High-throughput metagenomic technologies for complex microbial community analysis: open and closed formats. Academic Article uri icon


  • Understanding the structure, functions, activities and dynamics of microbial communities in natural environments is one of the grand challenges of 21st century science. To address this challenge, over the past decade, numerous technologies have been developed for interrogating microbial communities, of which some are amenable to exploratory work (e.g., high-throughput sequencing and phenotypic screening) and others depend on reference genes or genomes (e.g., phylogenetic and functional gene arrays). Here, we provide a critical review and synthesis of the most commonly applied "open-format" and "closed-format" detection technologies. We discuss their characteristics, advantages, and disadvantages within the context of environmental applications and focus on analysis of complex microbial systems, such as those in soils, in which diversity is high and reference genomes are few. In addition, we discuss crucial issues and considerations associated with applying complementary high-throughput molecular technologies to address important ecological questions.

published proceedings

  • mBio

altmetric score

  • 24.25

author list (cited authors)

  • Zhou, J., He, Z., Yang, Y., Deng, Y. e., Tringe, S. G., & Alvarez-Cohen, L.

citation count

  • 344

complete list of authors

  • Zhou, Jizhong||He, Zhili||Yang, Yunfeng||Deng, Ye||Tringe, Susannah G||Alvarez-Cohen, Lisa

publication date

  • January 2015

published in