Microbiome datasets are compositional: and this is not optional
Datasets collected by high-throughput sequencing (HTS) of 16S rRNA gene amplimers,
metagenomes or metatranscriptomes are commonplace and being used to study human …
metagenomes or metatranscriptomes are commonplace and being used to study human …
Compositional analysis: a valid approach to analyze microbiome high-throughput sequencing data
A workshop held at the 2015 annual meeting of the Canadian Society of Microbiologists
highlighted compositional data analysis methods and the importance of exploratory data …
highlighted compositional data analysis methods and the importance of exploratory data …
Enhancing diversity analysis by repeatedly rarefying next generation sequencing data describing microbial communities
Amplicon sequencing has revolutionized our ability to study DNA collected from
environmental samples by providing a rapid and sensitive technique for microbial …
environmental samples by providing a rapid and sensitive technique for microbial …
Seasonal shifts in the gut microbiome indicate plastic responses to diet in wild geladas
Background Adaptive shifts in gut microbiome composition are one route by which animals
adapt to seasonal changes in food availability and diet. However, outside of dietary shifts …
adapt to seasonal changes in food availability and diet. However, outside of dietary shifts …
A field guide for the compositional analysis of any-omics data
Background Next-generation sequencing (NGS) has made it possible to determine the
sequence and relative abundance of all nucleotides in a biological or environmental …
sequence and relative abundance of all nucleotides in a biological or environmental …
A phylogenetic transform enhances analysis of compositional microbiota data
Surveys of microbial communities (microbiota), typically measured as relative abundance of
species, have illustrated the importance of these communities in human health and disease …
species, have illustrated the importance of these communities in human health and disease …
Balances: a new perspective for microbiome analysis
High-throughput sequencing technologies have revolutionized microbiome research by
allowing the relative quantification of microbiome composition and function in different …
allowing the relative quantification of microbiome composition and function in different …
Microbiome multi-omics network analysis: statistical considerations, limitations, and opportunities
The advent of large-scale microbiome studies affords newfound analytical opportunities to
understand how these communities of microbes operate and relate to their environment …
understand how these communities of microbes operate and relate to their environment …
Methodology challenges in studying human gut microbiota–effects of collection, storage, DNA extraction and next generation sequencing technologies
The information on microbiota composition in the human gastrointestinal tract predominantly
originates from the analyses of human faeces by application of next generation sequencing …
originates from the analyses of human faeces by application of next generation sequencing …
Gut microbiota in mucosa and feces of newly diagnosed, treatment-naïve adult inflammatory bowel disease and irritable bowel syndrome patients
The knowledge on how gut microbes contribute to the inflammatory bowel disease (IBD) at
the onset of disease is still scarce. We compared gut microbiota in newly diagnosed …
the onset of disease is still scarce. We compared gut microbiota in newly diagnosed …