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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Viral metagenomic analysis of fecal samples reveals an enteric virome signature in irritable bowel syndrome
Mina Hojat Ansari,Mehregan Ebrahimi,Mehregan Ebrahimi,Mohammad Reza Fattahi,Michael G. Gardner,Michael G. Gardner,Ali Reza Safarpour,Mohammad Ali Faghihi,Kamran Bagheri Lankarani +8 more
TL;DR: A significant decrease in the diversity and abundance of enteric virome particularly in eukaryotic viruses of Megavirales in patients with irritable bowel syndrome is observed, shedding light on a new hypothesis that the alteration of the viral taxa contributes to the pathogenesis of irritable Bowel Syndrome.
Journal ArticleDOI
Composition and variation of respiratory microbiota in healthy military personnel.
Jun Hang,Nela Zavaljevski,Yu Yang,Valmik Desai,Richard C. Ruck,Louis R. Macareo,Richard G. Jarman,Jaques Reifman,Robert A. Kuschner,Paul B. Keiser +9 more
TL;DR: The derived microbiome profiles were consistent both internally and with previous reports, suggesting their utility for further analyses and association studies based on sequence and demographic data.
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Impacts of Anthropogenic Pollutants on Benthic Prokaryotic Communities in Mediterranean Touristic Ports
Elena Tamburini,Lapo Doni,Lapo Doni,Raffaela Lussu,Federico Meloni,Giovanna Salvatorica Cappai,Alessandra Carucci,Enrico Casalone,Giorgio Mastromei,Francesco Vitali,Francesco Vitali +10 more
TL;DR: This study provides the first assessment of the effects exerted by multiple organic and inorganic contaminations on benthic prokaryotes in ports over a large spatial scale and designates bacterial community as a candidate tool for the monitoring of the sediment quality status in harbors.
Journal ArticleDOI
Gut microbiota components are associated with fixed airway obstruction in asthmatic patients living in the tropics
Emiro Buendía,Josefina Zakzuk,Homero San-Juan-Vergara,Eduardo E. Zurek,Nadim J. Ajami,Luis Caraballo +5 more
TL;DR: In this tropical asthmatic population, components of human gut microbiota are associated with the presence of a FAO phenotype and lower specific IgE response to mites and Ascaris.
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Microbiota composition of the koala ( Phascolarctos cinereus ) ocular and urogenital sites, and their association with Chlamydia infection and disease
TL;DR: It was found that reproductive status in females and sexual maturation in males, were defining features in the koala urogenital microbiota, which is suggestive of members of the microbiota being involved in the acceleration or prevention of infections progressing to disease.
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
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.
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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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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