Since the renaissance of microbiome research in the past decade, much insight has
accumulated in comprehending forces sha** the architecture and functionality of resident …

Complex microbial communities shape the dynamics of various environments, ranging from
the mammalian gastrointestinal tract to the soil. Advances in DNA sequencing technologies …

Microbiome differential abundance analysis methods for two groups are well-established in
the literature. However, many microbiome studies involve more than two groups, sometimes …

Characterizing biomarkers based on microbiome profiles has great potential for translational
medicine and precision medicine. Here, we present microbiomeMarker, an R/Bioconductor …

Identifying differentially abundant microbes is a common goal of microbiome studies.
Multiple methods are used interchangeably for this purpose in the literature. Yet, there are …

Microbiome research is now moving beyond the compositional analysis of microbial taxa in
a sample. Increasing evidence from large human microbiome studies suggests that …

The gut microbiome has been shown to influence the response of tumors to anti–PD-1
(programmed cell death–1) immunotherapy in preclinical mouse models and observational …

There is increasing interest in the potential contribution of the gut microbiome to autism
spectrum disorder (ASD). However, previous studies have been underpowered and have …

Differential abundance (DA) analysis of microbiome data continues to be a challenging
problem due to the complexity of the data. In this article we define the notion of “sampling …

Microplastics contaminate environments worldwide and are ingested by numerous species,
whose health is affected in multiple ways. A key dimension of health that may be affected is …