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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Temporal Variations in Cigarette Tobacco Bacterial Community Composition and Tobacco-Specific Nitrosamine Content Are Influenced by Brand and Storage Conditions.
Jessica Chopyk,Suhana Chattopadhyay,Prachi Kulkarni,Eoghan M. Smyth,Eoghan M. Smyth,Lauren E. Hittle,Joseph N. Paulson,Mihai Pop,Stephanie S. Buehler,Pamela I. Clark,Emmanuel F. Mongodin,Amy R. Sapkota +11 more
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Active virus-host interactions at sub-freezing temperatures in Arctic peat soil.
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TL;DR: In this paper, stable isotope probing (SIP) targeted metagenomics was used to reveal the genomic potential of active soil microbial populations under simulated winter conditions, with an emphasis on viruses and virus-host dynamics.
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Reservoirs of antimicrobial resistance genes in retail raw milk.
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The closed eye harbours a unique microbiome in dry eye disease.
Kent A. Willis,Cameron K Postnikoff,Amelia Freeman,Gabriel Rezonzew,Kelly K. Nichols,Amit Gaggar,Charitharth Vivek Lal +6 more
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Metagenomic Sequencing Detects Respiratory Pathogens in Hematopoietic Cellular Transplant Patients
Charles Langelier,Matt S. Zinter,Katrina Kalantar,Gregory A Yank,Stephanie A. Christenson,Brian D. O’Donovan,Corin V. White,Michael R. Wilson,Anil Sapru,Christopher C. Dvorak,Steve Miller,Charles Y. Chiu,Joseph L. DeRisi +12 more
TL;DR: The results suggest that combining unbiased microbial pathogen detection with assessment of host gene biomarkers of immune response may hold promise for enhancing the diagnosis of post-HCT respiratory infections.
References
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QIIME allows analysis of high-throughput community sequencing data.
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Metagenomic biomarker discovery and explanation
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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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