The number of microbiome-related studies has notably increased the availability of data on
human microbiome composition and function. These studies provide the essential material …

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

The high-dimensional data created by high-throughput technologies require visualization
tools that reveal data structure and patterns in an intuitive form. We present PHATE, a …

Very low-carbohydrate, high-fat ketogenic diets (KDs) induce a pronounced shift in
metabolic fuel utilization that elevates circulating ketone bodies; however, the …

Diet is a key determinant of human gut microbiome variation. However, the fine-scale
relationships between daily food choices and human gut microbiome composition remain …

Differential abundance analysis is controversial throughout microbiome research. Gold
standard approaches require laborious measurements of total microbial load, or absolute …

Relatives have more similar gut microbiomes than nonrelatives, but the degree to which this
similarity results from shared genotypes versus shared environments has been …

Datasets collected by high-throughput sequencing (HTS) of 16S rRNA gene amplimers,
metagenomes or metatranscriptomes are commonplace and being used to study human …

Marker-gene and metagenomic sequencing have profoundly expanded our ability to
measure biological communities. But the measurements they provide differ from the truth …

Increasingly, researchers are discovering associations between microbiome and a wide
range of human diseases such as obesity, inflammatory bowel diseases, HIV, and so on …