Assessing Microbial Diversity Through Nucleotide Variation

You are welcome to download my Ph.D. dissertation. Please do not hesitate to contact me if you have questions regarding the methods and tools and how they might be applied to your data sets.

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Also there is a recent publication, in which oligotyping is demonstrated:

Eren AM, Zozaya M, Taylor CM, Dowd SE, Martin DH, et al. (2011), PLoS ONE 6(10): e26732. doi:10.1371/journal.pone.0026732

Unfortunately, due to the -somewhat ancient- graduate school policy, I had no other choice than the traditional copyright management option (which was forcing me to keep all rights of this dissertation reserved under my name). But I would like to declare here that I do licence my dissertation under the Creative Commons Licence BY/NC/SA 3.0, and offer my mere intellectual output to the academic community, hoping that future generations of scholars may have greater access to this work.

Microbes are the most abundant and most diverse form of life on Earth, constituting the largest portion of the total biomass of the entire planet. They are present in every niche in nature, including very extreme environments, and they govern biogeochemical transformations in ecosystems. The human body is home to a diverse assemblage of microbial species as well. In fact, the number of microbial cells in the gastrointestinal tract, oral cavity, skin, airway passages and urogenital system is approximately an order of magnitude greater than the number of cells that make up the human body itself, and changes in the composition and relative abundance of these microbial communities are highly associated with intestinal and respiratory disorders and diseases of the skin and mucus membranes. In the early 1990's, cultivation-independent methods, especially those based on PCR-amplification and sequences of phylogenetically informative 16S rRNA genes, made it possible to assess the composition of microbial species in natural environments, advances in high-throughput sequencing technologies in recent years have increased sequencing capacity and microbial detection by orders of magnitude. However, the effectiveness of current computational methods available to analyze the vast amounts of sequence data is poor and investigating the diversity within microbial communities remains challenging. In addition to offering an easy-to-use visualization and statistical analysis framework for microbial community analyses, the study described herein aims to present a biologically relevant computational approach for assessing microbial diversity at finer scales of microbial communities through nucleotide variation in 16S rRNA genes.

To Gülşan Eren, my little sister whom I never had a chance to spend enough time with.

I would like to thank my advisor Christopher M. Taylor for his help, guidance and his open mindedness. When I decided to change my research focus to microbial ecology in the middle of my Ph.D. education, he accepted the offer to be my advisor, facilitated an energetic collaboration with Michael J. Ferris and let me be a part of it.

I owe my deepest gratitude to Michael J. Ferris. It has been almost 2 years since I started working under his supervision, and I can clearly see that meeting with Michael J. Ferris was one of the most important milestones of my life. Among many other reasons, I am very thankful to him for tolerating my excitement, patiently teaching me and introducing me to the world of microbes.

I would also like to thank the invaluable members of my Ph.D. committee, Christopher M. Summa, Daniel Bilar and Huimin Chen. I wish I had been wise enough to benefit from their vision just a little more.

I honestly do not think that I would be able to finish this Ph.D. if it were not for the support of Seth Pincus, director of the Research Institute of Children's at Children's Hospital, and Mahdi Abdelguerfi, chair of the Department of Computer Science, University of New Orleans.

I am grateful to my dear colleagues Marcela Zozaya-Hinchliffe, Caroline E. Hennigan and Johana Norori for their support. Thanks to all faculty and staff of Children's Hospital and the Department of Computer Science in University of New Orleans.

My appreciation also extends to James Nachtwey, Richard Feynman, Kurt Vonnegut and Oğuz Atay for all the inspiration and strong influence.

I would also like to express my deep gratitude to those whom I met, and who had an impact on the course of my life: Nefin Huvaj, Mihail Guber, Mevzun Yüksel, Necdet Yücel, Doruk Fişek, Koray Löker, Oğuzhan Erdinç, Alp Öztarhan, Barış Metin, S. Çağlar Onur, Gürer Özen, Erkan Tekman, Murat Gündüz, Kevin Simpson and Aslı Şahin. Thank you very much.

There are people that I cannot thank enough. Therefore I will not dare to try. However, I would like to mention their names here: B. Duygu Özpolat, Arpat Özgül and Ashley Wright.

Finally, I frankly admit that I am here, writing this page in this library carrel, simply because I was lucky.

Thanks to serendipity.

A. Murat Eren was born in Turkey. During his undergraduate education he developed an interest in operating systems and cryptography and became proficient in GNU/Linux based operating systems and network security.

After graduating from university he became an advocate of the philosophy behind free/open-source software movement and joined forces of Turkish Linux Users Association (LKD) to create awareness towards open source as an economically and philosophically better alternative for universities and governmental agencies in Turkey.

In 2003, he started working at The National Research Institute of Electronics and Cryptology (UEKAE), an institute of The Scientific and Technological Research Council of Turkey (TÜBİTAK), as a part of a small developer team gathered to implement a Linux-based operating system, Pardus, to be used by the Turkish government and the public.

Following the first stable release of Pardus he moved to New Orleans and began his Ph.D. education at the Department of Computer Science in University of New Orleans in 2007.

After two years of Ph.D. education he developed a sudden interest in biological sciences, and decided to lend his expertise in computation to the exciting field of microbial ecology.

He likes photography, and has serious issues with any kind of authority.

I wrote my dissertation -almost- in one sitting. During this process I took a self-portrait and a screenshot of my dissertation everyday.