Using pyrosequencing and quantitative PCR to analyze microbial communities

    Authors

    H. S. Zhang

    Comments

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    Abbreviated Journal Title

    Front. Environ. Sci. Eng. China

    Keywords

    polymerase chain reaction (PCR); microbial communities; pyrosequencing; gut; microbial fuel cell; sludge; POLYMERASE-CHAIN-REACTION; RESPIRING BACTERIA ARB; FUEL-CELLS; RARE; BIOSPHERE; BIOFILM ANODE; RIBOSOMAL-RNA; DIVERSITY; MICROORGANISMS; CONVERSION; SAMPLES; Engineering, Environmental; Environmental Sciences

    Abstract

    New high-throughput technologies continue to emerge for studying complex microbial communities. In particular, massively parallel pyrosequencing enables very high numbers of sequences, providing a more complete view of community structures and a more accurate inference of the functions than has been possible just a few years ago. In parallel, quantitative real-time polymerase chain reaction (QPCR) allows quantitative monitoring of specific community members over time, space, or different environmental conditions. In this review, the principles of these two methods and their complementary applications in studying microbial ecology in bioenvironmental systems are discussed. The parallel sequencing of amplicon libraries and using barcodes to differentiate multiple samples in a pyrosequencing run are explained. The best procedures and chemistries for QPCR amplifications are also described and advantages of applying automation to increase accuracy are addressed. Three examples in which pyrosequencing and QPCR were used together to define and quantify members of microbial communities are provided: in the human large intestine, in a methanogenic digester whose sludge was made more bioavailable by a high-voltage pretreatment, and on the biofilm anode of a microbial electrolytic cell. The key findings in these systems and how both methods were used in concert to achieve those findings are highlighted.

    Journal Title

    Frontiers of Environmental Science & Engineering in China

    Volume

    5

    Issue/Number

    1

    Publication Date

    1-1-2011

    Document Type

    Review

    Language

    English

    First Page

    21

    Last Page

    27

    WOS Identifier

    WOS:000287753800002

    ISSN

    1673-7415

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