In this article, the problem of state estimation of a microbial consortium is discussed. This microbial consortium is composed of two strains, called producer and cleaner, in continuous culture. The producer strain grows by consuming glucose, while the cleaner grows by consuming the acetate excreted by the producer and toxifies the environment. Considering two available measurements, the total biomass and a fluorescent reporter, an observability analysis is cast and state estimators are proposed for each state component of this system. Although the system is shown to be detectable using solely the total biomass as measurement, the advantage of measuring the fluorescent reporter on the observer design is highlighted. A numerical experiment illustrates the methodology.