Comparing Published Gut Microbiome Taxonomic Data Across Multinational Studies

Abstract

Background: Nurse researchers are well poised to study the connection of the microbiome to health and disease. Evaluating published microbiome results can assist with study design and hypothesis generation.

Objectives: This article aims to present and define important analysis considerations in microbiome study planning and to identify genera shared across studies despite methodological differences. This methods article will highlight a workflow that the nurse scientist can use to combine and evaluate taxonomy tables for microbiome study or research proposal planning.

Methods: We compiled taxonomy tables from 13 published gut microbiome studies that had used Ion Torrent sequencing technology. We searched for studies that had amplified multiple hypervariable (V) regions of the 16S rRNA gene when sequencing the bacteria from healthy gut samples.

Results: We obtained 15 taxonomy tables from the 13 studies, comprised of samples from four continents and eight V regions. Methodology among studies was highly variable, including differences in V regions amplified, geographic location, and population demographics. Nevertheless, of the 354 total genera identified from the 15 data sets, 25 were shared in all V regions and the four continents. When relative abundance differences across the V regions were compared, Dorea and Roseburia were statistically different. Taxonomy tables from Asian subjects had increased average abundances of Prevotella and lowered abundances of Bacteroides compared with the European, North American, and South American study subjects.

Discussion: Evaluating taxonomy tables from previously published literature is essential for study planning. The genera found from different V regions and continents highlight geography and V region as important variables to consider in microbiome study design. The 25 shared genera across the various studies may represent genera commonly found in healthy gut microbiomes. Understanding the factors that may affect the results from a variety of microbiome studies will allow nurse scientists to plan research proposals in an informed manner. This work presents a valuable framework for future cross-study comparisons conducted across the globe.

Figure 1.. Stepwise Workflow of Data Accrual and Manipulation Process

Text in italics are results or output from example workflow. Abbreviations: IT = Ion Torrent; HMP = Human Microbiome Project; SD = Standard Deviation; V = hypervariable region. Figure created with Biorender.

Figure 2.. Venn Diagram by V region and Continent.

A.) Four-way Venn Diagram of different V region combinations (i.e., V12, V23, V3, V4, and excluding the IT Kit). Overlap of any portion of the ovals indicates shared genera. Numbers within the union indicates how many genera were shared between V regions labeled, or the intersection indicates how many were unique to that region. Numbers within the Venn Diagram represent those 13 data sets that amplified regions V1-V4. The number outside of the Venn Diagram are those genera found unique to the ITKit. B.) Venn diagram showing the comparisons for each of the four continents surveyed in this study. C.) Venn diagram of the 25 genera found intersecting all V regions and all continents. The number outside of the Venn are the number genera not found on all V regions and Continents. Abbreviations: N. America=North America; S. America=South America.

Figure 3.. Stacked Bar Charts of Bacteria Relative Abundance: V Region Analysis.

A.) Average relative abundance of 25 intersecting genera in all V regions and all continents, by specific V region (x-axis). B.) Average relative abundance of 25 intersecting genera for each of the data sets, organized by continent. Abbreviations: IT Kit = Ion Torrent Kit, amplifying V2,3,4,6/7,8,9; V = hypervariable

Figure 3.. Stacked Bar Charts of Bacteria Relative Abundance: V Region Analysis.

A.) Average relative abundance of 25 intersecting genera in all V regions and all continents, by specific V region (x-axis). B.) Average relative abundance of 25 intersecting genera for each of the data sets, organized by continent. Abbreviations: IT Kit = Ion Torrent Kit, amplifying V2,3,4,6/7,8,9; V = hypervariable

Figure 4:. Average Relative Abundance of HMP versus Continent of origin.

A.) Logarithm base 10 average relative abundance of HMP (y-axis) versus logarithm base 10 average relative abundance of North America (x-axis). B.) Logarithm base 10 average relative abundance of HMP (y-axis) versus logarithm base 10 average relative abundance of Asia (x-axis). C.) Logarithm base 10 average relative abundance of HMP (y-axis) versus logarithm base 10 average relative abundance of South America (x-axis). D.) Logarithm base 10 average relative abundance of HMP (y-axis) versus logarithm base 10 average relative abundance of Europe (x-axis).