Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, 101 David L. Boren Boulevard, Norman, OK 73019, USA.
ISME J. 2010 Sep;4(9):1167-79. doi: 10.1038/ismej.2010.46. Epub 2010 Apr 29.
A new generation of functional gene arrays (FGAs; GeoChip 3.0) has been developed, with approximately 28 000 probes covering approximately 57 000 gene variants from 292 functional gene families involved in carbon, nitrogen, phosphorus and sulfur cycles, energy metabolism, antibiotic resistance, metal resistance and organic contaminant degradation. GeoChip 3.0 also has several other distinct features, such as a common oligo reference standard (CORS) for data normalization and comparison, a software package for data management and future updating and the gyrB gene for phylogenetic analysis. Computational evaluation of probe specificity indicated that all designed probes would have a high specificity to their corresponding targets. Experimental analysis with synthesized oligonucleotides and genomic DNAs showed that only 0.0036-0.025% false-positive rates were observed, suggesting that the designed probes are highly specific under the experimental conditions examined. In addition, GeoChip 3.0 was applied to analyze soil microbial communities in a multifactor grassland ecosystem in Minnesota, USA, which showed that the structure, composition and potential activity of soil microbial communities significantly changed with the plant species diversity. As expected, GeoChip 3.0 is a high-throughput powerful tool for studying microbial community functional structure, and linking microbial communities to ecosystem processes and functioning.
新一代功能基因芯片（FGAs；GeoChip 3.0）已经开发出来，它包含约 28000 个探针，涵盖了参与碳、氮、磷和硫循环、能量代谢、抗生素抗性、金属抗性和有机污染物降解的 292 个功能基因家族的约 57000 个基因变体。GeoChip 3.0 还有其他几个独特的特点，例如用于数据归一化和比较的通用寡核苷酸参考标准（CORS）、用于数据管理和未来更新的软件包以及用于系统发育分析的gyrB 基因。探针特异性的计算评估表明，所有设计的探针都将对其相应的靶标具有很高的特异性。用合成寡核苷酸和基因组 DNA 进行的实验分析表明，仅观察到 0.0036-0.025%的假阳性率，这表明在所检查的实验条件下，设计的探针具有很高的特异性。此外，GeoChip 3.0 被应用于分析美国明尼苏达州多因素草地生态系统中的土壤微生物群落，结果表明，土壤微生物群落的结构、组成和潜在活性随着植物物种多样性而显著变化。正如预期的那样，GeoChip 3.0 是研究微生物群落功能结构的高通量强大工具，并将微生物群落与生态系统过程和功能联系起来。
