Abstract: A method and system for annotation and classification of biomedical text having bacterial associations have been provided. The method is microbiome specific method for extraction of information from biomedical text which provides an improvement in accuracy of the reported bacterial associations. The present disclosure uses a unique set of domain features to accurately identify bacterial associations from the biomedical text. The disclosure further provides a method to use the set of domain features to improve a microbiome crowd sourcing setup and create a refined microbial association network. The refined bacterial association network can also be made corresponding to a disease or healthy state, which can be used for an improved understanding of the bacterial community structure and design therapeutic interventions. This refined bacterial association networks for a disease can then be used for clinical, therapeutic and diagnostic applications for treatment of the disease.