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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Jonathan S. Bromberg,Lauren E. Hittle,Yanbao Xiong,Vikas Saxena,Eoghan M. Smyth,Lushen Li,Tianshu Zhang,Chelsea Wagner,W. Florian Fricke,Thomas Simon,C. Colin Brinkman,Emmanuel F. Mongodin +11 more
TL;DR: Analysis of mesenteric and peripheral lymph node structure showed that B. pseudolongum gavage resulted in a higher laminin α4/α5 ratio in the lymph node cortical ridge, indicative of a suppressive environment, while D. desulfuricans results in a lower lamination ratio, supportive of inflammation.
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Multi-marker eDNA metabarcoding survey to assess the environmental impact of three offshore gas platforms in the North Adriatic Sea (Italy).
Tristan Cordier,Fabrizio Frontalini,Kristina Cermakova,Laure Apothéloz-Perret-Gentil,Mauro Treglia,Enrico Scantamburlo,Vladimiro Bonamin,Jan Pawlowski +7 more
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A Comparative Study of Serum Biochemistry, Metabolome and Microbiome Parameters of Clinically Healthy, Normal Weight, Overweight, and Obese Companion Dogs.
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Identification of rumen microbial biomarkers linked to methane emission in Holstein dairy cows
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