The article discusses the challenges and tools used in microbial community profiling for human microbiome projects. It highlights the importance of understanding the human microbiome, which consists of trillions of microbial cells that outnumber human cells and play a crucial role in metabolic functions. The review covers various approaches to community profiling, including small-subunit rRNA studies and metagenomic studies, and addresses key questions such as whether there is a core microbiome shared by all individuals. It also discusses the challenges of analyzing microbial communities, including the variability between individuals and the difficulty of detecting rare species. The article emphasizes the importance of using high-throughput sequencing and computational methods to analyze microbial communities and provides guidance on choosing the appropriate sequencing technology, read length, and data analysis methods. It also discusses the importance of standardizing methods for comparing microbial communities and the challenges of taxonomic classification. The review concludes with the importance of integrating data from different studies to better understand the human microbiome and its role in health and disease.The article discusses the challenges and tools used in microbial community profiling for human microbiome projects. It highlights the importance of understanding the human microbiome, which consists of trillions of microbial cells that outnumber human cells and play a crucial role in metabolic functions. The review covers various approaches to community profiling, including small-subunit rRNA studies and metagenomic studies, and addresses key questions such as whether there is a core microbiome shared by all individuals. It also discusses the challenges of analyzing microbial communities, including the variability between individuals and the difficulty of detecting rare species. The article emphasizes the importance of using high-throughput sequencing and computational methods to analyze microbial communities and provides guidance on choosing the appropriate sequencing technology, read length, and data analysis methods. It also discusses the importance of standardizing methods for comparing microbial communities and the challenges of taxonomic classification. The review concludes with the importance of integrating data from different studies to better understand the human microbiome and its role in health and disease.