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“We aim to support the integration of microbiome collection and analysis in human cohort studies to advance clinical and translational research towards a better understanding of microbiome function in human health and disease.”
Additional support for Platform 2 provided by Dr. John Conly and Dr. Thomas J. Louie at the University of Calgary, Dr. Eytan Wine at the University of Alberta, and Dr. Qingling Duan at Queen’s University.
Get access to existing human cohort data and associated metadata, including the CHILD study and the Alberta BLOOM study. See below for more details, or contact us.
CHILD Study: The CHILD study is a longitudinal cohort study funded by AllerGen and CIHR. It began in 2008 and includes over 3,400 Canadian children. The CHILD study includes data collected from biological samples (including microbiome samples from various body sites), questionnaires, home assessments, and clinical assessments.
Alberta BLOOM Study: The Alberta BLOOM (Begin a Life of health with Observation and Optimization of the Microbiome) is a “research initiative aiming to understand how the microbiome of children born premature develops over the first years of life in comparison to the microbiome of children born at term.” This CIHR-funded study follows children from birth to preschool-age.
Experimental Design Consultation: Get help designing new microbiome studies using human cohorts, with specific attention to sample size, power calculations, feasibility studies, sample collection, etc. Contact us for details.
Data Analysis Assistance: Get advice on the analysis of new or existing human microbiome data gathered from cohort studies. Contact us for details.
Note: Advice and support for data analysis will be conducted in concert with Platform 4 (Functional Omics) and Platform 5 (Computational Development) to ensure the latest methods and tools are used to account for the unique compositional and functional nature of microbiome data, and to control for biases.
The rise to power of the microbiome: power and sample size calculation for microbiome studies
Ferdous et al. Mucosal Immunology. 22 July 2022.
“How many people do I need in my microbiome study?” This review is a resource to help researchers conduct sample size calculations, and includes statistical approaches to calculate sample sizes for typical microbiome studies, as well as relevant R scripts to help with some of these calculations.
Beta-diversity distance matrices for microbiome sample size and power calculations — How to obtain good estimates
Jiang et al. Computational and Structural Biotechnology Journal. 23 May 2022.
This review describes and illustrates three strategies for obtaining realistic distance matrices when designing a microbiome study. Using data from the American Gut project, we provide tables of observed distances for use by researchers planning their own studies, as well as R codes for generating similar matrices in other datasets. Furthermore, for simulated data, we compare methods, provide R codes, and demonstrate how challenging it is to obtain realistic distance distributions without any benchmark data. This code and illustrative distance tables are provided by the IMPACTT Consortium as a resource to the microbiome research community.
ReACH (Research Advancement through cohort Cataloguing and Harmonization) is a multidisciplinary research initiative funded under CIHR‘s Healthy Life Trajectories Initiative (HeLTI) that aims to help researchers investigating the Developmental Origins of Health and Disease (DOHaD). The initiative brings together a multidisciplinary team of researchers working together to develop resources to leverage collaborations and optimize use of Canadian research data. ReACH has created an open-access metadata catalogue, as well as developed resources to support data harmonization and co-analysis across studies. See the original publication here.
SyMBIOTA (Synergy in Microbiota Research) is a research program that investigates “early life determinants in the development of the infant gut microbiota and how the developing microbiota and its metabolites influence later childhood disease.” SyMBIOTA uses the CHILD cohort study as a research platform.
Let Them Eat Dirt: Saving our Children from an Oversanitized World is a bestselling book written by Dr. Brett Finlay and Platform 2 Co-Lead Dr. Marie-Claire Arrieta geared towards parents of young children. It explains how the millions of microbes that live in our bodies influence childhood development, and why an imbalance of these microbes, sometimes cause by an oversanitized environment, can lead to multiple chronic conditions.
Let Them Eat Dirt: The Hunt for our Missing Microbes is a documentary based on the bestselling book. Learn more here.
Contact us if you don’t have access to these articles.
Bergeron et al. 2021. Cohort Profile: Research Advancement through Cohort Cataloguing and Harmonization (ReACH). Int J Epidemiol. 50(2): 396-397.
Obiakor et al. 2018. The Association Between Early Life Antibiotic Use and Allergic Disease in Young Children: Recent Insights and their Implications. Expert Rev Clin Immunol. 14(10):841-855.
Patrick et al. 2020. Decreasing Antibiotic Use, the Gut Microbiota, and Asthma Incidence in Children: Evidence from Population-Based and Prospective Cohort Studies. Lancet Respir Med. 8(11): 1094-1105.
Laforest-Lapointe & Arrieta. 2017. Patterns of Early-Life Gut Microbial Colonization during Human Immune Development: An Ecological Perspective. Front Immunol. 9(788): 1-13.
Kozyrskyj. 2015. Can We Predict Future Allergies from our Infant Gut Microbiota? Expert Rev Resp Med. 9(6): 667-670.
