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Reprogramming Microbial Metabolic Pathways pp 73–94Cite as

Monitoring Microbial Diversity of Bioreactors Using Metagenomic Approaches

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Part of the book series: Subcellular Biochemistry ((SCBI,volume 64))

Abstract

With the rapid development of molecular techniques, particularly ‘omics’ technologies, the field of microbial ecology is growing rapidly. The applications of next generation sequencing have allowed researchers to produce massive amounts of genetic data on individual microbes, providing information about microbial communities and their interactions through in situ and in vitro measurements. The ability to identify novel microbes, functions, and enzymes, along with developing an understanding of microbial interactions and functions, is necessary for efficient production of useful and high value products in bioreactors. The ability to optimize bioreactors fully and understand microbial interactions and functions within these systems will establish highly efficient industrial processes for the production of bioproducts. This chapter will provide an overview of bioreactors and metagenomic technologies to help the reader understand microbial communities, interactions, and functions in bioreactors.

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Abbreviations

BLAST:

basic local alignment search tool

COG:

clusters of orthologous groups

IMG:

integrated microbial genomes

JGI:

joint genome institute

mcrA :

methyl coenzyme-M reductase

NCBI:

national center for biotechnology information

RDP10:

ribosomal database project

SAMS:

sequence analysis and management system

Y:

yield

Y p/N:

mass of bioproduct per mass of nitrogen utilized

Y p/O2 :

mass of bioproduct per mass of oxygen utilized

Y p/s:

mass of bioproduct produced per mass of carbon substrate utilized

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Acknowledgements

We thank the Utah State University Bioenergy program, the Utah Science Technology and Research (USTAR) initiative, the Sustainable Waste-to-Bioproducts Engineering Center (SWBEC), and the US Department of Energy (DOE) for financial support.

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  1. Department of Biological Engineering, Utah State University, 4105 Old Main Hill, Logan, UT, 84322-4105, USA

    Joshua T. Ellis, Ronald C. Sims & Charles D. Miller

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  1. Joshua T. Ellis
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  2. Ronald C. Sims
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Correspondence to Charles D. Miller .

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  1. , State Key Laboratory, Jiangnan University, Lihu Avenue 1800, Wuxi, 214122, Jiangsu, China, People's Republic

    Xiaoyuan Wang

  2. School of Biotechnology, Jiangnan University, Lihu Avenue 1800, Wuxi, 214122, China, People's Republic

    Jian Chen

  3. , Div. of Life Sciences, King's College London, Stamford Street 150, London, SE1 9NH, United Kingdom

    Peter Quinn

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Ellis, J.T., Sims, R.C., Miller, C.D. (2012). Monitoring Microbial Diversity of Bioreactors Using Metagenomic Approaches. In: Wang, X., Chen, J., Quinn, P. (eds) Reprogramming Microbial Metabolic Pathways. Subcellular Biochemistry, vol 64. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-5055-5_4

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