Author Correction: Microbiome differential abundance methods produce different results across 38 datasetsIdentifying differentially abundant microbes is a common goal of microbiome studies. Multiple methods are used interchangeably for this purpose in the literature. Yet, there are few large-scale studies ...
Differential abundance methods aim at detecting associations between the abundances of bacterial species and subject grouping factors. The results of such methods are important to identify the microbiome as a prognostic or diagnostic biomarker or to demonstrate efficacy of prodrug or antibiotic drugs. ...
Microbiome differential abundance analysis methods for two groups are well-established in the literature. However, many microbiome studies involve more than two groups, sometimes even ordered groups such as stages of a disease, and require different types of comparison. Standard pairwise comparisons are...
Effects on differential abundance testing: We build on a previous work to evaluate seven proposed statistical methods using rarefied as well as raw data. Our simulation studies suggest that the false discovery rates of many differential abundance-testing methods are not increased by rarefying itself, ...
(1|cage/mice). Specific contrasts were selected using theemmeansfunction (specs = ~ receiver:donor:time point) withoutPvalue correction. After obtaining all contrasts of interest for all taxa/pathways, allPvalues were corrected using fdr. Finally, to test the differential abundance of species Pre...
We then conducted differential analysis in metaCyc pathways (Methods). Out of the 435 tested metaCyc pathways, 69 had differential abundance between oCRC and age-matched controls in both cohorts (FDR adjusted P < 0.05, Supplementary Data 6). Among these, while only one pathway, PWY-7316...
Heat map of significant differential abundance of metabolites with decreasing pH (community and sponge). Identities of metabolites 1–29 are outlined below: 01 — (1S,2S)-2-(methylamino)-1-phenylpropan-1-ol hydrochloride; 02 — benzalkonium chloride (C12); 03 — diphenhydramine|2-benzhydryloxy-...
qiime songbird multinomial \ --i-table redsea.biom.qza \ --m-metadata-file data/redsea/redsea_metadata.txt \ --p-formula "Depth+Temperature+Salinity+Oxygen+Fluorescence+Nitrate" \ --p-epochs 10000 \ --p-differential-prior 0.5 \ --p-training-column Testing \ --p-summary-interval 1 \...
The abundance of a given species in an ecosystem generally reflects its fitness and adaptive capacity to the respective environmental conditions. Therefore, we explored patterns of differential abundance (Methods section) and found 589 bacterial genera with higher abundances in cryospheric compared to non...
2. Materials and Methods 2.1. Study Subjects All experimental procedures were approved by the Ethics Committee of the Anhui Agricultural University, Hefei, China (approval number AHAUB2022008). Adult rams with no significant differences in age, weight, height, length, and chest circumference were ob...