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Trained in molecular biology, my thesis work with Carl Woese at the University of Illinois Urbana, and post doctoral research with Norman Pace at the National Jewish Hospital in Denver focused on primary structure changes during maturation of precursor to mature ribosomal RNAs in Escherichia coli and Bacillus subtilis, and ultimately on the first isolation of an in vitro rRNA processing system. I subsequently developed a keen interest in understanding the evolution and complexity of microorganisms. While at the National Jewish Hospital and the University of Colorado in Denver (1976-1989), my laboratory advanced molecular phylogenetic techniques both at the bench and through the use of the use of 64 bit computing to develop a reference framework that describes the evolution of microbial eukaryotes. My research group documented the earliest diverging eukaryotic lineages, provided the first evidence of a specific link between animals and fungi to the exclusion of all other eukaryotes, discovered the stramenopiles (a novel assemblage of heterotrophic and photosynthetic eukaryotes), documented the relationship between ciliates, dinoflagellates and malaria-causing parasites, and demonstrated that the pathogen Pneumocystis is fungal rather than apicomplexan.  After moving to the Marine Biological Laboratory in 1989, I extended these techniques to define relationships for marine protists and cnidarian forms, and to survey eukaryotic microbial diversity in extreme environments.  My laboratory’s work on protist evolution culminated with determining the complete genome sequence of the early diverging human parasite Giardia lamblia.  Other fundamental discoveries and contributions that emerged from my molecular evolution studies include the first evidence that self-splicing group I introns undergo lateral transfer between eukaryotic rRNA genes; the demonstration that structurally distinct rRNAs in the apicomplexan parasite Plasmodium falciparum are differentially regulated depending upon life cycle stage; and the first use of PCR to amplify and sequence ribosomal RNA genes.

Nearly a decade ago, I re-focused efforts of my laboratory towards improving our understanding of microbial diversity and how communities shift their composition and structure in response to altered environmental influences. At that time, I was convinced the molecular strategies for inventorying complex microbial communities likely underestimated total microbial diversity because of the superficial amount of DNA sequencing relative to the enormous population size of a typical microbial community.  We initially took advantage of novel strategies patterned after SAGE techniques to sequence multiple hypervariable regions from a single rDNA template.  Each hypervariable region served as a proxy for the occurrence on a microbial rRNA gene in an environmental DNA sample.  Soon after working out that technology including the requisite analytical paradigms, the introduction of next generation DNA pyrosequencing (454 technology) allowed my group to ask the simple question: how many different kinds of microbes really occurred in marine environments? Instead of sequencing a few hundred or a few thousand templates, we were able to generate sequences for 104-106 templates.  The most stunning result described more than 40,000 different kinds of microbes in a liter of sea water from the diffuse flow of a sea mount.

These very large data sets also describe long-tailed distributions where a small number of taxa or operational taxonomic units (OTUs) dominate complex microbial communities, while an extraordinarily large number of OTUs occur in very low frequency and define the composition of a “rare biosphere”.   These surveys have fueled lively debates about the biological significance of the rare biosphere and have raised questions about analytical methodologies.  Simple explanations for the rare biosphere often focus on artifacts introduced through PCR amplification and sequencing of targeted genes or inclusion of singleton sequences in diversity estimates.  We have shown that quality control techniques can render sequences of very high accuracy and improved clustering algorithms can avoid the pitfalls of complete linkage analyses that can inflate the number of estimated OTUs.  Subsequent work in our laboratory and others show that rare taxa represent populations that have the capacity to shift from being rare to becoming dominant in response to changes in the environment. They also can reflect biogeographical distribution patterns.  

My current research focuses on major unsolved questions in microbial ecology: What is the diversity and distribution of microbial lineages in the Human Microbiome? How are microbes adapted (physiological, genomic) to the Human Microbiome? How are micro organisms linked to their chemical environment? We address the very same questions  in studies of microbial communities in the oceans and in the deep subsurface. The only difference between these systems are the field sites! Most relevant to the University of Chicago, we collaborate with Eugene Chang and Murat Eren on genomic-based studies that seek to understand the influence of microbial populations in the progression of ulcerative colitis. Both host genetics and properties of the human gut microbiome influence the development and course of Inflammatory Bowel Disease (IBD). For patients with medically recalcitrant ulcerative colitis (UC), an optional surgical colectomy and ileal pouch-anal anastomosis procedure (IPAA) removes the colon and creates an ileal pouch, which functions as a pseudo-rectum. Approximately 40-50 percent of UC patients eventually develop Pouchitis, which is an inflammatory response resembling the original IBD. Based on our published and preliminary data, we hypothesize that the emergence of specific pathobionts that existed before or acquired virulence elements after IPAA promote immune and inflammatory responses in the ileal pouch in genetically susceptible individuals to cause pouchitis. The initial formation of the ileal pouch represents the non-disease state but with a metastable microbiota that after 4 months resembles a stable, colonic-like microbiome. Non-competing explanations for pouch inflammation include 1) acquisition of pathobionts that promote host inflammatory response, and 2) changes in host physiology may trigger shifts in microbial community functions or foster growth of pathobionts that cause and perpetuate IBD. This project seeks to determine how pathobionts arise during inflammation through analysis of luminal and mucosal microbiome samples collected before initial surgery, after formation of the pouch and longitudinal sample from inflamed and non-inflamed periods. In contrast to large cross association studies where natural microbiome variability between individual exceeds differences between healthy and inflamed states, this experimental design allows each patient to serve as their own internal control thus increasing the resolving power of microbiome analyses.

A second major effort involved my serving as co-chair (with Kai-Uwe Hinrichs, University of Bremen) Deep Life Community of the Deep Carbon Observatory organized by the Carnegie Institution of Washington.  As part of this effort we explored unusual microbial communities that live deep beneath the surface of the earth. The overall goal is to understand how biotic and abiotic processes influence the deep carbon cycle.  Most of this work involves continued use of next generation DNA sequencing using Illumina technology and informatics including oversight of the web site Visualization of Microbial Population Structures ().