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As other reference-based approaches, one potential limitation of VALENCIA is that it is not able to classify communities which were not included in the training dataset. Though VALENCIA was demonstrated to be applicable on different populations, age ranges, and 16S rRNA regions, misclassification could happen for samples with novel bacteria or different community structures. The only potential issues we observed were related to the presence of community profiles which did not completely match those in the reference. For example, CST IV communities from some African populations tend to have a higher relative abundance of Prevotella spp. than CST IV communities from North American women [21, 25, 32]. We have shown, in our analysis of test dataset 3, that VALENCIA assigns these communities to one of the subtypes of CST IV depending on the presence and abundance of other taxa. However, an argument could be made for the addition of a novel CST and reference centroid which is Prevotella-dominated as defined by samples from African women. VALENCIA can be expanded by the addition of novel CSTs not found in the training dataset, when appropriate. This could be achieved either by adding data defining these novel CSTs to the existing training dataset or by constructing new training datasets from samples originating from a specific population of interest. As we collect more data from women across the globe, we plan to expand, update, and maintain VALENCIA.
MF, JR, and RB devised the study. MF designed and wrote VALENCIA. MF, BM, and PG performed the data analysis. SB and JH compiled the data and metadata. MH generated the data. MF, BM, and JR wrote the manuscript with edits from RB, SB, and JH. All authors read and approved the final manuscript.
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