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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Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown
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Analysis of composition of microbiomes: a novel method for studying microbial composition.
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Human gut microbes impact host serum metabolome and insulin sensitivity
Helle Krogh Pedersen,Valborg Gudmundsdottir,Henrik Nielsen,Tuulia Hyötyläinen,Tuulia Hyötyläinen,Trine G. Nielsen,Benjamin A. H. Jensen,Kristoffer Forslund,Falk Hildebrand,Falk Hildebrand,Edi Prifti,Edi Prifti,Gwen Falony,Florence Levenez,Joël Doré,Ismo Mattila,Ismo Mattila,Damian R. Plichta,Päivi Pöhö,Päivi Pöhö,Lars Hellgren,Manimozhiyan Arumugam,Shinichi Sunagawa,Sara Vieira-Silva,Torben Jørgensen,Torben Jørgensen,Jacob Bak Holm,Kajetan Trošt,Karsten Kristiansen,Susanne Brix,Jeroen Raes,Jeroen Raes,Jun Wang,Torben Hansen,Torben Hansen,Peer Bork,Søren Brunak,Søren Brunak,Matej Orešič,Matej Orešič,Matej Orešič,S. Dusko Ehrlich,S. Dusko Ehrlich,Oluf Pedersen +43 more
TL;DR: It is shown how the human gut microbiome impacts the serum metabolome and associates with insulin resistance in 277 non-diabetic Danish individuals and suggested that microbial targets may have the potential to diminish insulin resistance and reduce the incidence of common metabolic and cardiovascular disorders.
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