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.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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DOI
Autor*in
Hess, M.; Sczyrba, AlexanderUniBi ; Egan, R.; Kim, T. W.; Chokhawala, H.; Schroth, G.; Luo, S.; Clark, D. S.; Chen, F.; Zhang, T.; Mackie, R. I.; Pennacchio, L. A.
Alle
Einrichtung
Technische Fakultät > Computational Metagenomics
Centrum für Biotechnologie > Arbeitsgruppe A. Sczyrba
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.
Stichworte
4-beta-Cellobiosidase/genetics/metabolism; Cellulose 1; Cellulose/*metabolism; Cellulases/chemistry/*genetics/metabolism; Cellulase/genetics/metabolism; Carbohydrate Metabolism; Cattle/*microbiology; Bacterial Proteins/chemistry/genetics/metabolism; *Biomass; Bacteria/enzymology/*genetics/isolation & purification/metabolism; Animals; Amino Acid Sequence; Bacterial; Genome; *Metagenome; Molecular Sequence Annotation; Metagenomics/methods; Molecular Sequence Data; Poaceae/microbiology; Bacterial; Genes; Rumen/metabolism/*microbiology; Sequence Analysis; DNA
Erscheinungsjahr
2011
Zeitschriftentitel
Science
Band
331
Ausgabe
6016
Seite(n)
463-467
ISSN
0036-8075
eISSN
1095-9203
Page URI
https://pub.uni-bielefeld.de/record/1991643

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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. https://doi.org/10.1126/science.1200387
Hess, M., Sczyrba, Alexander, 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.
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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Comtet-Marre S, Parisot N, Lepercq P, Chaucheyras-Durand F, Mosoni P, Peyretaillade E, Bayat AR, Shingfield KJ, Peyret P, Forano E., Front Microbiol 8(), 2017
PMID: 28197133
High throughput 16SrRNA gene sequencing reveals the correlation between Propionibacterium acnes and sarcoidosis.
Zhao MM, Du SS, Li QH, Chen T, Qiu H, Wu Q, Chen SS, Zhou Y, Zhang Y, Hu Y, Su YL, Shen L, Zhang F, Weng D, Li HP., Respir Res 18(1), 2017
PMID: 28143482
Comparative study of the gut microbiome potentially related to milk protein in Murrah buffaloes (Bubalus bubalis) and Chinese Holstein cattle.
Zhang J, Xu C, Huo D, Hu Q, Peng Q., Sci Rep 7(), 2017
PMID: 28176851
Discovery of genes coding for carbohydrate-active enzyme by metagenomic analysis of lignocellulosic biomasses.
Montella S, Ventorino V, Lombard V, Henrissat B, Pepe O, Faraco V., Sci Rep 7(), 2017
PMID: 28198423
Functional gene profiling through metaRNAseq approach reveals diet-dependent variation in rumen microbiota of buffalo (Bubalus bubalis).
Hinsu AT, Parmar NR, Nathani NM, Pandit RJ, Patel AB, Patel AK, Joshi CG., Anaerobe 44(), 2017
PMID: 28246035
In depth analysis of rumen microbial and carbohydrate-active enzymes profile in Indian crossbred cattle.
Jose VL, More RP, Appoothy T, Arun AS., Syst Appl Microbiol 40(3), 2017
PMID: 28284522
A Review of Bioinformatics Tools for Bio-Prospecting from Metagenomic Sequence Data.
Roumpeka DD, Wallace RJ, Escalettes F, Fotheringham I, Watson M., Front Genet 8(), 2017
PMID: 28321234
Activity screening of environmental metagenomic libraries reveals novel carboxylesterase families.
Popovic A, Hai T, Tchigvintsev A, Hajighasemi M, Nocek B, Khusnutdinova AN, Brown G, Glinos J, Flick R, Skarina T, Chernikova TN, Yim V, Brüls T, Paslier DL, Yakimov MM, Joachimiak A, Ferrer M, Golyshina OV, Savchenko A, Golyshin PN, Yakunin AF., Sci Rep 7(), 2017
PMID: 28272521
metaSPAdes: a new versatile metagenomic assembler.
Nurk S, Meleshko D, Korobeynikov A, Pevzner PA., Genome Res 27(5), 2017
PMID: 28298430
Comparative analysis of fecal microbial communities in cattle and Bactrian camels.
Ming L, Yi L, Siriguleng, Hasi S, He J, Hai L, Wang Z, Guo F, Qiao X, Jirimutu., PLoS One 12(3), 2017
PMID: 28301489
Utilizing Anaerobic Fungi for Two-stage Sugar Extraction and Biofuel Production from Lignocellulosic Biomass.
Ranganathan A, Smith OP, Youssef NH, Struchtemeyer CG, Atiyeh HK, Elshahed MS., Front Microbiol 8(), 2017
PMID: 28443088
Enhancing microbial production of biofuels by expanding microbial metabolic pathways.
Yu P, Chen X, Li P., Biotechnol Appl Biochem 64(5), 2017
PMID: 27507087
Genome-Centric Analysis of a Thermophilic and Cellulolytic Bacterial Consortium Derived from Composting.
Lemos LN, Pereira RV, Quaggio RB, Martins LF, Moura LMS, da Silva AR, Antunes LP, da Silva AM, Setubal JC., Front Microbiol 8(), 2017
PMID: 28469608
A Metagenomics Investigation of Carbohydrate-Active Enzymes along the Gastrointestinal Tract of Saudi Sheep.
Al-Masaudi S, El Kaoutari A, Drula E, Al-Mehdar H, Redwan EM, Lombard V, Henrissat B., Front Microbiol 8(), 2017
PMID: 28473812
Metagenomic Sequencing of Diamondback Moth Gut Microbiome Unveils Key Holobiont Adaptations for Herbivory.
Xia X, Gurr GM, Vasseur L, Zheng D, Zhong H, Qin B, Lin J, Wang Y, Song F, Li Y, Lin H, You M., Front Microbiol 8(), 2017
PMID: 28491055
TRIENNIAL GROWTH AND DEVELOPMENT SYMPOSIUM: Molecular mechanisms related to bovine intramuscular fat deposition in the longissimus muscle.
Baik M, Kang HJ, Park SJ, Na SW, Piao M, Kim SY, Fassah DM, Moon YS., J Anim Sci 95(5), 2017
PMID: 28727015
Defluviitalea raffinosedens sp. nov., a thermophilic, anaerobic, saccharolytic bacterium isolated from an anaerobic batch digester treating animal manure and rice straw.
Ma S, Huang Y, Wang C, Fan H, Dai L, Zhou Z, Liu X, Deng Y., Int J Syst Evol Microbiol 67(5), 2017
PMID: 27902335
Host Immune Selection of Rumen Bacteria through Salivary Secretory IgA.
Fouhse JM, Smiegielski L, Tuplin M, Guan LL, Willing BP., Front Microbiol 8(), 2017
PMID: 28553275
Pretreatment of Hardwood and Miscanthus with Trametes versicolor for Bioenergy Conversion and Densification Strategies.
Kalinoski RM, Flores HD, Thapa S, Tuegel ER, Bilek MA, Reyes-Mendez EY, West MJ, Dumonceaux TJ, Canam T., Appl Biochem Biotechnol 183(4), 2017
PMID: 28528383
Generation and Characterization of Acid Tolerant Fibrobacter succinogenes S85.
Wu CW, Spike T, Klingeman DM, Rodriguez M, Bremer VR, Brown SD., Sci Rep 7(1), 2017
PMID: 28536480
Discovery and characterization of family 39 glycoside hydrolases from rumen anaerobic fungi with polyspecific activity on rare arabinosyl substrates.
Jones DR, Uddin MS, Gruninger RJ, Pham TTM, Thomas D, Boraston AB, Briggs J, Pluvinage B, McAllister TA, Forster RJ, Tsang A, Selinger LB, Abbott DW., J Biol Chem 292(30), 2017
PMID: 28588026
Diet shifts provoke complex and variable changes in the metabolic networks of the ruminal microbiome.
Wolff SM, Ellison MJ, Hao Y, Cockrum RR, Austin KJ, Baraboo M, Burch K, Lee HJ, Maurer T, Patil R, Ravelo A, Taxis TM, Truong H, Lamberson WR, Cammack KM, Conant GC., Microbiome 5(1), 2017
PMID: 28595639
Diversity of microbial carbohydrate-active enzymes in Danish anaerobic digesters fed with wastewater treatment sludge.
Wilkens C, Busk PK, Pilgaard B, Zhang WJ, Nielsen KL, Nielsen PH, Lange L., Biotechnol Biofuels 10(), 2017
PMID: 28649277
An isolated cellulolytic Escherichia coli from bovine rumen produces ethanol and hydrogen from corn straw.
Pang J, Liu ZY, Hao M, Zhang YF, Qi QS., Biotechnol Biofuels 10(), 2017
PMID: 28652866
Lignocellulose-Degrading Microbial Communities in Landfill Sites Represent a Repository of Unexplored Biomass-Degrading Diversity.
Ransom-Jones E, McCarthy AJ, Haldenby S, Doonan J, McDonald JE., mSphere 2(4), 2017
PMID: 28776044
Buwchitin: A Ruminal Peptide with Antimicrobial Potential against Enterococcus faecalis.
Oyama LB, Crochet JA, Edwards JE, Girdwood SE, Cookson AR, Fernandez-Fuentes N, Hilpert K, Golyshin PN, Golyshina OV, Privé F, Hess M, Mantovani HC, Creevey CJ, Huws SA., Front Chem 5(), 2017
PMID: 28748180
Improved genome recovery and integrated cell-size analyses of individual uncultured microbial cells and viral particles.
Stepanauskas R, Fergusson EA, Brown J, Poulton NJ, Tupper B, Labonté JM, Becraft ED, Brown JM, Pachiadaki MG, Povilaitis T, Thompson BP, Mascena CJ, Bellows WK, Lubys A., Nat Commun 8(1), 2017
PMID: 28729688
Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation.
Svartström O, Alneberg J, Terrapon N, Lombard V, de Bruijn I, Malmsten J, Dalin AM, El Muller E, Shah P, Wilmes P, Henrissat B, Aspeborg H, Andersson AF., ISME J 11(11), 2017
PMID: 28731473
Molecular cloning, heterologous expression, and functional characterization of a cellulolytic enzyme (Cel PRII) from buffalo rumen metagenome.
Shah RK, Patel AK, Davla DM, Parikh IK, Subramanian RB, Patel KC, Jakhesara SJ, Joshi CG., 3 Biotech 7(4), 2017
PMID: 28733938
Genetic diversity of catechol 1,2-dioxygenase in the fecal microbial metagenome.
Xu B, Xiong C, Deng M, Li J, Tang X, Wu Q, Zhou J, Yang Y, Ding J, Han N, Huang Z., J Basic Microbiol 57(10), 2017
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
A Systems Biology Approach Reveals Differences in the Dynamics of Colonization and Degradation of Grass vs. Hay by Rumen Microbes with Minor Effects of Vitamin E Supplementation.
Belanche A, Newbold CJ, Lin W, Rees Stevens P, Kingston-Smith AH., Front Microbiol 8(), 2017
PMID: 28824585
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
Total rRNA-Seq Analysis Gives Insight into Bacterial, Fungal, Protozoal and Archaeal Communities in the Rumen Using an Optimized RNA Isolation Method.
Elekwachi CO, Wang Z, Wu X, Rabee A, Forster RJ., Front Microbiol 8(), 2017
PMID: 28983291
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
Beyond Fermentation: Other Important Services Provided to Endothermic Herbivores by their Gut Microbiota.
Dearing MD, Kohl KD., Integr Comp Biol 57(4), 2017
PMID: 28662572
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
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 8(), 2017
PMID: 29167663
Impacts of diarrhea on the immune system, intestinal environment, and expression of PGRPs in New Zealand rabbits.
Chen Y, Zhao B, Wu Y, Hu S, Mu L, Zhu C, Pan Y, Wu X., PeerJ 5(), 2017
PMID: 29201570
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
Comparative Metagenomics of Cellulose- and Poplar Hydrolysate-Degrading Microcosms from Gut Microflora of the Canadian Beaver (Castor canadensis) and North American Moose (Alces americanus) after Long-Term Enrichment.
Wong MT, Wang W, Couturier M, Razeq FM, Lombard V, Lapebie P, Edwards EA, Terrapon N, Henrissat B, Master ER., Front Microbiol 8(), 2017
PMID: 29326667
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
Refining the phylum Chlorobi by resolving the phylogeny and metabolic potential of the representative of a deeply branching, uncultivated lineage.
Hiras J, Wu YW, Eichorst SA, Simmons BA, Singer SW., ISME J 10(4), 2016
PMID: 26325358
Metagenomics for the development of new biocatalysts to advance lignocellulose saccharification for bioeconomic development.
Montella S, Amore A, Faraco V., Crit Rev Biotechnol 36(6), 2016
PMID: 26381035
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
Dynamic changes of the dominant functioning microbial community in the compost of a 90-m(3) aerobic solid state fermentor revealed by integrated meta-omics.
Zhang L, Zhang H, Wang Z, Chen G, Wang L., Bioresour Technol 203(), 2016
PMID: 26720133
Recent Developments in Using Advanced Sequencing Technologies for the Genomic Studies of Lignin and Cellulose Degrading Microorganisms.
Kameshwar AK, Qin W., Int J Biol Sci 12(2), 2016
PMID: 26884714
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
Dung-inhabiting fungi: a potential reservoir of novel secondary metabolites for the control of plant pathogens.
Sarrocco S., Pest Manag Sci 72(4), 2016
PMID: 26662623
Metagenomic analysis of microbial consortia enriched from compost: new insights into the role of Actinobacteria in lignocellulose decomposition.
Wang C, Dong D, Wang H, Müller K, Qin Y, Wang H, Wu W., Biotechnol Biofuels 9(), 2016
PMID: 26834834
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
A comparison of rumen microbial profiles in dairy cows as retrieved by 454 Roche and Ion Torrent (PGM) sequencing platforms.
Indugu N, Bittinger K, Kumar S, Vecchiarelli B, Pitta D., PeerJ 4(), 2016
PMID: 26870608
PhyloPythiaS+: a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes.
Gregor I, Dröge J, Schirmer M, Quince C, McHardy AC., PeerJ 4(), 2016
PMID: 26870609
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
Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes.
Lin HH, Liao YC., Sci Rep 6(), 2016
PMID: 27067514
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
Biological processes for advancing lignocellulosic waste biorefinery by advocating circular economy.
Liguori R, Faraco V., Bioresour Technol 215(), 2016
PMID: 27131870
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 VGH, 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
Novel nitrifiers and comammox in a full-scale hybrid biofilm and activated sludge reactor revealed by metagenomic approach.
Chao Y, Mao Y, Yu K, Zhang T., Appl Microbiol Biotechnol 100(18), 2016
PMID: 27287850
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
Substrate-Driven Convergence of the Microbial Community in Lignocellulose-Amended Enrichments of Gut Microflora from the Canadian Beaver (Castor canadensis) and North American Moose (Alces americanus).
Wong MT, Wang W, Lacourt M, Couturier M, Edwards EA, Master ER., Front Microbiol 7(), 2016
PMID: 27446004
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
Defined enzyme cocktail from the anaerobic fungus Orpinomyces sp. strain C1A effectively releases sugars from pretreated corn stover and switchgrass.
Morrison JM, Elshahed MS, Youssef NH., Sci Rep 6(), 2016
PMID: 27381262
Functional and modular analyses of diverse endoglucanases from Ruminococcus albus 8, a specialist plant cell wall degrading bacterium.
Iakiviak M, Devendran S, Skorupski A, Moon YH, Mackie RI, Cann I., Sci Rep 6(), 2016
PMID: 27439730
Virtual microfluidics for digital quantification and single-cell sequencing.
Xu L, Brito IL, Alm EJ, Blainey PC., Nat Methods 13(9), 2016
PMID: 27479330
A multifunctional GH39 glycoside hydrolase from the anaerobic gut fungus Orpinomyces sp. strain C1A.
Morrison JM, Elshahed MS, Youssef N., PeerJ 4(), 2016
PMID: 27547582
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
Employment of Near Full-Length Ribosome Gene TA-Cloning and Primer-Blast to Detect Multiple Species in a Natural Complex Microbial Community Using Species-Specific Primers Designed with Their Genome Sequences.
Zhang H, He H, Yu X, Xu Z, Zhang Z., Mol Biotechnol 58(11), 2016
PMID: 27696215
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
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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
Microbial profiles of liquid and solid fraction associated biomaterial in buffalo rumen fed green and dry roughage diets by tagged 16S rRNA gene pyrosequencing.
Singh KM, Jisha TK, Reddy B, Parmar N, Patel A, Patel AK, Joshi CG., Mol Biol Rep 42(1), 2015
PMID: 25249226
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
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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
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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
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Taxator-tk: precise taxonomic assignment of metagenomes by fast approximation of evolutionary neighborhoods.
Dröge J, Gregor I, McHardy AC., Bioinformatics 31(6), 2015
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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
Metagenomic analysis of the sludge microbial community in a lab-scale denitrifying phosphorus removal reactor.
Lv XM, Shao MF, Li J, Li CL., Appl Biochem Biotechnol 175(7), 2015
PMID: 25820294
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
Towards an integrated understanding of the consequences of fungus domestication on the fungus-growing termite gut microbiota.
Poulsen M., Environ Microbiol 17(8), 2015
PMID: 25581852
Metagenomic analysis of the Rhinopithecus bieti fecal microbiome reveals a broad diversity of bacterial and glycoside hydrolase profiles related to lignocellulose degradation.
Xu B, Xu W, Li J, Dai L, Xiong C, Tang X, Yang Y, Mu Y, Zhou J, Ding J, Wu Q, Huang Z., BMC Genomics 16(), 2015
PMID: 25887697
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
RUMINANT NUTRITION SYMPOSIUM: How to use data on the rumen microbiome to improve our understanding of ruminant nutrition.
Firkins JL, Yu Z., J Anim Sci 93(4), 2015
PMID: 26020167
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
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Deciphering Cyanide-Degrading Potential of Bacterial Community Associated with the Coking Wastewater Treatment Plant with a Novel Draft Genome.
Wang Z, Liu L, Guo F, Zhang T., Microb Ecol 70(3), 2015
PMID: 25910603
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
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Improving the genetic representation of rare taxa within complex microbial communities using DNA normalization methods
Gagic D, Maclean PH, Li D, Attwood GT, Moon CD., Mol Ecol Resour 15(3), 2015
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Catching the tip of the iceberg - evaluation of sample preparation protocols for metaproteomic studies of the rumen microbiota.
Deusch S, Seifert J., Proteomics 15(20), 2015
PMID: 25765363
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
Discovery of new protein families and functions: new challenges in functional metagenomics for biotechnologies and microbial ecology.
Ufarté L, Potocki-Veronese G, Laville É., Front Microbiol 6(), 2015
PMID: 26097471
Diversity and functions of bacterial community in drinking water biofilms revealed by high-throughput sequencing.
Chao Y, Mao Y, Wang Z, Zhang T., Sci Rep 5(), 2015
PMID: 26067561
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 VGH, 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
High Genetic Diversity of Microbial Cellulase and Hemicellulase Genes in the Hindgut of Holotrichia parallela Larvae.
Sheng P, Li Y, Marshall SD, Zhang H., Int J Mol Sci 16(7), 2015
PMID: 26197317
Biocatalysts for biomass deconstruction from environmental genomics.
Armstrong Z, Mewis K, Strachan C, Hallam SJ., Curr Opin Chem Biol 29(), 2015
PMID: 26231123
Illumina MiSeq Phylogenetic Amplicon Sequencing Shows a Large Reduction of an Uncharacterised Succinivibrionaceae and an Increase of the Methanobrevibacter gottschalkii Clade in Feed Restricted Cattle.
McCabe MS, Cormican P, Keogh K, O'Connor A, O'Hara E, Palladino RA, Kenny DA, Waters SM., PLoS One 10(7), 2015
PMID: 26226343
From cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems.
Garza DR, Dutilh BE., Cell Mol Life Sci 72(22), 2015
PMID: 26254872
Deep insights into carbohydrate metabolism in the rumen of Mehsani buffalo at different diet treatments.
Parmar NR, Nirmal Kumar JI, Joshi CG., Genom Data 6(), 2015
PMID: 26697334
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 MOA., 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
Phylogeny-structured carbohydrate metabolism across microbiomes collected from different units in wastewater treatment process.
Xia Y, Chin FY, Chao Y, Zhang T., Biotechnol Biofuels 8(), 2015
PMID: 26500698
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
Long-Term Enrichment on Cellulose or Xylan Causes Functional and Taxonomic Convergence of Microbial Communities from Anaerobic Digesters.
Jia Y, Wilkins D, Lu H, Cai M, Lee PKH., Appl Environ Microbiol 82(5), 2015
PMID: 26712547
Enrichment and characterization of an anaerobic cellulolytic microbial consortium SQD-1.1 from mangrove soil.
Gao ZM, Xu X, Ruan LW., Appl Microbiol Biotechnol 98(1), 2014
PMID: 23529681
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
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Gastrointestinal tract microbiota and probiotics in production animals.
Yeoman CJ, White BA., Annu Rev Anim Biosci 2(), 2014
PMID: 25384152
Metagenomic analysis on seasonal microbial variations of activated sludge from a full-scale wastewater treatment plant over 4 years.
Ju F, Guo F, Ye L, Xia Y, Zhang T., Environ Microbiol Rep 6(1), 2014
PMID: 24596265
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
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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
Co-inoculating ruminal content neither provides active hydrolytic microbes nor improves methanization of ¹³C-cellulose in batch digesters.
Chapleur O, Bize A, Serain T, Mazéas L, Bouchez T., FEMS Microbiol Ecol 87(3), 2014
PMID: 24219327
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
Analysis of the bovine rumen microbiome reveals a diversity of Sus-like polysaccharide utilization loci from the bacterial phylum Bacteroidetes.
Rosewarne CP, Pope PB, Cheung JL, Morrison M., J Ind Microbiol Biotechnol 41(3), 2014
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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
Extracting data from the muck: deriving biological insight from complex microbial communities and non-model organisms with next generation sequencing.
Solomon KV, Haitjema CH, Thompson DA, O'Malley MA., Curr Opin Biotechnol 28(), 2014
PMID: 24503479
Advancing lignocellulose bioconversion through direct assessment of enzyme action on insoluble substrates.
Goacher RE, Selig MJ, Master ER., Curr Opin Biotechnol 27(), 2014
PMID: 24525082
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
A phylogenomic view of ecological specialization in the Lachnospiraceae, a family of digestive tract-associated bacteria.
Meehan CJ, Beiko RG., Genome Biol Evol 6(3), 2014
PMID: 24625961
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
Exploration of Natural Biomass Utilization Systems (NBUS) for advanced biofuel--from systems biology to synthetic design.
Xie S, Syrenne R, Sun S, Yuan JS., Curr Opin Biotechnol 27(), 2014
PMID: 24657913
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
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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
Metabolic characteristics of a glycogen-accumulating organism in Defluviicoccus cluster II revealed by comparative genomics.
Wang Z, Guo F, Mao Y, Xia Y, Zhang T., Microb Ecol 68(4), 2014
PMID: 24889288
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
Bacterial community composition in the gut content and ambient sediment of sea cucumber Apostichopus japonicus revealed by 16S rRNA gene pyrosequencing.
Gao F, Li F, Tan J, Yan J, Sun H., PLoS One 9(6), 2014
PMID: 24967593
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
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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
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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
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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
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Pros and cons of ion-torrent next generation sequencing versus terminal restriction fragment length polymorphism T-RFLP for studying the rumen bacterial community.
de la Fuente G, Belanche A, Girwood SE, Pinloche E, Wilkinson T, Newbold CJ., PLoS One 9(7), 2014
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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
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Metagenomic identification of a novel salt tolerance gene from the human gut microbiome which encodes a membrane protein with homology to a brp/blh-family β-carotene 15,15'-monooxygenase.
Culligan EP, Sleator RD, Marchesi JR, Hill C., PLoS One 9(7), 2014
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MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm.
Wu YW, Tang YH, Tringe SG, Simmons BA, Singer SW., Microbiome 2(), 2014
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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
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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
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Enzymatic degradation of (ligno)cellulose.
Bornscheuer U, Buchholz K, Seibel J., Angew Chem Int Ed Engl 53(41), 2014
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Marek's disease virus influences the core gut microbiome of the chicken during the early and late phases of viral replication.
Perumbakkam S, Hunt HD, Cheng HH., FEMS Microbiol Ecol 90(1), 2014
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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
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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
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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
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Draft Genome Sequence of Uncultivated Firmicutes (Peptococcaceae SCADC) Single Cells Sorted from Methanogenic Alkane-Degrading Cultures.
Tan B, Charchuk R, Li C, Nesbø C, Abu Laban N, Foght J., Genome Announc 2(5), 2014
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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
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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
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Dynamic flux balance analysis for synthetic microbial communities.
Henson MA, Hanly TJ., IET Syst Biol 8(5), 2014
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Evidence of carbon fixation pathway in a bacterium from candidate phylum SBR1093 revealed with genomic analysis.
Wang Z, Guo F, Liu L, Zhang T., PLoS One 9(10), 2014
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Diversity of glycosyl hydrolase enzymes from metagenome and their application in food industry.
Sathya TA, Khan M., J Food Sci 79(11), 2014
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Thermophilic microbial cellulose decomposition and methanogenesis pathways recharacterized by metatranscriptomic and metagenomic analysis.
Xia Y, Wang Y, Fang HH, Jin T, Zhong H, Zhang T., Sci Rep 4(), 2014
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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
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Evaluation of a hybrid approach using UBLAST and BLASTX for metagenomic sequences annotation of specific functional genes.
Yang Y, Jiang XT, Zhang T., PLoS One 9(10), 2014
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Integrated 'omics analysis for studying the microbial community response to a pH perturbation of a cellulose-degrading bioreactor culture.
Boaro AA, Kim YM, Konopka AE, Callister SJ, Ahring BK., FEMS Microbiol Ecol 90(3), 2014
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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
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Gill bacteria enable a novel digestive strategy in a wood-feeding mollusk.
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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
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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
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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
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AKE - the Accelerated k-mer Exploration web-tool for rapid taxonomic classification and visualization.
Langenkämper D, Goesmann A, Nattkemper TW., BMC Bioinformatics 15(), 2014
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Rumen microbial (meta)genomics and its application to ruminant production.
Morgavi DP, Kelly WJ, Janssen PH, Attwood GT., Animal 7 Suppl 1(), 2013
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Breeding for genetic improvement of forage plants in relation to increasing animal production with reduced environmental footprint.
Kingston-Smith AH, Marshall AH, Moorby JM., Animal 7 Suppl 1(), 2013
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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
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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
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Advances in monitoring environmental microbes.
Hazen TC, Rocha AM, Techtmann SM., Curr Opin Biotechnol 24(3), 2013
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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
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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
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The future of livestock breeding: genomic selection for efficiency, reduced emissions intensity, and adaptation.
Hayes BJ, Lewin HA, Goddard ME., Trends Genet 29(4), 2013
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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
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Phylogenetic distribution of potential cellulases in bacteria.
Berlemont R, Martiny AC., Appl Environ Microbiol 79(5), 2013
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Gut microbiota, host health, and polysaccharides.
Xu X, Xu P, Ma C, Tang J, Zhang X., Biotechnol Adv 31(2), 2013
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The human microbiome: from symbiosis to pathogenesis.
Eloe-Fadrosh EA, Rasko DA., Annu Rev Med 64(), 2013
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Ammonia assimilation in rumen bacteria: a review.
Pengpeng W, Tan Z., Anim Biotechnol 24(2), 2013
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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
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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
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Aerobic deconstruction of cellulosic biomass by an insect-associated Streptomyces.
Takasuka TE, Book AJ, Lewin GR, Currie CR, Fox BG., Sci Rep 3(), 2013
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ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies.
Clark SC, Egan R, Frazier PI, Wang Z., Bioinformatics 29(4), 2013
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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
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Mining of novel thermo-stable cellulolytic genes from a thermophilic cellulose-degrading consortium by metagenomics.
Xia Y, Ju F, Fang HH, Zhang T., PLoS One 8(1), 2013
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Advances in the diagnosis of key gastrointestinal nematode infections of livestock, with an emphasis on small ruminants.
Roeber F, Jex AR, Gasser RB., Biotechnol Adv 31(8), 2013
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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
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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
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The future is now: single-cell genomics of bacteria and archaea.
Blainey PC., FEMS Microbiol Rev 37(3), 2013
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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
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The Pacific Ocean virome (POV): a marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology.
Hurwitz BL, Sullivan MB., PLoS One 8(2), 2013
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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
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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
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Development of highly efficient, low-cost lignocellulolytic enzyme systems in the post-genomic era.
Liu G, Qin Y, Li Z, Qu Y., Biotechnol Adv 31(6), 2013
PMID: 23507038
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
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Advances in metabolic pathway and strain engineering paving the way for sustainable production of chemical building blocks.
Chen Y, Nielsen J., Curr Opin Biotechnol 24(6), 2013
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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
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Comparative digestive physiology.
Karasov WH, Douglas AE., Compr Physiol 3(2), 2013
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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
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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
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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
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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
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Computational meta'omics for microbial community studies.
Segata N, Boernigen D, Tickle TL, Morgan XC, Garrett WS, Huttenhower C., Mol Syst Biol 9(), 2013
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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
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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
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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
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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
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Meta-omic characterization of prokaryotic gene clusters for natural product biosynthesis.
Schofield MM, Sherman DH., Curr Opin Biotechnol 24(6), 2013
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An efficient proteomic approach to analyze agriculture crop biomass.
Flodrova D, Bobalova J., Protein J 32(5), 2013
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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
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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
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Mastering methodological pitfalls for surviving the metagenomic jungle.
Delmont TO, Simonet P, Vogel TM., Bioessays 35(8), 2013
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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
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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
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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
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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
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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
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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
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BioPig: a Hadoop-based analytic toolkit for large-scale sequence data.
Nordberg H, Bhatia K, Wang K, Wang Z., Bioinformatics 29(23), 2013
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Exploring variation-aware contig graphs for (comparative) metagenomics using MaryGold.
Nijkamp JF, Pop M, Reinders MJ, de Ridder D., Bioinformatics 29(22), 2013
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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
Differential recovery of bacterial and archaeal 16S rRNA genes from ruminal digesta in response to glycerol as cryoprotectant.
McKain N, Genc B, Snelling TJ, Wallace RJ., J Microbiol Methods 95(3), 2013
PMID: 24161897
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
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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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Metagenomics of rumen bacteriophage from thirteen lactating dairy cattle.
Ross EM, Petrovski S, Moate PJ, Hayes BJ., BMC Microbiol 13(), 2013
PMID: 24180266
Metagenomic insights into the carbohydrate-active enzymes carried by the microorganisms adhering to solid digesta in the rumen of cows.
Wang L, Hatem A, Catalyurek UV, Morrison M, Yu Z., PLoS One 8(11), 2013
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Comparative metabolite fingerprinting of the rumen system during colonisation of three forage grass (Lolium perenne L.) varieties.
Kingston-Smith AH, Davies TE, Rees Stevens P, Mur LA., PLoS One 8(11), 2013
PMID: 24312434
Genome resolved analysis of a premature infant gut microbial community reveals a Varibaculum cambriense genome and a shift towards fermentation-based metabolism during the third week of life.
Brown CT, Sharon I, Thomas BC, Castelle CJ, Morowitz MJ, Banfield JF., Microbiome 1(1), 2013
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Characterization of the core rumen microbiome in cattle during transition from forage to concentrate as well as during and after an acidotic challenge.
Petri RM, Schwaiger T, Penner GB, Beauchemin KA, Forster RJ, McKinnon JJ, McAllister TA., PLoS One 8(12), 2013
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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 8(12), 2013
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High-throughput single-cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton.
Martinez-Garcia M, Swan BK, Poulton NJ, Gomez ML, Masland D, Sieracki ME, Stepanauskas R., ISME J 6(1), 2012
PMID: 21716306
Characterization of the rumen microbiota of pre-ruminant calves using metagenomic tools.
Li RW, Connor EE, Li C, Baldwin Vi RL, Sparks ME., Environ Microbiol 14(1), 2012
PMID: 21906219
Unveiling in situ interactions between marine protists and bacteria through single cell sequencing.
Martinez-Garcia M, Brazel D, Poulton NJ, Swan BK, Gomez ML, Masland D, Sieracki ME, Stepanauskas R., ISME J 6(3), 2012
PMID: 21938022
Metagenomic analysis of Surti buffalo (Bubalus bubalis) rumen: a preliminary study.
Singh KM, Ahir VB, Tripathi AK, Ramani UV, Sajnani M, Koringa PG, Jakhesara S, Pandya PR, Rank DN, Murty DS, Kothari RK, Joshi CG., Mol Biol Rep 39(4), 2012
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Phage-bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome.
Berg Miller ME, Yeoman CJ, Chia N, Tringe SG, Angly FE, Edwards RA, Flint HJ, Lamed R, Bayer EA, White BA., Environ Microbiol 14(1), 2012
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Characterization of the fecal bacteria communities of forage-fed horses by pyrosequencing of 16S rRNA V4 gene amplicons.
Shepherd ML, Swecker WS, Jensen RV, Ponder MA., FEMS Microbiol Lett 326(1), 2012
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A metagenome of a full-scale microbial community carrying out enhanced biological phosphorus removal.
Albertsen M, Hansen LB, Saunders AM, Nielsen PH, Nielsen KL., ISME J 6(6), 2012
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Effect of exogenous electron shuttles on growth and fermentative metabolism in Clostridium sp. BC1.
Yarlagadda VN, Gupta A, Dodge CJ, Francis AJ., Bioresour Technol 108(), 2012
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The bacterial chemical repertoire mediates metabolic exchange within gut microbiomes.
Rath CM, Dorrestein PC., Curr Opin Microbiol 15(2), 2012
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The Fibrobacteres: an important phylum of cellulose-degrading bacteria.
Ransom-Jones E, Jones DL, McCarthy AJ, McDonald JE., Microb Ecol 63(2), 2012
PMID: 22213055
Metatranscriptomics reveals the diversity of genes expressed by eukaryotes in forest soils.
Damon C, Lehembre F, Oger-Desfeux C, Luis P, Ranger J, Fraissinet-Tachet L, Marmeisse R., PLoS One 7(1), 2012
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The Evolutionary Innovation of Nutritional Symbioses in Leaf-Cutter Ants.
Aylward FO, Currie CR, Suen G., Insects 3(1), 2012
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