In harmony? A scoping review of methods to combine multiple 16S amplicon data sets

Robust evidence on relationships between the human microbiome and health are critical for understanding and improving the human condition. However, there is little information about methodological approaches to combine and analyze multiple microbiome data sets. To address this gap, we conducted a scoping review of studies that combine sequencing data from multiple data sets to understand the study objectives, data sources and selection, feature -table assembly methods, and analyses. References were identified through a systematic search of literature published between 2011 and 2022. Our final review included 60 articles. Despite the wide-spread use of the word “meta-analysis,” we found that only 24 studies used a systematic process to select their data sets, suggesting multiple meanings of the term within the field. While more than two thirds of studies used at least one publicly available data source, 19 had to request data from the original authors. Most studies (60%) combined data sets from multiple disjoint hypervariable regions. The number of hypervariable regions combined was not associated with the table construction method, but feature table construction method and the number of hypervariable regions influenced analytical resolution. Our results suggest the microbiome community needs to examine the use of terminology and analytic approaches for combining data sets; that additional work is needed to explore the impact of data source on bias in combined studies; and invite an independent evaluation of the methods used for feature table construction across disjoint regions.