Microbiome Analysis from Sample Acquisition to Bioinformatics

A Microbiome Analysis combines sample collection and processing, NextGen sequencing and bioinformatics analysis to provide unprecedented details of the composition of microbiota at different sites on the human body. While at first, it might appear that the components required for “in house” microbiome analysis may be beyond the capabilities of some research laboratories, in reality, the requisite components for establishing a microbiome analysis pipeline may already exist at many institutions, eliminating the need for investigators to contract out for microbiome analysis.

In the following sections we describe a Microbiome Analysis analytical pipeline from acquisition of samples, multiplex DNA sequencing using the Illumina MiSeq sequencing platform and bioinformatics data analysis to accommodate a wide spectrum of clinical and basic science investigators.

Samples can be acquired from saliva (Basic Protocol 1), buccal swabs (Alternate Protocol 1), vaginal or skin samples (Basic Protocol 2), or fecal specimens (Basic Protocol 3 and Alternate Protocol 2). Support Protocols 1 and 2 provide information about transport of samples. Basic Protocols 4–6 describe DNA preparation, generation of the amplicon library and sample prep for NextGen sequencing. Support Protocol 3 describes how to quantify the DNA using PicoGreen. Finally, computational protocols using the QWRAP QIIME Wrapper are provided in Basic Protocols 7 and 8.

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