Accurate characterization of microbial communities is vital for understanding their role in human, plant, animal, and environmental health. Current methods, such as 16S amplicon sequencing and whole-genome shotgun sequencing (WGS), have limitations in cost-effectiveness and precision. This study introduced Abridged Shotgun Sequencing (ASSS) as a cost-efficient alternative for precise taxonomic profiling. The research aims to determine the optimal sequencing depth for reliable taxonomic profiles. The ASSS analysis pipeline outperforms existing tools in classification accuracy and computational efficiency. It successfully replicates distinctions in human microbiomes across body sites, recovers alpha diversity, and identifies microbial markers associated with medical conditions such as type 2 diabetes. Importantly, ASSS provides species-level accuracy comparable to deep WGS sequencing, yet at a fraction of the cost, making it an attractive choice for large-scale studies. Abridged Shotgun Sequencing (ASSS) offers a highly efficient and cost-effective approach for obtaining species-level taxonomic profiles in low-depth shotgun metagenomic datasets. it recommends microbiome researchers, particularly those studying human microbiomes, consider US as a viable alternative to amplicon sequencing. This innovation opens new avenues for precise and economical microbiome research, facilitating comprehensive investigations into microbial community roles in diverse ecosystems and health contexts.