Differential abundance analysis for microbial marker-gene surveys
TLDR
It is shown that metagenomeSeq outperforms the tools currently used in this field and relies on a novel normalization technique and a statistical model that accounts for undersampling in large-scale marker-gene studies.Abstract:
We introduce a methodology to assess differential abundance in sparse high-throughput microbial marker-gene survey data. Our approach, implemented in the metagenomeSeq Bioconductor package, relies on a novel normalization technique and a statistical model that accounts for undersampling-a common feature of large-scale marker-gene studies. Using simulated data and several published microbiota data sets, we show that metagenomeSeq outperforms the tools currently used in this field.read more
Citations
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A broken promise: microbiome differential abundance methods do not control the false discovery rate.
TL;DR: To further improve method benchmarking, a new simulation tool is introduced that allows to generate correlated count data following any univariate count distribution; the correlation structure may be inferred from real data.
Journal ArticleDOI
Experimental design and quantitative analysis of microbial community multiomics.
Himel Mallick,Himel Mallick,Siyuan Ma,Siyuan Ma,Eric A. Franzosa,Eric A. Franzosa,Tommi Vatanen,Xochitl C. Morgan,Curtis Huttenhower,Curtis Huttenhower +9 more
TL;DR: Current best practices for experimental design in microbiome molecular epidemiology are surveyed, including technologies for generating, analyzing, and integrating microbiome multiomics data.
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Proteobacteria explain significant functional variability in the human gut microbiome
TL;DR: These results establish limits on functional redundancy and predict specific genes and taxa that may explain physiological differences between gut microbiomes that are applicable to shotgun metagenomes from any environment and can integrate data from multiple studies.
Journal ArticleDOI
Large-scale benchmarking reveals false discoveries and count transformation sensitivity in 16S rRNA gene amplicon data analysis methods used in microbiome studies.
Jonathan Thorsen,Asker Daniel Brejnrod,Martin S. Mortensen,Morten Arendt Rasmussen,Jakob Stokholm,Waleed Abu Al-Soud,Søren J. Sørensen,Hans Bisgaard,Johannes Waage +8 more
TL;DR: The robustness of available methods for inference in differential relative abundance analysis and beta-diversity-based sample separation is assessed using a rigorous benchmarking framework based on large clinical 16S microbiome datasets from different sources, providing an easily extensible framework for benchmarking of new methods and future microbiome datasets.
Journal ArticleDOI
The maternal vaginal microbiome partially mediates the effects of prenatal stress on offspring gut and hypothalamus
Eldin Jašarević,Christopher D. Howard,Kathleen E. Morrison,Kathleen E. Morrison,Ana M. Misic,Tiffany Weinkopff,Phillip Scott,Phillip Scott,Christopher A. Hunter,Christopher A. Hunter,Daniel P. Beiting,Daniel P. Beiting,Tracy L. Bale +12 more
TL;DR: It is suggested that the maternal vaginal microbiota contribute to the lasting effects of prenatal stress on gut and hypothalamus in male mice, as observed after chronic stress in adulthood.
References
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Journal ArticleDOI
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
TL;DR: EdgeR as mentioned in this paper is a Bioconductor software package for examining differential expression of replicated count data, which uses an overdispersed Poisson model to account for both biological and technical variability and empirical Bayes methods are used to moderate the degree of overdispersion across transcripts, improving the reliability of inference.
Journal ArticleDOI
QIIME allows analysis of high-throughput community sequencing data.
J. Gregory Caporaso,Justin Kuczynski,Jesse Stombaugh,Kyle Bittinger,Frederic D. Bushman,Elizabeth K. Costello,Noah Fierer,Antonio Gonzalez Peña,Julia K. Goodrich,Jeffrey I. Gordon,Gavin A. Huttley,Scott T. Kelley,Dan Knights,Jeremy E. Koenig,Ruth E. Ley,Catherine A. Lozupone,Daniel McDonald,Brian D. Muegge,Meg Pirrung,Jens Reeder,Joel Sevinsky,Peter J. Turnbaugh,William A. Walters,Jeremy Widmann,Tanya Yatsunenko,Jesse R. Zaneveld,Rob Knight,Rob Knight +27 more
TL;DR: An overview of the analysis pipeline and links to raw data and processed output from the runs with and without denoising are provided.
Journal ArticleDOI
Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
TL;DR: The RDP Classifier can rapidly and accurately classify bacterial 16S rRNA sequences into the new higher-order taxonomy proposed in Bergey's Taxonomic Outline of the Prokaryotes, and the majority of the classification errors appear to be due to anomalies in the current taxonomies.
Journal ArticleDOI
Differential expression analysis for sequence count data.
Simon Anders,Wolfgang Huber +1 more
TL;DR: A method based on the negative binomial distribution, with variance and mean linked by local regression, is proposed and an implementation, DESeq, as an R/Bioconductor package is presented.
Journal ArticleDOI
Metagenomic biomarker discovery and explanation
Nicola Segata,Jacques Izard,Jacques Izard,Levi Waldron,Dirk Gevers,Larisa Miropolsky,Wendy S. Garrett,Curtis Huttenhower +7 more
TL;DR: A new method for metagenomic biomarker discovery is described and validates by way of class comparison, tests of biological consistency and effect size estimation to address the challenge of finding organisms, genes, or pathways that consistently explain the differences between two or more microbial communities.
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