Strain/Species-Specific Probe Design for Microbial Identification Microarrays |
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| Authors: | Qichao Tu Zhili He Ye Deng Jizhong Zhou |
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| Institution: | Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USAa;Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, California, USAb;State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, Chinac |
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| Abstract: | Specific identification of microorganisms in the environment is important but challenging, especially at the species/strain level. Here, we have developed a novel k-mer-based approach to select strain/species-specific probes for microbial identification with diagnostic microarrays. Application of this approach to human microbiome genomes showed that multiple (≥10 probes per strain) strain-specific 50-mer oligonucleotide probes could be designed for 2,012 of 3,421 bacterial strains of the human microbiome, and species-specific probes could be designed for most of the other strains. The method can also be used to select strain/species-specific probes for sequenced genomes in any environments, such as soil and water. |
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