Low-abundant bacteria drive compositional changes in the gut microbiota after dietary alteration

[1]  Jacquelynn Benjamino,et al.  Microbiome Analyses for Toxicological Studies , 2018, Current protocols in toxicology.

[2]  Marti J. Anderson,et al.  Permutational Multivariate Analysis of Variance (PERMANOVA) , 2017 .

[3]  Nicholas D. Embleton,et al.  Longitudinal development of the gut microbiome and metabolome in preterm neonates with late onset sepsis and healthy controls , 2017, Microbiome.

[4]  E. Khafipour,et al.  Short Term High Fat Diet Induces Obesity-Enhancing Changes in Mouse Gut Microbiota That are Partially Reversed by Cessation of the High Fat Diet , 2017, Lipids.

[5]  W. Cookson,et al.  Bacterial microbiota of the upper respiratory tract and childhood asthma , 2017, The Journal of allergy and clinical immunology.

[6]  Xiaowei Zhang,et al.  Where less may be more: how the rare biosphere pulls ecosystems strings , 2017, The ISME Journal.

[7]  Jian Xu,et al.  Diversity and resilience of the wood‐feeding higher termite Mironasutitermes shangchengensis gut microbiota in response to temporal and diet variations , 2016, Ecology and evolution.

[8]  J. Graf.  Lessons from Digestive-Tract Symbioses Between Bacteria and Invertebrates. , 2016, Annual review of microbiology.

[9]  Elizabeth A. Ottesen,et al.  The Core Gut Microbiome of the American Cockroach, Periplaneta americana, Is Stable and Resilient to Dietary Shifts , 2016, Applied and Environmental Microbiology.

[10]  E. Rosenberg,et al.  Microbes Drive Evolution of Animals and Plants: the Hologenome Concept , 2016, mBio.

[11]  Jacquelynn Benjamino,et al.  Characterization of the Core and Caste-Specific Microbiota in the Termite, Reticulitermes flavipes , 2016, Front. Microbiol..

[12]  F. Servant,et al.  The Characterization of Novel Tissue Microbiota Using an Optimized 16S Metagenomic Sequencing Pipeline , 2015, PloS one.

[13]  A. Brune,et al.  Diet is the primary determinant of bacterial community structure in the guts of higher termites , 2015, Molecular ecology.

[14]  K. Theis,et al.  Host Biology in Light of the Microbiome: Ten Principles of Holobionts and Hologenomes , 2015, PLoS biology.

[15]  Geoffrey E. Hinton,et al.  Deep Learning , 2015, Nature.

[16]  A. Moya,et al.  Diet shapes the gut microbiota of the omnivorous cockroach Blattella germanica. , 2015, FEMS microbiology ecology.

[17]  Daniel T. Larose,et al.  Data Mining and Predictive Analytics , 2015 .

[18]  M. Scharf.  Omic research in termites: an overview and a roadmap , 2015, Front. Genet..

[19]  Tiago P. Peixoto,et al.  The graph-tool python library , 2014 .

[20]  Sharon L. Grim,et al.  Analysis, Optimization and Verification of Illumina-Generated 16S rRNA Gene Amplicon Surveys , 2014, PloS one.

[21]  J. Clemente,et al.  The Long-Term Stability of the Human Gut Microbiota , 2013 .

[22]  A. Kostic,et al.  Exploring host-microbiota interactions in animal models and humans. , 2013, Genes & development.

[23]  Yunpeng Cai,et al.  The hindgut lumen prokaryotic microbiota of the termite Reticulitermes flavipes and its responses to dietary lignocellulose composition , 2013, Molecular ecology.

[24]  J. Vivanco,et al.  Variations in Diversity and Richness of Gut Bacterial Communities of Termites (Reticulitermes flavipes) Fed with Grassy and Woody Plant Substrates , 2013, Microbial Ecology.

[25]  Didier L. Baho,et al.  Fundamentals of Microbial Community Resistance and Resilience , 2012, Front. Microbio..

[26]  G. M. Luna,et al.  High bacterial biodiversity increases degradation performance of hydrocarbons during bioremediation of contaminated harbor marine sediments. , 2012, Environmental pollution.

[27]  Peter E. Larsen,et al.  Predicting bacterial community assemblages using an artificial neural network approach. , 2012, Methods in molecular biology.

[28]  Peter E. Larsen,et al.  Predicting bacterial community assemblages using an artificial neural network approach , 2012, Nature Methods.

[29]  I. Mizrahi,et al.  Composition and Similarity of Bovine Rumen Microbiota across Individual Animals , 2012, PloS one.

[30]  Eric P. Nawrocki,et al.  An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea , 2011, The ISME Journal.

[31]  J. Faith,et al.  Predicting a Human Gut Microbiota’s Response to Diet in Gnotobiotic Mice , 2011, Science.

[32]  P. Bakker,et al.  Deciphering the Rhizosphere Microbiome for Disease-Suppressive Bacteria , 2011, Science.

[33]  S. Bertilsson,et al.  Function-specific response to depletion of microbial diversity , 2011, The ISME Journal.

[34]  J. Parkhill,et al.  Dominant and diet-responsive groups of bacteria within the human colonic microbiota , 2011, The ISME Journal.

[35]  Pedro M. Valero-Mora,et al.  ggplot2: Elegant Graphics for Data Analysis , 2010 .

[36]  M. Wagner,et al.  A ‘rare biosphere’ microorganism contributes to sulfate reduction in a peatland , 2010, The ISME Journal.

[37]  William A. Walters,et al.  Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample , 2010, Proceedings of the National Academy of Sciences.

[38]  Hadley Wickham,et al.  ggplot2 - Elegant Graphics for Data Analysis (2nd Edition) , 2017 .

[39]  E. Rosenberg,et al.  Role of microorganisms in the evolution of animals and plants: the hologenome theory of evolution. , 2008, FEMS microbiology reviews.

[40]  M. Ohkuma.  Symbioses of flagellates and prokaryotes in the gut of lower termites. , 2008, Trends in microbiology.

[41]  John D. Hunter,et al.  Matplotlib: A 2D Graphics Environment , 2007, Computing in Science & Engineering.

[42]  Susan M. Huse,et al.  Microbial diversity in the deep sea and the underexplored “rare biosphere” , 2006, Proceedings of the National Academy of Sciences.

[43]  Eoin L. Brodie,et al.  Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB , 2006, Applied and Environmental Microbiology.

[44]  D. Faith,et al.  Phylogenetic diversity (PD) and biodiversity conservation: some bioinformatics challenges , 2006, Evolutionary bioinformatics online.

[45]  M. Blaxter,et al.  Ancient origin of glycosyl hydrolase family 9 cellulase genes. , 2005, Molecular biology and evolution.

[46]  Zhongtang Yu,et al.  Improved extraction of PCR-quality community DNA from digesta and fecal samples. , 2004, BioTechniques.

[47]  Jared R. Leadbetter,et al.  Description of Treponema azotonutricium sp. nov. and Treponema primitia sp. nov., the First Spirochetes Isolated from Termite Guts , 2004, Applied and Environmental Microbiology.

[48]  J. Breznak,et al.  Physiology and Nutrition of Treponema primitia, an H2/ CO2-Acetogenic Spirochete from Termite Hindguts , 2004, Applied and Environmental Microbiology.

[49]  T. Kudo,et al.  Differential role of symbiotic fungi in lignin degradation and food provision for fungus-growing termites (Macrotermitinae: Isoptera) , 2003 .

[50]  M. Ohkuma.  Termite symbiotic systems: efficient bio-recycling of lignocellulose , 2003, Applied Microbiology and Biotechnology.

[51]  J. Leadbetter,et al.  Acetogenesis from H2 plus CO2 by spirochetes from termite guts. , 1999, Science.

[52]  J. Tiedje,et al.  Influence of diet on the structure and function of the bacterial hindgut community of crickets , 1998 .

[53]  B. Kolli,et al.  Lignocellulose degradation by microorganisms from termite hills and termite guts: A survey on the present state of art , 1994 .

[54]  A. Beckenbach,et al.  Evolution of the mitochondrial cytochrome oxidase II gene among 10 orders of insects. , 1992, Molecular phylogenetics and evolution.

[55]  M. Kane,et al.  Effect of host diet on production of organic acids and methane by cockroach gut bacteria , 1991, Applied and environmental microbiology.

[56]  Yann LeCun,et al.  Second Order Properties of Error Surfaces: Learning Time and Generalization , 1990, NIPS 1990.

[57]  Ļ. Cleveland.  THE FEEDING HABIT OF TERMITE CASTES AND ITS RELATION TO THEIR INTESTINAL FLAGELLATES , 1925 .

[58]  Guigang Zhang,et al.  Deep Learning , 2016, Int. J. Semantic Comput..

[59]  J. Handelsman,et al.  Beyond the Venn diagram: the hunt for a core microbiome. , 2012, Environmental microbiology.

[60]  Jonathan M. Chase,et al.  Navigating the multiple meanings of β diversity: a roadmap for the practicing ecologist. , 2011, Ecology letters.

[61]  V. Dillon,et al.  The gut bacteria of insects: nonpathogenic interactions. , 2004, Annual review of entomology.