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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Zero-inflated negative binomial regression for differential abundance testing in microbiome studies
TL;DR: Application to two real datasets indicate that the proposed Zero-inflated Negative Binomial regression for identifying differentially abundant taxa between two or more populations is capable of detecting biologically meaningful taxa, consistent with previous studies.
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A two-stage microbial association mapping framework with advanced FDR control
TL;DR: A two-stage microbial association mapping framework which uses grouping information from the taxonomic tree to strengthen statistical power in association tests at the target rank and achieves additional efficiency by utilizing the intrinsic taxonomic structure of microbiome data is proposed.
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You must choose, but choose wisely: model-based approaches for microbial community analysis
TL;DR: It is shown that model assessment is important for qualifying interpretations and can further guide refinements in subsequent analyses as well as advocating for model-based approaches in data analyses of the soil microbiome.
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Gut and immune effects of bioactive milk factors in preterm pigs exposed to prenatal inflammation.
Shuqiang Ren,Yan Hui,Sandra Goericke-Pesch,Stanislava Pankratova,Witold Kot,Xiaoyu Pan,Thomas Thymann,Per T. Sangild,Per T. Sangild,Duc Ninh Nguyen +9 more
TL;DR: It is concluded that supplementation with bioactive ingredients from bovine milk supports gut, immunity and NEC resistance in neonates born preterm after gram-negative infection before birth and exerted only modest effects on gut and systemic immune parameters in preterm pigs exposed to prenatal inflammation.
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Microbial Community Dynamics During Lake Ice Freezing.
Tim Butler,Anna-Catharina Wilhelm,Amber C. Dwyer,Paige N Webb,Andrew L. Baldwin,Stephen M. Techtmann +5 more
TL;DR: Environmental conditions along with microbial abundance and microbial community composition was determined and relatives of microbes involved in nitrogen cycling bloomed during times of ice cover as sequences related to known nitrifying taxa were significantly enriched during ice cover.
References
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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.
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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
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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.
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Simon Anders,Wolfgang Huber +1 more
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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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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