TY - JOUR AU - Ohland, C. L. AU - Jobin, C. PY - 2015 DA - 2015// TI - Microbial activities and intestinal homeostasis: a delicate balance between health and disease JO - Cell Mol Gastroenterol Hepatol VL - 1 UR - https://doi.org/10.1016/j.jcmgh.2014.11.004 DO - 10.1016/j.jcmgh.2014.11.004 ID - Ohland2015 ER - TY - JOUR AU - Tan, J. AU - McKenzie, C. AU - Potamitis, M. AU - Thorburn, A. N. AU - Mackay, C. R. AU - Macia, L. PY - 2014 DA - 2014// TI - The role of short-chain fatty acids in health and disease JO - Adv Immunol VL - 121 UR - https://doi.org/10.1016/B978-0-12-800100-4.00003-9 DO - 10.1016/B978-0-12-800100-4.00003-9 ID - Tan2014 ER - TY - JOUR AU - Bergman, E. N. PY - 1990 DA - 1990// TI - Energy contributions of volatile fatty acids from the gastrointestinal tract in various species JO - Physiol Rev VL - 70 ID - Bergman1990 ER - TY - JOUR AU - Li, C. J. AU - Li, R. W. AU - Baldwin, R. L. AU - Blomberg le, A. AU - Wu, S. AU - Li, W. PY - 2016 DA - 2016// TI - Transcriptomic sequencing reveals a set of unique genes activated by butyrate-induced histone modification JO - Gene Regul Syst Bio VL - 10 ID - Li2016 ER - TY - JOUR AU - Lu, Z. AU - Gui, H. AU - Yao, L. AU - Yan, L. AU - Martens, H. AU - Aschenbach, J. R. AU - Shen, Z. PY - 2015 DA - 2015// TI - Short-chain fatty acids and acidic pH upregulate UT-B, GPR41, and GPR4 in rumen epithelial cells of goats JO - Am J Phys Regul Integr Comp Phys VL - 308 ID - Lu2015 ER - TY - JOUR AU - Malhi, M. AU - Gui, H. AU - Yao, L. AU - Aschenbach, J. R. AU - Gabel, G. AU - Shen, Z. PY - 2013 DA - 2013// TI - Increased papillae growth and enhanced short-chain fatty acid absorption in the rumen of goats are associated with transient increases in cyclin D1 expression after ruminal butyrate infusion JO - J Dairy Sci VL - 96 UR - https://doi.org/10.3168/jds.2013-6700 DO - 10.3168/jds.2013-6700 ID - Malhi2013 ER - TY - JOUR AU - MacDonald, V. E. AU - Howe, L. J. PY - 2009 DA - 2009// TI - Histone acetylation: where to go and how to get there JO - Epigenetics VL - 4 UR - https://doi.org/10.4161/epi.4.3.8484 DO - 10.4161/epi.4.3.8484 ID - MacDonald2009 ER - TY - JOUR AU - Samuel, B. S. AU - Shaito, A. AU - Motoike, T. AU - Rey, F. E. AU - Backhed, F. AU - Manchester, J. K. AU - Hammer, R. E. AU - Williams, S. C. AU - Crowley, J. AU - Yanagisawa, M. AU - Gordon, J. I. PY - 2008 DA - 2008// TI - Effects of the gut microbiota on host adiposity are modulated by the short-chain fatty-acid binding G protein-coupled receptor, Gpr41 JO - Proc Natl Acad Sci U S A VL - 105 UR - https://doi.org/10.1073/pnas.0808567105 DO - 10.1073/pnas.0808567105 ID - Samuel2008 ER - TY - JOUR AU - Tolhurst, G. AU - Heffron, H. AU - Lam, Y. S. AU - Parker, H. E. AU - Habib, A. M. AU - Diakogiannaki, E. AU - Cameron, J. AU - Grosse, J. AU - Reimann, F. AU - Gribble, F. M. PY - 2012 DA - 2012// TI - Short-chain fatty acids stimulate glucagon-like peptide-1 secretion via the G-protein-coupled receptor FFAR2 JO - Diabetes VL - 61 UR - https://doi.org/10.2337/db11-1019 DO - 10.2337/db11-1019 ID - Tolhurst2012 ER - TY - JOUR AU - Mao, S. Y. AU - Huo, W. J. AU - Zhu, W. Y. PY - 2016 DA - 2016// TI - Microbiome-metabolome analysis reveals unhealthy alterations in the composition and metabolism of ruminal microbiota with increasing dietary grain in a goat model JO - Environ Microbiol VL - 18 UR - https://doi.org/10.1111/1462-2920.12724 DO - 10.1111/1462-2920.12724 ID - Mao2016 ER - TY - JOUR AU - Mohammadzadeh, H. AU - Yanez-Ruiz, D. R. AU - Martinez-Fernandez, G. AU - Abecia, L. PY - 2014 DA - 2014// TI - Molecular comparative assessment of the microbial ecosystem in rumen and faeces of goats fed alfalfa hay alone or combined with oats JO - Anaerobe VL - 29 UR - https://doi.org/10.1016/j.anaerobe.2013.11.012 DO - 10.1016/j.anaerobe.2013.11.012 ID - Mohammadzadeh2014 ER - TY - JOUR AU - Zhang, R. AU - Zhu, W. AU - Zhu, W. AU - Liu, J. AU - Mao, S. PY - 2014 DA - 2014// TI - Effect of dietary forage sources on rumen microbiota, rumen fermentation and biogenic amines in dairy cows JO - J Sci Food Agric VL - 94 UR - https://doi.org/10.1002/jsfa.6508 DO - 10.1002/jsfa.6508 ID - Zhang2014 ER - TY - BOOK PY - 1988 DA - 1988// TI - Administration of affairs concerning experimental animals PB - Commission SSaT ed CY - Beijing ID - ref13 ER - TY - JOUR AU - Yang, W. AU - Shen, Z. AU - Martens, H. PY - 2012 DA - 2012// TI - An energy-rich diet enhances expression of Na(+)/H(+) exchanger isoform 1 and 3 messenger RNA in rumen epithelium of goat JO - J Anim Sci VL - 90 UR - https://doi.org/10.2527/jas.2011-3854 DO - 10.2527/jas.2011-3854 ID - Yang2012 ER - TY - JOUR AU - Mori, H. AU - Maruyama, F. AU - Kato, H. AU - Toyoda, A. AU - Dozono, A. AU - Ohtsubo, Y. AU - Nagata, Y. AU - Fujiyama, A. AU - Tsuda, M. AU - Kurokawa, K. PY - 2014 DA - 2014// TI - Design and experimental application of a novel non-degenerate universal primer set that amplifies prokaryotic 16S rRNA genes with a low possibility to amplify eukaryotic rRNA genes JO - DNA Res VL - 21 UR - https://doi.org/10.1093/dnares/dst052 DO - 10.1093/dnares/dst052 ID - Mori2014 ER - TY - JOUR AU - Magoc, T. AU - Salzberg, S. L. PY - 2011 DA - 2011// TI - FLASH: fast length adjustment of short reads to improve genome assemblies JO - Bioinformatics VL - 27 UR - https://doi.org/10.1093/bioinformatics/btr507 DO - 10.1093/bioinformatics/btr507 ID - Magoc2011 ER - TY - JOUR AU - McMurdie, P. J. AU - Holmes, S. PY - 2013 DA - 2013// TI - Phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data JO - PLoS One VL - 8 UR - https://doi.org/10.1371/journal.pone.0061217 DO - 10.1371/journal.pone.0061217 ID - McMurdie2013 ER - TY - JOUR AU - Edgar, R. C. PY - 2004 DA - 2004// TI - MUSCLE: a multiple sequence alignment method with reduced time and space complexity JO - BMC Bioinformatics VL - 5 UR - https://doi.org/10.1186/1471-2105-5-113 DO - 10.1186/1471-2105-5-113 ID - Edgar2004 ER - TY - JOUR AU - Stamatakis, A. PY - 2014 DA - 2014// TI - RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies JO - Bioinformatics VL - 30 UR - https://doi.org/10.1093/bioinformatics/btu033 DO - 10.1093/bioinformatics/btu033 ID - Stamatakis2014 ER - TY - JOUR AU - Paradis, E. AU - Claude, J. AU - Strimmer, K. PY - 2004 DA - 2004// TI - APE: analyses of phylogenetics and evolution in R language JO - Bioinformatics VL - 20 UR - https://doi.org/10.1093/bioinformatics/btg412 DO - 10.1093/bioinformatics/btg412 ID - Paradis2004 ER - TY - JOUR AU - Kim, D. AU - Pertea, G. AU - Trapnell, C. AU - Pimentel, H. AU - Kelley, R. AU - Salzberg, S. L. PY - 2013 DA - 2013// TI - TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions JO - Genome Biol VL - 14 UR - https://doi.org/10.1186/gb-2013-14-4-r36 DO - 10.1186/gb-2013-14-4-r36 ID - Kim2013 ER - TY - JOUR AU - Trapnell, C. AU - Williams, B. A. AU - Pertea, G. AU - Mortazavi, A. AU - Kwan, G. AU - Baren, M. J. AU - Salzberg, S. L. AU - Wold, B. J. AU - Pachter, L. PY - 2010 DA - 2010// TI - Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation JO - Nat Biotechnol VL - 28 UR - https://doi.org/10.1038/nbt.1621 DO - 10.1038/nbt.1621 ID - Trapnell2010 ER - TY - JOUR AU - Letunic, I. AU - Bork, P. PY - 2016 DA - 2016// TI - Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees JO - Nucleic Acids Res VL - 44 UR - https://doi.org/10.1093/nar/gkw290 DO - 10.1093/nar/gkw290 ID - Letunic2016 ER - TY - JOUR AU - Xie, C. AU - Mao, X. AU - Huang, J. AU - Ding, Y. AU - Wu, J. AU - Dong, S. AU - Kong, L. AU - Gao, G. AU - Li, C. Y. AU - Wei, L. PY - 2011 DA - 2011// TI - KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases JO - Nucleic Acids Res VL - 39 UR - https://doi.org/10.1093/nar/gkr483 DO - 10.1093/nar/gkr483 ID - Xie2011 ER - TY - JOUR AU - Shannon, P. AU - Markiel, A. AU - Ozier, O. AU - Baliga, N. S. AU - Wang, J. T. AU - Ramage, D. AU - Amin, N. AU - Schwikowski, B. AU - Ideker, T. PY - 2003 DA - 2003// TI - Cytoscape: a software environment for integrated models of biomolecular interaction networks JO - Genome Res VL - 13 UR - https://doi.org/10.1101/gr.1239303 DO - 10.1101/gr.1239303 ID - Shannon2003 ER - TY - BOOK AU - Oksanen, J. AU - Blanchet, G. F. AU - Friendly, M. AU - Kindt, R. AU - Legendre, P. AU - McGlinn, D. AU - Minchin, P. R. AU - O'Hara, R. B. AU - Simpson, G. L. AU - Solymos, P. PY - 2016 DA - 2016// TI - Vegan: community ecology package ID - Oksanen2016 ER - TY - BOOK AU - Wickham, H. PY - 2009 DA - 2009// TI - ggplot2: elegant graphics for data analysis PB - Springer-Verlag CY - New York UR - https://doi.org/10.1007/978-0-387-98141-3 DO - 10.1007/978-0-387-98141-3 ID - Wickham2009 ER - TY - JOUR AU - Wang, A. AU - Gu, Z. AU - Heid, B. AU - Akers, R. M. AU - Jiang, H. PY - 2009 DA - 2009// TI - Identification and characterization of the bovine G protein-coupled receptor GPR41 and GPR43 genes JO - J Dairy Sci VL - 92 UR - https://doi.org/10.3168/jds.2009-2037 DO - 10.3168/jds.2009-2037 ID - Wang2009 ER - TY - JOUR AU - Weimer, P. J. PY - 1996 DA - 1996// TI - Why don’t ruminal bacteria digest cellulose faster? JO - J Dairy Sci VL - 79 UR - https://doi.org/10.3168/jds.S0022-0302(96)76509-8 DO - 10.3168/jds.S0022-0302(96)76509-8 ID - Weimer1996 ER - TY - JOUR AU - Duncan, S. H. AU - Barcenilla, A. AU - Stewart, C. S. AU - Pryde, S. E. AU - Flint, H. J. PY - 2002 DA - 2002// TI - Acetate utilization and butyryl coenzyme a (CoA):acetate-CoA transferase in butyrate-producing bacteria from the human large intestine JO - Appl Environ Microbiol VL - 68 UR - https://doi.org/10.1128/AEM.68.10.5186-5190.2002 DO - 10.1128/AEM.68.10.5186-5190.2002 ID - Duncan2002 ER - TY - JOUR AU - Leong, L. E. AU - Denman, S. E. AU - Hugenholtz, P. AU - McSweeney, C. S. PY - 2016 DA - 2016// TI - Amino acid and peptide utilization profiles of the fluoroacetate-degrading bacterium Synergistetes strain MFA1 under varying conditions JO - Microb Ecol VL - 71 UR - https://doi.org/10.1007/s00248-015-0641-4 DO - 10.1007/s00248-015-0641-4 ID - Leong2016 ER - TY - JOUR AU - Spring, S. AU - Bunk, B. AU - Sproer, C. AU - Schumann, P. AU - Rohde, M. AU - Tindall, B. J. AU - Klenk, H. P. PY - 2016 DA - 2016// TI - Characterization of the first cultured representative of Verrucomicrobia subdivision 5 indicates the proposal of a novel phylum JO - ISME J VL - 10 UR - https://doi.org/10.1038/ismej.2016.84 DO - 10.1038/ismej.2016.84 ID - Spring2016 ER - TY - BOOK AU - Han, Z. AU - Chen, J. PY - 1988 DA - 1988// TI - Rumen digestion and metabolism PB - Science Publishing Company in China CY - China ID - Han1988 ER - TY - JOUR AU - Inan, M. S. AU - Rasoulpour, R. J. AU - Yin, L. AU - Hubbard, A. K. AU - Rosenberg, D. W. AU - Giardina, C. PY - 2000 DA - 2000// TI - The luminal short-chain fatty acid butyrate modulates NF-kappaB activity in a human colonic epithelial cell line JO - Gastroenterology VL - 118 UR - https://doi.org/10.1016/S0016-5085(00)70142-9 DO - 10.1016/S0016-5085(00)70142-9 ID - Inan2000 ER - TY - JOUR AU - Segain, J. P. AU - Raingeard de la Bletiere, D. AU - Bourreille, A. AU - Leray, V. AU - Gervois, N. AU - Rosales, C. AU - Ferrier, L. AU - Bonnet, C. AU - Blottiere, H. M. AU - Galmiche, J. P. PY - 2000 DA - 2000// TI - Butyrate inhibits inflammatory responses through NFkappaB inhibition: implications for Crohn’s disease JO - Gut VL - 47 UR - https://doi.org/10.1136/gut.47.3.397 DO - 10.1136/gut.47.3.397 ID - Segain2000 ER - TY - JOUR AU - Bordonaro, M. AU - Lazarova, D. L. AU - Sartorelli, A. C. PY - 2008 DA - 2008// TI - Hyperinduction of Wnt activity: a new paradigm for the treatment of colorectal cancer? JO - Oncol Res VL - 17 ID - Bordonaro2008 ER - TY - JOUR AU - Lazarova, D. L. AU - Bordonaro, M. AU - Carbone, R. AU - Sartorelli, A. C. PY - 2004 DA - 2004// TI - Linear relationship between Wnt activity levels and apoptosis in colorectal carcinoma cells exposed to butyrate JO - Int J Cancer VL - 110 UR - https://doi.org/10.1002/ijc.20152 DO - 10.1002/ijc.20152 ID - Lazarova2004 ER - TY - JOUR AU - Yonezawa, T. AU - Haga, S. AU - Kobayashi, Y. AU - Katoh, K. AU - Obara, Y. PY - 2008 DA - 2008// TI - Unsaturated fatty acids promote proliferation via ERK1/2 and Akt pathway in bovine mammary epithelial cells JO - Biochem Biophys Res Commun VL - 367 UR - https://doi.org/10.1016/j.bbrc.2007.12.190 DO - 10.1016/j.bbrc.2007.12.190 ID - Yonezawa2008 ER - TY - JOUR AU - Taoka, H. AU - Yokoyama, Y. AU - Morimoto, K. AU - Kitamura, N. AU - Tanigaki, T. AU - Takashina, Y. AU - Tsubota, K. AU - Watanabe, M. PY - 2016 DA - 2016// TI - Role of bile acids in the regulation of the metabolic pathways JO - World J Diabetes VL - 7 UR - https://doi.org/10.4239/wjd.v7.i13.260 DO - 10.4239/wjd.v7.i13.260 ID - Taoka2016 ER - TY - JOUR AU - Priatel, J. J. AU - Chui, D. AU - Hiraoka, N. AU - Simmons, C. J. AU - Richardson, K. B. AU - Page, D. M. AU - Fukuda, M. AU - Varki, N. M. AU - Marth, J. D. PY - 2000 DA - 2000// TI - The ST3Gal-I sialyltransferase controls CD8+ T lymphocyte homeostasis by modulating O-glycan biosynthesis JO - Immunity VL - 12 UR - https://doi.org/10.1016/S1074-7613(00)80180-6 DO - 10.1016/S1074-7613(00)80180-6 ID - Priatel2000 ER - TY - JOUR AU - Merrill, A. H. PY - 2002 DA - 2002// TI - De novo sphingolipid biosynthesis: a necessary, but dangerous, pathway JO - J Biol Chem VL - 277 UR - https://doi.org/10.1074/jbc.R200009200 DO - 10.1074/jbc.R200009200 ID - Merrill2002 ER - TY - JOUR AU - Zheng, W. AU - Kollmeyer, J. AU - Symolon, H. AU - Momin, A. AU - Munter, E. AU - Wang, E. AU - Kelly, S. AU - Allegood, J. C. AU - Liu, Y. AU - Peng, Q. PY - 2006 DA - 2006// TI - Ceramides and other bioactive sphingolipid backbones in health and disease: lipidomic analysis, metabolism and roles in membrane structure, dynamics, signaling and autophagy JO - Biochim Biophys Acta VL - 1758 UR - https://doi.org/10.1016/j.bbamem.2006.08.009 DO - 10.1016/j.bbamem.2006.08.009 ID - Zheng2006 ER - TY - JOUR AU - Berthe, W. AU - Sevrain, C. M. AU - Chantome, A. AU - Bouchet, A. M. AU - Gueguinou, M. AU - Fourbon, Y. AU - Potier-Cartereau, M. AU - Haelters, J. P. AU - Couthon-Gourves, H. AU - Vandier, C. AU - Jaffres, P. A. PY - 2016 DA - 2016// TI - New disaccharide-based ether lipids as SK3 ion channel inhibitors JO - ChemMedChem VL - 11 UR - https://doi.org/10.1002/cmdc.201600147 DO - 10.1002/cmdc.201600147 ID - Berthe2016 ER - TY - JOUR AU - Vadder, F. AU - Kovatcheva-Datchary, P. AU - Goncalves, D. AU - Vinera, J. AU - Zitoun, C. AU - Duchampt, A. AU - Backhed, F. AU - Mithieux, G. PY - 2014 DA - 2014// TI - Microbiota-generated metabolites promote metabolic benefits via gut-brain neural circuits JO - Cell VL - 156 UR - https://doi.org/10.1016/j.cell.2013.12.016 DO - 10.1016/j.cell.2013.12.016 ID - Vadder2014 ER - TY - JOUR AU - Kimura, I. AU - Ozawa, K. AU - Inoue, D. AU - Imamura, T. AU - Kimura, K. AU - Maeda, T. AU - Terasawa, K. AU - Kashihara, D. AU - Hirano, K. AU - Tani, T. PY - 2013 DA - 2013// TI - The gut microbiota suppresses insulin-mediated fat accumulation via the short-chain fatty acid receptor GPR43 JO - Nat Commun VL - 4 UR - https://doi.org/10.1038/ncomms2852 DO - 10.1038/ncomms2852 ID - Kimura2013 ER - TY - JOUR AU - Kasubuchi, M. AU - Hasegawa, S. AU - Hiramatsu, T. AU - Ichimura, A. AU - Kimura, I. PY - 2015 DA - 2015// TI - Dietary gut microbial metabolites, short-chain fatty acids, and host metabolic regulation JO - Nutrients VL - 7 UR - https://doi.org/10.3390/nu7042839 DO - 10.3390/nu7042839 ID - Kasubuchi2015 ER - TY - JOUR AU - Barcenilla, A. AU - Pryde, S. E. AU - Martin, J. C. AU - Duncan, S. H. AU - Stewart, C. S. AU - Henderson, C. AU - Flint, H. J. PY - 2000 DA - 2000// TI - Phylogenetic relationships of butyrate-producing bacteria from the human gut JO - Appl Environ Microbiol VL - 66 UR - https://doi.org/10.1128/AEM.66.4.1654-1661.2000 DO - 10.1128/AEM.66.4.1654-1661.2000 ID - Barcenilla2000 ER - TY - JOUR AU - Guzman, J. R. AU - Conlin, V. S. AU - Jobin, C. PY - 2013 DA - 2013// TI - Diet, microbiome, and the intestinal epithelium: an essential triumvirate? JO - Biomed Res Int VL - 2013 UR - https://doi.org/10.1155/2013/425146 DO - 10.1155/2013/425146 ID - Guzman2013 ER -