Dr. Wodan Ling, assistant professor of population health sciences, has received an R01 to develop robust statistical methods for longitudinal microbiome studies.
Large-scale longitudinal microbiome studies have the potential to provide an enhanced understanding of how changes in the microbiome are related to disease development and treatment efficacy. However, a gap persists in the availability of statistical and computational tools that can analyze these studies effectively.
“We have been analyzing longitudinal microbiome data for years, but there are issues with the data that have not been addressed,” Dr. Ling said. “We don’t have a pipeline we can use from the beginning to the end of the analytical process. It’s important to find means to identify the biomedical signals while capturing time dynamics and individual-specific effects observed in our data.”
Dr. Ling and her team will develop a suite of statistical tools tailored for longitudinal microbiome studies. The tools will address batch effects, which occur when non-biological factors in an experiment cause changes in the data, resulting in misleading outcomes. They will also provide improved identification of individual taxa associated with biomedical exposures or outcomes over time. Moreover, the suite will allow researchers to identify microbiome composition dynamics and visualize longitudinal microbiome data.
Her research is informed by and will enable the analysis of three longitudinal microbiome profiling studies. The first is a graft-versus-host disease study, which will elucidate how the gut microbiome interacts with complications and therapies in patients who received a bone marrow transplant. The second is a study on the association between the gut microbiome and post-transplant complications in kidney transplant recipients. The third examines the environmental factors associated with type I diabetes in children.
“The first two studies focus on transplants and, in turn, immunocompromised patients,” Dr. Ling explained. “Their microbiome takes on an incredibly vital role after their operation. The third study applies to another vulnerable population: patients who are only three months old. We’re examining, from birth, how their gut microbiome is developing and later associated with type I diabetes. Altogether, we want to observe patients whose microbiome reflect significant health implications over time.”
Dr. Ling will work with Dr. John R. Lee, associate professor of medicine, Dr. Michael C. Wu, professor of biostatistics at the Fred Hutchinson Cancer Center, and Dr. Ni Zhao, associate professor of biostatistics at Johns Hopkins Bloomberg School of Public Health. She also extends gratitude to Dr. Judy Zhong, chief of the Division of Biostatistics, Dr. Rulla Tamimi, chief of the Division of Epidemiology, the departmental faculty aim workshop members, and the grants and finance team for their continued support.
“Although our focus is on microbiome, these methods can be applied to other omics fields,” Dr. Ling said, emphasizing the interdisciplinary nature of her research. With the context of the additional studies, the suite will allow for improved etiology and development of microbiota-based therapies. Though there are challenges that come with advancing her research, she is excited to refine a pipeline that is seamless and cohesive.
- Highlights