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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.


FIV vaccine with receptor epitopes results in neutralizing antibodies but does not confer resistance to challenge.

Miller C, Emanuelli M, Fink E, Musselman E, Mackie R, Troyer R, Elder J, VandeWoude S.

NPJ Vaccines. 2018 Apr 30;3:16. doi: 10.1038/s41541-018-0051-y. 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.


Untangling the cecal microbiota of feral chickens by culturomic and metagenomic analyses.

Ferrario C, Alessandri G, Mancabelli L, Gering E, Mangifesta M, Milani C, Lugli GA, Viappiani A, Duranti S, Turroni F, Ossiprandi MC, Hiyashi R, Mackie R, van Sinderen D, Ventura M.

Environ Microbiol. 2017 Nov;19(11):4771-4783. doi: 10.1111/1462-2920.13943. Epub 2017 Oct 13.


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.


Targeted Enrichment for Pathogen Detection and Characterization in Three Felid Species.

Lee JS, Mackie RS, Harrison T, Shariat B, Kind T, Kehl T, Löchelt M, Boucher C, VandeWoude S.

J Clin Microbiol. 2017 Jun;55(6):1658-1670. doi: 10.1128/JCM.01463-16. Epub 2017 Mar 22.


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.


Bacteroides intestinalis DSM 17393, a member of the human colonic microbiome, upregulates multiple endoxylanases during growth on xylan.

Wang K, Pereira GV, Cavalcante JJ, Zhang M, Mackie R, Cann I.

Sci Rep. 2016 Sep 29;6:34360. doi: 10.1038/srep34360.


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.


Integrating heterogeneous drug sensitivity data from cancer pharmacogenomic studies.

Pozdeyev N, Yoo M, Mackie R, Schweppe RE, Tan AC, Haugen BR.

Oncotarget. 2016 Aug 9;7(32):51619-51625. doi: 10.18632/oncotarget.10010.


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.


A role for attention during wilderness navigation: Comparing effects of BDNF, KIBRA, and CHRNA4.

Rovira E, Mackie RS, Clark N, Squire PN, Hendricks MD, Pulido AM, Greenwood PM.

Neuropsychology. 2016 Sep;30(6):709-19. doi: 10.1037/neu0000277. Epub 2016 Apr 28.


Age, introduction of solid feed and weaning are more important determinants of gut bacterial succession in piglets than breed and nursing mother as revealed by a reciprocal cross-fostering model.

Bian G, Ma S, Zhu Z, Su Y, Zoetendal EG, Mackie R, Liu J, Mu C, Huang R, Smidt H, Zhu W.

Environ Microbiol. 2016 May;18(5):1566-77. doi: 10.1111/1462-2920.13272. Epub 2016 Mar 21.


Dose-Response Modeling for Inhalational Anthrax in Rabbits Following Single or Multiple Exposures.

Gutting BW, Rukhin A, Marchette D, Mackie RS, Thran B.

Risk Anal. 2016 Nov;36(11):2031-2038. doi: 10.1111/risa.12564. Epub 2016 Feb 17.


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.


Genome-wide meta-analysis identifies five new susceptibility loci for cutaneous malignant melanoma.

Law MH, Bishop DT, Lee JE, Brossard M, Martin NG, Moses EK, Song F, Barrett JH, Kumar R, Easton DF, Pharoah PDP, Swerdlow AJ, Kypreou KP, Taylor JC, Harland M, Randerson-Moor J, Akslen LA, Andresen PA, Avril MF, Azizi E, Scarrà GB, Brown KM, Dębniak T, Duffy DL, Elder DE, Fang S, Friedman E, Galan P, Ghiorzo P, Gillanders EM, Goldstein AM, Gruis NA, Hansson J, Helsing P, Hočevar M, Höiom V, Ingvar C, Kanetsky PA, Chen WV; GenoMEL Consortium; Essen-Heidelberg Investigators; SDH Study Group; Q-MEGA and QTWIN Investigators; AMFS Investigators; ATHENS Melanoma Study Group, Landi MT, Lang J, Lathrop GM, Lubiński J, Mackie RM, Mann GJ, Molven A, Montgomery GW, Novaković S, Olsson H, Puig S, Puig-Butille JA, Qureshi AA, Radford-Smith GL, van der Stoep N, van Doorn R, Whiteman DC, Craig JE, Schadendorf D, Simms LA, Burdon KP, Nyholt DR, Pooley KA, Orr N, Stratigos AJ, Cust AE, Ward SV, Hayward NK, Han J, Schulze HJ, Dunning AM, Bishop JAN, Demenais F, Amos CI, MacGregor S, Iles MM.

Nat Genet. 2015 Sep;47(9):987-995. doi: 10.1038/ng.3373. Epub 2015 Aug 3.


Four core genotypes mouse model: localization of the Sry transgene and bioassay for testicular hormone levels.

Itoh Y, Mackie R, Kampf K, Domadia S, Brown JD, O'Neill R, Arnold AP.

BMC Res Notes. 2015 Mar 7;8:69. doi: 10.1186/s13104-015-0986-2.


Development and validation of a melanoma risk score based on pooled data from 16 case-control studies.

Davies JR, Chang YM, Bishop DT, Armstrong BK, Bataille V, Bergman W, Berwick M, Bracci PM, Elwood JM, Ernstoff MS, Green A, Gruis NA, Holly EA, Ingvar C, Kanetsky PA, Karagas MR, Lee TK, Le Marchand L, Mackie RM, Olsson H, Østerlind A, Rebbeck TR, Reich K, Sasieni P, Siskind V, Swerdlow AJ, Titus L, Zens MS, Ziegler A, Gallagher RP, Barrett JH, Newton-Bishop J.

Cancer Epidemiol Biomarkers Prev. 2015 May;24(5):817-24. doi: 10.1158/1055-9965.EPI-14-1062. Epub 2015 Feb 24.


Evaluation of Inhaled Versus Deposited Dose Using the Exponential Dose-Response Model for Inhalational Anthrax in Nonhuman Primate, Rabbit, and Guinea Pig.

Gutting BW, Rukhin A, Mackie RS, Marchette D, Thran B.

Risk Anal. 2015 May;35(5):811-27. doi: 10.1111/risa.12326. Epub 2014 Dec 24.


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.


The effect on melanoma risk of genes previously associated with telomere length.

Iles MM, Bishop DT, Taylor JC, Hayward NK, Brossard M, Cust AE, Dunning AM, Lee JE, Moses EK, Akslen LA; AMFS Investigators, Andresen PA, Avril MF, Azizi E, Scarrà GB, Brown KM, Dębniak T, Elder DE, Friedman E, Ghiorzo P, Gillanders EM, Goldstein AM, Gruis NA, Hansson J, Harland M, Helsing P, Hočevar M, Höiom V; IBD investigators, Ingvar C, Kanetsky PA, Landi MT, Lang J, Lathrop GM, Lubiński J, Mackie RM, Martin NG, Molven A, Montgomery GW, Novaković S, Olsson H, Puig S, Puig-Butille JA; QMEGA and QTWIN Investigators, Radford-Smith GL, Randerson-Moor J; SDH Study Group, van der Stoep N, van Doorn R, Whiteman DC, MacGregor S, Pooley KA, Ward SV, Mann GJ, Amos CI, Pharoah PD, Demenais F, Law MH, Newton Bishop JA, Barrett JH; GenoMEL Consortium.

J Natl Cancer Inst. 2014 Sep 17;106(10). pii: dju267. doi: 10.1093/jnci/dju267. Print 2014 Oct.


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.


Fine mapping of genetic susceptibility loci for melanoma reveals a mixture of single variant and multiple variant regions.

Barrett JH, Taylor JC, Bright C, Harland M, Dunning AM, Akslen LA, Andresen PA, Avril MF, Azizi E, Bianchi Scarrà G, Brossard M, Brown KM, Dębniak T, Elder DE, Friedman E, Ghiorzo P, Gillanders EM, Gruis NA, Hansson J, Helsing P, Hočevar M, Höiom V, Ingvar C, Landi MT, Lang J, Lathrop GM, Lubiński J, Mackie RM, Molven A, Novaković S, Olsson H, Puig S, Puig-Butille JA, van der Stoep N, van Doorn R, van Workum W, Goldstein AM, Kanetsky PA, Pharoah PD, Demenais F, Hayward NK, Newton Bishop JA, Bishop DT, Iles MM; GenoMEL Consortium.

Int J Cancer. 2015 Mar 15;136(6):1351-60. doi: 10.1002/ijc.29099. Epub 2014 Aug 14.


'This isn't what mine looked like': a qualitative study of symptom appraisal and help seeking in people recently diagnosed with melanoma.

Walter FM, Birt L, Cavers D, Scott S, Emery J, Burrows N, Cavanagh G, MacKie R, Weller D, Campbell C.

BMJ Open. 2014 Jul 21;4(7):e005566. doi: 10.1136/bmjopen-2014-005566.


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.


PIAS1 regulates breast tumorigenesis through selective epigenetic gene silencing.

Liu B, Tahk S, Yee KM, Yang R, Yang Y, Mackie R, Hsu C, Chernishof V, O'Brien N, Jin Y, Fan G, Lane TF, Rao J, Slamon D, Shuai K.

PLoS One. 2014 Feb 24;9(2):e89464. doi: 10.1371/journal.pone.0089464. eCollection 2014.


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.


Herbivorous rodents (Neotoma spp.) harbour abundant and active foregut microbiota.

Kohl KD, Miller AW, Marvin JE, Mackie R, Dearing MD.

Environ Microbiol. 2014 Sep;16(9):2869-78. doi: 10.1111/1462-2920.12376. Epub 2014 Jan 23.


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.


PIAS1 SUMO ligase regulates the self-renewal and differentiation of hematopoietic stem cells.

Liu B, Yee KM, Tahk S, Mackie R, Hsu C, Shuai K.

EMBO J. 2014 Jan 13;33(2):101-13. doi: 10.1002/embj.201283326. Epub 2013 Dec 15.


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.


Modeling low-dose mortality and disease incubation period of inhalational anthrax in the rabbit.

Gutting BW, Marchette D, Sherwood R, Andrews GA, Director-Myska A, Channel SR, Wolfe D, Berger AE, Mackie RS, Watson BJ, Rukhin A.

J Theor Biol. 2013 Jul 21;329:20-31. doi: 10.1016/j.jtbi.2013.03.020. Epub 2013 Apr 6.


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