Statistical evaluation of diet-microbe associations.
BACKGROUND
Statistical evaluation of the association between microbial abundance and dietary variables can be done in various ways. Currently, there is no consensus on which methods are to be preferred in which circumstances. Application of particular methods seems to be based on the tradition of a particular research group, availability of experience with particular software, or depending on the outcomes of the analysis.


RESULTS
We applied four popular methods including edgeR, limma, metagenomeSeq and shotgunFunctionalizeR, to evaluate the association between dietary variables and abundance of microbes. We found large difference in results between the methods. Our simulation studies revealed that no single method was optimal.


CONCLUSIONS
We advise researchers to run multiple analyses and focus on the significant findings identified by multiple methods in order to achieve a better control of false discovery rate, although the false discovery rate can still be substantial.
['Zhang|Xiang|X|0000-0002-3878-9196', 'Nieuwdorp|Max|M|', 'Groen|Albert K|AK|', 'Zwinderman|Aeiko H|AH|']
D003198:Computer Simulation D004032:Diet D006801:Humans D054892:Metagenome D064307:Microbiota D012336:RNA, Ribosomal, 16S D012984:Software
Association Simulation Diet Microbiome Sequencing