Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases Export

@article{citeulike:4230417, abstract = {10.1073/pnas.0806191105 The complex microbiome of the rumen functions as an effective system for the conversion of plant cell wall biomass to microbial protein, short chain fatty acids, and gases. As such, it provides a unique genetic resource for plant cell wall degrading microbial enzymes that could be used in the production of biofuels. The rumen and gastrointestinal tract harbor a dense and complex microbiome. To gain a greater understanding of the ecology and metabolic potential of this microbiome, we used comparative metagenomics (phylotype analysis and SEED subsystems-based annotations) to examine randomly sampled pyrosequence data from 3 fiber-adherent microbiomes and 1 pooled liquid sample (a mixture of the liquid microbiome fractions from the same bovine rumens). Even though the 3 animals were fed the same diet, the community structure, predicted phylotype, and metabolic potentials in the rumen were markedly different with respect to nutrient utilization. A comparison of the glycoside hydrolase and cellulosome functional genes revealed that in the rumen microbiome, initial colonization of fiber appears to be by organisms possessing enzymes that attack the easily available side chains of complex plant polysaccharides and not the more recalcitrant main chains, especially cellulose. Furthermore, when compared with the termite hindgut microbiome, there are fundamental differences in the glycoside hydrolase content that appear to be diet driven for either the bovine rumen (forages and legumes) or the termite hindgut (wood).}, author = {Brulc, Jennifer M. and Antonopoulos, Dionysios A. and Berg Miller, Margret E. and Wilson, Melissa K. and Yannarell, Anthony C. and Dinsdale, Elizabeth A. and Edwards, Robert E. and Frank, Edward D. and Emerson, Joanne B. and Wacklin, Pirjo and Coutinho, Pedro M. and Henrissat, Bernard and Nelson, Karen E. and White, Bryan A.}, citeulike-article-id = {4230417}, citeulike-linkout-0 = {http://dx.doi.org/10.1073/pnas.0806191105}, citeulike-linkout-1 = {http://www.pnas.org/content/106/6/1948.full.abstract}, citeulike-linkout-2 = {http://www.pnas.org/content/106/6/1948.full.full.pdf}, citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/19181843}, citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=19181843}, day = {10}, doi = {10.1073/pnas.0806191105}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences}, keywords = {biofuels, comparative-metagenomics, gut-microbes, pyrosequencing, seed}, month = {February}, number = {6}, pages = {1948--1953}, posted-at = {2009-03-27 12:47:21}, priority = {2}, title = {Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases}, url = {http://dx.doi.org/10.1073/pnas.0806191105}, volume = {106}, year = {2009} }

TY - JOUR ID - citeulike:4230417 L3 - citeulike-article-id:4230417 N2 - 10.1073/pnas.0806191105 The complex microbiome of the rumen functions as an effective system for the conversion of plant cell wall biomass to microbial protein, short chain fatty acids, and gases. As such, it provides a unique genetic resource for plant cell wall degrading microbial enzymes that could be used in the production of biofuels. The rumen and gastrointestinal tract harbor a dense and complex microbiome. To gain a greater understanding of the ecology and metabolic potential of this microbiome, we used comparative metagenomics (phylotype analysis and SEED subsystems-based annotations) to examine randomly sampled pyrosequence data from 3 fiber-adherent microbiomes and 1 pooled liquid sample (a mixture of the liquid microbiome fractions from the same bovine rumens). Even though the 3 animals were fed the same diet, the community structure, predicted phylotype, and metabolic potentials in the rumen were markedly different with respect to nutrient utilization. A comparison of the glycoside hydrolase and cellulosome functional genes revealed that in the rumen microbiome, initial colonization of fiber appears to be by organisms possessing enzymes that attack the easily available side chains of complex plant polysaccharides and not the more recalcitrant main chains, especially cellulose. Furthermore, when compared with the termite hindgut microbiome, there are fundamental differences in the glycoside hydrolase content that appear to be diet driven for either the bovine rumen (forages and legumes) or the termite hindgut (wood). IS - 6 JF - Proceedings of the National Academy of Sciences SN - 1091-6490 EP - 1953 TI - Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases VL - 106 SP - 1948 KW - biofuels KW - comparative-metagenomics KW - gut-microbes KW - pyrosequencing KW - seed AU - Brulc, Jennifer AU - Antonopoulos, Dionysios AU - Berg Miller, Margret AU - Wilson, Melissa AU - Yannarell, Anthony AU - Dinsdale, Elizabeth AU - Edwards, Robert AU - Frank, Edward AU - Emerson, Joanne AU - Wacklin, Pirjo AU - Coutinho, Pedro AU - Henrissat, Bernard AU - Nelson, Karen AU - White, Bryan PY - 2009/02/10/ UR - http://dx.doi.org/10.1073/pnas.0806191105 ER -