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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Xylo-oligosaccharides and virginiamycin differentially modulate gut microbial composition in chickens
TL;DR: There was a significant change in the relative abundance of certain bacteria, but the overall microbial diversity was not affected by treatment with either XOS or VIRG, and the presence or absence of specific microbial genus was not determined.
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Structural robustness of the gut mucosal microbiota is associated with Crohn's disease remission after surgery
Stanislas Mondot,Stanislas Mondot,Stanislas Mondot,Patricia Lepage,Patricia Lepage,P. Seksik,Matthieu Allez,Xavier Treton,Yoram Bouhnik,J-F Colombel,Marion Leclerc,Marion Leclerc,P Pochart,P Pochart,Joël Doré,Joël Doré,Philippe Marteau +16 more
TL;DR: ICR modifies the gut microbiome and highlights target species, including Faecalibacterium prausnitzii and Ruminococcus gnavus, which may allow precise modulations of the overall microbial ecosystem towards remission pattern.
Journal ArticleDOI
Bioinformatic Approaches Including Predictive Metagenomic Profiling Reveal Characteristics of Bacterial Response to Petroleum Hydrocarbon Contamination in Diverse Environments.
Arghya Mukherjee,Bobby Chettri,James S. Langpoklakpam,Pijush Basak,Aravind Prasad,Ashis K. Mukherjee,Maitree Bhattacharyya,Arvind Kumar Singh,Dhrubajyoti Chattopadhyay +8 more
TL;DR: This study has comprehensively described phylogenetic and functional compositions of these habitats and inferred a multitude of metagenomic features including 255 taxa and 414 functional modules which can be used as biomarkers for effective distinction between the 12 oil polluted sites.
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Feed additives shift gut microbiota and enrich antibiotic resistance in swine gut
Yi Zhao,Jian-Qiang Su,Xin-Li An,Fu-Yi Huang,Christopher Rensing,Kristian K. Brandt,Yong-Guan Zhu +6 more
TL;DR: The results suggest that increased levels of in-feed additives could aggravate the enrichment of ARGs and MGEs in swine gut.
Journal ArticleDOI
A single early-in-life macrolide course has lasting effects on murine microbial network topology and immunity.
Victoria E. Ruiz,Thomas Battaglia,Zachary D. Kurtz,Luc Bijnens,Amy Ou,Isak Engstrand,Xuhui Zheng,Tadasu Iizumi,Briana J. Mullins,Christian L. Müller,Ken Cadwell,Richard Bonneau,Guillermo I. Perez-Perez,Martin J. Blaser,Martin J. Blaser +14 more
TL;DR: It is demonstrated that a single pulsed macrolide antibiotic treatment (PAT) course early in life is sufficient to lead to durable alterations to the murine intestinal microbiota, ileal gene expression, specific intestinal T-cell populations, and secretory IgA expression.
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