Additive Main Effects and Multiplicative Interaction Model (AMMI) analysis of bacterial T-RFLP data

sets. Using the software T-Rex (T-RFLP analysis Expedited) [15], T-RFLP profiles were first analyzed individually and then grouped according to antibiotic exposure, vaccine season and vaccine status in the software R. The quadrates illustrate the centroids of the individual data points and represent the following: A) prevaccine era, not vaccinated, no antibiotic exposure. B) vaccine era, not vaccinated, no antibiotic exposure. C) vaccine era, vaccinated, no antibiotic exposure. A_ab) prevaccine era, not vaccinated, antibiotic exposure. B_ab) vaccine era, not vaccinated, antibiotic exposure. C_ab) vaccine era, vaccinated, antibiotic exposure. According to AMMI, antibiotic exposure (grey versus black) and vaccine season (A and A_ab versus others) significantly influences the microbiota (see text and Table 3).