Use and Applications of JMP® in Microbial Ecology

Microbial ecology is the ecology of microorganisms; that is, the study of the relationship among microorganisms and between microorganisms and their environment. Millions of dollars and countless hours are currently spent by enthusiast scientists, microbiologists and bioinformaticians from all over the world to elucidate the characteristics and biological mechanisms behind the ecology of microorganisms. Microorganisms are omnipresent in the biosphere. They can be found in virtually every environment, from bright-colored hot springs to the skin and guts of animals. However, perhaps because of their close relationship with our bodies, the microorganisms inhabiting the intestinal tract have received much more scrutiny than any other group of microorganisms on Earth. More importantly, gastrointestinal microorganisms have been widely studied because they strongly modulate health and disease in humans and other animals. JMP® (SAS Institute) is a powerful software that offers a variety of tools and applications that have been used in many fields of study. Surprisingly, JMP® has only been scarcely used in the field of Microbial Ecology. In this paper, I will discuss the use and applications offered by JMP® 9.0.0 in the study of microbial ecology with a strong emphasis on gut microbial ecology. Topics will include basic statistics, graphical tools, and multivariate methods such as clustering and principal components. Real data sets obtained from animal studies will be utilized to demonstrate the usefulness of the software. Additionally, examples will be given from other fields of study for people outside the field of Microbial Ecology.