… Susan P Holmes Susan P Holmes … Benjamin J Callahan, Paul J McMurdie, Susan P Holmes,
Exact sequence variants should replace operational taxonomic units in marker-gene data …

We present the open-source software package DADA2 for modeling and correcting Illumina-sequenced
amplicon errors ( https://github.com/benjjneb/dada2 ). DADA2 infers sample …

Background The accuracy of microbial community surveys based on marker-gene and
metagenomic sequencing (MGS) suffers from the presence of contaminants—DNA sequences …

Despite the critical role of the human microbiota in health, our understanding of microbiota
compositional dynamics during and after pregnancy is incomplete. We conducted a case-…

High-throughput sequencing of PCR-amplified taxonomic markers (like the 16S rRNA gene)
has enabled a new level of analysis of complex bacterial communities known as …

We consider a continuous space which models the set of all phylogenetic trees having a
fixed set of leaves. This space has a natural metric of nonpositive curvature, giving a way of …

The spatiotemporal structure of the human microbiome 1 , 2 , proteome 3 and metabolome
4 , 5 reflects and determines regional intestinal physiology and may have implications for …

Background In a series of studies of the gut microbiome, “enterotypes” have been used to
classify gut microbiome samples that cluster together in ordination analyses. Initially, three …

Preterm birth (PTB) is the leading cause of neonatal morbidity and mortality. Previous studies
have suggested that the maternal vaginal microbiota contributes to the pathophysiology of …

BACKGROUND Elevated levels of inflammatory cytokines have been associated with poor
outcomes among COVID-19 patients. It is unknown, however, how these levels compare with …