The SuperChip for microbial community structure, and function from all environments.
Terry C. Hazen,Terry C. Hazen +1 more
TLDR
A cheap and portable assay would impact countless areas, including clean water technologies, emerging diseases, bioenergy, infectious disease diagnosis, climate change, food safety, environmental clean‐up and bioterrorism, but it will require a very large group of multidiscplenary scientists from multiple institutions crossing many international boundaries and funding over a 5‐year period of more than $100 million.Abstract:
Summary
We have the technology and capability to develop an all-in-one microarray that can provide complete information on a microbial community, including algae, protozoa, bacteria, archaea, fungi, viruses, antimicrobial resistance, biotoxins and functional activity. With lab-on-a-chip, nanotechnology integrating a variety of the latest methods for a large number of sample types (water, sediment, waste water, food, blood, etc.) it is possible to make a desktop instrument that would have universal applications. There are two major thrusts to this grand challenge that will allow us to take advantage of the latest biotechnological breakthroughs in real time. The first is a bioengineering thrust that will take advantage of the large multidisciplinary laboratories in developing key technologies. Miniaturization will reduce reagent costs and increase sensitivity and reaction kinetics for rapid turnaround time. New and evolving technologies will allow us to port the designs for state-of-the-art microarrays today to completely new nanotechnology inspired platforms as they mature. The second thrust is in bioinformatics to use our existing expertise to take advantage of the rapidly evolving landscape of bioinformatics data. This increasing capacity of the data set will allow us to resolve microbial species to greatly improved levels and identify functional genes beyond the hypothetical protein level. A cheap and portable assay would impact countless areas, including clean water technologies, emerging diseases, bioenergy, infectious disease diagnosis, climate change, food safety, environmental clean-up and bioterrorism. In my opinion it is possible but it will require a very large group of multidiscplenary scientists from multiple institutions crossing many international boundaries and funding over a 5-year period of more than $100 million. Given the impact that this SuperChip could have it is well worth the price!!!read more
Citations
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Journal ArticleDOI
Applications of functional gene microarrays for profiling microbial communities.
TL;DR: This review focuses on applications of FGA technology for profiling microbial communities, including target preparation, hybridization and data processing, and data analysis.
Journal ArticleDOI
Variation in microbial community from predominantly mesophilic to thermotolerant and moderately thermophilic species in an industrial copper heap bioleaching operation
Mauricio Acosta,Pedro A. Galleguillos,Yousef Ghorbani,Pierina Tapia,Yasna Contador,Antonio Velásquez,Cristian Espoz,Carlos Pinilla,Cecilia Demergasso +8 more
TL;DR: In this paper, a comprehensive monitoring program has been performed at an industrial bio-leaching heap at the Escondida mine in Chile since 2006, in order to study possible changes to the indigenous microbial population.
Journal ArticleDOI
Characteristic of filamentous fungal diversity and dynamics associated with wheat Qu and the traditional fermentation of Chinese rice wine
TL;DR: This research presents a novel and scalable method forFermentation Technology of Rice Wine that can be applied to Food Safety and Nutrition and has shown promising results in terms of quality and efficiency.
Book ChapterDOI
Chapter 1 - Applications of Functional Gene Microarrays for Profiling Microbial Communities
Joy D. Van Nostrand,Jizhong Zhou +1 more
TL;DR: This chapter focuses on functional gene arrays, which probe for structural genes involved in particular functions of interest, which are used to examine samples from numerous environments including the deep sea, Antarctic locations, metals-contaminated sites, climate change experimental sites, human environments, and other clinical applications.
References
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Journal ArticleDOI
Deep-sea oil plume enriches indigenous oil-degrading bacteria.
Terry C. Hazen,Eric A. Dubinsky,Todd Z. DeSantis,Gary L. Andersen,Yvette M. Piceno,Navjeet Singh,Janet K. Jansson,Alexander J. Probst,Sharon Borglin,Julian L. Fortney,William T. Stringfellow,William T. Stringfellow,Markus Bill,Mark E. Conrad,Lauren M. Tom,Krystle L. Chavarria,Thana R. Alusi,Regina Lamendella,Dominique C. Joyner,Chelsea Spier,Jacob Bælum,Manfred Auer,Marcin Zemla,Romy Chakraborty,Eric Sonnenthal,Patrik D'haeseleer,Hoi-Ying N. Holman,Shariff Osman,Zhenmei Lu,Joy D. Van Nostrand,Ye Deng,Jizhong Zhou,Jizhong Zhou,Olivia U. Mason +33 more
TL;DR: It is reported that the dispersed hydrocarbon plume stimulated deep-sea indigenous γ-Proteobacteria that are closely related to known petroleum degraders, and the potential exists for intrinsic bioremediation of the oil plume in the deep-water column without substantial oxygen drawdown.
Journal ArticleDOI
Urban aerosols harbor diverse and dynamic bacterial populations
Eoin L. Brodie,Todd Z. DeSantis,Jordan Moberg Parker,Ingrid X. Zubietta,Yvette M. Piceno,Gary L. Andersen +5 more
TL;DR: Using multivariate regression techniques, it is demonstrated that temporal and meteorological influences can be stronger factors than location in shaping the biological composition of the air the authors breathe.
Journal ArticleDOI
Microbial gene functions enriched in the Deepwater Horizon deep-sea oil plume
Zhenmei Lu,Zhenmei Lu,Ye Deng,Joy D. Van Nostrand,Zhili He,James W. Voordeckers,Aifen Zhou,Yong-Jin Lee,Olivia U. Mason,Eric A. Dubinsky,Krystle L. Chavarria,Lauren M. Tom,Julian L. Fortney,Regina Lamendella,Janet K. Jansson,Patrik D'haeseleer,Terry C. Hazen,Jizhong Zhou,Jizhong Zhou,Jizhong Zhou +19 more
TL;DR: It is shown that the microbial community functional composition and structure were dramatically altered in a deep-sea oil plume resulting from the spill, indicating a great potential for intrinsic bioremediation or natural attenuation in the deep sea.
Journal ArticleDOI
Advances in monitoring environmental microbes.
TL;DR: This review focuses on the biases associated with sample collection, nucleic acid extraction, processing, sequencing analyses, and Chip technologies used in microbial ecology studies.
Journal ArticleDOI
PCR Amplification-Independent Methods for Detection of Microbial Communities by the High-Density Microarray PhyloChip
Kristen M. DeAngelis,Kristen M. DeAngelis,Cindy H. Wu,Harry R. Beller,Harry R. Beller,Eoin L. Brodie,Romy Chakraborty,Todd Z. DeSantis,Julian L. Fortney,Terry C. Hazen,Terry C. Hazen,Shariff Osman,Mary E. Singer,Lauren M. Tom,Gary L. Andersen +14 more
TL;DR: Direct hybridization of dscDNA and RNA is a viable alternative to PCR-amplified microbial community analysis, providing identification of the active populations within microbial communities that attenuate pollutants, drive global biogeochemical cycles, or proliferate disease states.