Recent advances have made it possible to analyze high-throughput marker-gene
sequencing data without resorting to the customary construction of molecular operational�…

Clostridium butyricum is a butyrate-producing human gut symbiont that has been safely
used as a probiotic for decades. C. butyricum strains have been investigated for potential�…

Background The analysis of microbial communities through DNA sequencing brings many
challenges: the integration of different types of data with methods from ecology, genetics�…

Current practice in the normalization of microbiome count data is inefficient in the statistical
sense. For apparently historical reasons, the common approach is either to use simple�…

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

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�…

High-throughput DNA sequencing technologies, coupled with advanced bioinformatics
tools, have enabled rapid advances in microbial ecology and our understanding of the�…

Vinyl chloride (VC) is a human carcinogen and widespread priority pollutant. Here we report
the first, to our knowledge, complete genome sequences of microorganisms able to respire�…

We present a detailed description of a new Bioconductor package, phyloseq, for integrated
data and analysis of taxonomically-clustered phylogenetic sequencing data in conjunction�…