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My laboratory addresses fundamental questions in environmental microbiology and microbial evolution. Projects are all related to examining the effects of microbial contamination in water, and range from marker and technology development and validation to studying antibiotic resistant genes and host-fecal bacteria coevolution. Rapid detection of molecular markers for fecal bacteria and pathogens is the new paradigm for monitoring water quality.
To date, investigators have concentrated on identifying human and agricultural contamination. In many areas, however, significant contamination may come from overlooked sources: wild animals and birds. To investigate this problem and provide new tools, we developed and published two new avian assays: GFC, based on Catellicoccus, which targets fecal bacteria found in gulls, and GFD, based on Helicobacter, which targets avian fecal bacteria found in gulls, ducks, geese, and chickens. A focus of the lab is identifying other frequently overlooked sources of contamination such as rodents, and estimating their impact and associated health risk.
Occurrence and persistence of fecal bacteria markers in hosts and water: Another research focus is on understanding the occurrence, survival, spread, and correlation among fecal pathogens, molecular markers, and public health indicators in natural waters. For qPCR of markers to be used quantitatively across environments, both the temporal and geographic frequency and the relative persistence and decay of the markers must be understood. Our past work used mesocosms to compare decay of human and ruminant markers under varying environmental conditions. We are currently focusing on markers from different bacterial groups that occur in the same host species.
Sample interference in environmental QPCR: Sample interference in environmental applications of quantitative PCR prevents rapid, accurate estimations of genes and transcripts. We developed a spike-and-recovery approach using a mutant strain of Escherichia coli that contains a chromosomal insertion of a mutant GFP gene. This approach, coupled with previously developed kinetic outlier detection (KOD) methods, allowed sensitive detection of PCR inhibition at much lower inhibitor concentrations than alternative approaches using Cq values or amplification efficiencies. We are currently testing the approach in environmental water studies. These methods will be useful in a wide variety of environmental “omics”.