Metagenomic biomarker discovery and explanation
Nicola Segata,Jacques Izard,Jacques Izard,Levi Waldron,Dirk Gevers,Larisa Miropolsky,Wendy S. Garrett,Curtis Huttenhower +7 more
Reads0
Chats0
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
Citations
More filters
Journal ArticleDOI
Effect of time-restricted feeding on metabolic risk and circadian rhythm associated with gut microbiome in healthy males
Falak Zeb,Xiaoyue Wu,Lijun Chen,Sadia Fatima,Ijaz-Ul Haq,Aochang Chen,Fatima Majeed,Qing Feng,Min Li +8 more
TL;DR: It is shown that TRF ameliorated the serum lipid and liver profiles of the individuals and regulates circadian rhythm associated with gut microbiome modulation, which could be a safe remedy for the prevention of metabolic diseases related to dyslipidemia.
Journal ArticleDOI
Calorie restriction slows age-related microbiota changes in an Alzheimer's disease model in female mice.
Laura M. Cox,Marissa J. Schafer,Jiho Sohn,Julia Vincentini,Howard L. Weiner,Stephen D. Ginsberg,Martin J. Blaser,Martin J. Blaser +7 more
TL;DR: It is found that female Tg2576 mice have more substantial age-related microbiome changes compared to wildtype (WT) mice, including an increase in Bacteroides, which were normalized by CR, and long-term CR may alter the gut environment and prevent the expansion of microbes that contribute to age- related cognitive decline.
Journal ArticleDOI
Structure and Function of the Fecal Microbiota in Diarrheic Neonatal Piglets.
Qiaoli Yang,Xiaoyu Huang,Shengguo Zhao,Wenyang Sun,Zunqiang Yan,Pengfei Wang,Li Shenggui,Wangzhou Huang,Shengwei Zhang,Lixia Liu,Shuangbao Gun +10 more
TL;DR: A potential role for Prevotella is identified in the community-wide microbial aberration and dysfunction that underpins the pathogenesis of piglet diarrheic conditions and may provide biomarkers of neonatal piglet diarrhea.
Journal ArticleDOI
Tree phyllosphere bacterial communities: exploring the magnitude of intra- and inter-individual variation among host species.
TL;DR: The results suggest that individual samples from consistent positions within the tree canopy from multiple individuals per species can be used to accurately quantify variation in phyllosphere bacterial community structure.
Journal ArticleDOI
GOsummaries: an R Package for Visual Functional Annotation of Experimental Data
TL;DR: A novel R package, 'GOsummaries' is introduced that visualises the GO enrichment results as concise word clouds that can be combined together if the number of gene lists is larger, and improves significantly the interpretability of PCA results.
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.
Related Papers (5)
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
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