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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Journal ArticleDOI
Analysis of microbial compositions: a review of normalization and differential abundance analysis.
TL;DR: Some recent methods for differential abundance analysis are reviewed and described and their strengths and weaknesses are described.
Journal ArticleDOI
Statistical evaluation of methods for identification of differentially abundant genes in comparative metagenomics
TL;DR: It is shown that sample size, effect size, and gene abundance greatly affect the performance of all methods, and several of the methods also show non-optimal model assumptions and biased false discovery rate estimates, which can result in too large numbers of false positives.
Journal ArticleDOI
Contributions of the maternal oral and gut microbiome to placental microbial colonization in overweight and obese pregnant women
Luisa F. Gomez-Arango,Helen L. Barrett,Helen L. Barrett,H. David McIntyre,Leonie K. Callaway,Leonie K. Callaway,Mark Morrison,Marloes Dekker Nitert +7 more
TL;DR: It is demonstrated that the placental microbiome exhibits a higher resemblance and phylogenetic proximity with the pregnant oral microbiome, suggesting that placental colonization may have multiple niche sources.
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The Core and Seasonal Microbiota of Raw Bovine Milk in Tanker Trucks and the Impact of Transfer to a Milk Processing Facility
Mary E. Kable,Yanin Srisengfa,Miles Laird,Jose Zaragoza,Jeremy McLeod,Jessie Heidenreich,Maria L. Marco +6 more
TL;DR: Raw bovine milk samples from 899 tanker trucks arriving at two dairy processors in San Joaquin Valley of California during three seasons were analyzed by community 16S rRNA gene sequencing, revealing highly diverse bacterial populations, which exhibited seasonal differences.
Journal ArticleDOI
Apple endophytic microbiota of different rootstock/scion combinations suggests a genotype-specific influence.
Jia Liu,Ahmed Abdelfattah,John L. Norelli,Erik Burchard,Leonardo Schena,Samir Droby,Michael Wisniewski +6 more
TL;DR: The similarity of the microbiota in samples with a similar pedigree suggests the possibility of some level of co-evolution or selection as proposed by the “holobiont” concept in which metaorganisms have co-Evolved.
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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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