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Items: 33

1.

Human and Extracellular DNA Depletion for Metagenomic Analysis of Complex Clinical Infection Samples Yields Optimized Viable Microbiome Profiles.

Nelson MT, Pope CE, Marsh RL, Wolter DJ, Weiss EJ, Hager KR, Vo AT, Brittnacher MJ, Radey MC, Hayden HS, Eng A, Miller SI, Borenstein E, Hoffman LR.

Cell Rep. 2019 Feb 19;26(8):2227-2240.e5. doi: 10.1016/j.celrep.2019.01.091.

2.

Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis.

Matamouros S, Hayden HS, Hager KR, Brittnacher MJ, Lachance K, Weiss EJ, Pope CE, Imhaus AF, McNally CP, Borenstein E, Hoffman LR, Miller SI.

Proc Natl Acad Sci U S A. 2018 Feb 13;115(7):1605-1610. doi: 10.1073/pnas.1714373115. Epub 2018 Jan 29.

3.

Clinical and Fecal Microbial Changes With Diet Therapy in Active Inflammatory Bowel Disease.

Suskind DL, Cohen SA, Brittnacher MJ, Wahbeh G, Lee D, Shaffer ML, Braly K, Hayden HS, Klein J, Gold B, Giefer M, Stallworth A, Miller SI.

J Clin Gastroenterol. 2018 Feb;52(2):155-163. doi: 10.1097/MCG.0000000000000772.

4.

In vivo protein interaction network analysis reveals porin-localized antibiotic inactivation in Acinetobacter baumannii strain AB5075.

Wu X, Chavez JD, Schweppe DK, Zheng C, Weisbrod CR, Eng JK, Murali A, Lee SA, Ramage E, Gallagher LA, Kulasekara HD, Edrozo ME, Kamischke CN, Brittnacher MJ, Miller SI, Singh PK, Manoil C, Bruce JE.

Nat Commun. 2016 Nov 11;7:13414. doi: 10.1038/ncomms13414.

5.

GUTSS: An Alignment-Free Sequence Comparison Method for Use in Human Intestinal Microbiome and Fecal Microbiota Transplantation Analysis.

Brittnacher MJ, Heltshe SL, Hayden HS, Radey MC, Weiss EJ, Damman CJ, Zisman TL, Suskind DL, Miller SI.

PLoS One. 2016 Jul 8;11(7):e0158897. doi: 10.1371/journal.pone.0158897. eCollection 2016.

6.

Genomic Analysis of Salmonella enterica Serovar Typhimurium Characterizes Strain Diversity for Recent U.S. Salmonellosis Cases and Identifies Mutations Linked to Loss of Fitness under Nitrosative and Oxidative Stress.

Hayden HS, Matamouros S, Hager KR, Brittnacher MJ, Rohmer L, Radey MC, Weiss EJ, Kim KB, Jacobs MA, Sims-Day EH, Yue M, Zaidi MB, Schifferli DM, Manning SD, Walson JL, Miller SI.

MBio. 2016 Mar 8;7(2):e00154. doi: 10.1128/mBio.00154-16.

7.

Metagenomic evidence for taxonomic dysbiosis and functional imbalance in the gastrointestinal tracts of children with cystic fibrosis.

Manor O, Levy R, Pope CE, Hayden HS, Brittnacher MJ, Carr R, Radey MC, Hager KR, Heltshe SL, Ramsey BW, Miller SI, Hoffman LR, Borenstein E.

Sci Rep. 2016 Mar 4;6:22493. doi: 10.1038/srep22493.

8.

Regional Isolation Drives Bacterial Diversification within Cystic Fibrosis Lungs.

Jorth P, Staudinger BJ, Wu X, Hisert KB, Hayden H, Garudathri J, Harding CL, Radey MC, Rezayat A, Bautista G, Berrington WR, Goddard AF, Zheng C, Angermeyer A, Brittnacher MJ, Kitzman J, Shendure J, Fligner CL, Mittler J, Aitken ML, Manoil C, Bruce JE, Yahr TL, Singh PK.

Cell Host Microbe. 2015 Sep 9;18(3):307-19. doi: 10.1016/j.chom.2015.07.006. Epub 2015 Aug 20.

9.

Low Level Engraftment and Improvement following a Single Colonoscopic Administration of Fecal Microbiota to Patients with Ulcerative Colitis.

Damman CJ, Brittnacher MJ, Westerhoff M, Hayden HS, Radey M, Hager KR, Marquis SR, Miller SI, Zisman TL.

PLoS One. 2015 Aug 19;10(8):e0133925. doi: 10.1371/journal.pone.0133925. eCollection 2015.

10.

Resources for Genetic and Genomic Analysis of Emerging Pathogen Acinetobacter baumannii.

Gallagher LA, Ramage E, Weiss EJ, Radey M, Hayden HS, Held KG, Huse HK, Zurawski DV, Brittnacher MJ, Manoil C.

J Bacteriol. 2015 Jun 15;197(12):2027-35. doi: 10.1128/JB.00131-15. Epub 2015 Apr 6.

11.

An underlying mechanism for the increased mutagenesis of lagging-strand genes in Bacillus subtilis.

Million-Weaver S, Samadpour AN, Moreno-Habel DA, Nugent P, Brittnacher MJ, Weiss E, Hayden HS, Miller SI, Liachko I, Merrikh H.

Proc Natl Acad Sci U S A. 2015 Mar 10;112(10):E1096-105. doi: 10.1073/pnas.1416651112. Epub 2015 Feb 23.

12.

Fecal microbial transplant effect on clinical outcomes and fecal microbiome in active Crohn's disease.

Suskind DL, Brittnacher MJ, Wahbeh G, Shaffer ML, Hayden HS, Qin X, Singh N, Damman CJ, Hager KR, Nielson H, Miller SI.

Inflamm Bowel Dis. 2015 Mar;21(3):556-63. doi: 10.1097/MIB.0000000000000307.

13.

Cross-species comparison of the Burkholderia pseudomallei, Burkholderia thailandensis, and Burkholderia mallei quorum-sensing regulons.

Majerczyk CD, Brittnacher MJ, Jacobs MA, Armour CD, Radey MC, Bunt R, Hayden HS, Bydalek R, Greenberg EP.

J Bacteriol. 2014 Nov;196(22):3862-71. doi: 10.1128/JB.01974-14. Epub 2014 Sep 2.

14.

Genomic analysis of the emergence of 20th century epidemic dysentery.

Rohmer L, Jacobs MA, Brittnacher MJ, Fong C, Hayden HS, Hocquet D, Weiss EJ, Radey M, Germani Y, Talukder KA, Hager AJ, Kemner JM, Sims-Day EH, Matamouros S, Hager KR, Miller SI.

BMC Genomics. 2014 May 10;15:355. doi: 10.1186/1471-2164-15-355.

15.

Gastrointestinal pathology in juvenile and adult CFTR-knockout ferrets.

Sun X, Olivier AK, Yi Y, Pope CE, Hayden HS, Liang B, Sui H, Zhou W, Hager KR, Zhang Y, Liu X, Yan Z, Fisher JT, Keiser NW, Song Y, Tyler SR, Goeken JA, Kinyon JM, Radey MC, Fligg D, Wang X, Xie W, Lynch TJ, Kaminsky PM, Brittnacher MJ, Miller SI, Parekh K, Meyerholz DK, Hoffman LR, Frana T, Stewart ZA, Engelhardt JF.

Am J Pathol. 2014 May;184(5):1309-22. doi: 10.1016/j.ajpath.2014.01.035. Epub 2014 Mar 15.

16.

Escherichia coli dysbiosis correlates with gastrointestinal dysfunction in children with cystic fibrosis.

Hoffman LR, Pope CE, Hayden HS, Heltshe S, Levy R, McNamara S, Jacobs MA, Rohmer L, Radey M, Ramsey BW, Brittnacher MJ, Borenstein E, Miller SI.

Clin Infect Dis. 2014 Feb;58(3):396-9. doi: 10.1093/cid/cit715. Epub 2013 Oct 30.

17.

Genome sequence of Francisella tularensis subspecies holarctica strain FSC200, isolated from a child with tularemia.

Svensson K, Sjödin A, Byström M, Granberg M, Brittnacher MJ, Rohmer L, Jacobs MA, Sims-Day EH, Levy R, Zhou Y, Hayden HS, Lim R, Chang J, Guenthener D, Kang A, Haugen E, Gillett W, Kaul R, Forsman M, Larsson P, Johansson A.

J Bacteriol. 2012 Dec;194(24):6965-6. doi: 10.1128/JB.01040-12.

18.

Strain-dependent diversity in the Pseudomonas aeruginosa quorum-sensing regulon.

Chugani S, Kim BS, Phattarasukol S, Brittnacher MJ, Choi SH, Harwood CS, Greenberg EP.

Proc Natl Acad Sci U S A. 2012 Oct 9;109(41):E2823-31. doi: 10.1073/pnas.1214128109. Epub 2012 Sep 17.

19.

Functional genetic screen of human diversity reveals that a methionine salvage enzyme regulates inflammatory cell death.

Ko DC, Gamazon ER, Shukla KP, Pfuetzner RA, Whittington D, Holden TD, Brittnacher MJ, Fong C, Radey M, Ogohara C, Stark AL, Akey JM, Dolan ME, Wurfel MM, Miller SI.

Proc Natl Acad Sci U S A. 2012 Aug 28;109(35):E2343-52. doi: 10.1073/pnas.1206701109. Epub 2012 Jul 25.

20.

Identification of a p-coumarate degradation regulon in Rhodopseudomonas palustris by Xpression, an integrated tool for prokaryotic RNA-seq data processing.

Phattarasukol S, Radey MC, Lappala CR, Oda Y, Hirakawa H, Brittnacher MJ, Harwood CS.

Appl Environ Microbiol. 2012 Oct;78(19):6812-8. doi: 10.1128/AEM.01418-12. Epub 2012 Jul 13.

21.

Evolution of Burkholderia pseudomallei in recurrent melioidosis.

Hayden HS, Lim R, Brittnacher MJ, Sims EH, Ramage ER, Fong C, Wu Z, Crist E, Chang J, Zhou Y, Radey M, Rohmer L, Haugen E, Gillett W, Wuthiekanun V, Peacock SJ, Kaul R, Miller SI, Manoil C, Jacobs MA.

PLoS One. 2012;7(5):e36507. doi: 10.1371/journal.pone.0036507. Epub 2012 May 15.

22.

PGAT: a multistrain analysis resource for microbial genomes.

Brittnacher MJ, Fong C, Hayden HS, Jacobs MA, Radey M, Rohmer L.

Bioinformatics. 2011 Sep 1;27(17):2429-30. doi: 10.1093/bioinformatics/btr418. Epub 2011 Jul 15.

23.

Structure of a Burkholderia pseudomallei trimeric autotransporter adhesin head.

Edwards TE, Phan I, Abendroth J, Dieterich SH, Masoudi A, Guo W, Hewitt SN, Kelley A, Leibly D, Brittnacher MJ, Staker BL, Miller SI, Van Voorhis WC, Myler PJ, Stewart LJ.

PLoS One. 2010 Sep 20;5(9). pii: e12803. doi: 10.1371/journal.pone.0012803.

24.

A genome-wide in vitro bacterial-infection screen reveals human variation in the host response associated with inflammatory disease.

Ko DC, Shukla KP, Fong C, Wasnick M, Brittnacher MJ, Wurfel MM, Holden TD, O'Keefe GE, Van Yserloo B, Akey JM, Miller SI.

Am J Hum Genet. 2009 Aug;85(2):214-27. doi: 10.1016/j.ajhg.2009.07.012. Epub 2009 Aug 6.

25.

Genome-wide screen in Francisella novicida for genes required for pulmonary and systemic infection in mice.

Kraemer PS, Mitchell A, Pelletier MR, Gallagher LA, Wasnick M, Rohmer L, Brittnacher MJ, Manoil C, Skerett SJ, Salama NR.

Infect Immun. 2009 Jan;77(1):232-44. doi: 10.1128/IAI.00978-08. Epub 2008 Oct 27.

26.

Burkholderia thailandensis as a model system for the study of the virulence-associated type III secretion system of Burkholderia pseudomallei.

Haraga A, West TE, Brittnacher MJ, Skerrett SJ, Miller SI.

Infect Immun. 2008 Nov;76(11):5402-11. doi: 10.1128/IAI.00626-08. Epub 2008 Sep 8.

27.

Large-insert genome analysis technology detects structural variation in Pseudomonas aeruginosa clinical strains from cystic fibrosis patients.

Hayden HS, Gillett W, Saenphimmachak C, Lim R, Zhou Y, Jacobs MA, Chang J, Rohmer L, D'Argenio DA, Palmieri A, Levy R, Haugen E, Wong GK, Brittnacher MJ, Burns JL, Miller SI, Olson MV, Kaul R.

Genomics. 2008 Jun;91(6):530-7. doi: 10.1016/j.ygeno.2008.02.005. Epub 2008 Apr 29.

28.

Determination and comparison of the Francisella tularensis subsp.novicida U112 proteome to other bacterial proteomes.

Rohmer L, Guina T, Chen J, Gallis B, Taylor GK, Shaffer SA, Miller SI, Brittnacher MJ, Goodlett DR.

J Proteome Res. 2008 May;7(5):2016-24. doi: 10.1021/pr700760z. Epub 2008 Apr 2.

PMID:
18380474
29.

PSAT: a web tool to compare genomic neighborhoods of multiple prokaryotic genomes.

Fong C, Rohmer L, Radey M, Wasnick M, Brittnacher MJ.

BMC Bioinformatics. 2008 Mar 26;9:170. doi: 10.1186/1471-2105-9-170.

30.

A Francisella mutant in lipid A carbohydrate modification elicits protective immunity.

Kanistanon D, Hajjar AM, Pelletier MR, Gallagher LA, Kalhorn T, Shaffer SA, Goodlett DR, Rohmer L, Brittnacher MJ, Skerrett SJ, Ernst RK.

PLoS Pathog. 2008 Feb 8;4(2):e24. doi: 10.1371/journal.ppat.0040024.

31.

MglA regulates Francisella tularensis subsp. novicida (Francisella novicida) response to starvation and oxidative stress.

Guina T, Radulovic D, Bahrami AJ, Bolton DL, Rohmer L, Jones-Isaac KA, Chen J, Gallagher LA, Gallis B, Ryu S, Taylor GK, Brittnacher MJ, Manoil C, Goodlett DR.

J Bacteriol. 2007 Sep;189(18):6580-6. Epub 2007 Jul 20.

32.

Comparison of Francisella tularensis genomes reveals evolutionary events associated with the emergence of human pathogenic strains.

Rohmer L, Fong C, Abmayr S, Wasnick M, Larson Freeman TJ, Radey M, Guina T, Svensson K, Hayden HS, Jacobs M, Gallagher LA, Manoil C, Ernst RK, Drees B, Buckley D, Haugen E, Bovee D, Zhou Y, Chang J, Levy R, Lim R, Gillett W, Guenthener D, Kang A, Shaffer SA, Taylor G, Chen J, Gallis B, D'Argenio DA, Forsman M, Olson MV, Goodlett DR, Kaul R, Miller SI, Brittnacher MJ.

Genome Biol. 2007;8(6):R102.

33.

Type IV pili-mediated secretion modulates Francisella virulence.

Hager AJ, Bolton DL, Pelletier MR, Brittnacher MJ, Gallagher LA, Kaul R, Skerrett SJ, Miller SI, Guina T.

Mol Microbiol. 2006 Oct;62(1):227-37.

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