Title

Using pyrosequencing and quantitative PCR to analyze microbial communities

Authors

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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