Comparative genomic approaches for investigating evolution in the microbial and viral populations of the rumen

Miller, Margret E.

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https://hdl.handle.net/2142/18486 Copy

Description

Title

Comparative genomic approaches for investigating evolution in the microbial and viral populations of the rumen

Author(s)

Miller, Margret E.

Issue Date

2011-01-21T22:42:30Z

Director of Research (if dissertation) or Advisor (if thesis)

White, Bryan A.

Doctoral Committee Chair(s)

White, Bryan A.

Committee Member(s)

• Drackley, James K.
• Roca, Alfred L.
• Yannarell, Anthony C.

Department of Study

Animal Sciences

Discipline

Animal Sciences

Degree Granting Institution

University of Illinois at Urbana-Champaign

Degree Name

Ph.D.

Degree Level

Dissertation

Keyword(s)

• comparative genomics
• Metagenomics
• bacteriophages
• evolution
• rumen

Abstract

The rumen is home to a diverse population of microorganisms encompassing all three domains of life: Bacteria, Archaea, and Eukarya. Viruses have also been documented to be present in large numbers; however, little is currently known about their role in the dynamics of the rumen ecosystem. This research aimed to use a comparative genomics approach in order to assess the potential evolutionary mechanisms at work in the rumen environment. We proposed to do this by first assessing the diversity and potential for horizontal gene transfer (HGT) of multiple strains of the cellulolytic rumen bacterium, Ruminococcus flavefaciens, and then by conducting a survey of rumen viral metagenome (virome) and subsequent comparison of the virome and microbiome sequences to ascertain if there was genetic information shared between these populations. We hypothesize that the bacteriophages play an integral role in the community dynamics of the rumen, as well as driving the evolution of the rumen microbiome through HGT. In our analysis of the Ruminococcus flavefaciens genomes, there were several mobile elements and clustered regularly interspaced short palindromic repeat (CRISPR) sequences detected, both of which indicate interactions with bacteriophages. The rumen virome sequences revealed a great deal of diversity in the viral populations. Additionally, the microbial and viral populations appeared to be closely associated; the dominant viral types were those that infect the dominant microbial phyla. The correlation between the distribution of taxa in the microbiome and virome sequences as well as the presence of CRISPR loci in the R. flavefaciens genomes, suggested that there is a “kill-the-winner” community dynamic between the viral and microbial populations in the rumen. Additionally, upon comparison of the rumen microbiome and rumen virome sequences, we found that there are many sequence similarities between these populations indicating a potential for phage-mediated HGT. These results suggest that the phages represent a gene pool in the rumen that could potentially contain genes that are important for adaptation and survival in the rumen environment, as well as serving as a molecular ‘fingerprint’ of the rumen ecosystem.

Graduation Semester

2010-12

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http://hdl.handle.net/2142/18486

Copyright and License Information

Copyright 2010 Margret Ellen Berg Miller

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