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Generation of an E. coli platform strain for improved sucrose utilization using adaptive laboratory evolution.

Mohamed ET, Mundhada H, Landberg J, Cann I, Mackie RI, Nielsen AT, Herrgård MJ, Feist AM.

Microb Cell Fact. 2019 Jun 29;18(1):116. doi: 10.1186/s12934-019-1165-2.


Diverse hydrogen production and consumption pathways influence methane production in ruminants.

Greening C, Geier R, Wang C, Woods LC, Morales SE, McDonald MJ, Rushton-Green R, Morgan XC, Koike S, Leahy SC, Kelly WJ, Cann I, Attwood GT, Cook GM, Mackie RI.

ISME J. 2019 Oct;13(10):2617-2632. doi: 10.1038/s41396-019-0464-2. Epub 2019 Jun 26.


Combined Genomic, Transcriptomic, Proteomic, and Physiological Characterization of the Growth of Pecoramyces sp. F1 in Monoculture and Co-culture With a Syntrophic Methanogen.

Li Y, Li Y, Jin W, Sharpton TJ, Mackie RI, Cann I, Cheng Y, Zhu W.

Front Microbiol. 2019 Mar 6;10:435. doi: 10.3389/fmicb.2019.00435. eCollection 2019.


Identification of Halophilic Microbes in Lung Fibrotic Tissue by Oligotyping.

D'Alessandro-Gabazza CN, Méndez-García C, Hataji O, Westergaard S, Watanabe F, Yasuma T, Toda M, Fujimoto H, Nishihama K, Fujiwara K, Taguchi O, Kobayashi T, Mackie RI, Cann I, Gabazza EC.

Front Microbiol. 2018 Aug 30;9:1892. doi: 10.3389/fmicb.2018.01892. eCollection 2018.


"Candidatus Paraporphyromonas polyenzymogenes" encodes multi-modular cellulases linked to the type IX secretion system.

Naas AE, Solden LM, Norbeck AD, Brewer H, Hagen LH, Heggenes IM, McHardy AC, Mackie RI, Paša-Tolić L, Arntzen MØ, Eijsink VGH, Koropatkin NM, Hess M, Wrighton KC, Pope PB.

Microbiome. 2018 Mar 1;6(1):44. doi: 10.1186/s40168-018-0421-8.


Let them eat fruit.

Mackie RI, Cann I.

Nat Microbiol. 2018 Feb;3(2):127-129. doi: 10.1038/s41564-018-0108-8. No abstract available.


Metabolic networks for nitrogen utilization in Prevotella ruminicola 23.

Kim JN, Méndez-García C, Geier RR, Iakiviak M, Chang J, Cann I, Mackie RI.

Sci Rep. 2017 Aug 10;7(1):7851. doi: 10.1038/s41598-017-08463-3.


Enzymatic Mechanism for Arabinan Degradation and Transport in the Thermophilic Bacterium Caldanaerobius polysaccharolyticus.

Wefers D, Dong J, Abdel-Hamid AM, Paul HM, Pereira GV, Han Y, Dodd D, Baskaran R, Mayer B, Mackie RI, Cann I.

Appl Environ Microbiol. 2017 Aug 31;83(18). pii: e00794-17. doi: 10.1128/AEM.00794-17. Print 2017 Sep 15.


Biochemical and Structural Analyses of Two Cryptic Esterases in Bacteroides intestinalis and their Synergistic Activities with Cognate Xylanases.

Wefers D, Cavalcante JJV, Schendel RR, Deveryshetty J, Wang K, Wawrzak Z, Mackie RI, Koropatkin NM, Cann I.

J Mol Biol. 2017 Aug 4;429(16):2509-2527. doi: 10.1016/j.jmb.2017.06.017. Epub 2017 Jun 29.


Outer membrane vesicles from Fibrobacter succinogenes S85 contain an array of carbohydrate-active enzymes with versatile polysaccharide-degrading capacity.

Arntzen MØ, Várnai A, Mackie RI, Eijsink VGH, Pope PB.

Environ Microbiol. 2017 Jul;19(7):2701-2714. doi: 10.1111/1462-2920.13770. Epub 2017 May 29.


Multiple cellobiohydrolases and cellobiose phosphorylases cooperate in the ruminal bacterium Ruminococcus albus 8 to degrade cellooligosaccharides.

Devendran S, Abdel-Hamid AM, Evans AF, Iakiviak M, Kwon IH, Mackie RI, Cann I.

Sci Rep. 2016 Oct 17;6:35342. doi: 10.1038/srep35342.


Orenia metallireducens sp. nov. Strain Z6, a Novel Metal-Reducing Member of the Phylum Firmicutes from the Deep Subsurface.

Dong Y, Sanford RA, Boyanov MI, Kemner KM, Flynn TM, O'Loughlin EJ, Chang YJ, Locke RA Jr, Weber JR, Egan SM, Mackie RI, Cann I, Fouke BW.

Appl Environ Microbiol. 2016 Oct 14;82(21):6440-6453. Print 2016 Nov 1.


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. 2016 Jul 21;6:29979. doi: 10.1038/srep29979.


Lignocellulose-derived thin stillage composition and efficient biological treatment with a high-rate hybrid anaerobic bioreactor system.

Oosterkamp MJ, Méndez-García C, Kim CH, Bauer S, Ibáñez AB, Zimmerman S, Hong PY, Cann IK, Mackie RI.

Biotechnol Biofuels. 2016 Jun 6;9:120. doi: 10.1186/s13068-016-0532-z. eCollection 2016.


Cellulose degradation in the human gut: Ruminococcus champanellensis expands the cellulosome paradigm.

Cann I, Bernardi RC, Mackie RI.

Environ Microbiol. 2016 Feb;18(2):307-10. doi: 10.1111/1462-2920.13152. Epub 2016 Jan 18. No abstract available.


The gut microbiota appears to compensate for seasonal diet variation in the wild black howler monkey (Alouatta pigra).

Amato KR, Leigh SR, Kent A, Mackie RI, Yeoman CJ, Stumpf RM, Wilson BA, Nelson KE, White BA, Garber PA.

Microb Ecol. 2015 Feb;69(2):434-43. doi: 10.1007/s00248-014-0554-7. Epub 2014 Dec 19.


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. 2015 Feb;69(2):444-56. doi: 10.1007/s00248-014-0547-6. Epub 2014 Dec 19.


Functional potential of soil microbial communities in the maize rhizosphere.

Li X, Rui J, Xiong J, Li J, He Z, Zhou J, Yannarell AC, Mackie RI.

PLoS One. 2014 Nov 10;9(11):e112609. doi: 10.1371/journal.pone.0112609. eCollection 2014.


Structural and biochemical basis for mannan utilization by Caldanaerobius polysaccharolyticus strain ATCC BAA-17.

Chekan JR, Kwon IH, Agarwal V, Dodd D, Revindran V, Mackie RI, Cann I, Nair SK.

J Biol Chem. 2014 Dec 12;289(50):34965-77. doi: 10.1074/jbc.M114.579904. Epub 2014 Oct 23.


Fe-oxide grain coatings support bacterial Fe-reducing metabolisms in 1.7-2.0 km-deep subsurface quartz arenite sandstone reservoirs of the Illinois Basin (USA).

Dong Y, Sanford RA, Locke RA 2nd, Cann IK, Mackie RI, Fouke BW.

Front Microbiol. 2014 Sep 30;5:511. doi: 10.3389/fmicb.2014.00511. eCollection 2014.


The role of gut microbes in satisfying the nutritional demands of adult and juvenile wild, black howler monkeys (Alouatta pigra).

Amato KR, Leigh SR, Kent A, Mackie RI, Yeoman CJ, Stumpf RM, Wilson BA, Nelson KE, White BA, Garber PA.

Am J Phys Anthropol. 2014 Dec;155(4):652-64. doi: 10.1002/ajpa.22621. Epub 2014 Sep 23.


Xylan utilization in human gut commensal bacteria is orchestrated by unique modular organization of polysaccharide-degrading enzymes.

Zhang M, Chekan JR, Dodd D, Hong PY, Radlinski L, Revindran V, Nair SK, Mackie RI, Cann I.

Proc Natl Acad Sci U S A. 2014 Sep 2;111(35):E3708-17. doi: 10.1073/pnas.1406156111. Epub 2014 Aug 18.


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. 2014 Jul 22;5:307. doi: 10.3389/fmicb.2014.00307. eCollection 2014.


Enrichment of specific bacterial and eukaryotic microbes in the rhizosphere of switchgrass (Panicum virgatum L.) through root exudates.

Mao Y, Li X, Smyth EM, Yannarell AC, Mackie RI.

Environ Microbiol Rep. 2014 Jun;6(3):293-306. doi: 10.1111/1758-2229.12152. Epub 2014 Mar 19.


Nitrogen utilization and metabolism in Ruminococcus albus 8.

Kim JN, Henriksen ED, Cann IK, Mackie RI.

Appl Environ Microbiol. 2014 May;80(10):3095-102. doi: 10.1128/AEM.00029-14. Epub 2014 Mar 7.


Dietary supplementation of usnic acid, an antimicrobial compound in lichens, does not affect rumen bacterial diversity or density in reindeer.

Glad T, Barboza P, Mackie RI, Wright AD, Brusetti L, Mathiesen SD, Sundset MA.

Curr Microbiol. 2014 Jun;68(6):724-8. doi: 10.1007/s00284-014-0534-7. Epub 2014 Feb 9.


Two new xylanases with different substrate specificities from the human gut bacterium Bacteroides intestinalis DSM 17393.

Hong PY, Iakiviak M, Dodd D, Zhang M, Mackie RI, Cann I.

Appl Environ Microbiol. 2014 Apr;80(7):2084-93. doi: 10.1128/AEM.03176-13. Epub 2014 Jan 24.


Molecular and biochemical analyses of CbCel9A/Cel48A, a highly secreted multi-modular cellulase by Caldicellulosiruptor bescii during growth on crystalline cellulose.

Yi Z, Su X, Revindran V, Mackie RI, Cann I.

PLoS One. 2013 Dec 16;8(12):e84172. doi: 10.1371/journal.pone.0084172. eCollection 2013.


Mutational and structural analyses of Caldanaerobius polysaccharolyticus Man5B reveal novel active site residues for family 5 glycoside hydrolases.

Oyama T, Schmitz GE, Dodd D, Han Y, Burnett A, Nagasawa N, Mackie RI, Nakamura H, Morikawa K, Cann I.

PLoS One. 2013 Nov 20;8(11):e80448. doi: 10.1371/journal.pone.0080448. eCollection 2013.


Halomonas sulfidaeris-dominated microbial community inhabits a 1.8 km-deep subsurface Cambrian Sandstone reservoir.

Dong Y, Kumar CG, Chia N, Kim PJ, Miller PA, Price ND, Cann IK, Flynn TM, Sanford RA, Krapac IG, Locke RA 2nd, Hong PY, Tamaki H, Liu WT, Mackie RI, Hernandez AG, Wright CL, Mikel MA, Walker JL, Sivaguru M, Fried G, Yannarell AC, Fouke BW.

Environ Microbiol. 2014 Jun;16(6):1695-708. doi: 10.1111/1462-2920.12325. Epub 2013 Dec 12.


Probiotic dosing of Ruminococcus flavefaciens affects rumen microbiome structure and function in reindeer.

Præsteng KE, Pope PB, Cann IK, Mackie RI, Mathiesen SD, Folkow LP, Eijsink VG, Sundset MA.

Microb Ecol. 2013 Nov;66(4):840-9.


Monitoring the perturbation of soil and groundwater microbial communities due to pig production activities.

Hong PY, Yannarell AC, Dai Q, Ekizoglu M, Mackie RI.

Appl Environ Microbiol. 2013 Apr;79(8):2620-9. doi: 10.1128/AEM.03760-12. Epub 2013 Feb 8.


Environmental and Public Health Implications of Water Reuse: Antibiotics, Antibiotic Resistant Bacteria, and Antibiotic Resistance Genes.

Hong PY, Al-Jassim N, Ansari MI, Mackie RI.

Antibiotics (Basel). 2013 Jul 31;2(3):367-99. doi: 10.3390/antibiotics2030367. Review.


Reconstitution of a thermostable xylan-degrading enzyme mixture from the bacterium Caldicellulosiruptor bescii.

Su X, Han Y, Dodd D, Moon YH, Yoshida S, Mackie RI, Cann IK.

Appl Environ Microbiol. 2013 Mar;79(5):1481-90. doi: 10.1128/AEM.03265-12. Epub 2012 Dec 21.


Heterologous gene expression in filamentous fungi.

Su X, Schmitz G, Zhang M, Mackie RI, Cann IK.

Adv Appl Microbiol. 2012;81:1-61. doi: 10.1016/B978-0-12-394382-8.00001-0. Review.


Supplementing with non-glycoside hydrolase proteins enhances enzymatic deconstruction of plant biomass.

Su X, Zhang J, Mackie RI, Cann IK.

PLoS One. 2012;7(8):e43828. doi: 10.1371/journal.pone.0043828. Epub 2012 Aug 27.


Biochemical and structural insights into xylan utilization by the thermophilic bacterium Caldanaerobius polysaccharolyticus.

Han Y, Agarwal V, Dodd D, Kim J, Bae B, Mackie RI, Nair SK, Cann IK.

J Biol Chem. 2012 Oct 12;287(42):34946-60. doi: 10.1074/jbc.M112.391532. Epub 2012 Aug 22.


Impact of different bioenergy crops on N-cycling bacterial and archaeal communities in soil.

Mao Y, Yannarell AC, Davis SC, Mackie RI.

Environ Microbiol. 2013 Mar;15(3):928-42. doi: 10.1111/j.1462-2920.2012.02844.x. Epub 2012 Aug 14.


Molecular and biochemical analyses of the GH44 module of CbMan5B/Cel44A, a bifunctional enzyme from the hyperthermophilic bacterium Caldicellulosiruptor bescii.

Ye L, Su X, Schmitz GE, Moon YH, Zhang J, Mackie RI, Cann IK.

Appl Environ Microbiol. 2012 Oct;78(19):7048-59. doi: 10.1128/AEM.02009-12. Epub 2012 Jul 27.


Evolution of Salmonella enterica virulence via point mutations in the fimbrial adhesin.

Kisiela DI, Chattopadhyay S, Libby SJ, Karlinsey JE, Fang FC, Tchesnokova V, Kramer JJ, Beskhlebnaya V, Samadpour M, Grzymajlo K, Ugorski M, Lankau EW, Mackie RI, Clegg S, Sokurenko EV.

PLoS Pathog. 2012;8(6):e1002733. doi: 10.1371/journal.ppat.1002733. Epub 2012 Jun 7.


Salmonella strains isolated from Galápagos iguanas show spatial structuring of serovar and genomic diversity.

Lankau EW, Cruz Bedon L, Mackie RI.

PLoS One. 2012;7(5):e37302. doi: 10.1371/journal.pone.0037302. Epub 2012 May 16.


Monitoring airborne biotic contaminants in the indoor environment of pig and poultry confinement buildings.

Hong PY, Li X, Yang X, Shinkai T, Zhang Y, Wang X, Mackie RI.

Environ Microbiol. 2012 Jun;14(6):1420-31. doi: 10.1111/j.1462-2920.2012.02726.x. Epub 2012 Mar 14.


Ecological drift and local exposures drive enteric bacterial community differences within species of Galápagos iguanas.

Lankau EW, Hong PY, Mackie RI.

Mol Ecol. 2012 Apr;21(7):1779-88. doi: 10.1111/j.1365-294X.2012.05502.x. Epub 2012 Feb 27.


Carriage of antibiotic-resistant enteric bacteria varies among sites in Galapagos reptiles.

Wheeler E, Hong PY, Bedon LC, Mackie RI.

J Wildl Dis. 2012 Jan;48(1):56-67.


Biochemical and mutational analyses of a multidomain cellulase/mannanase from Caldicellulosiruptor bescii.

Su X, Mackie RI, Cann IK.

Appl Environ Microbiol. 2012 Apr;78(7):2230-40. doi: 10.1128/AEM.06814-11. Epub 2012 Jan 13.


Purification, characterization, and expression of multiple glutamine synthetases from Prevotella ruminicola 23.

Kim JN, Cann IK, Mackie RI.

J Bacteriol. 2012 Jan;194(1):176-84. doi: 10.1128/JB.05916-11. Epub 2011 Oct 21.


Pyrosequencing-based analysis of the mucosal microbiota in healthy individuals reveals ubiquitous bacterial groups and micro-heterogeneity.

Hong PY, Croix JA, Greenberg E, Gaskins HR, Mackie RI.

PLoS One. 2011;6(9):e25042. doi: 10.1371/journal.pone.0025042. Epub 2011 Sep 22.


Changes in N-transforming archaea and bacteria in soil during the establishment of bioenergy crops.

Mao Y, Yannarell AC, Mackie RI.

PLoS One. 2011;6(9):e24750. doi: 10.1371/journal.pone.0024750. Epub 2011 Sep 14.


Functional analyses of multiple lichenin-degrading enzymes from the rumen bacterium Ruminococcus albus 8.

Iakiviak M, Mackie RI, Cann IK.

Appl Environ Microbiol. 2011 Nov;77(21):7541-50. doi: 10.1128/AEM.06088-11. Epub 2011 Sep 2.

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