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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Soil exposure modifies the gut microbiota and supports immune tolerance in a mouse model.
Noora Ottman,Noora Ottman,Lasse Ruokolainen,Alina Suomalainen,Hanna Sinkko,Piia Karisola,Jenni Lehtimäki,Maili Lehto,Ilkka Hanski,Harri Alenius,Nanna Fyhrquist,Nanna Fyhrquist +11 more
TL;DR: Exposure to soil polarizes the immune system toward TH1 and a higher level of anti‐inflammatory signaling, alleviating TH2‐type allergic responses, and provides evidence of the role of environmentally acquired microbes in alleviating against TH1‐driven inflammation, which relates to allergic diseases.
Journal ArticleDOI
Spatial and compositional variation in the fungal communities of organic and conventionally grown apple fruit at the consumer point-of-purchase.
TL;DR: Results of the present study represent an advancement of the current knowledge on the fungal microbiota in collected fruit tissues of apple and suggest that management practices may have been a contributing factor in determining the taxa present.
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Relocation, high‐latitude warming and host genetic identity shape the foliar fungal microbiome of poplars
Miklós Bálint,László Bartha,Robert B. O'Hara,Matthew S. Olson,Matthew S. Olson,Jürgen Otte,Markus Pfenninger,Amanda L. Robertson,Amanda L. Robertson,Peter Tiffin,Imke Schmitt +10 more
TL;DR: Examination of the effect of host relocation and high‐latitude warming on the complex fungal endophytic microbiome associated with leaves of an ecologically dominant boreal forest tree suggests that climate change effects on host–microbiome systems may be mediated by the interaction of environmental factors and the population genetic processes of the hosts.
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Characterization of bacterial microbiota compositions along the intestinal tract in pigs and their interactions and functions
Daniel Crespo-Piazuelo,Jordi Estellé,Manuel Revilla,Manuel Revilla,Lourdes Criado-Mesas,Yuliaxis Ramayo-Caldas,Cristina Óvilo,Ana Isabel Fernández,Maria Ballester,Josep María Folch,Josep María Folch +10 more
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A clinician's guide to microbiome analysis.
TL;DR: The major decision points confronting new entrants to the field or for those designing new projects in microbiome research are summarized and recommendations based on current technology options and the experience of sequencing platform choices are provided.
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.
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
TL;DR: An overview of the analysis pipeline and links to raw data and processed output from the runs with and without denoising are provided.
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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Differential expression analysis for sequence count data.
Simon Anders,Wolfgang Huber +1 more
TL;DR: A method based on the negative binomial distribution, with variance and mean linked by local regression, is proposed and an implementation, DESeq, as an R/Bioconductor package is presented.
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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