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 ...
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...
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...
Canonical correspondence analysis and related multivariate methods in aquatic ecology Canonical correspondence analysis (CCA) is a multivariate method to elucidate the relationships between biological assemblages of species and their environ... CJF Braak,PFM Verdonschot - 《Aquatic Sciences》 被引量: 3055...
Microbial diversity and differential abundance analyses Alpha diversity indices (i.e. Observed ASV [richness], Shannon, Inverse of Simpson and Pielou’s evenness), rarefaction curves and beta diversity (determined by PCoA based on Bray-Curtis dissimilarities) were computed as previously described by Fe...
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...
Moreover, intriguing findings were obtained through different differential abundance (DA) analyses. Particularly, the ANCOM-BC analysis identified amplicon sequence variants (ASVs) with significantly distinct abundances. Of particular interest was the observation of higher abundances of ASVs affiliated with ...
Abstract Background Materials and methods Results Discussion Conclusions Availability of data and materials Abbreviations References Acknowledgements Funding Author information Ethics declarations Additional information Supplementary Information Rights and permissions About this article AdvertisementMicrobiome...
there is not even resolution in the study to say anything meaningful about that microbe in the context of differential abundance analysis. The--min-feature-countfilter is appliedafterthe--min-sample-countis applied, so it's possible for (for example) a sample to get filtered out which in tur...
It is important to point out that the treatment methods discussed in this review do not always give satisfying results, and, when a response occurs, it may not be permanent and it might be heterogeneous [21,30]. It could be correlated with patients’ lifestyle—their diet, sleep cycle, ex...