Evolutionary genomics of Streptococcus
Functional, comparative, and evolutionary genomics of Streptococcus mutans
Protozoan genomics
Campylobacter coli Data Sets

Evolutionary genomics of Streptococcus

In the preface of their 1991 book entitled “The Comparative Method in Evolutionary Biology”, Harvey and Pagel state: “Comparative studies have taught us most of what we know about adaptation”. This is equally true this many years later, whether the realm of study is bird behavior, or molecular adaptation. Identifying which genes and sites within genes are of key functional significance and linked to pathogenesis across a pathogen’s genome is fundamental to our understanding of disease biology. Comparative genomic sequence analysis plays a pivotal role in this endeavor.

Streptococci are a diverse group of bacteria, comprising over 70 species, and include taxa which are members of human and animal commensal microflora, as well a variety of important human, zoonotic, and agricultural pathogens. Recent molecular phylogenies support several taxonomic divisions within the genus, including Pyogenes, Bovis, Mutans, Salivarius, Anginosus, and Mitis. The major human pathogens occur in the Pyogenes, Mitis and Mutans groups.

Employing data acquired via NGS techniques this project investigates comparative genomics across a wide range of animal and human pathogens of the genus Streptococcus with the goal of identifying the molecular specifics associated with host adaptation and host specific pathogenesis. As part of this process we consider such things as (1) the role of positive selection versus lateral gene transfer (2) the demographic history of groups of interest (3) phylogenomic approaches to reconstructing gene gains and losses in the diversification of the genus Streptococcus (4) the evolution of the core versus the dispensable genome.

This work has been, or is currently, supported by NIH (NIAID) and USDA.


Functional, comparative, and evolutionary genomics of Streptococcus mutans.

Streptococcus mutans is known to be one of the most prevalent bacteria in human oral flora and is widely recognized as a key etiological agent of human dental caries. The purpose of this project is to use comparative genomic and transcriptomic approaches to gain insights on basic biology, evolutionary history and pathogenesis of this organism. An important aspect of this work involves an ongoing collaboration with the laboratory of Dr. Robert Burne at the University of Florida. Dr. Burne’s lab performs experiments designed to assess the functional role of various loci identified in evolutionary comparisons of the core, unique core, and dispensable genomes of S. mutans strains of varying phenotypes.  This work is supported by the NIH (NIAID and NIDCR).


Protozoan genomics

A new area of research for the Stanhope lab involves comparative genomics of protozoans. The two protozoans in question are Blastocystis and Plasmodium – specifically avian malaria. Blastocystis is a member of the Stramenopiles, found in the gastrointestinal tract of a wide range of organisms including humans, farm animals, birds, rodents, reptiles, amphibians, and fish. The organism has a very wide geographic distribution, and in humans, is found at relatively low rates in developed countries, but up to more than 50% in less developed countries. The role of Blastocystis in human disease is somewhat controversial but there are a number of studies that have suggested a link to a variety of health problems including Irritable Bowel Syndrome. We are exploring different ways to culture the organism and are conducting comparative genomic analysis across different strains of B. hominis. This work involves collaborations with Dr. Rune Stensvold from the Statens Serum Institut and Dr. Graham Clark, from the London School of Hygiene and Tropical Medicine.

Plasmodium genomics involves a number of putative new species of Plasmodium isolated by Holly Lutz, a graduate student in the lab, from various species of birds. We are currently exploring ways to obtain pure cultures for genome sequencing.


Data Sets

Campylobacter coli Illumina denovo assemblies used in the paper "Expanded MLST genotyping and comparative genomic hybridization of Campylobacter coli isolates from multiple hosts"

cco4 (gziped fasta files)
cco74 (gziped fasta files)

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