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Characterization of the Vaginal Microbiome in Pregnancy

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Characterization of the Vaginal Microbiome in Pregnancy CHARACTERIZATION OF THE VAGINAL MICROBIOME IN PREGNANCY A Thesis Submitted to the College of Graduate and Postdoctoral Studies In Partial Fulfillment of the Requirements For the Degree of Doctor of Philosophy In the Department of Veterinary Microbiology University of Saskatchewan Saskatoon By ALINE COSTA DE FREITAS © Copyright Aline C. Freitas, February, 2018. All rights reserved. PERMISSION TO USE In presenting this thesis in partial fulfillment of the requirements for a Postgraduate degree from the University of Saskatchewan, I agree that the Libraries of this University may make it freely available for inspection. I further agree that permission for copying of this thesis/dissertation in any manner, in whole or in part, for scholarly purposes may be granted by the professor or professors who supervised my thesis work or, in their absence, by the Head of the Department or the Dean of the College in which my thesis work was done. It is understood that any copying or publication or use of this thesis or parts thereof for financial gain shall not be allowed without my written permission. It is also understood that due recognition shall be given to me and to the University of Saskatchewan in any scholarly use which may be made of any material in my thesis/dissertation. Requests for permission to copy or to make other uses of materials in this thesis in whole or part should be addressed to: Head of Department of Veterinary Microbiology University of Saskatchewan Saskatoon, Saskatchewan S7N 5B4 Canada OR Dean College of Graduate and Postdoctoral Studies University of Saskatchewan 116 Thorvaldson Building, 110 Science Place Saskatoon, Saskatchewan S7N 5C9 Canada i ABSTRACT The vaginal microbiome plays an important role in women’s reproductive health. Imbalances in this microbiota are associated with bacterial vaginosis, increased susceptibility to sexually transmitted infections, and negative reproductive outcomes. The causes of such variations, however, are poorly understood. A healthy vaginal microbiota is defined as Lactobacillus-dominated and an overgrowth of other species is often associated with unhealthy conditions. An appreciation of “atypical” microbiomes in healthy women, such as Bifidobacterium-dominated, has been gradually increasing. Although bifidobacteria play an important role in gut health, vaginal bifidobacteria have not yet been fully characterized. In this study, a baseline description of the “healthy” vaginal microbiome in pregnancy has been established based on cpn60 gene amplicon sequencing. The vaginal microbiota of pregnant women relative to non-pregnant women had lower richness and diversity, higher Lactobacillus abundance and lower Mollicutes/Ureaplasma prevalence. This gives a better understanding of the vaginal microbiome in healthy pregnancies and provides a control group for a subsequent comparison to women who experienced preterm birth. An association between Mollicutes and preterm was confirmed, and further suggested that a more rich and diverse microbiome is associated with prematurity. To better understand the relationship between reproductive outcomes and microbiota, an improved definition of the healthy microbiome is also needed, which should include evaluation of “atypical” microbiomes, such as Bifidobacterium-dominated. Phenotypic characterization of vaginal bifidobacteria indicated that they have health promoting characteristics similar to beneficial vaginal lactobacilli. Considering the importance of bifidobacteria as one of the primary colonizers of the neonatal gut, the genomes of vaginal and gut isolates of Bifidobacterium breve and Bifidobacterium longum were compared. Results indicated that vaginal and gut microbiomes are colonized by a shared community of Bifidobacterium, which may be transferred from mother to infant. Taken together, the results presented in this thesis provide a better understanding of the vaginal microbiome of pregnant women with low and high risk for preterm birth. It also improves the understanding of a healthy microbiome by phenotypically characterizing vaginal bifidobacteria, and contributes to elucidate aspects of bifidobacteria ecology by comparing the genomes of vaginal and gut bifidobacteria. ii ACKNOWLEDGEMENTS This thesis project could only be completed with the collaboration and support of many people to whom I am very grateful. First and foremost, I would like to thank my supervisor Dr. Janet Hill for giving me the opportunity to be part of the Hill lab. I am grateful for her guidance, patience, kindness, ability to transform any moment in a teaching moment, encouragement in moments of uncertainty, replying/reviewing materials in a record time, teaching me so much about Science and pushing me beyond my comfort zone (which today I really appreciate!). Thank you! I also would like to thank the members of my Research Advisory Committee – Dr. Joseph Rubin, Dr. Aaron White, Dr. Jo-Anne Dillon and Dr. Vikram Misra – for their insightful comments that undoubtedly improved the quality of this work. To the VOGUE team, in special Dr. Bocking and Dr. Money, thank you for providing me the opportunity to participate in this interdisciplinary group which immensely contributed to my professional development. Thanks to the Hill lab members/alumni and aggregates: Bonnie, John, Matthew, Teenus, Isha, Matheus, Jason, Lisa, Mo, Niradha, Salahuddin, Maodong, Shakya, Pashupati, Sonu, Arinjay, Roman, Carolina, Lana, Linda and GMP members. Every seminar, lab meeting, “office” talks and chit chatting contributed for my professional and personal growth, and made everything more enjoyable and fun! A special thanks to Champika Fernando who not only taught me so much in the lab, but also became a good friend who gave me encouragement and support throughout my PhD. To my family back home – mom, dad and “little” sister. I know that moving so far away was not easy for you and I am sorry I missed so many important moments. Thank you for your unlimited support that always help me to keep going. Last but not least, I would like to thank my fiancé Eduardo who helped me after we moved to Canada when I could barely speak English. I am thankful for your support in so many challenging moments in the past few years. Your strength and love were fundamental for my success in completing this PhD. Thank you for sharing your life with me and I am looking forward to our next adventures together! iii TABLE OF CONTENTS PERMISSION TO USE ............................................................................................................. i ABSTRACT .............................................................................................................................. ii ACKNOWLEDGEMENTS ..................................................................................................... iii LIST OF TABLES .................................................................................................................. vii LIST OF FIGURES ............................................................................................................... viii LIST OF ABBREVIATIONS .................................................................................................. ix CHAPTER 1. Introduction and literature review ................................................................... 1 1.1. Introduction .......................................................................................................................... 1 1.2. The vaginal microbiome ....................................................................................................... 3 The healthy microbiota ................................................................................................................... 3 The vaginal microbiome in dysbiosis .............................................................................................. 5 Pregnancy and the vaginal microbiome ........................................................................................... 9 Approaches to studying the vaginal microbiome ........................................................................... 10 1.3. Preterm birth ...................................................................................................................... 13 Definition ..................................................................................................................................... 13 Hypothesis of mechanisms ............................................................................................................ 13 Microorganisms and preterm birth ................................................................................................ 16 1.4. The genus Bifidobacterium ................................................................................................. 20 History.......................................................................................................................................... 20 Significance of lactic acid bacteria ................................................................................................ 21 Mother to infant bifidobacteria transmission.................................................................................. 23 Genetic diversity of bifidobacteria ................................................................................................ 25 OBJECTIVES ......................................................................................................................... 28 CHAPTER 2. The vaginal microbiome of pregnant women
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