PPEM 497: Special Topics (Fall 2017, Section Studying and Shaping Microbiomes of the Environment)

Formal courses given infrequently to explore, in depth, a comparatively narrow subject which may be topical or of special interest.


  • Plant Pathology and Environmental Microbiology


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 PPEM 497 Special Topics: Studying and Shaping Microbiomes of the Environment, 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. Finally, we will execute microbiome-based research projects for faculty who lack expertise in this area, and you will have the opportunity to participate in the presentation and/or publication of generated data when appropriate.

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.

Course Logistics

Instructor: Dr. Terrence Bell, Assistant Professor, Department of Plant Pathology and Environmental Microbiology
Office: 317 Buckhout Laboratory
Phone: 814-865-9653
Office hours: Please make an appointment to discuss course material outside of class hours, or feel free to e-mail me for clarification at any time.

Class Meeting Times: Tues/Thurs | 9:05-10:20 a.m.
Class Location: 216 Osmond Lab
Prerequisites: You should have a solid background in ecology, microbiology, or both. If you have not taken BIOL 220W or MICRB 201, enrollment requires permission of the instructor.

Course Objectives

At the conclusion of this course, students will be able to:

  • Interpret microbiome terminology and figures;
  • Understand and present a summary of a microbiome-based journal article;
  • Analyze microbiome-based high-throughput sequencing data using freely available software;
  • Apply microbiome analysis tools to unknown data;
  • Use unfamiliar microbiome analysis tools that provide sufficient online support;
  • Select appropriate analysis methods for microbiome-based sequencing data;
  • Create a meaningful and testable hypothesis for a microbiome analysis study;
  • Express their interpretation of microbiome data in oral, written, and graphical contexts.

Faculty-Serving Research Projects

Some course assignments will be focused around actual faculty research, and students will be eligible as authors of publishable work, pending faculty approval. This project has been funded by the Schreyer Institute.

Environment Health and Safety (EHS) Course

Students should either provide evidence of the EHS Lab Safety Training (Initial or Refresher), or complete the training by September 15. This will allow students to participate in wet-lab work to prepare samples for sequencing for in-class projects.

Required Course Materials

No materials are strictly required for the course, but students will benefit from access to Mac computers outside of class hours. You may use Windows if you prefer (XP or later), but keep in mind that certain components of the pipelines used in class will deviate from general lab/assignment instructions, and may require slightly more troubleshooting on your part. I will distribute appropriate reading materials ahead of class sections, and students seeking additional background information can see me for recommendations. Some sources that may be useful include:

  1. For developing an aptitude using R to perform ecological analyses, I strongly recommend the following book: Numerical Ecology with R by Daniel Borcard, François Gillet, Pierre Legendre. The book provides detailed descriptions of the approaches that we will use; however, all scripts and required data are freely available online.
  2. For a general background on lecture topics, I would recommend the following textbook (certainly not required), since it does a nice job of integrating recent advances in environmental microbiology: Environmental Microbiology: From Genomes to Biogeochemistry (2nd ed.) by Eugene Madsen. In particular, I would recommend these sections:
    • 1.1-1.3
    • 3.1, 3.3, 3.4, 3.6, 3.7
    • 6.1, 6.3, 6.4, 6.5, 6.7
    • 8.1, 8.2, 8.6

Course Grading

Grades will be determined as follows:

Lab worksheets 15
Participation (project design and wet lab work) 10
Midterm 15
Final quiz (December 7-no final exam) 10
Assignment 1 10
Assignment 2 15
Assignment 3 25

Course Lab Worksheets

These will be available prior to each relevant lab section. Not all lab sections will have a worksheet component (first is August 31). These can mostly be completed in class, but should be submitted by the Sunday after the relevant lab section (midnight) at the latest.

Course Participation

This will be based on attendance, contributions to class discussions, and participation in the preparation of sequencing data.

Course Midterm and Quiz

The midterm will cover material (including assigned readings) from lectures 1-9, and a final quiz will cover material (and readings) from lectures 10-13.

Course Assignments

Short assignment descriptions are provided below. More details will be made available through the term.

  1. Journal Article Communication. Students will read and interpret an article that uses NGS methods to explore either natural or agricultural soil microbiomes, and will teach aspects of what they have learned in a speed presentation format.
  2. Learning New Software. Students will explore data analysis software that has not been learned in class, apply it to our research projects, and answer a number of short questions related to the work. Some suggestions of software will be provided, but students keen to use other software can do so pending my approval.
  3. Write a Short Article Centered on Research Project. Students will produce a short scientific article with sequence data generated through our in-class research projects. This will be done in the style of Short Communications submitted to The ISME Journal:
    • Abstract: 150 words maximum;
    • Article: 1000 words maximum, excluding, references, figures and tables;
    • Tables and Figures: 2 maximum (can use multiple panels);
    • References: 20 maximum. For an example, see: Taylor JD et al. 2014. Seasonal microbial community dynamics correlate with phytoplankton-derived polysaccharides in surface coastal waters. The ISME Journal 8: 245-248.

Course Computer Support

Support is available through Student Technology Services for difficulties with software installation or other computer issues.

Course Calendar

Tues Aug 22 Lecture 1: Course introduction
Thur Aug 24 Faculty members present research projects
Lab 1: Primer on the Command Terminal and Exploring New Software
Tues Aug 29 Lecture 2: Sequencing technologies and microbiome data
Thur Aug 31 Lab 2: Mothur basics and 16S rRNA processing tutorial
Sun Sept 3 Worksheet 1 due (from Thursday class)
Tues Sept 5 Brainstorm ideas in class for experimental design
Lecture 3: Asking good questions with microbiome data
Thur Sept 7 Lab 3: Problem solving with the Mothur Wiki
Sun Sept 10 Worksheet 2 due (from Thursday class)
Tues Sept 12 Complete 1/2 page project proposal for faculty member
Lecture 4: Early microbiome studies in terrestrial environments
Thur Sept 14 Sign up for wet lab processing of sequencing data
Lab 4: Comparing 'species' assignments across analysis platforms
Fri Sept 15 Deadline for EHS training
Sun Sept 17 Worksheet 3 due (from Thursday class)
Tues Sept 19 Lecture 5: Interpreting microbiome figures and analyses
Present project proposal to faculty member (10 min + 5 min questions)
Thur Sept 21 Lab 5: Journal article presentations
Tues Sept 26 Feedback from myself and faculty member on design
Lecture 6: Journal article presentations (continued)
Thur Sept 28 NO CLASS
Tues Oct 3 Lecture 7: Relating sequencing data to function
Thur Oct 5 Lab 7: R basics and introductory tutorial
Tues Oct 10 Return final project design to faculty member and instructor
Lecture 8: Ecological principles and their relevance to microbiome research
Thur Oct 12 Lab 8: Applying R package 'vegan' to microbiomes
Sun Oct 15 Worksheet 4 due (from Thursday class)
Tues Oct 17 Lecture 9: Managed microbiomes
Thur Oct 19 Lab 9: Exploring new R packages
Sun Oct 22 Worksheet 5 due (from Thursday class)
Tues Oct 24 Lecture 10: Trials and possibilities in microbiome manipulation
Thur Oct 26 Lab 10: Initial processing of project data
Tues Oct 31 Midterm (Lectures 1-10)
Thur Nov 2 Lab 11: Capabilities of IMG and/or project data work
Tues Nov 7 Lecture 11: Writing a scientific article from microbiome data: the process
Thur Nov 9 Lab 12: Metagenome/metatranscriptome analysis in IMG/MER
Sun Nov 12 Worksheet 6 due (from Thursday class)
Tues Nov 14 Lecture 12: The phytobiome: are microbes essential or not?
Thur Nov 16 Lab 13: Investigating metagenomes in MG-RAST
Sun Nov 19 Worksheet 7 due (from Thursday class)
Tues Nov 21 NO CLASS - Thanksgiving
Thur Nov 23 NO CLASS - Thanksgiving
Tues Nov 28 Lecture 13: Large-scale microbiome projects: findings and limitations
Thur Nov 30 Lab 14: TBD
Tues Dec 5 Peer review session for assignment 3
Thur Dec 7 Final Quiz (Lecture 10-13 material)

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