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FFHI Ph.D. Student Nick Bokulich Publishes Study in Nature Methods

by jiopark — last modified Jan 22, 2015 12:59 PM
FFHI-associated graduate student Nick Bokulich is first author of an important study advancing bioinformatic methods to directly characterize the diversity of microbes in natural sites. The study was recently published in the prestigious journal Nature Methods.

The paper, “Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing”, includes FFHI-affiliated co-authors Bokulich and David Mills and a number of leading researchers in the area of microbial ecology including Rob Knight (University of Colorado Boulder), Jeffrey Gordon (Washington University in St. Louis), Dirk Gevers (the Broad Institute at MIT and Harvard) and Greg Caporaso (Northern Arizona University and Argonne National Laboratory). The methods presented in this paper enable researchers to optimally describe the microbial ecology of any natural site using the latest next generation sequencing approaches.

Nick Bokulich, a 2nd year PhD student in the Food Science Graduate Group, works in the laboratory of Dr. David Mills.  His research examines the microbial ecology associated with food fermentations and gut health as well as the development of bioinformatics tools to carry out those analyses.  Recently Nick became the first recipient of the Dannon Probiotics fellowship – a program created to support the education of outstanding students researching in the area of probiotics and gut health.   

Regarding this work Dr. Mills remarked “These methods further our ability to survey complex microbial ecosystems through an enhanced understanding of how sequencing data quality impacts the accuracy and reliability of biological conclusions. These steps are especially critical to large-scale studies to normalize sequencing data produced from multiple instruments, experiments, or locations.”

Co-author Greg Caporaso also commented "Nick's efforts here are truly heroic.  His recommendations for quality control have now become the default settings in the widely-used Quantitative Insights Into Microbial Ecology (QIIME) bioinformatics software package and are in widespread use in the Earth Microbiome Project." 

This research is an outcome of existing collaborations among the principal labs working on a Gates Foundation funded-project to examine innovative new strategies to benefit infant nutrition in less developed countries.