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Bacterial Community Ecology of the Colon in Mus Musculus Brigham Young University BYU ScholarsArchive Theses and Dissertations 2017-07-01 Bacterial Community Ecology of the Colon in Mus musculus Rachel Marie Nettles Brigham Young University Follow this and additional works at: https://scholarsarchive.byu.edu/etd Part of the Biology Commons BYU ScholarsArchive Citation Nettles, Rachel Marie, "Bacterial Community Ecology of the Colon in Mus musculus" (2017). Theses and Dissertations. 6912. https://scholarsarchive.byu.edu/etd/6912 This Thesis is brought to you for free and open access by BYU ScholarsArchive. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of BYU ScholarsArchive. For more information, please contact [email protected], [email protected]. Bacterial Community Ecology of the Colon in Mus musculus TITLE PAGE Rachel Marie Nettles A thesis submitted to the faculty of Brigham Young University in partial fulfillment of the requirements for the degree of Master of Science Roger T. Koide, Chair John Chaston Laura Bridgewater Department of Biology Brigham Young University Copyright © 2017 Rachel Marie Nettles All Rights Reserved ABSTRACT Bacterial Community Ecology of the Colon in Mus musculus Rachel Marie Nettles Department of Biology, BYU Master of Science The gut microbiome is a community of closely interacting microbes living in the gastrointestinal tract. Its structure has direct relevance to health. Disturbances to the microbiome, such as due to antibiotic use, have been implicated in various diseases. The goal of this study was to determine how the gut microbiome reacts to and recovers from disturbance caused by antibiotics. Because diet also influences the microbiome, this study included the interaction between diet and antibiotics. Half of the mice in each diet treatment were given antibiotics to disturb their microbiomes. After cessation of antibiotics, mice were paired in combinations within diets to determine whether the microbiomes of control mice influenced the disturbed microbiomes of formerly antibiotic mice. Chapter 1. Diet significantly altered the structure of the gut microbiome but its effect was significantly smaller than the effect of antibiotics. There was a significant interaction between diet and antibiotics; the antibiotic effect was larger in the cornstarch diet than in the glucose diet. Dysbiotic microbiomes resulting from antibiotics were characterized by an increase in Bacteroidetes and Proteobacteria, and a decrease in Firmicutes. Antibiotic administration also resulted in an initial increase OTU diversity, mainly because it reduced the abundance of dominant OTUs, resulting in greater evenness. Chapter 2. Seven weeks after the cessation of antibiotics (experiment termination), the effect of the antibiotics on the microbiome was still evident. The structure of the dysbiotic microbiome had not returned to that of control mice. Antibiotics significantly increased the relative abundance of some taxa and significant decreased the relative abundance of others. It was unexpected that the taxonomic hierarchy within the microbiome did not recover after 7 weeks following cessation of antibiotics. It would appear, therefore, that antibiotics established a new, semi-stable hierarchy. Chapter 3. When paired together, the assumption was that dysbiotic microbiomes of antibiotic mice would be positively influenced by microbiomes of control mice, based on the assumption that the control mouse wou ld act as a probiotic for the antibiotic mouse, either via coprophagy or consumption of food contaminated by feces. Contrary to that hypothesis, the microbiomes of control mice became more similar to that of antibiotic mice. One can offer at least two hypotheses to explain this result, but neither was tested. First, compared to the control microbiome, the dysbiotic microbiome may have been more stable and thus more resistant to change due to invasion by OTUs from the control microbiome. Other research has shown that dysbiotic microbiomes have a high degree of stability. If this were true, the use of probiotics is questionable. Second, one or more of the antibiotics could still have been active at the initial phase of pairing, and coprophagy caused the microbiome of the control mice to rapidly become dysbiotic. If this is true, the experiment should have been conducted with a waiting period between the cessation of antibiotic administration and pairing. Keywords: antibiotics, community structure, competition, diet, diversity, gut, microbiome, Mus ACKNOWLEDGEMENTS I want to thank Dr. John Chaston for his help and mentorship throughout the sequencing process. I would also like to thank Courtney Carroll for her assistance throughout the sequencing process. A huge thank you to Dr. Blair Lawley who taught me the ins and outs of QIIME, and to and Dr. Gerald Tannock who graciously hosted me in his lab. Thank you to Laura Bridgewater for her willingness to be on my committee, and for her mentorship. I am grateful for the assistance of the Hancock lab and the Christensen lab in getting this project off to a successful start. Thank you to Eliza Clark, and especially to Kevin Ricks. I could not have done this without you. And most of all, a huge thank you to Dr. Roger Koide, who took the plunge with me into the word of the gut microbiome. You are a truly amazing mentor and have taught me more in my four years with you than anyone else in my entire college education. I hope your tux is ready. Thank you to everyone who took part in this project. Your contributions are greatly appreciated. TABLE OF CONTENTS TITLE PAGE ................................................................................................................................... i ABSTRACT .................................................................................................................................... ii ACKNOWLEDGEMENTS ........................................................................................................... iii TABLE OF CONTENTS ............................................................................................................... iv LIST OF TABLES ....................................................................................................................... viii LIST OF FIGURES ....................................................................................................................... xi Introduction ..................................................................................................................................... 1 Methods .......................................................................................................................................... 5 Mice and Treatments................................................................................................................... 5 Sampling ..................................................................................................................................... 6 Figure 1. .................................................................................................................................. 7 Figure 2. .................................................................................................................................. 7 Sequencing .................................................................................................................................. 8 Community Analysis .................................................................................................................. 9 Chapter 1 ....................................................................................................................................... 10 Introduction ............................................................................................................................... 10 Figure 1. ................................................................................................................................ 10 Results ....................................................................................................................................... 11 Table 1. ................................................................................................................................. 11 Table 2. ................................................................................................................................. 12 Figure 2. ................................................................................................................................ 12 Table 3. ................................................................................................................................. 12 Figure 3. ................................................................................................................................ 13 Table 4. ................................................................................................................................. 13 Table 5. ................................................................................................................................. 13 Table 6. ................................................................................................................................. 14 Table 7. ................................................................................................................................. 14 Table 8. ................................................................................................................................. 15 Table 9. ................................................................................................................................
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