Metagenomic biomarker discovery and explanation
Nicola Segata,Jacques Izard,Jacques Izard,Levi Waldron,Dirk Gevers,Larisa Miropolsky,Wendy S. Garrett,Curtis Huttenhower +7 more
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TLDR
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.Abstract:
This study describes and validates a new method for metagenomic biomarker discovery by way of class comparison, tests of biological consistency and effect size estimation. This addresses the challenge of finding organisms, genes, or pathways that consistently explain the differences between two or more microbial communities, which is a central problem to the study of metagenomics. We extensively validate our method on several microbiomes and a convenient online interface for the method is provided at http://huttenhower.sph.harvard.edu/lefse/.read more
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Environmental temperature alters the digestive performance and gut microbiota of a terrestrial amphibian.
TL;DR: The relationship between environmental temperature and digestive performance in red-backed salamanders may be mediated by temperature-induced changes in the abundance of chitin-digesting gut microbiota, suggesting that gut microbiota may mediate the relationship between temperature and digestion in ectotherms.
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Light-driven anaerobic microbial oxidation of manganese.
Mirna Daye,Vanja Klepac-Ceraj,Mihkel Pajusalu,Sophie Rowland,Anna Farrell-Sherman,Nicolas J. Beukes,Nobumichi Tamura,Gregory P. Fournier,Tanja Bosak +8 more
TL;DR: Anoxygenic photosynthetic microorganisms can biomineralize manganese oxides without molecular oxygen being present and without high-potential photosynthesis reaction centres, which sheds doubt on proposed dates for the origins of oxygenic photosynthesis.
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Cafeteria diet and probiotic therapy: cross talk among memory, neuroplasticity, serotonin receptors and gut microbiota in the rat
TL;DR: Results show that probiotics can be beneficial in situations of gut dysbiosis where memory deficits are evident but may be detrimental in healthy subjects.
Journal ArticleDOI
Wheat and Rice Growth Stages and Fertilization Regimes Alter Soil Bacterial Community Structure, But Not Diversity.
TL;DR: In this article, the authors examined microbial community structure and diversity across eight representative growth stages of wheat-rice rotation under four different fertilization treatments: no nitrogen fertilizer (NNF), chemical fertilizer (CF), organic-inorganic mixed fertilizer (OIMF), and organic fertilizer (OF).
Journal ArticleDOI
A meta-analysis reveals the environmental and host factors shaping the structure and function of the shrimp microbiota.
Fernanda Cornejo-Granados,Luigui Gallardo-Becerra,Miriam Leonardo-Reza,Juan Pablo Ochoa-Romo,Adrián Ochoa-Leyva +4 more
TL;DR: This is the first meta-analysis of the microbiota from freshwater and marine shrimps using all publically available sequences of the 16S ribosomal gene (16S rRNA gene), and it is demonstrated that despite the impact of technical and bioinformatics factors, the biological factors were also statistically significant in shaping the microbiota.
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Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
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