A New Generation of Functional Gene Array GeoChip 5.0

Shi, Z.; H. Yin, J.D. Van Nostrand, J.W. Voordeckers, Q. Tu, Y. Deng, M. Yuan, A. Zhou, P. Zhang, N. Xiao, D. Ning, Z. He, L. Wu and J. Zhou (2019) Functional Gene Array-Based Ultrasensitive and Quantitative Detection of Microbial Populations in Complex Communities. International Society for Microbial Ecology Journal. [doi]:10.1128/mSystems.00296-19 {PMID}:31213523PMCID:PMC6581690 OSTI:1580884

Associating variations in microbial functional gene structure with environmental variables. (a) CCA based on selected environmental variables. A total of 7 environmental factors (U, pH, redox, Se, O2, DIC, and DOC) were selected from 41 measured variables. The top two axes (CCA1 and CCA2) were included and accounted for 50.7% and 13.8% microbial functional gene structure variation, respectively. (b) Partial CCA-based VPA assigning variance to U, pH, and DOC.

The rapid development of metagenomic technologies, including microarrays, over the past decade has greatly expanded our understanding of complex microbial systems. However, because of the ever-expanding number of novel microbial sequences discovered each year, developing a microarray that is representative of real microbial communities, is specific and sensitive, and provides quantitative information remains a challenge. The newly developed GeoChip 5.0 is the most comprehensive microarray available to date for examining the functional capabilities of microbial communities important to biogeochemistry, ecology, environmental sciences, and human health. The GeoChip 5 is highly specific, sensitive, and quantitative based on both computational and experimental assays. Use of the array on a contaminated groundwater sample provided novel insights on the impacts of environmental contaminants on groundwater microbial communities.