Microbiome-relevant courses offered at Purdue

Agricultural & Biological Engineering (ABE) 440 – Cell and Molecular Design Principles: This course examines the design principles underlying the organizations and dynamics of biological networks with an emphasis on genetic/molecular circuits. Topics include the structure and tuning of network motifs and relationship to performance parameters such as robustness to internal noise, temporal response, noise filtering, bi-stability, pattern generation and temporal programs. Examples are presented from the study of natural systems and the design of new synthetic systems. Prerequisite: MA 265 & MA 266 or MA 262 & MA 303; AND BIOL 230 or BIOL 231 or BCHM 307 or BIOL 221. Typically offered: Spring. Credits: 3.00

Agricultural & Biological Engineering (ABE) 547 – Models and Microbiomes: Learn how computational, physical, and biological models apply to a microbiome of your interest. Successful completion of the course will enable you to review primary papers and books for state-of-the-art developments in the field, and analyze the relationships between multiple modeling approaches for the microbiome. Prerequisite: None. Typically offered: Fall. Credits: 3.00.

Agronomy (AGRY) 649 – Molecular Microbial Ecology: This course will focus on the theoretical basis, application and data interpretation of the most commonly used molecular genetic techniques (e.g., PCR, hybridization, nucleic acid sequencing/analysis, genetic fingerprinting, etc.) for studying microorganisms from and in the environment. The major ecological scales of microbes to be discussed are the application of molecular genetic techniques to study and understand:  1.  Individual microbes, 2.  Microbial populations, and 3.  Microbial communities (microbiomes). Prerequisite: AGRY 32000 or AGRY 58000 or BCHM 56200 or BIOL 24100 or BIOL 43800 or BIOL 54900. Prerequisite: None. Typically offered: Fall. Credits: 3.00

Animal Sciences (ANSC) 595 – Molecular Microbiome Analysis: The overall goal of the course is to provide students with an advanced understanding of microbial ecology in the animal microbiome and how to analyze next-generation sequencing data of amplicon libraries. Upon completion of this course students should be able to 1) understand and critically review peer-reviewed publications in microbiome studies, 2) design a microbiome experiment, with considerations for microbiome controls and reproducibility, 3) analyze next-gen sequencing data from gene amplicon libraries, 4) use R to manage datasets, preform analyses, and produce descriptive graphics, and 5) develop basic computational literacy in bash and R scripting, and cluster computing. Prerequisite: None. Typically offered: Spring. Credits: 3.00.

Animal Sciences (ANSC)/Food Science (FS) 660 – Intestinal Microbiology and Immunology: Discussion and critique of recent journal articles related to intestinal microbiology/immunology. The specific areas covered under this forum are: (i) Intestinal microbiology and microbiome, (ii) Food microbiology as it related to gastrointestinal diseases and persistence, (iii) Probiotics and prebiotics – related to intestinal health or pathogen control, and (iv) Mucosal immunity with major emphasis on intestinal immunology and gut health. Prerequisite: None. Typically offered: Fall. Credits: 1.00

Food Science (FS) 491 – Anaerobic Microbiology: Anaerobic microorganisms perform essential roles in Earth’s chemistry and biology, being central to global element cycling. Furthermore, these microbes are involved in diverse biotransformations of relevance to humans in industrial and agricultural settings, such as in the gut/rumen microbiome, food fermentations, soil fertilization, biofuels production, and wastewater treatment. In this course, we will investigate the unique physiological attributes of anaerobic microbes with diverse metabolisms and their roles in processes of importance to ecology and society. We will use project-based approaches to connect the fundamental physiology of anaerobes with natural and engineered processes, with the goal of designing and managing processes for increased efficiency, productivity, stability, and societal benefit. Prerequisite: None. Typically offered: Fall. Credits: 3.00

Food Science (FS) 591 – Microbial Genomics and Metabolism: The rapid advent of increasingly inexpensive and high-throughput DNA sequencing techniques has ushered in an era in which complete genome sequences for large numbers of microbes are known. This development, used as a reference for global methods to measure gene expression and metabolic function in biological systems like transcriptomics, proteomics, and metabolomics, has revolutionized the study of microbial physiology and ecology. Yet having genome sequence alone has not unlocked all the secrets of microbial physiology, as much genomic “dark matter” exists in which the function of many genes can only be poorly predicted – if at all. In this course we will cover the basic principles of genome organization and evolution in microbes, how (meta)genome sequences are generated and annotated, how gene functions are predicted, and how microbial behavior is studied “in the wild” using systems biology techniques. We will discuss how these genome-enabled techniques inform our understanding of microbe-microbe and microbe-host interactions. This microbiology course will appeal to those interested in genome-function relationships in individual microbial species, in interactions with hosts, as well as community microbial behavior in microbiomes. Prerequisite: None. Typically offered: Spring, odd years. Credits: 3.00