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Title: The PathoChip, a functional gene array for assessing pathogenic properties of diverse microbial communities

item LEE, YONG-JIN - University Of Oklahoma
item VAN NOSTRAND, JOY - University Of Oklahoma
item TU, QICHAO - University Of Oklahoma
item LU, ZHENMEI - University Of Oklahoma
item CHENG, LEI - University Of Oklahoma
item YUAN, TONG - University Of Oklahoma
item DENG, YE - University Of Oklahoma
item Carter, Michelle
item HE, ZHILI - University Of Oklahoma
item WU, LIYOU - University Of Oklahoma
item ZHOU, JIZHONG - University Of Oklahoma

Submitted to: The ISME Journal: Multidisciplinary Journal of Microbial Ecology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/20/2013
Publication Date: 6/13/2013
Citation: Lee, Y., Van Nostrand, J.D., Tu, Q., Lu, Z., Cheng, L., Yuan, T., Deng, Y., Carter, M.Q., He, Z., Wu, L., Zhou, J. 2013. The PathoChip, a functional gene array for assessing pathogenic properties of diverse microbial communities. The ISME Journal: Multidisciplinary Journal of Microbial Ecology. doi: 10.1038/ismej.2013.88.

Interpretive Summary: Bacterial pathogens are widespread in natural environments. We have constructed a microarray that contains almost 4,000 gene probes targeting known bacterial virulence factors including toxins and proteins known to enhance pathogens survival in host and natural environments. We evaluated the specificity of the DNA probes and demonstrated that about 98% of probes are specific at least at the species level. We then applied this Microarray, designated as the Virulence Chip, to investigate the virulence potential of three distinct microbial communities. We detected an array of virulence genes in all three samples examined, including natural soil, sea water, and human saliva. We found that, 1) for soil samples, both virulence gene diversity and abundance increased in response to elevated temperature; 2) for deep sea water, virulence gene diversity was significantly altered by the oil contamination; and 3) for saliva samples, the evenness of virulence genes was significantly (P = 0.017) different between caries-active group and caries-free group, but there was no significant difference in the richness or the diversity between the two groups. This study demonstrated that the Virulence Chip is a useful tool to identify virulence genes in microbial populations, to determine the pathogenic potential of a natural microbial community, and to examine the dynamics of virulence gene in response to perturbations.

Technical Abstract: Pathogens present in the environment pose a serious threat to human, plant and animal health as evidenced by recent outbreaks. Since many pathogens can survive and proliferate in the environment, it is important to understand the population dynamics of pathogens and their pathogenic potential in the environment. To assess pathogenic potential in diverse habitats, we developed a functional gene array (the Virulence Chip) constructed with key virulence genes related to major virulence factors such as adherence, colonization, motility, invasion, toxin, immune evasion, and iron uptake. A total of 3,715 best probes were designed from 13 virulence factors, covering 7,417 coding sequences from 778 microbial species (1,351 strains). The specificity of the developed gene array was computationally verified, and approximately 98% of the probes adopted in the Virulence Chip provided specificity at or below the species level, proving its excellent capability for the detection of target sequences with high discrimination power. We then applied this array to environmental and clinical samples from soil, oil plume, and saliva to assess the occurrence of virulence genes in natural environments. Virulence genes were detected in all samples, but more abundant and diverse in stressed conditions compared to their corresponding controls. Statistical analyses showed that microbial communities were responsive to different environmental perturbations, which drove change in abundance and distribution of virulence genes. The Virulence Chip provides a useful tool to identify virulence genes in microbial populations, examines virulence gene dynamics in response to environmental perturbations, and determines pathogenic potential of microbial communities in the environment.