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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Prenatal dietary supplements influence the infant airway microbiota in a randomized factorial clinical trial
Mathis Hjort Hjelmsø,Shiraz A. Shah,Jonathan Thorsen,Morten Arendt Rasmussen,Gisle Vestergaard,Martin S. Mortensen,Asker Daniel Brejnrod,Susanne Brix,Bo L. Chawes,Klaus Bønnelykke,Søren J. Sørensen,Jakob Stokholm,Hans Bisgaard +12 more
TL;DR: Mediation analysis reveals the changed airway microbiota to be a minor and non-significant mediator of the protective effect of the dietary interventions on risk of asthma, demonstrating the potential of prenatal dietary supplements as manipulators of the early airway bacterial colonization.
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Host-microbiota interactions shed light on mortality events in the striped venus clam Chamelea gallina.
Massimo Milan,Morgan Smits,Morgan Smits,Giulia Dalla Rovere,Silvia Iori,Angela Zampieri,Lisa Carraro,Camillo Martino,Chiara Papetti,Andrea Ianni,Nicola Ferri,Marco Iannaccone,Tomaso Patarnello,Romina Brunetta,Claudio Ciofi,Lisa Grotta,Giuseppe Arcangeli,Luca Bargelloni,Barbara Cardazzo,Giuseppe Martino +19 more
TL;DR: A broader approach based on the combination of RNA‐sequencing and 16S microbiota analyses to decipher the factors underlying mass mortality in the striped venus clam, Chamelea gallina, along the Adriatic coast is proposed.
Journal ArticleDOI
Variability in Metagenomic Count Data and Its Influence on the Identification of Differentially Abundant Genes.
TL;DR: An hierarchical overdispersed Poisson model is introduced to explore the variability in metagenomic data and provides suggestions for accurate and reliable identification of differentially abundant genes.
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Environmental pollution effects on plant microbiota: the case study of poplar bacterial-fungal response to silver nanoparticles
Francesco Vitali,Aida Raio,Federico Sebastiani,Paolo Cherubini,Duccio Cavalieri,Claudia Cocozza +5 more
TL;DR: This study offers new insights into the effects of Ag-NPs on both phyllosphere and rhizosphere poplar-associated microbiota and may represent a first attempt to understand the behavior of microbial communities of a tree species growing in a polluted environment.
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Genetic adaptation of microbial populations present in high-intensity catfish production systems with therapeutic oxytetracycline treatment.
TL;DR: Results of this study suggested that aquaculture waste, especially waste containing therapeutic antibiotics, has a significant impact on microbial population structures and their genetic structures.
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
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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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