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Marker gene amplicon sequencing is often preferred over whole genome sequencing for microbial community characterization, due to its lower cost while still enabling assessment of uncultivable organisms. This technique involves many experimental steps, each of which can be source of errors and bias. We present an up-to-date overview of the whole experimental pipeline, from sampling to sequencing reads, and give information allowing for informed choices at each step of both planning and execution of a microbial community assessment study. When applicable, we also suggest ways of avoiding inherent pitfalls in amplicon sequencing. This article is protected by copyright. All rights reserved.
This article was published in the following journal.
Name: Journal of applied microbiology
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The collective designation of three organizations with common membership: the European Economic Community (Common Market), the European Coal and Steel Community, and the European Atomic Energy Community (Euratom). It was known as the European Community until 1994. It is primarily an economic union with the principal objectives of free movement of goods, capital, and labor. Professional services, social, medical and paramedical, are subsumed under labor. The constituent countries are Austria, Belgium, Denmark, Finland, France, Germany, Greece, Ireland, Italy, Luxembourg, Netherlands, Portugal, Spain, Sweden, and the United Kingdom. (The World Almanac and Book of Facts 1997, p842)
Systematic identification of a population's needs or the assessment of individuals to determine the proper level of services needed.
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A frequent complication of drug therapy for microbial infection. It may result from opportunistic colonization following immunosuppression by the primary pathogen and can be influenced by the time interval between infections, microbial physiology, or host resistance. Experimental challenge and in vitro models are sometimes used in virulence and infectivity studies.
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Bioinformatics is the application of computer software and hardware to the management of biological data to create useful information. Computers are used to gather, store, analyze and integrate biological and genetic information which can then be applied...