tools designed for microbiome analysis;
  2. Learn how to approach an unfamiliar sequence analysis tool and use it;
  3. Interpret, describe, and assess results from microbiome research, and communicate your understanding to peers;
  4. Understand the major achievements of microbiome analysis in natural and engineered soil systems, as well as its potential for the future;
  5. Develop your scientific writing in order to present your own microbiome sequence data.

Disability Statement

Penn State welcomes students with disabilities into the University’s educational programs. Every Penn State campus has an office for students with disabilities. The Student Disability Resources website provides contact information for every Penn State campus. For further information, please visit the Student Disability Resources website.

In order to receive consideration for reasonable accommodations, you must contact the appropriate disability services office at the campus where you are officially enrolled, participate in an intake interview, and provide documentation. If the documentation supports your request for reasonable accommodations, your campus’s disability services office will provide you with an accommodation letter. Please share this letter with your instructors and discuss the accommodations with them as early in your courses as possible. You must follow this process for every semester that you request accommodations.

Academic Integrity

Penn State and the College of Agricultural Sciences take violations of academic integrity very seriously. Faculty, alumni, staff and fellow students expect each student to uphold the university’s standards of academic integrity both in and outside of the classroom.

Academic integrity is the pursuit of scholarly activity in an open, honest, and responsible manner. Academic integrity is a basic guiding principle for all academic activity at The Pennsylvania State University, and all members of the university community are expected to act in accordance with this principle. Consistent with this expectation, students should act with personal integrity; respect other students' dignity, rights, and property; and help create and maintain an environment in which all can succeed through the fruits of their efforts. Academic integrity includes a commitment not to engage in or tolerate acts of falsification, plagiarism, misrepresentation, or deception. Such acts of dishonesty violate the fundamental ethical principles of the university community and compromise the worth of work completed by others (see Faculty Senate Policy 49‐20 and G‐9 Procedures).

Academic Integrity Guidelines for the College of Agricultural Sciences

Contact Information

Terrence H. Bell, Ph.D.
  • Assistant Professor of Phytobiomes
Phone: 814-865-9653