Development and applications of functional gene microarrays in the analysis of the functional diversity, composition, and structure of microbial communities
Development and applications of functional gene microarrays in the analysis of the functional diversity, composition, and structure of microbial communities
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DOI：
10.1007/s11783-011-0301-y
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发表时间：
2011-03-01
影响因子：
--
通讯作者：
Zhou, Jizhong
中科院分区：
文献类型：
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作者：
He, Zhili;Van Nostrand, Joy D.;Zhou, Jizhong
功能基因芯片（FGAs）是一种特殊类型的微阵列，含有与微生物功能过程相关的关键基因的探针，如碳、氮、硫、磷和金属的生物地球化学循环，环境污染物的生物降解，能量处理和应激反应。GeoChips被认为是最全面的FGA。实验建立的探针设计标准和计算流水线集成序列检索，探针设计和验证，阵列构建，数据分析和自动更新被用来开发GeoChip技术。GeoChip已被系统地评估，并被证明是一个强大的工具，用于快速，特异性，灵敏度和定量分析的微生物群落在一个高通量的方式。几代GeoChip已被开发并应用于研究来自不同栖息地的各种微生物群落的功能多样性，组成，结构，功能和动态，如水，土壤，海洋，生物反应器，人类微生物组和极端生态系统。GeoChip能够解决与全球变化，生物能源，生物修复，农业经营，土地利用，人类健康，环境恢复和生态理论相关的基本问题，并将微生物群落结构与环境因素和生态系统功能联系起来。
Functional gene arrays (FGAs) are a special type of microarrays containing probes for key genes involved in microbial functional processes, such as biogeochemical cycling of carbon, nitrogen, sulfur, phosphorus, and metals, biodegradation of environmental contaminants, energy processing, and stress responses. GeoChips are considered as the most comprehensive FGAs. Experimentally established probe design criteria and a computational pipeline integrating sequence retrieval, probe design and verification, array construction, data analysis, and automatic update are used to develop the GeoChip technology. GeoChip has been systematically evaluated and demonstrated to be a powerful tool for rapid, specific, sensitive, and quantitative analysis of microbial communities in a high-throughput manner. Several generations of GeoChip have been developed and applied to investigate the functional diversity, composition, structure, function, and dynamics of a variety of microbial communities from different habitats, such as water, soil, marine, bioreactor, human microbiome, and extreme ecosystems. GeoChip is able to address fundamental questions related to global change, bioenergy, bioremediation, agricultural operation, land use, human health, environmental restoration, and ecological theories and to link the microbial community structure to environmental factors and ecosystem functioning.