Interactions between species introduce spurious associations in microbiome studies

Microbiota contribute to many dimensions of host phenotype, including disease. To link specific microbes to specific phenotypes, microbiome-wide association studies compare microbial abundances between two groups of samples. Abundance differences, however, reflect not only direct associations with the phenotype, but also indirect effects due to microbial interactions. We found that microbial interactions could easily generate a large number of spurious associations that provide no mechanistic insight. Using techniques from statistical physics, we developed a method to remove indirect associations and applied it to the largest dataset on pediatric inflammatory bowel disease. Our method corrected the inflation of p-values in standard association tests and showed that only a small subset of associations is directly linked to the disease. Direct associations had a much higher accuracy in separating cases from controls and pointed to immunomodulation, butyrate production, and the brain-gut axis as important factors in the inflammatory bowel disease.Comment: 4 main text figures, 15 supplementary figures (i.e appendix) and 6 supplementary tables. Overall 49 pages including reference

Photon-Photon Correlations as a Probe of Vacuum Induced Coherence Effects

We present new experimental implications of the effects of vacuum induced coherence on the photon -photon correlation in the pi-polarized fluorescence in j = 1/2 to j = 1/2 transition. These effects should be thus observable in measurements of photon statistics in for example Hg and Ba ion traps.Comment: 7 pages, 6 figures, submitted to Physical Review