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Manassas Park, VA, United States

Naqvi A.,Microbiome Analysis Center | Rangwala H.,Microbiome Analysis Center | Rangwala H.,George Mason University | Spear G.,Rush University Medical Center | And 2 more authors.
Chemistry and Biodiversity | Year: 2010

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. © 2010 Verlag Helvetica Chimica Acta AG. Source


Gillevet P.,George Mason University | Gillevet P.,Microbiome Analysis Center | Sikaroodi M.,George Mason University | Sikaroodi M.,Microbiome Analysis Center | And 2 more authors.
Chemistry and Biodiversity | Year: 2010

Recent advances in molecular techniques have now made it possible to interrogate the human microbiome in depth to better understand the interactions with the host organism and its role in diseases. We now report the utility of Length Heterogeneity Polymerase Chain Reaction (LH-PCR) to survey samples and a proprietary Multitagged Pyrosequencing (MTPS) methodology to interrogate the gut microbiome in healthy and disease states. We present an overview of our studies demonstrating the application of these molecular-biology techniques to an example disease state such as Inflammatory Bowel Disease (IBD). The findings show that there is a core mucosal bacterial microbiome (i.e., a mucosal biofilm) that is distinct from the luminal microbiome in health, and that the mucosal microbiome appears to be dysbiotic in IBD. We propose that the mucosal microbiome forms a synergistic and stable interaction with the host immune system, while the lumen microbiome varies based on diet or other environmental factors. We define this composite ecosystem of the human microbiome and human host as the Human Metabiome. © 2010 Verlag Helvetica Chimica Acta AG. Source


Naqvi A.,Microbiome Analysis Center | Rangwala H.,Microbiome Analysis Center | Rangwala H.,George Mason University | Keshavarzian A.,Rush University Medical Center | And 2 more authors.
Chemistry and Biodiversity | Year: 2010

In this article, we used a network-based approach to characterize the microflora abundance in colonic mucosal samples and correlate potential interactions between the identified species with respect to the healthy and diseased states. We analyzed the modelled network by computing several local and global network statistics, identified recurring patterns or motifs, fit the network models to a family of well-studied graph models. This study has demonstrated, for the first time, an approach that differentiated the gut microbiota in alcoholic subjects and healthy subjects using topological network analysis of the gut microbiome. © 2010 Verlag Helvetica Chimica Acta AG. Source

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