The invention relates to the field of machine learning and comprises supervised learning. In particular, the invention relates to a computer-implemented method for generating a classifier for at least one target microbe by employing supervised machine learning, e.g., an artificial neural network, a classifier that is obtainable by said method, and applications of the inventive classifier. Thus, the invention further relates to a method for quantifying the abundance of at least one target microbe in a sample, and a method for analyzing the microbial composition in a sample. Further provided herein are diagnostic uses of the classifier, i.e. a method for diagnosing a microbial disease in a subject. In addition, the invention relates to a set of standards comprised in the classifier, a computer-readable storage medium, and/or a kit.