Analysis of Multitag Pyrosequence Data from Human Cervical Lavage Samples

Abstract

We have been using the Roche GS-FLX sequencing platform to produce tens of thousands of sequencing reads from samples of both bacterial communities (microbiome) and fungal communities (mycobiome) of stool, gut mucosa, vaginal washes, and oral washes from a large number of subjects. This vast volume of data from diverse sources has necessitated the development of an analysis pipeline in order to systematically and rapidly identify the taxa within the samples and to correlate the sample data with clinical and environmental features. Specifically, we have developed automated analytical tools for data tracking, taxonomical analysis, and feature clustering of bacteria in the human microbiome and demonstrate the pipeline using Cervical Vaginal Lavage (CVL) samples. This analysis pipeline will not only provide insight to our specific CVL dataset, but is applicable to other microbiome samples and will ultimately broaden our understanding of how the microbiome influences human health.

Bacterial Population in Intestines of the Black Tiger Shrimp (Penaeus monodon) under Different Growth Stages

“…To provide comprehensive coverage of bacterial communities, a high-throughput pyrosequencing method has been employed to obtain a higher number of sequence-reads [23]. The method has recently gained popularity for an in-depth characterization of various microbial communities such as those in the human [24], [25], [26], fermented food [27], soil [28], [29], [30], [31], extreme environments [32], the deep marine biosphere [33], [34], wastewater treatment bioreactors, [35] and plant biospheres [36], [37]. Furthermore, to enable an analysis of multiple samples in parallel within a single run, a barcode tag with a short unique nucleotide sequence was added to distinguish each sample [31].…”

Diversity and biogeochemical structuring of bacterial communities across the Porangahau ridge accretionary prism, New Zealand

“…The length of sequences averaged 262 bp. The sequence analysis pipeline is described by Naqvi et al (2010). Briefly, sequences shorter than 75 bp, with quality scores <25 and those with multiple Ns were removed before analysis.…”

Role of Next-Generation Sequencing in Understanding the Interactions between Human Papillomavirus and the Cervicovaginal Microbiome

“…When evaluated over a long period of time (up to 7 years), the cervical microbiome displays fluctuation between community types [29]. A previous study, using pyrosequencing on cervicovaginal lavage samples, describes the abundance of Bacteroides and Cytophaga , along with high G+C bacteria [32]. …”