GeoChip 4.0 as a high-density comprehensive functional gene array for profiling microbial communities

Background/Question/Methods

Microorganisms constitute the most abundant life forms on Earth’s biosphere and in human body environments, and play integral roles in their ecosystems, but it remains challenging to understand the functional diversity, structure and metabolic potential of microbial communities at a community level. We have developed a comprehensive functional gene array, GeoChip 4.0 to profile microbial communities. GeoChip 4.0 contains 120,054 distinct probes covering 200,393 gene variants involved in a variety of functional processes, such as biogeochemical cycling of carbon, nitrogen, sulfur, phosphorous and various metals, stress responses, and human health. Among them, a subset of 36,062 probes are specifically designed for the human microbiome, called HuMiChip, which covers 47,979 gene variants with 139 functional gene families involved in 19 functional processes.  Also, a subset of 22,855 probes were designed to target 79,628 sequences for 46 genes involved in microbial responses to changes of temperature, osmolarity, oxidative status, nutrient limitation and general stress responses, which is termed as StressChip. In addition, GeoChip 4.0 contains probes for bacterial phages and virulence. As a new version, GeoChip 4.0 is constructed by NimbleGen with a format of 12x135K, and evaluated both computationally and experimentally.

Results/Conclusions

The developed GeoChip 4.0 has been applied to analyze environmental samples from oil spill sites, groundwater, and human gut. First, to examine the impact of oil spill in the Gulf of Mexico on marine ecosystems, GeoChip 4.0 analyses showed that the microbial community functional diversity and structure were dramatically altered, and a variety of metabolic genes involved in both aerobic and anaerobic hydrocarbon degradation were highly enriched in the oil plume, indicating the potential of intrinsic bioremediation in the deep sea. Second, GeoChip 4.0 was used to profile polylactate-stimulated Cr (VI)-reducing microbial communities in a DOE contaminated site at Hanford, indicating that the diversity and structure of microbial communities shifted at different time points after polylactate injection. Cytochrome and Cr reductase genes were enriched after polylactate injection. Third, GeoChip 4.0 was used to analyze gut flora in patients with alcoholic and HBV-related liver cirrhosis compared to the control group, indicating that liver cirrhosis exerted enormous influences on metabolic potential of the gut microbiome, and that the weakening of the metabolic potential in gut microbiota of cirrhotic patients may contribute to malnutrition in end-stage liver disease. All results demonstrated that GeoChip is a rapid and powerful tool for profiling microbial communities.