Publication Date

Summer 2014

Degree Type


Degree Name

Master of Science (MS)


Biological Sciences


Cleber Ouverney


16S rRNA, SR1, Uncultivable bacteria

Subject Areas

Molecular biology; Microbiology


Complex and naturally occurring microbial communities are known to be predominantly composed of uncultured bacteria and archaea. A few representatives of uncultured prokaryotes (e.g., from the candidate divisions TM7 and SR1) have been found in environmental samples and in association with animals, including humans. It is not yet clear, however, how uncultured bacteria found at environmental sites relate phylogenetically to their counterparts associated with animal hosts. In this study, we investigated the diversity of the SR1 candidate division to better understand the divide between animal-associated and environmental lineages. We generated 16S rDNA gene clone libraries from samples obtained from the following two habitats: outflow from water in a sulfur cave and spring water sediment in open air. Out of the 421 SR1 clones sequenced, we identified 18 operational taxonomic units (OTUs) that were used in combination with SR1 reference sequences to build an SR1 phylogenetic tree.

Phylogenetic analyses indicated that SR1 members associated with animal hosts clustered separately from those collected at the environmental sites. Further in-depth investigation may help to better characterize these bacteria and establish their nutritional requirements and physiological role in their respective communities. In addition, the microbes associated with host animals that are easy to maintain in the laboratory (e.g., termites, cow rumen) or found in habitats easy to access may serve as model organisms for studying the mechanisms by which these bacteria interact with their respective hosts, especially if the sequence homology observed for 16S rDNA to other genes, such as those involved in pathogenicity or mutualism.