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, et al. (2011)
Science 331(6016): 463-467.

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Abstract / Bemerkung
The paucity of enzymes that efficiently deconstruct plant polysaccharides represents a major bottleneck for industrial-scale conversion of cellulosic biomass into biofuels. Cow rumen microbes specialize in degradation of cellulosic plant material, but most members of this complex community resist cultivation. To characterize biomass-degrading genes and genomes, we sequenced and analyzed 268 gigabases of metagenomic DNA from microbes adherent to plant fiber incubated in cow rumen. From these data, we identified 27,755 putative carbohydrate-active genes and expressed 90 candidate proteins, of which 57% were enzymatically active against cellulosic substrates. We also assembled 15 uncultured microbial genomes, which were validated by complementary methods including single-cell genome sequencing. These data sets provide a substantially expanded catalog of genes and genomes participating in the deconstruction of cellulosic biomass.
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6016
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463-467
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Hess M, Sczyrba A, Egan R, et al. Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science. 2011;331(6016):463-467.
Hess, M., Sczyrba, A., Egan, R., Kim, T. W., Chokhawala, H., Schroth, G., Luo, S., et al. (2011). Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science, 331(6016), 463-467. doi:10.1126/science.1200387
Hess, M., Sczyrba, A., Egan, R., Kim, T. W., Chokhawala, H., Schroth, G., Luo, S., Clark, D. S., Chen, F., Zhang, T., et al. (2011). Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science 331, 463-467.
Hess, M., et al., 2011. Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science, 331(6016), p 463-467.
M. Hess, et al., “Metagenomic discovery of biomass-degrading genes and genomes from cow rumen”, Science, vol. 331, 2011, pp. 463-467.
Hess, M., Sczyrba, A., Egan, R., Kim, T.W., Chokhawala, H., Schroth, G., Luo, S., Clark, D.S., Chen, F., Zhang, T., Mackie, R.I., Pennacchio, L.A., Tringe, S.G., Visel, A., Woyke, T., Wang, Z., Rubin, E.M.: Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science. 331, 463-467 (2011).
Hess, M., Sczyrba, Alexander, Egan, R., Kim, T. W., Chokhawala, H., Schroth, G., Luo, S., Clark, D. S., Chen, F., Zhang, T., Mackie, R. I., Pennacchio, L. A., Tringe, S. G., Visel, A., Woyke, T., Wang, Z., and Rubin, E. M. “Metagenomic discovery of biomass-degrading genes and genomes from cow rumen”. Science 331.6016 (2011): 463-467.

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PMID: 28745827
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.
Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C, Genome Standards Consortium, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T., Nat Biotechnol 35(8), 2017
PMID: 28787424
Analysis of large 16S rRNA Illumina data sets: Impact of singleton read filtering on microbial community description.
Auer L, Mariadassou M, O'Donohue M, Klopp C, Hernandez-Raquet G., Mol Ecol Resour 17(6), 2017
PMID: 28695665
Metagenome Analysis: a Powerful Tool for Enzyme Bioprospecting.
Madhavan A, Sindhu R, Parameswaran B, Sukumaran RK, Pandey A., Appl Biochem Biotechnol 183(2), 2017
PMID: 28815469
Metagenomic mining pectinolytic microbes and enzymes from an apple pomace-adapted compost microbial community.
Zhou M, Guo P, Wang T, Gao L, Yin H, Cai C, Gu J, Lü X., Biotechnol Biofuels 10(), 2017
PMID: 28852421
A Structural and Functional Elucidation of the Rumen Microbiome Influenced by Various Diets and Microenvironments.
Deusch S, Camarinha-Silva A, Conrad J, Beifuss U, Rodehutscord M, Seifert J., Front Microbiol 8(), 2017
PMID: 28883813
Optimization of a metatranscriptomic approach to study the lignocellulolytic potential of the higher termite gut microbiome.
Marynowska M, Goux X, Sillam-Dussès D, Rouland-Lefèvre C, Roisin Y, Delfosse P, Calusinska M., BMC Genomics 18(1), 2017
PMID: 28863779
Facing the challenge of sustainable bioenergy production: Could halophytes be part of the solution?
Debez A, Belghith I, Friesen J, Montzka C, Elleuche S., J Biol Eng 11(), 2017
PMID: 28883890
Metatranscriptomics Reveals the Functions and Enzyme Profiles of the Microbial Community in Chinese Nong-Flavor Liquor Starter.
Huang Y, Yi Z, Jin Y, Huang M, He K, Liu D, Luo H, Zhao D, He H, Fang Y, Zhao H., Front Microbiol 8(), 2017
PMID: 28955318
Tools for Genomic and Transcriptomic Analysis of Microbes at Single-Cell Level.
Chen Z, Chen L, Zhang W., Front Microbiol 8(), 2017
PMID: 28979258
PCR and Omics Based Techniques to Study the Diversity, Ecology and Biology of Anaerobic Fungi: Insights, Challenges and Opportunities.
Edwards JE, Forster RJ, Callaghan TM, Dollhofer V, Dagar SS, Cheng Y, Chang J, Kittelmann S, Fliegerova K, Puniya AK, Henske JK, Gilmore SP, O'Malley MA, Griffith GW, Smidt H., Front Microbiol 8(), 2017
PMID: 28993761
Using metagenomics to investigate human and environmental resistomes.
Bengtsson-Palme J, Larsson DGJ, Kristiansson E., J Antimicrob Chemother 72(10), 2017
PMID: 28673041
The trajectory of microbial single-cell sequencing.
Woyke T, Doud DFR, Schulz F., Nat Methods 14(11), 2017
PMID: 29088131
Comparative characterization of bacterial communities in geese fed all-grass or high-grain diets.
Xu Q, Yuan X, Gu T, Li Y, Dai W, Shen X, Song Y, Zhang Y, Zhao W, Chang G, Chen G., PLoS One 12(10), 2017
PMID: 28972993
Endosphere microbiome comparison between symptomatic and asymptomatic roots of Brassica napus infected with Plasmodiophora brassicae.
Zhao Y, Gao Z, Tian B, Bi K, Chen T, Liu H, Xie J, Cheng J, Fu Y, Jiang D., PLoS One 12(10), 2017
PMID: 29065162
Recent advances in sequence assembly: principles and applications.
Chen Q, Lan C, Zhao L, Wang J, Chen B, Chen YP., Brief Funct Genomics 16(6), 2017
PMID: 28453648
Targeted metatranscriptomics of compost-derived consortia reveals a GH11 exerting an unusual exo-1,4-β-xylanase activity.
Mello BL, Alessi AM, Riaño-Pachón DM, deAzevedo ER, Guimarães FEG, Espirito Santo MC, McQueen-Mason S, Bruce NC, Polikarpov I., Biotechnol Biofuels 10(), 2017
PMID: 29118851
New microbial resource: microbial diversity, function and dynamics in Chinese liquor starter.
Huang Y, Yi Z, Jin Y, Zhao Y, He K, Liu D, Zhao D, He H, Luo H, Zhang W, Fang Y, Zhao H., Sci Rep 7(1), 2017
PMID: 29109406
Progressive Colonization of Bacteria and Degradation of Rice Straw in the Rumen by Illumina Sequencing.
Cheng Y, Wang Y, Li Y, Zhang Y, Liu T, Wang Y, Sharpton TJ, Zhu W., Front Microbiol 8(), 2017
PMID: 29163444
Dietary energy drives the dynamic response of bovine rumen viral communities.
Anderson CL, Sullivan MB, Fernando SC., Microbiome 5(1), 2017
PMID: 29179741
Disentangling metabolic functions of bacteria in the honey bee gut.
Kešnerová L, Mars RAT, Ellegaard KM, Troilo M, Sauer U, Engel P., PLoS Biol 15(12), 2017
PMID: 29232373
CoMet: a workflow using contig coverage and composition for binning a metagenomic sample with high precision.
Herath D, Tang SL, Tandon K, Ackland D, Halgamuge SK., BMC Bioinformatics 18(suppl 16), 2017
PMID: 29297295
Estimating the success of enzyme bioprospecting through metagenomics: current status and future trends.
Ferrer M, Martínez-Martínez M, Bargiela R, Streit WR, Golyshina OV, Golyshin PN., Microb Biotechnol 9(1), 2016
PMID: 26275154
Single-cell technologies in environmental omics.
Kodzius R, Gojobori T., Gene 576(2 pt 1), 2016
PMID: 26474748
Robust and effective methodologies for cryopreservation and DNA extraction from anaerobic gut fungi.
Solomon KV, Henske JK, Theodorou MK, O'Malley MA., Anaerobe 38(), 2016
PMID: 26620247
Metagenomic assessment of the functional potential of the rumen microbiome in Holstein dairy cows.
Pitta DW, Indugu N, Kumar S, Vecchiarelli B, Sinha R, Baker LD, Bhukya B, Ferguson JD., Anaerobe 38(), 2016
PMID: 26700882
Haplotype-Phased Synthetic Long Reads from Short-Read Sequencing.
Stapleton JA, Kim J, Hamilton JP, Wu M, Irber LC, Maddamsetti R, Briney B, Newton L, Burton DR, Brown CT, Chan C, Buell CR, Whitehead TA., PLoS One 11(1), 2016
PMID: 26789840
Biosynthesis of polyketides by trans-AT polyketide synthases.
Helfrich EJ, Piel J., Nat Prod Rep 33(2), 2016
PMID: 26689670
Metagenomic analysis and functional characterization of the biogas microbiome using high throughput shotgun sequencing and a novel binning strategy.
Campanaro S, Treu L, Kougias PG, De Francisci D, Valle G, Angelidaki I., Biotechnol Biofuels 9(), 2016
PMID: 26839589
Metagenomic Analysis Reveals Symbiotic Relationship among Bacteria in Microcystis-Dominated Community.
Xie M, Ren M, Yang C, Yi H, Li Z, Li T, Zhao J., Front Microbiol 7(), 2016
PMID: 26870018
Improved Environmental Genomes via Integration of Metagenomic and Single-Cell Assemblies.
Mende DR, Aylward FO, Eppley JM, Nielsen TN, DeLong EF., Front Microbiol 7(), 2016
PMID: 26904016
Comprehensive detection of bacterial carbohydrate-active enzyme coding genes expressed in cow rumen.
Shinkai T, Mitsumori M, Sofyan A, Kanamori H, Sasaki H, Katayose Y, Takenaka A., Anim Sci J 87(11), 2016
PMID: 26875748
Early-branching gut fungi possess a large, comprehensive array of biomass-degrading enzymes.
Solomon KV, Haitjema CH, Henske JK, Gilmore SP, Borges-Rivera D, Lipzen A, Brewer HM, Purvine SO, Wright AT, Theodorou MK, Grigoriev IV, Regev A, Thompson DA, O'Malley MA., Science 351(6278), 2016
PMID: 26912365
Recovering complete and draft population genomes from metagenome datasets.
Sangwan N, Xia F, Gilbert JA., Microbiome 4(), 2016
PMID: 26951112
Isolation and characterization of novel multifunctional recombinant family 26 glycoside hydrolase from Mehsani buffalo rumen metagenome.
Patel AB, Patel AK, Shah MP, Parikh IK, Joshi CG., Biotechnol Appl Biochem 63(2), 2016
PMID: 25644118
MeCorS: Metagenome-enabled error correction of single cell sequencing reads.
Bremges A, Singer E, Woyke T, Sczyrba A., Bioinformatics 32(14), 2016
PMID: 27153586
Oral Samples as Non-Invasive Proxies for Assessing the Composition of the Rumen Microbial Community.
Tapio I, Shingfield KJ, McKain N, Bonin A, Fischer D, Bayat AR, Vilkki J, Taberlet P, Snelling TJ, Wallace RJ., PLoS One 11(3), 2016
PMID: 26986467
Cellulose-Enriched Microbial Communities from Leaf-Cutter Ant (Atta colombica) Refuse Dumps Vary in Taxonomic Composition and Degradation Ability.
Lewin GR, Johnson AL, Soto RD, Perry K, Book AJ, Horn HA, Pinto-Tomás AA, Currie CR., PLoS One 11(3), 2016
PMID: 26999749
MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices.
Li D, Luo R, Liu CM, Leung CM, Ting HF, Sadakane K, Yamashita H, Lam TW., Methods 102(), 2016
PMID: 27012178
Decreased microbial diversity and Lactobacillus group in the intestine of geriatric giant pandas (Ailuropoda melanoleuca).
Peng Z, Zeng D, Wang Q, Niu L, Ni X, Zou F, Yang M, Sun H, Zhou Y, Liu Q, Yin Z, Pan K, Jing B., World J Microbiol Biotechnol 32(5), 2016
PMID: 27038949
Exploring the Secretomes of Microbes and Microbial Communities Using Filamentous Phage Display.
Gagic D, Ciric M, Wen WX, Ng F, Rakonjac J., Front Microbiol 7(), 2016
PMID: 27092113
Reconstruction of Bacterial and Viral Genomes from Multiple Metagenomes.
Gupta A, Kumar S, Prasoodanan VP, Harish K, Sharma AK, Sharma VK., Front Microbiol 7(), 2016
PMID: 27148174
Specific microbiome-dependent mechanisms underlie the energy harvest efficiency of ruminants.
Shabat SK, Sasson G, Doron-Faigenboim A, Durman T, Yaacoby S, Berg Miller ME, White BA, Shterzer N, Mizrahi I., ISME J 10(12), 2016
PMID: 27152936
Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data.
Frank JA, Pan Y, Tooming-Klunderud A, Eijsink VG, McHardy AC, Nederbragt AJ, Pope PB., Sci Rep 6(), 2016
PMID: 27156482
Cellular adhesiveness and cellulolytic capacity in Anaerolineae revealed by omics-based genome interpretation.
Xia Y, Wang Y, Wang Y, Chin FY, Zhang T., Biotechnol Biofuels 9(), 2016
PMID: 27222666
The Enigmatic Universe of the Herbivore Gut.
Glass NL., Trends Biochem Sci 41(7), 2016
PMID: 27257096
Deep metagenome and metatranscriptome analyses of microbial communities affiliated with an industrial biogas fermenter, a cow rumen, and elephant feces reveal major differences in carbohydrate hydrolysis strategies.
Güllert S, Fischer MA, Turaev D, Noebauer B, Ilmberger N, Wemheuer B, Alawi M, Rattei T, Daniel R, Schmitz RA, Grundhoff A, Streit WR., Biotechnol Biofuels 9(), 2016
PMID: 27279900
Convergent Evolution of Rumen Microbiomes in High-Altitude Mammals.
Zhang Z, Xu D, Wang L, Hao J, Wang J, Zhou X, Wang W, Qiu Q, Huang X, Zhou J, Long R, Zhao F, Shi P., Curr Biol 26(14), 2016
PMID: 27321997
Applying functional metagenomics to search for novel lignocellulosic enzymes in a microbial consortium derived from a thermophilic composting phase of sugarcane bagasse and cow manure.
Colombo LT, de Oliveira MN, Carneiro DG, de Souza RA, Alvim MC, Dos Santos JC, da Silva CC, Vidigal PM, da Silveira WB, Passos FM., Antonie Van Leeuwenhoek 109(9), 2016
PMID: 27350392
Discovery of new cellulases from the metagenome by a metagenomics-guided strategy.
Yang C, Xia Y, Qu H, Li AD, Liu R, Wang Y, Zhang T., Biotechnol Biofuels 9(), 2016
PMID: 27382415
Virtual microfluidics for digital quantification and single-cell sequencing.
Xu L, Brito IL, Alm EJ, Blainey PC., Nat Methods 13(9), 2016
PMID: 27479330
Exploring the Shift in Structure and Function of Microbial Communities Performing Biological Phosphorus Removal.
Mao Y, Wang Z, Li L, Jiang X, Zhang X, Ren H, Zhang T., PLoS One 11(8), 2016
PMID: 27547976
Molecular insights into the mechanism of thermal stability of actinomycete mannanase.
Kumagai Y, Uraji M, Wan K, Okuyama M, Kimura A, Hatanaka T., FEBS Lett 590(17), 2016
PMID: 27447091
Functional characterization of a gene locus from an uncultured gut Bacteroides conferring xylo-oligosaccharides utilization to Escherichia coli.
Tauzin AS, Laville E, Xiao Y, Nouaille S, Le Bourgeois P, Heux S, Portais JC, Monsan P, Martens EC, Potocki-Veronese G, Bordes F., Mol Microbiol 102(4), 2016
PMID: 27573446
Construction and Characterization of a Cellulolytic Consortium Enriched from the Hindgut of Holotrichia parallela Larvae.
Sheng P, Huang J, Zhang Z, Wang D, Tian X, Ding J., Int J Mol Sci 17(10), 2016
PMID: 27706065
From Genomes to Phenotypes: Traitar, the Microbial Trait Analyzer.
Weimann A, Mooren K, Frank J, Pope PB, Bremges A, McHardy AC., mSystems 1(6), 2016
PMID: 28066816
Temporal Metagenomic and Metabolomic Characterization of Fresh Perennial Ryegrass Degradation by Rumen Bacteria.
Mayorga OL, Kingston-Smith AH, Kim EJ, Allison GG, Wilkinson TJ, Hegarty MJ, Theodorou MK, Newbold CJ, Huws SA., Front Microbiol 7(), 2016
PMID: 27917166
Composting-Like Conditions Are More Efficient for Enrichment and Diversity of Organisms Containing Cellulase-Encoding Genes than Submerged Cultures.
Heiss-Blanquet S, Fayolle-Guichard F, Lombard V, Hébert A, Coutinho PM, Groppi A, Barre A, Henrissat B., PLoS One 11(12), 2016
PMID: 27936240
Nutrient availability shapes the microbial community structure in sugarcane bagasse compost-derived consortia.
Mello BL, Alessi AM, McQueen-Mason S, Bruce NC, Polikarpov I., Sci Rep 6(), 2016
PMID: 27941835
The environment shapes microbial enzymes: five cold-active and salt-resistant carboxylesterases from marine metagenomes.
Tchigvintsev A, Tran H, Popovic A, Kovacic F, Brown G, Flick R, Hajighasemi M, Egorova O, Somody JC, Tchigvintsev D, Khusnutdinova A, Chernikova TN, Golyshina OV, Yakimov MM, Savchenko A, Golyshin PN, Jaeger KE, Yakunin AF., Appl Microbiol Biotechnol 99(5), 2015
PMID: 25194841
The early impact of genomics and metagenomics on ruminal microbiology.
Denman SE, McSweeney CS., Annu Rev Anim Biosci 3(), 2015
PMID: 25387109
Investigating the function of an arabinan utilization locus isolated from a termite gut community.
Arnal G, Bastien G, Monties N, Abot A, Anton Leberre V, Bozonnet S, O'Donohue M, Dumon C., Appl Environ Microbiol 81(1), 2015
PMID: 25304507
Community analysis of plant biomass-degrading microorganisms from Obsidian Pool, Yellowstone National Park.
Vishnivetskaya TA, Hamilton-Brehm SD, Podar M, Mosher JJ, Palumbo AV, Phelps TJ, Keller M, Elkins JG., Microb Ecol 69(2), 2015
PMID: 25319238
A polysaccharide utilization locus from an uncultured bacteroidetes phylotype suggests ecological adaptation and substrate versatility.
Mackenzie AK, Naas AE, Kracun SK, Schückel J, Fangel JU, Agger JW, Willats WG, Eijsink VG, Pope PB., Appl Environ Microbiol 81(1), 2015
PMID: 25326301
Multi-functional glycoside hydrolase: Blon_0625 from Bifidobacterium longum subsp. infantis ATCC 15697.
Matsumoto T, Shimada S, Hata Y, Tanaka T, Kondo A., Enzyme Microb Technol 68(), 2015
PMID: 25435500
Ecological roles of dominant and rare prokaryotes in acid mine drainage revealed by metagenomics and metatranscriptomics.
Hua ZS, Han YJ, Chen LX, Liu J, Hu M, Li SJ, Kuang JL, Chain PS, Huang LN, Shu WS., ISME J 9(6), 2015
PMID: 25361395
Metagenomic-based study of the phylogenetic and functional gene diversity in Galápagos land and marine iguanas.
Hong PY, Mao Y, Ortiz-Kofoed S, Shah R, Cann I, Mackie RI., Microb Ecol 69(2), 2015
PMID: 25524569
News in livestock research - use of Omics-technologies to study the microbiota in the gastrointestinal tract of farm animals.
Deusch S, Tilocca B, Camarinha-Silva A, Seifert J., Comput Struct Biotechnol J 13(), 2015
PMID: 26900430
First insights into the microbial diversity in the omasum and reticulum of bovine using Illumina sequencing.
Peng S, Yin J, Liu X, Jia B, Chang Z, Lu H, Jiang N, Chen Q., J Appl Genet 56(3), 2015
PMID: 25604266
High-throughput metagenomic technologies for complex microbial community analysis: open and closed formats.
Zhou J, He Z, Yang Y, Deng Y, Tringe SG, Alvarez-Cohen L., MBio 6(1), 2015
PMID: 25626903
Metatranscriptomic analyses of plant cell wall polysaccharide degradation by microorganisms in the cow rumen.
Dai X, Tian Y, Li J, Luo Y, Liu D, Zheng H, Wang J, Dong Z, Hu S, Huang L., Appl Environ Microbiol 81(4), 2015
PMID: 25501482
Prepartum and postpartum rumen fluid microbiomes: characterization and correlation with production traits in dairy cows.
Lima FS, Oikonomou G, Lima SF, Bicalho ML, Ganda EK, Filho JC, Lorenzo G, Trojacanec P, Bicalhoa RC., Appl Environ Microbiol 81(4), 2015
PMID: 25501481
Comparative analysis of sugarcane bagasse metagenome reveals unique and conserved biomass-degrading enzymes among lignocellulolytic microbial communities.
Mhuantong W, Charoensawan V, Kanokratana P, Tangphatsornruang S, Champreda V., Biotechnol Biofuels 8(), 2015
PMID: 25709713
Discrete and structurally unique proteins (tāpirins) mediate attachment of extremely thermophilic Caldicellulosiruptor species to cellulose.
Blumer-Schuette SE, Alahuhta M, Conway JM, Lee LL, Zurawski JV, Giannone RJ, Hettich RL, Lunin VV, Himmel ME, Kelly RM., J Biol Chem 290(17), 2015
PMID: 25720489
DomSign: a top-down annotation pipeline to enlarge enzyme space in the protein universe.
Wang T, Mori H, Zhang C, Kurokawa K, Xing XH, Yamada T., BMC Bioinformatics 16(), 2015
PMID: 25888481
RUMINANT NUTRITION SYMPOSIUM: Use of genomics and transcriptomics to identify strategies to lower ruminal methanogenesis.
McAllister TA, Meale SJ, Valle E, Guan LL, Zhou M, Kelly WJ, Henderson G, Attwood GT, Janssen PH., J Anim Sci 93(4), 2015
PMID: 26020166
Wiretapping into microbial interactions by single cell genomics.
Stepanauskas R., Front Microbiol 6(), 2015
PMID: 25904902
CoMeta: classification of metagenomes using k-mers.
Kawulok J, Deorowicz S., PLoS One 10(4), 2015
PMID: 25884504
Exploring the sheep rumen microbiome for carbohydrate-active enzymes.
Lopes LD, de Souza Lima AO, Taketani RG, Darias P, da Silva LR, Romagnoli EM, Louvandini H, Abdalla AL, Mendes R., Antonie Van Leeuwenhoek 108(1), 2015
PMID: 25900454
Elviz - exploration of metagenome assemblies with an interactive visualization tool.
Cantor M, Nordberg H, Smirnova T, Hess M, Tringe S, Dubchak I., BMC Bioinformatics 16(), 2015
PMID: 25928663
Reconstructing rare soil microbial genomes using in situ enrichments and metagenomics.
Delmont TO, Eren AM, Maccario L, Prestat E, Esen ÖC, Pelletier E, Le Paslier D, Simonet P, Vogel TM., Front Microbiol 6(), 2015
PMID: 25983722
The bamboo-eating giant panda harbors a carnivore-like gut microbiota, with excessive seasonal variations.
Xue Z, Zhang W, Wang L, Hou R, Zhang M, Fei L, Zhang X, Huang H, Bridgewater LC, Jiang Y, Jiang C, Zhao L, Pang X, Zhang Z., MBio 6(3), 2015
PMID: 25991678
Synergistic function of four novel thermostable glycoside hydrolases from a long-term enriched thermophilic methanogenic digester.
Wang M, Lai GL, Nie Y, Geng S, Liu L, Zhu B, Shi Z, Wu XL., Front Microbiol 6(), 2015
PMID: 26052323
Rumen microbiome from steers differing in feed efficiency.
Myer PR, Smith TP, Wells JE, Kuehn LA, Freetly HC., PLoS One 10(6), 2015
PMID: 26030887
Metagenomic surveys of gut microbiota.
Mandal RS, Saha S, Das S., Genomics Proteomics Bioinformatics 13(3), 2015
PMID: 26184859
Biotechnological applications of functional metagenomics in the food and pharmaceutical industries.
Coughlan LM, Cotter PD, Hill C, Alvarez-Ordóñez A., Front Microbiol 6(), 2015
PMID: 26175729
Structural Features of a Bacteroidetes-Affiliated Cellulase Linked with a Polysaccharide Utilization Locus.
Naas AE, MacKenzie AK, Dalhus B, Eijsink VG, Pope PB., Sci Rep 5(), 2015
PMID: 26133573
Improved ethanol production from biomass by a rumen metagenomic DNA fragment expressed in Escherichia coli MS04 during fermentation.
Loaces I, Amarelle V, Muñoz-Gutierrez I, Fabiano E, Martinez A, Noya F., Appl Microbiol Biotechnol 99(21), 2015
PMID: 26175105
Biocatalysts for biomass deconstruction from environmental genomics.
Armstrong Z, Mewis K, Strachan C, Hallam SJ., Curr Opin Chem Biol 29(), 2015
PMID: 26231123
Metagenome approaches revealed a biological prospect for improvement on mesophilic cellulose degradation.
Wang Y, Xia Y, Ju F, Zhang T., Appl Microbiol Biotechnol 99(24), 2015
PMID: 26359182
Metatranscriptomic discovery of plant biomass-degrading capacity from grass carp intestinal microbiomes.
Wu S, Ren Y, Peng C, Hao Y, Xiong F, Wang G, Li W, Zou H, Angert ER., FEMS Microbiol Ecol 91(10), 2015
PMID: 26362922
Next-generation sequencing (NGS) for assessment of microbial water quality: current progress, challenges, and future opportunities.
Tan B, Ng C, Nshimyimana JP, Loh LL, Gin KY, Thompson JR., Front Microbiol 6(), 2015
PMID: 26441948
The players may change but the game remains: network analyses of ruminal microbiomes suggest taxonomic differences mask functional similarity.
Taxis TM, Wolff S, Gregg SJ, Minton NO, Zhang C, Dai J, Schnabel RD, Taylor JF, Kerley MS, Pires JC, Lamberson WR, Conant GC., Nucleic Acids Res 43(20), 2015
PMID: 26420832
Limited dissemination of the wastewater treatment plant core resistome.
Munck C, Albertsen M, Telke A, Ellabaan M, Nielsen PH, Sommer MO., Nat Commun 6(), 2015
PMID: 26419330
Anvi'o: an advanced analysis and visualization platform for 'omics data.
Eren AM, Esen ÖC, Quince C, Vineis JH, Morrison HG, Sogin ML, Delmont TO., PeerJ 3(), 2015
PMID: 26500826
PanCoreGen - Profiling, detecting, annotating protein-coding genes in microbial genomes.
Paul S, Bhardwaj A, Bag SK, Sokurenko EV, Chattopadhyay S., Genomics 106(6), 2015
PMID: 26456591
Metagenomic analysis of the rumen microbial community following inhibition of methane formation by a halogenated methane analog.
Denman SE, Martinez Fernandez G, Shinkai T, Mitsumori M, McSweeney CS., Front Microbiol 6(), 2015
PMID: 26528253
Lignin-modifying processes in the rhizosphere of arid land grasses.
Hudson CM, Kirton E, Hutchinson MI, Redfern JL, Simmons B, Ackerman E, Singh S, Williams KP, Natvig DO, Powell AJ., Environ Microbiol 17(12), 2015
PMID: 26279186
The rumen microbial metagenome associated with high methane production in cattle.
Wallace RJ, Rooke JA, McKain N, Duthie CA, Hyslop JJ, Ross DW, Waterhouse A, Watson M, Roehe R., BMC Genomics 16(), 2015
PMID: 26494241
Identification of low abundance microbiome in clinical samples using whole genome sequencing.
Zhang C, Cleveland K, Schnoll-Sussman F, McClure B, Bigg M, Thakkar P, Schultz N, Shah MA, Betel D., Genome Biol 16(), 2015
PMID: 26614063
Metagenomics and novel gene discovery: promise and potential for novel therapeutics.
Culligan EP, Sleator RD, Marchesi JR, Hill C., Virulence 5(3), 2014
PMID: 24317337
Biochemical and kinetic characterization of the multifunctional β-glucosidase/β-xylosidase/α-arabinosidase, Bgxa1.
Gruninger RJ, Gong X, Forster RJ, McAllister TA., Appl Microbiol Biotechnol 98(7), 2014
PMID: 23995226
Gastrointestinal tract microbiota and probiotics in production animals.
Yeoman CJ, White BA., Annu Rev Anim Biosci 2(), 2014
PMID: 25384152
EBI metagenomics--a new resource for the analysis and archiving of metagenomic data.
Hunter S, Corbett M, Denise H, Fraser M, Gonzalez-Beltran A, Hunter C, Jones P, Leinonen R, McAnulla C, Maguire E, Maslen J, Mitchell A, Nuka G, Oisel A, Pesseat S, Radhakrishnan R, Rocca-Serra P, Scheremetjew M, Sterk P, Vaughan D, Cochrane G, Field D, Sansone SA., Nucleic Acids Res 42(database issue), 2014
PMID: 24165880
Diet alters both the structure and taxonomy of the ovine gut microbial ecosystem.
Ellison MJ, Conant GC, Cockrum RR, Austin KJ, Truong H, Becchi M, Lamberson WR, Cammack KM., DNA Res 21(2), 2014
PMID: 24170804
Thermophilic lignocellulose deconstruction.
Blumer-Schuette SE, Brown SD, Sander KB, Bayer EA, Kataeva I, Zurawski JV, Conway JM, Adams MW, Kelly RM., FEMS Microbiol Rev 38(3), 2014
PMID: 24118059
New aspects and strategies for methane mitigation from ruminants.
Kumar S, Choudhury PK, Carro MD, Griffith GW, Dagar SS, Puniya M, Calabro S, Ravella SR, Dhewa T, Upadhyay RC, Sirohi SK, Kundu SS, Wanapat M, Puniya AK., Appl Microbiol Biotechnol 98(1), 2014
PMID: 24247990
Factors influencing the grass carp gut microbiome and its effect on metabolism.
Ni J, Yan Q, Yu Y, Zhang T., FEMS Microbiol Ecol 87(3), 2014
PMID: 24256454
Board-invited review: Opportunities and challenges in using exogenous enzymes to improve ruminant production.
Meale SJ, Beauchemin KA, Hristov AN, Chaves AV, McAllister TA., J Anim Sci 92(2), 2014
PMID: 24363327
Exploring bacterial lignin degradation.
Brown ME, Chang MC., Curr Opin Chem Biol 19(), 2014
PMID: 24780273
Proceedings of the 2013 A.S.P.E.N. Research workshop: the interface between nutrition and the gut microbiome: implications and applications for human health [corrected].
Alverdy J, Gilbert J, DeFazio JR, Sadowsky MJ, Chang EB, Morowitz MJ, Teitelbaum DH., JPEN J Parenter Enteral Nutr 38(2), 2014
PMID: 24379111
Metagenomic analysis of microbial consortium from natural crude oil that seeps into the marine ecosystem offshore Southern California.
Hawley ER, Piao H, Scott NM, Malfatti S, Pagani I, Huntemann M, Chen A, Glavina Del Rio T, Foster B, Copeland A, Jansson J, Pati A, Tringe S, Gilbert JA, Lorenson TD, Hess M., Stand Genomic Sci 9(3), 2014
PMID: 25197496
Recruiting human microbiome shotgun data to site-specific reference genomes.
Xie G, Lo CC, Scholz M, Chain PS., PLoS One 9(1), 2014
PMID: 24454771
Microbial enzymes: tools for biotechnological processes.
Adrio JL, Demain AL., Biomolecules 4(1), 2014
PMID: 24970208
Community structure and succession regulation of fungal consortia in the lignocellulose-degrading process on natural biomass.
Tian B, Wang C, Lv R, Zhou J, Li X, Zheng Y, Jin X, Wang M, Ye Y, Huang X, Liu P., ScientificWorldJournal 2014(), 2014
PMID: 24574925
Herbivorous rodents (Neotoma spp.) harbour abundant and active foregut microbiota.
Kohl KD, Miller AW, Marvin JE, Mackie R, Dearing MD., Environ Microbiol 16(9), 2014
PMID: 24373154
MetaCluster-TA: taxonomic annotation for metagenomic data based on assembly-assisted binning.
Wang Y, Leung H, Yiu S, Chin F., BMC Genomics 15 Suppl 1(), 2014
PMID: 24564377
Comparative genomic analysis reveals 2-oxoacid dehydrogenase complex lipoylation correlation with aerobiosis in archaea.
Borziak K, Posner MG, Upadhyay A, Danson MJ, Bagby S, Dorus S., PLoS One 9(1), 2014
PMID: 24489835
Genomic variability of monkeypox virus among humans, Democratic Republic of the Congo.
Kugelman JR, Johnston SC, Mulembakani PM, Kisalu N, Lee MS, Koroleva G, McCarthy SE, Gestole MC, Wolfe ND, Fair JN, Schneider BS, Wright LL, Huggins J, Whitehouse CA, Wemakoy EO, Muyembe-Tamfum JJ, Hensley LE, Palacios GF, Rimoin AW., Emerg Infect Dis 20(2), 2014
PMID: 24457084
Strain/species identification in metagenomes using genome-specific markers.
Tu Q, He Z, Zhou J., Nucleic Acids Res 42(8), 2014
PMID: 24523352
Diversity of rumen bacteria in canadian cervids.
Gruninger RJ, Sensen CW, McAllister TA, Forster RJ., PLoS One 9(2), 2014
PMID: 24586961
GeoChip 4: a functional gene-array-based high-throughput environmental technology for microbial community analysis.
Tu Q, Yu H, He Z, Deng Y, Wu L, Van Nostrand JD, Zhou A, Voordeckers J, Lee YJ, Qin Y, Hemme CL, Shi Z, Xue K, Yuan T, Wang A, Zhou J., Mol Ecol Resour 14(5), 2014
PMID: 24520909
Tackling soil diversity with the assembly of large, complex metagenomes.
Howe AC, Jansson JK, Malfatti SA, Tringe SG, Tiedje JM, Brown CT., Proc Natl Acad Sci U S A 111(13), 2014
PMID: 24632729
Metagenomic analysis of sludge from full-scale anaerobic digesters operated in municipal wastewater treatment plants.
Yang Y, Yu K, Xia Y, Lau FT, Tang DT, Fung WC, Fang HH, Zhang T., Appl Microbiol Biotechnol 98(12), 2014
PMID: 24633414
Straw- and slurry-associated prokaryotic communities differ during co-fermentation of straw and swine manure.
Li J, Rui J, Pei Z, Sun X, Zhang S, Yan Z, Wang Y, Liu X, Zheng T, Li X., Appl Microbiol Biotechnol 98(10), 2014
PMID: 24633443
Extensive microbial and functional diversity within the chicken cecal microbiome.
Sergeant MJ, Constantinidou C, Cogan TA, Bedford MR, Penn CW, Pallen MJ., PLoS One 9(3), 2014
PMID: 24657972
Captivity results in disparate loss of gut microbial diversity in closely related hosts.
Kohl KD, Skopec MM, Dearing MD., Conserv Physiol 2(1), 2014
PMID: 27293630
Feasibilities of consolidated bioprocessing microbes: from pretreatment to biofuel production.
Parisutham V, Kim TH, Lee SK., Bioresour Technol 161(), 2014
PMID: 24745899
Alignment-free visualization of metagenomic data by nonlinear dimension reduction.
Laczny CC, Pinel N, Vlassis N, Wilmes P., Sci Rep 4(), 2014
PMID: 24682077
Metagenomic analysis of buffalo rumen microbiome: Effect of roughage diet on Dormancy and Sporulation genes.
Singh KM, Reddy B, Patel AK, Panchasara H, Parmar N, Patel AB, Shah TM, Bhatt VD, Joshi CG., Meta Gene 2(), 2014
PMID: 25606408
Obtaining genomes from uncultivated environmental microorganisms using FACS-based single-cell genomics.
Rinke C, Lee J, Nath N, Goudeau D, Thompson B, Poulton N, Dmitrieff E, Malmstrom R, Stepanauskas R, Woyke T., Nat Protoc 9(5), 2014
PMID: 24722403
Reconstructing a Thauera genome from a hydrogenotrophic-denitrifying consortium using metagenomic sequence data.
Mao Y, Xia Y, Wang Z, Zhang T., Appl Microbiol Biotechnol 98(15), 2014
PMID: 24769905
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 545(1), 2014
PMID: 24797613
Metasecretome-selective phage display approach for mining the functional potential of a rumen microbial community.
Ciric M, Moon CD, Leahy SC, Creevey CJ, Altermann E, Attwood GT, Rakonjac J, Gagic D., BMC Genomics 15(), 2014
PMID: 24886150
Anaerobic gut fungi: Advances in isolation, culture, and cellulolytic enzyme discovery for biofuel production.
Haitjema CH, Solomon KV, Henske JK, Theodorou MK, O'Malley MA., Biotechnol Bioeng 111(8), 2014
PMID: 24788404
Identification of novel biomass-degrading enzymes from genomic dark matter: Populating genomic sequence space with functional annotation.
Piao H, Froula J, Du C, Kim TW, Hawley ER, Bauer S, Wang Z, Ivanova N, Clark DS, Klenk HP, Hess M., Biotechnol Bioeng 111(8), 2014
PMID: 24728961
Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome.
Shi W, Moon CD, Leahy SC, Kang D, Froula J, Kittelmann S, Fan C, Deutsch S, Gagic D, Seedorf H, Kelly WJ, Atua R, Sang C, Soni P, Li D, Pinares-Patiño CS, McEwan JC, Janssen PH, Chen F, Visel A, Wang Z, Attwood GT, Rubin EM., Genome Res 24(9), 2014
PMID: 24907284
High-throughput Methods Redefine the Rumen Microbiome and Its Relationship with Nutrition and Metabolism.
McCann JC, Wickersham TA, Loor JJ., Bioinform Biol Insights 8(), 2014
PMID: 24940050
Omics-based interpretation of synergism in a soil-derived cellulose-degrading microbial community.
Zhou Y, Pope PB, Li S, Wen B, Tan F, Cheng S, Chen J, Yang J, Liu F, Lei X, Su Q, Zhou C, Zhao J, Dong X, Jin T, Zhou X, Yang S, Zhang G, Yang H, Wang J, Yang R, Eijsink VG, Wang J., Sci Rep 4(), 2014
PMID: 24924356
Determining the culturability of the rumen bacterial microbiome.
Creevey CJ, Kelly WJ, Henderson G, Leahy SC., Microb Biotechnol 7(5), 2014
PMID: 24986151
Rumen cellulosomics: divergent fiber-degrading strategies revealed by comparative genome-wide analysis of six ruminococcal strains.
Dassa B, Borovok I, Ruimy-Israeli V, Lamed R, Flint HJ, Duncan SH, Henrissat B, Coutinho P, Morrison M, Mosoni P, Yeoman CJ, White BA, Bayer EA., PLoS One 9(7), 2014
PMID: 24992679
Viral tagging reveals discrete populations in Synechococcus viral genome sequence space.
Deng L, Ignacio-Espinoza JC, Gregory AC, Poulos BT, Weitz JS, Hugenholtz P, Sullivan MB., Nature 513(7517), 2014
PMID: 25043051
Phylogenomically guided identification of industrially relevant GH1 β-glucosidases through DNA synthesis and nanostructure-initiator mass spectrometry.
Heins RA, Cheng X, Nath S, Deng K, Bowen BP, Chivian DC, Datta S, Friedland GD, D'Haeseleer P, Wu D, Tran-Gyamfi M, Scullin CS, Singh S, Shi W, Hamilton MG, Bendall ML, Sczyrba A, Thompson J, Feldman T, Guenther JM, Gladden JM, Cheng JF, Adams PD, Rubin EM, Simmons BA, Sale KL, Northen TR, Deutsch S., ACS Chem Biol 9(9), 2014
PMID: 24984213
High potential source for biomass degradation enzyme discovery and environmental aspects revealed through metagenomics of Indian buffalo rumen.
Singh KM, Reddy B, Patel D, Patel AK, Parmar N, Patel A, Patel JB, Joshi CG., Biomed Res Int 2014(), 2014
PMID: 25136572
Distribution and diversity of members of the bacterial phylum Fibrobacteres in environments where cellulose degradation occurs.
Ransom-Jones E, Jones DL, Edwards A, McDonald JE., Syst Appl Microbiol 37(7), 2014
PMID: 25154048
Temporal dynamics of fibrolytic and methanogenic rumen microorganisms during in situ incubation of switchgrass determined by 16S rRNA gene profiling.
Piao H, Lachman M, Malfatti S, Sczyrba A, Knierim B, Auer M, Tringe SG, Mackie RI, Yeoman CJ, Hess M., Front Microbiol 5(), 2014
PMID: 25101058
Do rumen Bacteroidetes utilize an alternative mechanism for cellulose degradation?
Naas AE, Mackenzie AK, Mravec J, Schückel J, Willats WG, Eijsink VG, Pope PB., MBio 5(4), 2014
PMID: 25096880
Anaerobic fungi (phylum Neocallimastigomycota): advances in understanding their taxonomy, life cycle, ecology, role and biotechnological potential.
Gruninger RJ, Puniya AK, Callaghan TM, Edwards JE, Youssef N, Dagar SS, Fliegerova K, Griffith GW, Forster R, Tsang A, McAllister T, Elshahed MS., FEMS Microbiol Ecol 90(1), 2014
PMID: 25046344
Enzymatic degradation of (ligno)cellulose.
Bornscheuer U, Buchholz K, Seibel J., Angew Chem Int Ed Engl 53(41), 2014
PMID: 25136976
Enabling large-scale next-generation sequence assembly with Blacklight.
Couger MB, Pipes L, Squina F, Prade R, Siepel A, Palermo R, Katze MG, Mason CE, Blood PD., Concurr Comput 26(13), 2014
PMID: 25294974
Inference of phenotype-defining functional modules of protein families for microbial plant biomass degraders.
Konietzny SG, Pope PB, Weimann A, McHardy AC., Biotechnol Biofuels 7(1), 2014
PMID: 25342967
A comparative metagenome survey of the fecal microbiota of a breast- and a plant-fed Asian elephant reveals an unexpectedly high diversity of glycoside hydrolase family enzymes.
Ilmberger N, Güllert S, Dannenberg J, Rabausch U, Torres J, Wemheuer B, Alawi M, Poehlein A, Chow J, Turaev D, Rattei T, Schmeisser C, Salomon J, Olsen PB, Daniel R, Grundhoff A, Borchert MS, Streit WR., PLoS One 9(9), 2014
PMID: 25208077
Complementary symbiont contributions to plant decomposition in a fungus-farming termite.
Poulsen M, Hu H, Li C, Chen Z, Xu L, Otani S, Nygaard S, Nobre T, Klaubauf S, Schindler PM, Hauser F, Pan H, Yang Z, Sonnenberg AS, de Beer ZW, Zhang Y, Wingfield MJ, Grimmelikhuijzen CJ, de Vries RP, Korb J, Aanen DK, Wang J, Wang J, Boomsma JJ, Zhang G., Proc Natl Acad Sci U S A 111(40), 2014
PMID: 25246537
Substrate-Specific Development of Thermophilic Bacterial Consortia by Using Chemically Pretreated Switchgrass.
Eichorst SA, Joshua C, Sathitsuksanoh N, Singh S, Simmons BA, Singer SW., Appl Environ Microbiol 80(23), 2014
PMID: 25261509
Dynamic flux balance analysis for synthetic microbial communities.
Henson MA, Hanly TJ., IET Syst Biol 8(5), 2014
PMID: 25257022
Occurrence of lignin degradation genotypes and phenotypes among prokaryotes.
Tian JH, Pourcher AM, Bouchez T, Gelhaye E, Peu P., Appl Microbiol Biotechnol 98(23), 2014
PMID: 25343973
Characterization of the rumen microbiome of Indian Kankrej cattle (Bos indicus) adapted to different forage diet.
Patel V, Patel AK, Parmar NR, Patel AB, Reddy B, Joshi CG., Appl Microbiol Biotechnol 98(23), 2014
PMID: 25359471
Gill bacteria enable a novel digestive strategy in a wood-feeding mollusk.
O'Connor RM, Fung JM, Sharp KH, Benner JS, McClung C, Cushing S, Lamkin ER, Fomenkov AI, Henrissat B, Londer YY, Scholz MB, Posfai J, Malfatti S, Tringe SG, Woyke T, Malmstrom RR, Coleman-Derr D, Altamia MA, Dedrick S, Kaluziak ST, Haygood MG, Distel DL., Proc Natl Acad Sci U S A 111(47), 2014
PMID: 25385629
Convergent bacterial microbiotas in the fungal agricultural systems of insects.
Aylward FO, Suen G, Biedermann PH, Adams AS, Scott JJ, Malfatti SA, Glavina del Rio T, Tringe SG, Poulsen M, Raffa KF, Klepzig KD, Currie CR., MBio 5(6), 2014
PMID: 25406380
Cellulolytic potential under environmental changes in microbial communities from grassland litter.
Berlemont R, Allison SD, Weihe C, Lu Y, Brodie EL, Martiny JB, Martiny AC., Front Microbiol 5(), 2014
PMID: 25505459
Genomics review of holocellulose deconstruction by aspergilli.
Segato F, Damásio AR, de Lucas RC, Squina FM, Prade RA., Microbiol Mol Biol Rev 78(4), 2014
PMID: 25428936
AKE - the Accelerated k-mer Exploration web-tool for rapid taxonomic classification and visualization.
Langenkämper D, Goesmann A, Nattkemper TW., BMC Bioinformatics 15(), 2014
PMID: 25495116
Rumen microbial (meta)genomics and its application to ruminant production.
Morgavi DP, Kelly WJ, Janssen PH, Attwood GT., Animal 7 Suppl 1(), 2013
PMID: 23031271
Ecology of uncultured Prochlorococcus clades revealed through single-cell genomics and biogeographic analysis.
Malmstrom RR, Rodrigue S, Huang KH, Kelly L, Kern SE, Thompson A, Roggensack S, Berube PM, Henn MR, Chisholm SW., ISME J 7(1), 2013
PMID: 22895163
Coverage theories for metagenomic DNA sequencing based on a generalization of Stevens' theorem.
Wendl MC, Kota K, Weinstock GM, Mitreva M., J Math Biol 67(5), 2013
PMID: 22965653
Advances in monitoring environmental microbes.
Hazen TC, Rocha AM, Techtmann SM., Curr Opin Biotechnol 24(3), 2013
PMID: 23183250
Responses of the functional structure of soil microbial community to livestock grazing in the Tibetan alpine grassland.
Yang Y, Wu L, Lin Q, Yuan M, Xu D, Yu H, Hu Y, Duan J, Li X, He Z, Xue K, van Nostrand J, Wang S, Zhou J., Glob Chang Biol 19(2), 2013
PMID: 23504798
Comparative quantitative analysis of gene expression profiles of glycoside hydrolase family 10 xylanases in the sheep rumen during a feeding cycle.
Li Z, Zhao H, Yang P, Zhao J, Huang H, Xue X, Zhang X, Diao Q, Yao B., Appl Environ Microbiol 79(4), 2013
PMID: 23220966
Methanotrophic bacteria in oilsands tailings ponds of northern Alberta.
Saidi-Mehrabad A, He Z, Tamas I, Sharp CE, Brady AL, Rochman FF, Bodrossy L, Abell GC, Penner T, Dong X, Sensen CW, Dunfield PF., ISME J 7(5), 2013
PMID: 23254511
Phylogenetic distribution of potential cellulases in bacteria.
Berlemont R, Martiny AC., Appl Environ Microbiol 79(5), 2013
PMID: 23263967
Gut microbiota, host health, and polysaccharides.
Xu X, Xu P, Ma C, Tang J, Zhang X., Biotechnol Adv 31(2), 2013
PMID: 23280014
The human microbiome: from symbiosis to pathogenesis.
Eloe-Fadrosh EA, Rasko DA., Annu Rev Med 64(), 2013
PMID: 23327521
Ammonia assimilation in rumen bacteria: a review.
Pengpeng W, Tan Z., Anim Biotechnol 24(2), 2013
PMID: 23534958
PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes.
Segata N, Börnigen D, Morgan XC, Huttenhower C., Nat Commun 4(), 2013
PMID: 23942190
Boronated tartrolon antibiotic produced by symbiotic cellulose-degrading bacteria in shipworm gills.
Elshahawi SI, Trindade-Silva AE, Hanora A, Han AW, Flores MS, Vizzoni V, Schrago CG, Soares CA, Concepcion GP, Distel DL, Schmidt EW, Haygood MG., Proc Natl Acad Sci U S A 110(4), 2013
PMID: 23288898
Aerobic deconstruction of cellulosic biomass by an insect-associated Streptomyces.
Takasuka TE, Book AJ, Lewin GR, Currie CR, Fox BG., Sci Rep 3(), 2013
PMID: 23301151
Comparative genomic analysis of the microbiome [corrected] of herbivorous insects reveals eco-environmental adaptations: biotechnology applications.
Shi W, Xie S, Chen X, Sun S, Zhou X, Liu L, Gao P, Kyrpides NC, No EG, Yuan JS., PLoS Genet 9(1), 2013
PMID: 23326236
Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities.
Shakya M, Quince C, Campbell JH, Yang ZK, Schadt CW, Podar M., Environ Microbiol 15(6), 2013
PMID: 23387867
Simultaneous amplicon sequencing to explore co-occurrence patterns of bacterial, archaeal and eukaryotic microorganisms in rumen microbial communities.
Kittelmann S, Seedorf H, Walters WA, Clemente JC, Knight R, Gordon JI, Janssen PH., PLoS One 8(2), 2013
PMID: 23408926
The future is now: single-cell genomics of bacteria and archaea.
Blainey PC., FEMS Microbiol Rev 37(3), 2013
PMID: 23298390
De novo prediction of the genomic components and capabilities for microbial plant biomass degradation from (meta-)genomes.
Weimann A, Trukhina Y, Pope PB, Konietzny SG, McHardy AC., Biotechnol Biofuels 6(1), 2013
PMID: 23414703
Comparative analysis of microbial profiles in cow rumen fed with different dietary fiber by tagged 16S rRNA gene pyrosequencing.
Thoetkiattikul H, Mhuantong W, Laothanachareon T, Tangphatsornruang S, Pattarajinda V, Eurwilaichitr L, Champreda V., Curr Microbiol 67(2), 2013
PMID: 23471692
Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome.
Fitzsimons MS, Novotny M, Lo CC, Dichosa AE, Yee-Greenbaum JL, Snook JP, Gu W, Chertkov O, Davenport KW, McMurry K, Reitenga KG, Daughton AR, He J, Johnson SL, Gleasner CD, Wills PL, Parson-Quintana B, Chain PS, Detter JC, Lasken RS, Han CS., Genome Res 23(5), 2013
PMID: 23493677
Towards a metagenomic understanding on enhanced biomethane production from waste activated sludge after pH 10 pretreatment.
Wong MT, Zhang D, Li J, Hui RK, Tun HM, Brar MS, Park TJ, Chen Y, Leung FC., Biotechnol Biofuels 6(1), 2013
PMID: 23506434
Mountain pine beetles colonizing historical and naive host trees are associated with a bacterial community highly enriched in genes contributing to terpene metabolism.
Adams AS, Aylward FO, Adams SM, Erbilgin N, Aukema BH, Currie CR, Suen G, Raffa KF., Appl Environ Microbiol 79(11), 2013
PMID: 23542624
Comparative digestive physiology.
Karasov WH, Douglas AE., Compr Physiol 3(2), 2013
PMID: 23720328
Comparative metagenomic and metatranscriptomic analysis of hindgut paunch microbiota in wood- and dung-feeding higher termites.
He S, Ivanova N, Kirton E, Allgaier M, Bergin C, Scheffrahn RH, Kyrpides NC, Warnecke F, Tringe SG, Hugenholtz P., PLoS One 8(4), 2013
PMID: 23593407
Metagenomic analysis of a tropical composting operation at the são paulo zoo park reveals diversity of biomass degradation functions and organisms.
Martins LF, Antunes LP, Pascon RC, de Oliveira JC, Digiampietri LA, Barbosa D, Peixoto BM, Vallim MA, Viana-Niero C, Ostroski EH, Telles GP, Dias Z, da Cruz JB, Juliano L, Verjovski-Almeida S, da Silva AM, Setubal JC., PLoS One 8(4), 2013
PMID: 23637931
Direct amplification of new cellulase genes from woodland soil purified DNA.
Cucurachi M, Busconi M, Marudelli M, Soffritti G, Fogher C., Mol Biol Rep 40(7), 2013
PMID: 23645028
Discovery of (hemi-) cellulase genes in a metagenomic library from a biogas digester using 454 pyrosequencing.
Yan X, Geng A, Zhang J, Wei Y, Zhang L, Qian C, Wang Q, Wang S, Zhou Z., Appl Microbiol Biotechnol 97(18), 2013
PMID: 23653123
Computational meta'omics for microbial community studies.
Segata N, Boernigen D, Tickle TL, Morgan XC, Garrett WS, Huttenhower C., Mol Syst Biol 9(), 2013
PMID: 23670539
Mining for hemicellulases in the fungus-growing termite Pseudacanthotermes militaris using functional metagenomics.
Bastien G, Arnal G, Bozonnet S, Laguerre S, Ferreira F, Fauré R, Henrissat B, Lefèvre F, Robe P, Bouchez O, Noirot C, Dumon C, O'Donohue M., Biotechnol Biofuels 6(1), 2013
PMID: 23672637
Alternatives to antibiotics: a symposium on the challenges and solutions for animal production.
Seal BS, Lillehoj HS, Donovan DM, Gay CG., Anim Health Res Rev 14(1), 2013
PMID: 23702321
The genome of the anaerobic fungus Orpinomyces sp. strain C1A reveals the unique evolutionary history of a remarkable plant biomass degrader.
Youssef NH, Couger MB, Struchtemeyer CG, Liggenstoffer AS, Prade RA, Najar FZ, Atiyeh HK, Wilkins MR, Elshahed MS., Appl Environ Microbiol 79(15), 2013
PMID: 23709508
Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes.
Albertsen M, Hugenholtz P, Skarshewski A, Nielsen KL, Tyson GW, Nielsen PH., Nat Biotechnol 31(6), 2013
PMID: 23707974
Gut metagenome in European women with normal, impaired and diabetic glucose control.
Karlsson FH, Tremaroli V, Nookaew I, Bergström G, Behre CJ, Fagerberg B, Nielsen J, Bäckhed F., Nature 498(7452), 2013
PMID: 23719380
Meta-omic characterization of prokaryotic gene clusters for natural product biosynthesis.
Schofield MM, Sherman DH., Curr Opin Biotechnol 24(6), 2013
PMID: 23731715
An efficient proteomic approach to analyze agriculture crop biomass.
Flodrova D, Bobalova J., Protein J 32(5), 2013
PMID: 23681363
Genome sequencing of rumen bacteria and archaea and its application to methane mitigation strategies.
Leahy SC, Kelly WJ, Ronimus RS, Wedlock N, Altermann E, Attwood GT., Animal 7 Suppl 2(), 2013
PMID: 23739466
QualComp: a new lossy compressor for quality scores based on rate distortion theory.
Ochoa I, Asnani H, Bharadia D, Chowdhury M, Weissman T, Yona G., BMC Bioinformatics 14(), 2013
PMID: 23758828
Mastering methodological pitfalls for surviving the metagenomic jungle.
Delmont TO, Simonet P, Vogel TM., Bioessays 35(8), 2013
PMID: 23757040
Community dynamics of cellulose-adapted thermophilic bacterial consortia.
Eichorst SA, Varanasi P, Stavila V, Zemla M, Auer M, Singh S, Simmons BA, Singer SW., Environ Microbiol 15(9), 2013
PMID: 23763762
The gut microbiota of insects - diversity in structure and function.
Engel P, Moran NA., FEMS Microbiol Rev 37(5), 2013
PMID: 23692388
Microbial brokers of insect-plant interactions revisited.
Douglas AE., J Chem Ecol 39(7), 2013
PMID: 23793897
Single-cell genomics reveals complex carbohydrate degradation patterns in poribacterial symbionts of marine sponges.
Kamke J, Sczyrba A, Ivanova N, Schwientek P, Rinke C, Mavromatis K, Woyke T, Hentschel U., ISME J 7(12), 2013
PMID: 23842652
Biomining active cellulases from a mining bioremediation system.
Mewis K, Armstrong Z, Song YC, Baldwin SA, Withers SG, Hallam SJ., J Biotechnol 167(4), 2013
PMID: 23906845
Metagenomics of hydrocarbon resource environments indicates aerobic taxa and genes to be unexpectedly common.
An D, Caffrey SM, Soh J, Agrawal A, Brown D, Budwill K, Dong X, Dunfield PF, Foght J, Gieg LM, Hallam SJ, Hanson NW, He Z, Jack TR, Klassen J, Konwar KM, Kuatsjah E, Li C, Larter S, Leopatra V, Nesbø CL, Oldenburg T, Pagé AP, Ramos-Padron E, Rochman FF, Saidi-Mehrabad A, Sensen CW, Sipahimalani P, Song YC, Wilson S, Wolbring G, Wong ML, Voordouw G., Environ Sci Technol 47(18), 2013
PMID: 23889694
The genome and developmental transcriptome of the strongylid nematode Haemonchus contortus.
Schwarz EM, Korhonen PK, Campbell BE, Young ND, Jex AR, Jabbar A, Hall RS, Mondal A, Howe AC, Pell J, Hofmann A, Boag PR, Zhu XQ, Gregory T, Loukas A, Williams BA, Antoshechkin I, Brown C, Sternberg PW, Gasser RB., Genome Biol 14(8), 2013
PMID: 23985341
Metagenomic predictions: from microbiome to complex health and environmental phenotypes in humans and cattle.
Ross EM, Moate PJ, Marett LC, Cocks BG, Hayes BJ., PLoS One 8(9), 2013
PMID: 24023808
Meta4: a web application for sharing and annotating metagenomic gene predictions using web services.
Richardson EJ, Escalettes F, Fotheringham I, Wallace RJ, Watson M., Front Genet 4(), 2013
PMID: 24046776
High throughput sequencing methods and analysis for microbiome research.
Di Bella JM, Bao Y, Gloor GB, Burton JP, Reid G., J Microbiol Methods 95(3), 2013
PMID: 24029734
BioPig: a Hadoop-based analytic toolkit for large-scale sequence data.
Nordberg H, Bhatia K, Wang K, Wang Z., Bioinformatics 29(23), 2013
PMID: 24021384
Exploring variation-aware contig graphs for (comparative) metagenomics using MaryGold.
Nijkamp JF, Pop M, Reinders MJ, de Ridder D., Bioinformatics 29(22), 2013
PMID: 24058058
Seasonally variable intestinal metagenomes of the red palm weevil (Rhynchophorus ferrugineus).
Jia S, Zhang X, Zhang G, Yin A, Zhang S, Li F, Wang L, Zhao D, Yun Q, Tala, Wang J, Sun G, Baabdullah M, Yu X, Hu S, Al-Mssallem IS, Yu J., Environ Microbiol 15(11), 2013
PMID: 24102776
Microbial diversity in the era of omic technologies.
Nikolaki S, Tsiamis G., Biomed Res Int 2013(), 2013
PMID: 24260747
Looking large, to make more, out of gut metagenomics.
Morrison M., Curr Opin Microbiol 16(5), 2013
PMID: 24209636
A potential source for cellulolytic enzyme discovery and environmental aspects revealed through metagenomics of Brazilian mangroves.
Thompson CE, Beys-da-Silva WO, Santi L, Berger M, Vainstein MH, Guima Rães JA, Vasconcelos AT., AMB Express 3(1), 2013
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