Example of a terminal restriction fragment length polymorphism (TRFLP) electropherogram obtained from the V6-V8 16S rRNA gene PCR digested with Msp1. The DNA was obtained from five intestinal compartments of one horse. The length of the terminal restriction fragment is plotted on the x-axis in base pairs. The intensity of the fluorescent signal of the terminal restriction fragment is plotted on the y-axis. Each peak represents a bacterial cluster present in the respective intestinal compartment. The electropherogram was accompanied by a numerical report (length of the terminal restriction fragment, height and area of the peak) from which actual numbers were drawn for analysis. Qualitative analysis for absence or presence of peaks was performed in this study to compare the richness of the equine microbiota of different gastrointestinal compartments between and within animals. The similarity coefficient (Cs) was used for comparison and was calculated as: Cs = (2j/[a + b]), where ‘a’ is the number of T-RF peaks unique for sample 1, ‘b’ is the number of T-RF peaks unique for sample 2, and ‘j’ is the number of common T-RF peaks. The scale for the y-axis depends on the maximum intensity of the fluorescent signals (height of the peak) in each sample, therefore the height of the peaks should not be compared visually. The height or area of a peak corresponds to the relative abundance of the bacterial cluster it represents and can be used for quantitative analysis.