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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Spatial Variability of Antarctic Surface Snow Bacterial Communities
Lucie A Malard,Marie Šabacká,Iordanis Magiopoulos,Matthew C. Mowlem,A. J. Hodson,Martyn Tranter,Martin J. Siegert,David A. Pearce,David A. Pearce +8 more
TL;DR: A change in microbial community structure with geographical location was apparent and, notably, a decrease in alpha diversity at more remote southern latitudes and soil-related microorganisms dominated microbial assemblages suggesting terrestrial input, most likely from long-range aeolian transport into continental Antarctica.
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A Statistical Model for Describing and Simulating Microbial Community Profiles
Siyuan Ma,Siyuan Ma,Boyu Ren,Boyu Ren,Himel Mallick,Himel Mallick,Yo Sup Moon,Emma Schwager,Sagun Maharjan,Sagun Maharjan,Timothy L. Tickle,Timothy L. Tickle,Yiren Lu,Rachel N. Carmody,Eric A. Franzosa,Eric A. Franzosa,Lucas Janson,Curtis Huttenhower +17 more
TL;DR: SparseDOSSA as mentioned in this paper is a statistical model of microbial ecological population structure, which can be used to parameterize real-world microbial community profiles and to simulate new, realistic profiles of known structure for methods evaluation.
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Bacterial Butyrate in Parkinson's Disease Is Linked to Epigenetic Changes and Depressive Symptoms
Aoji Xie,Elizabeth Ensink,Peipei Li,Juozas Gordevičius,Lee Marshall,Sonia George,J. Andrew Pospisilik,Velma T. E. Aho,Madelyn C. Houser,Pedro A. B. Pereira,Knut Rudi,Lars Paulin,Malú G. Tansey,Petri Auvinen,Patrik Brundin,Lena Brundin,Viviane Labrie,Filip Scheperjans +17 more
TL;DR: The gut microbiome and its metabolites can impact brain health and are altered in Parkinson's disease patients and it has been recently demonstrated that PD patients have reduced fecal levels of the potent epigenetic modulator butyrate and its bacterial producers.
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Microbial Population Changes in Decaying Ascophyllum nodosum Result in Macroalgal-Polysaccharide-Degrading Bacteria with Potential Applicability in Enzyme-Assisted Extraction Technologies
Maureen W. Ihua,Freddy Guihéneuf,Halimah Mohammed,Lekha Menon Margassery,Stephen A. Jackson,Dagmar B. Stengel,David Clarke,Alan D. W. Dobson +7 more
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Priming of microbial microcystin degradation in biomass-fed gravity driven membrane filtration biofilms.
TL;DR: A subsequent experiment showed that MC removal developed significantly faster in mature biofilms that were pre-fed with biomass from the mutant strain than in unamended controls, indicating that MC degradation was a facultative trait of bacterial populations in GDMBiofilms.
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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