Abstract: There is described a method for selecting microbial isolates for use in oral killed vaccines against abnormal microbial colonization of mucosal surfaces by the microbes. The method comprises evaluating capacity of a plurality of different isolates of a microbe to activate antigen responsive cells to provide activation data for each microbial isolate, and the effectiveness of the isolates in reducing infection of a mucosal surface by the microbe to provide clearance data for each microbial isolate. An isolate, the activation data and clearance data for which correlate and is optimal for generating mucosal immunity against the microbe compared to the, or each, other of the isolates, or an isolate the activation data for which is optimal and a further isolate the clearance data for which is optimal, compared to the, or each, other of the isolates, respectively, is then selected for use in the vaccine.