Mitchell Lloyd Sogin

I committed most of my career investigating the evolution of protists, many of which cause disease in humans. Our early studies focused upon the use of ribosomal RNAs for inferring phylogenetic relationships & ultimately culminated with genome projects for human parasites such as Giardia lamblia. In 2003, the Census of Marine Life funded by the Alfred P Sloan foundation attracted my interest. Within a short timeframe, I received support to organize the International Census of Marine Microbes. The goal was to identify the diversity & relative abundance of microbes throughout the world’s oceans. We initially developed an efficient strategy for sequencing informative portions of ribosomal RNA genes in order to characterize a larger number of marine samples that typically surveyed by most molecular microbial surveys. Two years later with the introduction of the Roche Genome pyrosequencing systems, I realized it would be possible to take advantage of its massively parallel capacity to characterize rapidly evolving regions in small subunit rRNA coding regions from many thousands of DNA templates extracted from the environment. Each pyrotag served as a proxy for the occurrence of an rRNA coding regions from different microbes in an environmental sample. We pioneered this experimental strategy that described the rare biosphere. The rare biosphere is only accessible through ultra deep sequencing efforts & it posits that most microbial diversity is represented by low-abundance taxa that rarely occur in nature. Since that publication we have collected more than 380 million pyrotag sequences from ~1200 marine samples, animal microbiomes (humans & rats), soils, & complex sewage communities. We have developed analytical strategies for determining the taxonomic source of pyrotags & have established a web site Visualization of Microbial Population Structures (VAMPS) – http://vamps.mbl.edu which offers the community tools for comparing microbial community population structures. Our general next generation sequencing strategy now dominates the field of molecular microbial ecology including efforts underway within the Human Microbiome Project (HMP). We currently have active projects for exploring microbial population structures within influents to sewage treatment plants, ongoing studies of microbial diversity in the oceans and deep subsurface and deep subseafloor environments, and investigations of human microbiome in pouchitis patients, a model for Ulcerative Colitis.