Publication Date

Fall 2015

Degree Type


Degree Name

Master of Science (MS)


Biological Sciences


Cleber C. Ouverney


BLAST analysis, Chloroflexi, human analog, Phylogenetic analysis, uncultivable bacteria, wastewater

Subject Areas

Molecular biology; Microbiology


The phylum Chloroflexi is relatively unexplored, with the majority of its representatives being uncultivable. As a result, these microorganisms have not been characterized beyond their morphology and simple staining reactions, making the study of this phylum extremely challenging. Chloroflexi has been detected in the human oral cavity of patients suffering from peri-implantitis and in the vagina of patients suffering from bacterial vaginosis. Interestingly, Chloroflexi is also present in various environments such as freshwater lakes, soil, deep-sea sponges, hot springs and activated wastewater. Isolation of an environmental Chloroflexi with high 16S rRNA gene homology to a human-associated counterpart could be used as a model to understand its role in human health. The goal of this study was to better characterize Chloroflexi from activated wastewater, where it is known to be abundant, in order to elucidate the relatedness of an environmental analog to a potential human pathogen. Analysis using the 16S rRNA gene clone library generated 230 clones, out of which 67 clones were Chloroflexi. Based on BLAST analysis, about 93% (62 sequences) of the 67 Chloroflexi sequences were homologous to Chloroflexi phylotypes from other environmental sites. The remaining 7% (5 sequences) of Chloroflexi sequences were homologous to human-associated phylotypes derived from samples collected on human skin or human oral cavity. Overall, results suggest that activated wastewater serves as a potential habitat where one can find a human-associated Chloroflexi bacterium analog in order to better characterize this phylum and its contribution to human health.