Metagenomic biomarker discovery and explanation
Nicola Segata,Jacques Izard,Jacques Izard,Levi Waldron,Dirk Gevers,Larisa Miropolsky,Wendy S. Garrett,Curtis Huttenhower +7 more
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TLDR
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.Abstract:
This study describes and validates a new method for metagenomic biomarker discovery by way of class comparison, tests of biological consistency and effect size estimation. This addresses the challenge of finding organisms, genes, or pathways that consistently explain the differences between two or more microbial communities, which is a central problem to the study of metagenomics. We extensively validate our method on several microbiomes and a convenient online interface for the method is provided at http://huttenhower.sph.harvard.edu/lefse/.read more
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The combination of biochar and plant roots improves soil bacterial adaptation to PAH stress: Insights from soil enzymes, microbiome, and metabolome
TL;DR: It is suggested that biochar application can efficiently improve bacterial functions in rhizosphere soil, and the results facilitate the development of in situ remediation programs in soil contaminated with PAHs.
Journal ArticleDOI
Increases in bacterial community network complexity induced by biochar-based fertilizer amendments to karst calcareous soil
TL;DR: Wang et al. as mentioned in this paper explored the amendment of karst soils with biochar in combination with swine manure compost and chemical fertilizer with the aim of improving the microbial community structure and soil nutrient status of these soils.
Journal ArticleDOI
Characterization of intestinal microbiota in alcoholic patients with and without alcoholic hepatitis or chronic alcoholic pancreatitis.
Dragos Ciocan,Vinciane Rebours,Vinciane Rebours,Cosmin Sebastian Voican,Laura Wrzosek,Virginie Puchois,Anne-Marie Cassard,Gabriel Perlemuter +7 more
TL;DR: Bacterial diversity was lower in patients with CAP, who had a global intestinal microbiota composition different from that of AC, and sAH patients were found to have higher levels of Haemophilus.
Journal ArticleDOI
Interactions of plant growth-promoting rhizobacteria and soil factors in two leguminous plants.
TL;DR: Soil pH, P and K significantly affected the composition of the soybean rhizomicrobiome, whereas soil pH and N had a significant effect on the alfalfa rhizome, and the rhizomes assemblage and plant growth-associated microbes are differentially structured by soil properties and leguminous plant species.
Journal ArticleDOI
Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment.
Julia Fukuyama,Laurie Rumker,Kris Sankaran,Pratheepa Jeganathan,Les Dethlefsen,David A. Relman,David A. Relman,Susan Holmes +7 more
TL;DR: Through a holistic approach that integrates phylogenetic, metagenomic and abundance information, this work elucidate patterns of taxonomic and functional change that characterize the community recovery process across individuals and provides greater interpretability than existing methods.
References
More filters
Journal ArticleDOI
Matplotlib: A 2D Graphics Environment
TL;DR: Matplotlib is a 2D graphics package used for Python for application development, interactive scripting, and publication-quality image generation across user interfaces and operating systems.
BookDOI
Modern Applied Statistics with S
W. N. Venables,Brian D. Ripley +1 more
TL;DR: A guide to using S environments to perform statistical analyses providing both an introduction to the use of S and a course in modern statistical methods.
Book
Principal Component Analysis
TL;DR: In this article, the authors present a graphical representation of data using Principal Component Analysis (PCA) for time series and other non-independent data, as well as a generalization and adaptation of principal component analysis.
Journal ArticleDOI
Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
Patrick D. Schloss,Patrick D. Schloss,Sarah L. Westcott,Sarah L. Westcott,Thomas Ryabin,Justine R. Hall,Martin Hartmann,Emily B. Hollister,Ryan A. Lesniewski,Brian B. Oakley,Donovan H. Parks,Courtney J. Robinson,Jason W. Sahl,Blaz Stres,Gerhard G. Thallinger,David J. Van Horn,Carolyn F. Weber +16 more
TL;DR: M mothur is used as a case study to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the α and β diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments.
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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