Leveraging the microbiome to improve pregnancy outcomes in African American communities

August, 2020

Expectant mothers have a lot of things to consider when trying to keep themselves and their pregnancies healthy. With stress, food and environmental factors already being considered as influences on her overall health and wellbeing and that of her unborn child, one might think that the changes to her microbiome is the least of her worries. But, research shows that microbiome health during pregnancy can be an indicator to – and potentially influence – outcomes1

Some women, African American women in particular, can experience additional stressors and obstacles to healthy pregnancy outcomes2. At Emory University, Dr. Anna Knight is part of a team exploring the Emory University African American Microbiome in Pregnancy Cohort to identify changes to the microbiome that might affect outcomes.

How did you first get interested in science and microbiome research?

I’ve been interested in science for as long as I can remember. I majored in Human Biology at North Carolina State University, where I had the opportunity to work in a genetics lab studying colorectal cancer. This led me to pursue a Ph.D. in genetics at Emory University, where I first became interested in the microbiome after doing a rotation analyzing 16S rRNA sequencing for oral, vaginal, and gut microbiome swabs. I continued to work on the microbiome throughout my graduate career and have since made it a key area of focus for my own lab. I am constantly amazed by the potential implications it has for improving health.

Can you summarize your Ph.D. project?

I worked with the Emory University African American Microbiome in Pregnancy Cohort to examine changes in the oral, vaginal, and gut microbiomes associated with pregnancy and pregnancy complications. Participants provided self-collected swabs twice over pregnancy, as well as a blood sample for DNA methylation and gene expression analyses. They also answered a range of sociodemographic and stress-related scales. The goal of this study is to bridge the gap in knowledge of the etiology of pregnancy complications and the increased rates of pregnancy complications in African American women.

What is a typical day for you in the lab?

A typical day in lab for me combines both bench and computational work. I typically spend time extracting DNA and RNA, supervising trainees, and analyzing DNA methylation, gene expression, and microbiome data from pregnant women and their neonates. I also work on manuscripts or drafting grant proposals to fund new projects. Our lab is highly collaborative, and I often devote time to building collaborations with investigators in the Department of Gynecology and Obstetrics, School of Nursing, and Human Genetics.

What do you find most interesting about your project? What is the most interesting or surprising result you have found? 

I find exploring all of the new bioinformatics tools for analyzing the microbiome to be the most interesting part of the project. In 2019, we published a paper, “Stability of the Vaginal, Oral, and Gut Microbiota Across Pregnancy Among African American Women: The Effect of Socioeconomic Status and Antibiotic Exposure”2  detailing our early findings. We found that some sociodemographic characteristics are associated with changes in microbiome diversity over pregnancy. However, the main aims of the study are still being analyzed.

What kind of microbiome research do you perform and how does it impact health and disease or the environment? Where do you see this heading in the next five years?

My current microbiome research focuses on changes in the microbiome over pregnancy, and how the microbiome relates to pregnancy complications using the Emory University African American Microbiome in Pregnancy Cohort. Our first paper examining the impact of socioeconomic status on the microbiome was published in 20192, and we’ve learned so much about studying the microbiome during this process. We chose to study the microbiome during pregnancy due to the links between vaginal infections and periodontal disease to preterm birth, and the known changes in the gut microbiome over pregnancy. We hope that our research in this area can help identify interventions and lifestyle changes that modulate the microbiome and can decrease risk of pregnancy complications in African Americans. 

Within the next five years, we will have more than 500 participants with oral, vaginal, and gut microbiome swabs for two timepoints during pregnancy. We will use this cohort to identify associations between local microbiome composition and adverse pregnancy outcomes, including preterm birth, preeclampsia, and gestational diabetes. We will also examine the impact of stress and other biobehavioral factors on the microbiome that can be modified to reduce the risk of adverse pregnancy outcomes.

What are your hobbies?

My hobbies including traveling, baking and decorating cupcakes, and reading with a nice cup of tea.

What are the major challenges you face in your research with regards to sample collection, nucleic acid isolation and data analysis?

The major challenges we have faced have been identifying the best storage methods for home-collected samples and optimizing our extraction protocols. We have piloted different bead beating and lysis techniques, and have developed qPCR protocols to quantify bacterial DNA. On the analysis side, our biggest hurdle has been analyzing data from ~1,000 samples, and carefully determining the proper QC pipelines.

Which QIAGEN products do you use/have you used in the past and what did you like about the products?

Our lab uses QIAGEN products for many of our research projects. We use the QIAamp DNA Mini Kit and the DNeasy Blood and Tissue Kit to extract DNA from blood clots, Guthrie cards, and peripheral blood mononuclear cell samples. For our microbiome studies, we use the DNeasy PowerSoil Kit to extract DNA from oral, vaginal, and gut swabs. 

If you have similar challenges, we recommend the use of the new generation DNeasy 96 PowerSoil Pro Kit.

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1. Dunlop AL, Mulle JG, Ferranti EP, Edwards S, Dunn AB, Corwin EJ. (2015) Maternal Microbiome and Pregnancy Outcomes That Impact Infant Health: A Review. Adv Neonatal Care. 15(6), 377‐385.
2. Dunlop AL, Knight AK, Satten GA, et al. (2019) Stability of the vaginal, oral, and gut microbiota across pregnancy among African American women: the effect of socioeconomic status and antibiotic exposure. PeerJ. 7