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Viewing the human microbiome through three-dimensional glasses: integrating structural and functional studies to better define the properties of myriad carbohydrate-active enzymes.

Turnbaugh PJ, Henrissat B, Gordon JI.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1;66(Pt 10):1261-4. doi: 10.1107/S1744309110029088. Epub 2010 Jul 31.


Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes.

Tasse L, Bercovici J, Pizzut-Serin S, Robe P, Tap J, Klopp C, Cantarel BL, Coutinho PM, Henrissat B, Leclerc M, Doré J, Monsan P, Remaud-Simeon M, Potocki-Veronese G.

Genome Res. 2010 Nov;20(11):1605-12. doi: 10.1101/gr.108332.110. Epub 2010 Sep 14.


Bacteria of the human gut microbiome catabolize red seaweed glycans with carbohydrate-active enzyme updates from extrinsic microbes.

Hehemann JH, Kelly AG, Pudlo NA, Martens EC, Boraston AB.

Proc Natl Acad Sci U S A. 2012 Nov 27;109(48):19786-91. doi: 10.1073/pnas.1211002109. Epub 2012 Nov 12.


Complex carbohydrate utilization by the healthy human microbiome.

Cantarel BL, Lombard V, Henrissat B.

PLoS One. 2012;7(6):e28742. doi: 10.1371/journal.pone.0028742. Epub 2012 Jun 13.


The abundance and variety of carbohydrate-active enzymes in the human gut microbiota.

El Kaoutari A, Armougom F, Gordon JI, Raoult D, Henrissat B.

Nat Rev Microbiol. 2013 Jul;11(7):497-504. doi: 10.1038/nrmicro3050. Epub 2013 Jun 10. Review.


Comparative metagenomic analysis of plasmid encoded functions in the human gut microbiome.

Jones BV, Sun F, Marchesi JR.

BMC Genomics. 2010 Jan 19;11:46. doi: 10.1186/1471-2164-11-46.


Microbial and Carbohydrate Active Enzyme profile of buffalo rumen metagenome and their alteration in response to variation in the diet.

Patel DD, Patel AK, Parmar NR, Shah TM, Patel JB, Pandya PR, Joshi CG.

Gene. 2014 Jul 15;545(1):88-94. doi: 10.1016/j.gene.2014.05.003. Epub 2014 May 2.


Metagenomic Analysis of the Gut Microbiome of the Common Black Slug Arion ater in Search of Novel Lignocellulose Degrading Enzymes.

Joynson R, Pritchard L, Osemwekha E, Ferry N.

Front Microbiol. 2017 Nov 8;8:2181. doi: 10.3389/fmicb.2017.02181. eCollection 2017.


Characterizing kiwifruit carbohydrate utilization in vitro and its consequences for human faecal microbiota.

Rosendale DI, Blatchford PA, Sims IM, Parkar SG, Carnachan SM, Hedderley D, Ansell J.

J Proteome Res. 2012 Dec 7;11(12):5863-75. doi: 10.1021/pr300646m. Epub 2012 Oct 26.


Microbiome Structural and Functional Interactions across Host Dietary Niche Space.

Phillips CD, Hanson J, Wilkinson JE, Koenig L, Rees E, Webala P, Kingston T.

Integr Comp Biol. 2017 Oct 1;57(4):743-755. doi: 10.1093/icb/icx011.


Global Profiling of Carbohydrate Active Enzymes in Human Gut Microbiome.

Bhattacharya T, Ghosh TS, Mande SS.

PLoS One. 2015 Nov 6;10(11):e0142038. doi: 10.1371/journal.pone.0142038. eCollection 2015.


Integrating '-omics' and natural product discovery platforms to investigate metabolic exchange in microbiomes.

Yang JY, Karr JR, Watrous JD, Dorrestein PC.

Curr Opin Chem Biol. 2011 Feb;15(1):79-87. doi: 10.1016/j.cbpa.2010.10.025. Epub 2010 Nov 17. Review.


Development and validation of a microarray for the investigation of the CAZymes encoded by the human gut microbiome.

El Kaoutari A, Armougom F, Leroy Q, Vialettes B, Million M, Raoult D, Henrissat B.

PLoS One. 2013 Dec 31;8(12):e84033. doi: 10.1371/journal.pone.0084033. eCollection 2013.


The human microbiome: a hot spot of microbial horizontal gene transfer.

Liu L, Chen X, Skogerbø G, Zhang P, Chen R, He S, Huang DW.

Genomics. 2012 Nov;100(5):265-70. doi: 10.1016/j.ygeno.2012.07.012. Epub 2012 Jul 25.


Multifunctional nutrient-binding proteins adapt human symbiotic bacteria for glycan competition in the gut by separately promoting enhanced sensing and catalysis.

Cameron EA, Kwiatkowski KJ, Lee BH, Hamaker BR, Koropatkin NM, Martens EC.

MBio. 2014 Sep 9;5(5):e01441-14. doi: 10.1128/mBio.01441-14.


Metagenomic discovery of biomass-degrading genes and genomes from cow rumen.

Hess M, Sczyrba A, Egan R, Kim TW, Chokhawala H, Schroth G, Luo S, Clark DS, Chen F, Zhang T, Mackie RI, Pennacchio LA, Tringe SG, Visel A, Woyke T, Wang Z, Rubin EM.

Science. 2011 Jan 28;331(6016):463-7. doi: 10.1126/science.1200387.


Companion animals symposium: humanized animal models of the microbiome.

Gootenberg DB, Turnbaugh PJ.

J Anim Sci. 2011 May;89(5):1531-7. doi: 10.2527/jas.2010-3371. Epub 2010 Sep 10. Review.


The mind-body-microbial continuum.

Gonzalez A, Stombaugh J, Lozupone C, Turnbaugh PJ, Gordon JI, Knight R.

Dialogues Clin Neurosci. 2011;13(1):55-62.


Metagenomic analysis of the pygmy loris fecal microbiome reveals unique functional capacity related to metabolism of aromatic compounds.

Xu B, Xu W, Yang F, Li J, Yang Y, Tang X, Mu Y, Zhou J, Huang Z.

PLoS One. 2013;8(2):e56565. doi: 10.1371/journal.pone.0056565. Epub 2013 Feb 15.


Expansion of the protein repertoire in newly explored environments: human gut microbiome specific protein families.

Ellrott K, Jaroszewski L, Li W, Wooley JC, Godzik A.

PLoS Comput Biol. 2010 Jun 3;6(6):e1000798. doi: 10.1371/journal.pcbi.1000798.

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