The importance of longitudinal analysis in human microbiome studies

Human microbiome research has exploded over the past decade, revealing the fascinating influence of our bodily microbes on human health and disease from gut health to skin health to brain health. To date, however, a majority of human microbiome studies have been cross-sectional, analysing microbiomes at a single point in time. However, human microbiomes can change rapidly in response to different foods, drugs and their environment, and it is these changes over time that may tell us more about the influence of human microbiomes on health and disease, than microbial snapshots at a single point in time. This blog will outline the evidence showing changes in human microbiomes over time and discuss the importance of incorporating longitudinal sampling into your microbiome study.


Human microbiome research to date


Human microbiome research has provided fascinating insights into the influence of microbes on the human body, from belly to brain. However, most of this research to date has been cross-sectional, meaning microbiomes are examined at a single point in time. However, longitudinal studies, which study participants over a particular period of time, are a more powerful scientific tool, as they can allow scientists to examine how microbiomes change over time in response to age, disease, diet or any other factor. Indeed, the initial phase of the Human Microbiome Project, launched in 2007, aimed to profile the healthy microbiome in various body sites in humans, but did not examine how the human microbiome changed over time. This cross-sectional analysis has now been extended in Phase 2 of the Human Microbiome Project, in which microbiomes are being studied over time to see if they change in mothers giving birth preterm, or adults with inflammatory bowel disease and Type 2 diabetes. Like many other ecosystems, these changes in the microbiome over time are a more powerful way to understand whether they are related to disease.


Studies using longitudinal sampling


Recent microbiome studies incorporating longitudinal sampling have identified critical insights into how microbiomes change in response to their environment and even prior to the onset of certain diseases:




Previous cross-sectional research has demonstrated associations between the vaginal microbiome and preterm birth, with varying results across different populations. However, larger longitudinal analyses have more recently shown that the changes in vaginal microbiome composition over time through pregnancy provide more sensitive insights into microbial signatures that are associated with preterm birth.




The gut microbiome differs between individuals with different diets, such as vegetarians vs omnivores. However, cross-sectional studies do not determine whether these differences are due to diets alone or other differences in lifestyles between vegetarians, omnivores or those with other diets. However, longitudinal studies, which track changes in gut microbiome composition over the course of time with changes in diet tell us much more about the influence of foods on the gut microbiome and associated health outcomes.


Inflammatory disease onset


A number of inflammatory diseases including inflammatory bowel disease, asthma and arthritis have been associated with differences in gut microbiome composition. However, more recent evidence from longitudinal studies have shown changes in the gut microbiome that occur prior to the onset of these diseases or their symptoms, including type 1 diabetes onset in children and inflammatory bowel disease flare-ups in adults.


Human microbiomes can change daily (and even hourly…)


Monthly or weekly sampling can provide detailed insight into changes in human microbiome composition and function. However, a small number of research studies have examined daily changes in human microbiomes and found that there are changes apparent even from day-to-day in both infants and in adults consuming different diets. In fact, changes in the oral microbiome even change throughout a single 24 hour period, from morning to night. These studies suggest that studying microbiomes over multiple time-points is important to distinguish whether differences in microbiome profiles between individuals are due to differences in times or days of collection or due to other factors such as diet and disease.


Conducting your longitudinal microbiome study


As we learn more about the microbes that inhabit the human body and the role they play in human health and disease, it will become more important to study the changes in these microbes over time. The team at Microbiome Insights are leading experts in microbiome research studies from study design to analysis. If you are looking for advice on your microbiome research study, reach out to the team today.


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About Microbiome Insights

Microbiome Insights, Inc. is a global leader providing end-to-end microbiome sequencing and comprehensive bioinformatic analysis. The company is headquartered in Vancouver, Canada where samples from around the world are processed in its College of American Pathologist (CAP) accredited laboratory. Working with clients from pharma, biotech, nutrition, cosmetic and agriculture companies as well as with world leading academic and government research institutions, Microbiome Insights has supported over 772 microbiome studies from basic research to commercial R&D and clinical trials. The company's team of expert bioinformaticians and data scientists deliver industry leading insights including biomarker discovery, machine-learning based modelling and customized bioinformatics analysis.