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
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Diet-induced obesity, energy metabolism and gut microbiota in C57BL/6J mice fed Western diets based on lean seafood or lean meat mixtures.
Jacob Bak Holm,Alexander Krokedal Rønnevik,Alexander Krokedal Rønnevik,Hanne Sørup Tastesen,Even Fjære,Even Fjære,Kristin Røen Fauske,Ulrike Liisberg,Ulrike Liisberg,Lise Madsen,Lise Madsen,Karsten Kristiansen,Bjørn Liaset +12 more
TL;DR: Comparing the gut microbiomes of mice fed the two WDs revealed significant differences in the relative abundance of operational taxonomic units (OTUs) belonging to the orders Bacteroidales and Clostridiales, with genes involved in metabolism of aromatic amino acids exhibiting higher relative abundance in the microbiome of mice feeding the seafood WD.
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Bayesian Nonparametric Ordination for the Analysis of Microbial Communities
TL;DR: A Bayesian analysis for dependent distributions to endow frequently used ordinations with estimates of uncertainty is proposed and a Bayesian nonparametric prior for dependent normalized random measures is constructed, which is marginally equivalent to the normalized generalized Gamma process.
Journal ArticleDOI
Mentholation affects the cigarette microbiota by selecting for bacteria resistant to harsh environmental conditions and selecting against potential bacterial pathogens
Jessica Chopyk,Suhana Chattopadhyay,Prachi Kulkarni,Emma Claye,Kelsey R. Babik,Molly Reid,Eoghan M. Smyth,Eoghan M. Smyth,Lauren E. Hittle,Joseph N. Paulson,Raul Cruz-Cano,Mihai Pop,Stephanie S. Buehler,Pamela I. Clark,Amy R. Sapkota,Emmanuel F. Mongodin +15 more
TL;DR: Preliminary evidence that the mentholation of commercially available cigarettes can impact the bacterial community of these products is provided, with Pseudomonas was the most abundant genera and included Pseudomanas oryzihabitans and Pseudsomonas putida, regardless of mentholated status.
Journal ArticleDOI
Late weaning is associated with increased microbial diversity and Faecalibacterium prausnitzii abundance in the fecal microbiota of piglets.
Francesca Romana Massacci,Francesca Romana Massacci,Mustapha Berri,Gaetan Lemonnier,Elodie Guettier,Fany Blanc,Deborah Jardet,Marie Noelle Rossignol,Marie-José Mercat,Joël Doré,Patricia Lepage,Claire Rogel-Gaillard,Jordi Estellé +12 more
TL;DR: Overall, these results show that late weaning increased gut microbiota diversity and the abundance of F. prausnitzii, a microorganism with positive effects in humans, show that weaning can drastically change the gut microbiota.
Posted ContentDOI
Longitudinal differential abundance analysis of microbial marker-gene surveys using smoothing splines
TL;DR: A novel method for longitudinal marker-gene surveys based on smoothing splines that allows discovery and inference of time periods where specific microbial features are differentially abundant and is, to the authors' knowledge, the first flexible method of its kind implemented as a software capable of detecting time periods of differential abundance for microbial features species.
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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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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