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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Longitudinal metagenomic profiling of bovine milk to assess the impact of intramammary treatment using a third-generation cephalosporin
E.K. Ganda,Rafael Bisinotto,Svetlana Lima,Kristina Kronauer,Dean Harrison Decter,Georgios Oikonomou,Georgios Oikonomou,Ynte H. Schukken,Rodrigo C. Bicalho +8 more
TL;DR: A longitudinal description of the changes in the microbiome of milk that are associated with mastitis and antimicrobial therapy is provided and no differences were observed in culture-negative mastitis samples when compared to healthy milk.
Journal ArticleDOI
Resistome diversity in cattle and the environment decreases during beef production
Noelle R. Noyes,Xiang Yang,Lyndsey M. Linke,Roberta J. Magnuson,Adam Dettenwanger,Shaun R. Cook,Ifigenia Geornaras,Dale R. Woerner,Sheryl P. Gow,Tim A. McAllister,Hua Yang,Jaime Ruiz,Kenneth L. Jones,Christina Boucher,Paul S. Morley,Keith E. Belk +15 more
TL;DR: In this article, the utility and limitations of metagenomics for assessing public health risks regarding antimicrobial resistance, and demonstrates that environmental pathways may represent a greater risk than the food supply.
Journal ArticleDOI
Plant developmental stage drives the differentiation in ecological role of the maize microbiome.
Chao Xiong,Brajesh K. Singh,Ji-Zheng He,Ji-Zheng He,Yan-Lai Han,Pei-Pei Li,Li-Hua Wan,Guo-Zhong Meng,Si-Yi Liu,Jun-Tao Wang,Chuan-Fa Wu,Chuan-Fa Wu,An-Hui Ge,Li-Mei Zhang +13 more
TL;DR: In this paper, the authors examined both bacterial and fungal communities across soils, epiphytic and endophytic niches of leaf and root, and plastic leaf of fake plant (representing environment-originating microbes) at three developmental stages of maize at two contrasting sites, and explored the potential function of phylloplane microbiomes based on metagenomics.
Journal ArticleDOI
Impact of prematurity and nutrition on the developing gut microbiome and preterm infant growth
Alex Grier,Xing Qiu,Sanjukta Bandyopadhyay,Jeanne Holden-Wiltse,Haeja A. Kessler,Ann L. Gill,Brooke Hamilton,Heidie Huyck,Sara K. Misra,Thomas J. Mariani,Rita M. Ryan,Lori Scholer,Kristin Scheible,Yi-Horng Lee,Mary T. Caserta,Gloria S. Pryhuber,Steven R. Gill +16 more
TL;DR: The phase-dependent impact of nutrition on infant growth along with phase-specific metabolic functions suggests a pioneering potential for improving growth outcomes by tailoring nutrient intake to microbiota phase.
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A comprehensive analysis of breast cancer microbiota and host gene expression.
Kevin J. Thompson,James N. Ingle,Xiaojia Tang,Nicholas Chia,Patricio Jeraldo,Marina Walther-Antonio,Karunya K. Kandimalla,Stephen Johnson,Janet Yao,Sean C. Harrington,Vera J. Suman,Liewei Wang,Richard L. Weinshilboum,Judy C. Boughey,Jean Pierre A. Kocher,Heidi Nelson,Matthew P. Goetz,Krishna R. Kalari +17 more
TL;DR: The objective was to characterize the microbiota and associate the microbiota with the tumor expression profiles, for 668 breast tumor tissues and 72 non-cancerous adjacent tissues and further unraveling this complicated interplay should enable us to better diagnose and treat breast cancer patients.
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.
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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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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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