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Items: 1 to 50 of 309

1.

Compositional and Functional Differences in the Human Gut Microbiome Correlate with Clinical Outcome following Infection with Wild-Type Salmonella enterica Serovar Typhi.

Zhang Y, Brady A, Jones C, Song Y, Darton TC, Jones C, Blohmke CJ, Pollard AJ, Magder LS, Fasano A, Sztein MB, Fraser CM.

MBio. 2018 May 8;9(3). pii: e00686-18. doi: 10.1128/mBio.00686-18.

2.

Salmonella Typhi Colonization Provokes Extensive Transcriptional Changes Aimed at Evading Host Mucosal Immune Defense During Early Infection of Human Intestinal Tissue.

Nickerson KP, Senger S, Zhang Y, Lima R, Patel S, Ingano L, Flavahan WA, Kumar DKV, Fraser CM, Faherty CS, Sztein MB, Fiorentino M, Fasano A.

EBioMedicine. 2018 May;31:92-109. doi: 10.1016/j.ebiom.2018.04.005. Epub 2018 Apr 12.

3.

Primordial origin and diversification of plasmids in Lyme disease agent bacteria.

Casjens SR, Di L, Akther S, Mongodin EF, Luft BJ, Schutzer SE, Fraser CM, Qiu WG.

BMC Genomics. 2018 Mar 27;19(1):218. doi: 10.1186/s12864-018-4597-x.

4.

Publisher Correction: Enterotypes in the landscape of gut microbial community composition.

Costea PI, Hildebrand F, Arumugam M, Bäckhed F, Blaser MJ, Bushman FD, de Vos WM, Ehrlich SD, Fraser CM, Hattori M, Huttenhower C, Jeffery IB, Knights D, Lewis JD, Ley RE, Ochman H, O'Toole PW, Quince C, Relman DA, Shanahan F, Sunagawa S, Wang J, Weinstock GM, Wu GD, Zeller G, Zhao L, Raes J, Knight R, Bork P.

Nat Microbiol. 2018 Mar;3(3):388. doi: 10.1038/s41564-018-0114-x.

PMID:
29440750
5.

Enterotypes in the landscape of gut microbial community composition.

Costea PI, Hildebrand F, Arumugam M, Bäckhed F, Blaser MJ, Bushman FD, de Vos WM, Ehrlich SD, Fraser CM, Hattori M, Huttenhower C, Jeffery IB, Knights D, Lewis JD, Ley RE, Ochman H, O'Toole PW, Quince C, Relman DA, Shanahan F, Sunagawa S, Wang J, Weinstock GM, Wu GD, Zeller G, Zhao L, Raes J, Knight R, Bork P.

Nat Microbiol. 2018 Jan;3(1):8-16. doi: 10.1038/s41564-017-0072-8. Epub 2017 Dec 18. Review. Erratum in: Nat Microbiol. 2018 Feb 13;:.

6.

Aligner optimization increases accuracy and decreases compute times in multi-species sequence data.

Robinson KM, Hawkins AS, Santana-Cruz I, Adkins RS, Shetty AC, Nagaraj S, Sadzewicz L, Tallon LJ, Rasko DA, Fraser CM, Mahurkar A, Silva JC, Dunning Hotopp JC.

Microb Genom. 2017 Jul 8;3(9):e000122. doi: 10.1099/mgen.0.000122. eCollection 2017 Sep.

7.

Systemic and Terminal Ileum Mucosal Immunity Elicited by Oral Immunization With the Ty21a Typhoid Vaccine in Humans.

Booth JS, Patil SA, Ghazi L, Barnes R, Fraser CM, Fasano A, Greenwald BD, Sztein MB.

Cell Mol Gastroenterol Hepatol. 2017 Aug 16;4(3):419-437. doi: 10.1016/j.jcmgh.2017.08.002. eCollection 2017 Nov.

8.

Whole-Genome Sequences of Bacteremia Isolates of Bordetella holmesii.

Tettelin H, Hooven TA, Zhao X, Su Q, Sadzewicz L, Tallon LJ, Fraser CM, Ratner AJ.

Genome Announc. 2017 Sep 28;5(39). pii: e01023-17. doi: 10.1128/genomeA.01023-17.

9.

CloVR-Comparative: automated, cloud-enabled comparative microbial genome sequence analysis pipeline.

Agrawal S, Arze C, Adkins RS, Crabtree J, Riley D, Vangala M, Galens K, Fraser CM, Tettelin H, White O, Angiuoli SV, Mahurkar A, Fricke WF.

BMC Genomics. 2017 Apr 27;18(1):332. doi: 10.1186/s12864-017-3717-3.

10.

New var reconstruction algorithm exposes high var sequence diversity in a single geographic location in Mali.

Dara A, Drábek EF, Travassos MA, Moser KA, Delcher AL, Su Q, Hostelley T, Coulibaly D, Daou M, Dembele A, Diarra I, Kone AK, Kouriba B, Laurens MB, Niangaly A, Traore K, Tolo Y, Fraser CM, Thera MA, Djimde AA, Doumbo OK, Plowe CV, Silva JC.

Genome Med. 2017 Mar 28;9(1):30. doi: 10.1186/s13073-017-0422-4.

11.

Plasmid diversity and phylogenetic consistency in the Lyme disease agent Borrelia burgdorferi.

Casjens SR, Gilcrease EB, Vujadinovic M, Mongodin EF, Luft BJ, Schutzer SE, Fraser CM, Qiu WG.

BMC Genomics. 2017 Feb 15;18(1):165. doi: 10.1186/s12864-017-3553-5.

12.

Genome-wide diversity and gene expression profiling of Babesia microti isolates identify polymorphic genes that mediate host-pathogen interactions.

Silva JC, Cornillot E, McCracken C, Usmani-Brown S, Dwivedi A, Ifeonu OO, Crabtree J, Gotia HT, Virji AZ, Reynes C, Colinge J, Kumar V, Lawres L, Pazzi JE, Pablo JV, Hung C, Brancato J, Kumari P, Orvis J, Tretina K, Chibucos M, Ott S, Sadzewicz L, Sengamalay N, Shetty AC, Su Q, Tallon L, Fraser CM, Frutos R, Molina DM, Krause PJ, Ben Mamoun C.

Sci Rep. 2016 Oct 18;6:35284. doi: 10.1038/srep35284.

13.

Efficient Enrichment of Bacterial mRNA from Host-Bacteria Total RNA Samples.

Kumar N, Lin M, Zhao X, Ott S, Santana-Cruz I, Daugherty S, Rikihisa Y, Sadzewicz L, Tallon LJ, Fraser CM, Dunning Hotopp JC.

Sci Rep. 2016 Oct 7;6:34850. doi: 10.1038/srep34850.

14.

Annotated draft genome sequences of three species of Cryptosporidium: Cryptosporidium meleagridis isolate UKMEL1, C. baileyi isolate TAMU-09Q1 and C. hominis isolates TU502_2012 and UKH1.

Ifeonu OO, Chibucos MC, Orvis J, Su Q, Elwin K, Guo F, Zhang H, Xiao L, Sun M, Chalmers RM, Fraser CM, Zhu G, Kissinger JC, Widmer G, Silva JC.

Pathog Dis. 2016 Oct;74(7). pii: ftw080. Epub 2016 Aug 12.

15.

An integrated genomic and transcriptomic survey of mucormycosis-causing fungi.

Chibucos MC, Soliman S, Gebremariam T, Lee H, Daugherty S, Orvis J, Shetty AC, Crabtree J, Hazen TH, Etienne KA, Kumari P, O'Connor TD, Rasko DA, Filler SG, Fraser CM, Lockhart SR, Skory CD, Ibrahim AS, Bruno VM.

Nat Commun. 2016 Jul 22;7:12218. doi: 10.1038/ncomms12218.

16.

Facing the Heat: Does Desiccation and Thermal Stress Explain Patterns of Orientation in an Intertidal Invertebrate?

Fraser CM, Seebacher F, Lathlean J, Coleman RA.

PLoS One. 2016 Mar 9;11(3):e0150200. doi: 10.1371/journal.pone.0150200. eCollection 2016.

17.

Genomic insights into the Ixodes scapularis tick vector of Lyme disease.

Gulia-Nuss M, Nuss AB, Meyer JM, Sonenshine DE, Roe RM, Waterhouse RM, Sattelle DB, de la Fuente J, Ribeiro JM, Megy K, Thimmapuram J, Miller JR, Walenz BP, Koren S, Hostetler JB, Thiagarajan M, Joardar VS, Hannick LI, Bidwell S, Hammond MP, Young S, Zeng Q, Abrudan JL, Almeida FC, Ayllón N, Bhide K, Bissinger BW, Bonzon-Kulichenko E, Buckingham SD, Caffrey DR, Caimano MJ, Croset V, Driscoll T, Gilbert D, Gillespie JJ, Giraldo-Calderón GI, Grabowski JM, Jiang D, Khalil SM, Kim D, Kocan KM, Koči J, Kuhn RJ, Kurtti TJ, Lees K, Lang EG, Kennedy RC, Kwon H, Perera R, Qi Y, Radolf JD, Sakamoto JM, Sánchez-Gracia A, Severo MS, Silverman N, Šimo L, Tojo M, Tornador C, Van Zee JP, Vázquez J, Vieira FG, Villar M, Wespiser AR, Yang Y, Zhu J, Arensburger P, Pietrantonio PV, Barker SC, Shao R, Zdobnov EM, Hauser F, Grimmelikhuijzen CJ, Park Y, Rozas J, Benton R, Pedra JH, Nelson DR, Unger MF, Tubio JM, Tu Z, Robertson HM, Shumway M, Sutton G, Wortman JR, Lawson D, Wikel SK, Nene VM, Fraser CM, Collins FH, Birren B, Nelson KE, Caler E, Hill CA.

Nat Commun. 2016 Feb 9;7:10507. doi: 10.1038/ncomms10507.

18.

Potential Influence of Staphylococcus aureus Clonal Complex 30 Genotype and Transcriptome on Hematogenous Infections.

Sharma-Kuinkel BK, Mongodin EF, Myers JR, Vore KL, Canfield GS, Fraser CM, Rude TH, Fowler VG Jr, Gill SR.

Open Forum Infect Dis. 2015 Jun 24;2(3):ofv093. doi: 10.1093/ofid/ofv093. eCollection 2015 Sep.

19.

Erratum for Martin et al., Phylogenomic Identification of Regulatory Sequences in Bacteria: an Analysis of Statistical Power and an Application to Borrelia burgdorferi Sensu Lato.

Martin CL, Sukarna TY, Akther S, Ramrattan G, Pagan P, Di L, Mongodin EF, Fraser CM, Schutzer SE, Luft BJ, Casjens SR, Qiu WG.

MBio. 2015 Jul 21;6(4):e00999. doi: 10.1128/mBio.00999-15. No abstract available.

20.

The Oral Bacterial Communities of Children with Well-Controlled HIV Infection and without HIV Infection.

Goldberg BE, Mongodin EF, Jones CE, Chung M, Fraser CM, Tate A, Zeichner SL.

PLoS One. 2015 Jul 6;10(7):e0131615. doi: 10.1371/journal.pone.0131615. eCollection 2015.

21.

Examination of the Enterotoxigenic Escherichia coli Population Structure during Human Infection.

Sahl JW, Sistrunk JR, Fraser CM, Hine E, Baby N, Begum Y, Luo Q, Sheikh A, Qadri F, Fleckenstein JM, Rasko DA.

MBio. 2015 Jun 9;6(3):e00501. doi: 10.1128/mBio.00501-15.

22.

Pulmonary Nontuberculous Mycobacterial Infection. A Multisystem, Multigenic Disease.

Szymanski EP, Leung JM, Fowler CJ, Haney C, Hsu AP, Chen F, Duggal P, Oler AJ, McCormack R, Podack E, Drummond RA, Lionakis MS, Browne SK, Prevots DR, Knowles M, Cutting G, Liu X, Devine SE, Fraser CM, Tettelin H, Olivier KN, Holland SM.

Am J Respir Crit Care Med. 2015 Sep 1;192(5):618-28. doi: 10.1164/rccm.201502-0387OC.

23.

Functional dynamics of the gut microbiome in elderly people during probiotic consumption.

Eloe-Fadrosh EA, Brady A, Crabtree J, Drabek EF, Ma B, Mahurkar A, Ravel J, Haverkamp M, Fiorino AM, Botelho C, Andreyeva I, Hibberd PL, Fraser CM.

MBio. 2015 Apr 14;6(2). pii: e00231-15. doi: 10.1128/mBio.00231-15.

24.

Phylogenomic identification of regulatory sequences in bacteria: an analysis of statistical power and an application to Borrelia burgdorferi sensu lato.

Martin CL, Sukarna TY, Akther S, Ramrattan G, Pagan P, Di L, Mongodin EF, Fraser CM, Schutzer SE, Luft BJ, Casjens SR, Qiu WG.

MBio. 2015 Apr 14;6(2). pii: e00011-15. doi: 10.1128/mBio.00011-15. Erratum in: MBio. 2015;6(4):e00999. Martin, Che I [Corrected to Martin, Che L].

25.

New signaling pathways govern the host response to C. albicans infection in various niches.

Liu Y, Shetty AC, Schwartz JA, Bradford LL, Xu W, Phan QT, Kumari P, Mahurkar A, Mitchell AP, Ravel J, Fraser CM, Filler SG, Bruno VM.

Genome Res. 2015 May;25(5):679-89. doi: 10.1101/gr.187427.114. Epub 2015 Apr 9.

26.

Gut microbiota in multiple sclerosis: possible influence of immunomodulators.

Cantarel BL, Waubant E, Chehoud C, Kuczynski J, DeSantis TZ, Warrington J, Venkatesan A, Fraser CM, Mowry EM.

J Investig Med. 2015 Jun;63(5):729-34. doi: 10.1097/JIM.0000000000000192.

27.

Transcriptional attenuation controls macrolide inducible efflux and resistance in Streptococcus pneumoniae and in other Gram-positive bacteria containing mef/mel(msr(D)) elements.

Chancey ST, Bai X, Kumar N, Drabek EF, Daugherty SC, Colon T, Ott S, Sengamalay N, Sadzewicz L, Tallon LJ, Fraser CM, Tettelin H, Stephens DS.

PLoS One. 2015 Feb 19;10(2):e0116254. doi: 10.1371/journal.pone.0116254. eCollection 2015.

28.

Defining the phylogenomics of Shigella species: a pathway to diagnostics.

Sahl JW, Morris CR, Emberger J, Fraser CM, Ochieng JB, Juma J, Fields B, Breiman RF, Gilmour M, Nataro JP, Rasko DA.

J Clin Microbiol. 2015 Mar;53(3):951-60. doi: 10.1128/JCM.03527-14. Epub 2015 Jan 14.

29.

Genomic epidemiology of the Haitian cholera outbreak: a single introduction followed by rapid, extensive, and continued spread characterized the onset of the epidemic.

Eppinger M, Pearson T, Koenig SS, Pearson O, Hicks N, Agrawal S, Sanjar F, Galens K, Daugherty S, Crabtree J, Hendriksen RS, Price LB, Upadhyay BP, Shakya G, Fraser CM, Ravel J, Keim PS.

MBio. 2014 Nov 4;5(6):e01721. doi: 10.1128/mBio.01721-14.

30.

Single molecule sequencing and genome assembly of a clinical specimen of Loa loa, the causative agent of loiasis.

Tallon LJ, Liu X, Bennuru S, Chibucos MC, Godinez A, Ott S, Zhao X, Sadzewicz L, Fraser CM, Nutman TB, Dunning Hotopp JC.

BMC Genomics. 2014 Sep 12;15:788. doi: 10.1186/1471-2164-15-788.

31.

Probiotics: achieving a better regulatory fit.

Hoffmann DE, Fraser CM, Palumbo F, Ravel J, Rowthorn V, Schwartz J.

Food Drug Law J. 2014;69(2):237-72, ii.

PMID:
25163211
32.

BorreliaBase: a phylogeny-centered browser of Borrelia genomes.

Di L, Pagan PE, Packer D, Martin CL, Akther S, Ramrattan G, Mongodin EF, Fraser CM, Schutzer SE, Luft BJ, Casjens SR, Qiu WG.

BMC Bioinformatics. 2014 Jul 3;15:233. doi: 10.1186/1471-2105-15-233.

33.

Culture-independent evaluation of the appendix and rectum microbiomes in children with and without appendicitis.

Jackson HT, Mongodin EF, Davenport KP, Fraser CM, Sandler AD, Zeichner SL.

PLoS One. 2014 Apr 23;9(4):e95414. doi: 10.1371/journal.pone.0095414. eCollection 2014.

34.

Genome sequences of rhinovirus C isolates from wisconsin pediatric respiratory studies.

Liggett SB, Bochkov YA, Pappas T, Lemanske RF Jr, Gern JE, Sengamalay N, Zhao X, Su Q, Fraser CM, Palmenberg AC.

Genome Announc. 2014 Mar 27;2(2). pii: e00203-14. doi: 10.1128/genomeA.00203-14.

35.

Genome sequences of rhinovirus B isolates from wisconsin pediatric respiratory studies.

Liggett SB, Bochkov YA, Pappas T, Lemanske RF Jr, Gern JE, Sengamalay N, Zhao X, Su Q, Fraser CM, Palmenberg AC.

Genome Announc. 2014 Mar 27;2(2). pii: e00202-14. doi: 10.1128/genomeA.00202-14.

36.

Genome sequences of rhinovirus a isolates from wisconsin pediatric respiratory studies.

Liggett SB, Bochkov YA, Pappas T, Lemanske RF Jr, Gern JE, Sengamalay N, Zhao X, Su Q, Fraser CM, Palmenberg AC.

Genome Announc. 2014 Mar 27;2(2). pii: e00200-14. doi: 10.1128/genomeA.00200-14.

37.

High-level relatedness among Mycobacterium abscessus subsp. massiliense strains from widely separated outbreaks.

Tettelin H, Davidson RM, Agrawal S, Aitken ML, Shallom S, Hasan NA, Strong M, de Moura VC, De Groote MA, Duarte RS, Hine E, Parankush S, Su Q, Daugherty SC, Fraser CM, Brown-Elliott BA, Wallace RJ Jr, Holland SM, Sampaio EP, Olivier KN, Jackson M, Zelazny AM.

Emerg Infect Dis. 2014 Mar;20(3):364-71. doi: 10.3201/eid2003.131106.

38.

Draft Genome Sequence of Mortierella alpina Isolate CDC-B6842.

Etienne KA, Chibucos MC, Su Q, Orvis J, Daugherty S, Ott S, Sengamalay NA, Fraser CM, Lockhart SR, Bruno VM.

Genome Announc. 2014 Jan 23;2(1). pii: e01180-13. doi: 10.1128/genomeA.01180-13.

39.

Genome Sequence of Escherichia coli O157:H7 Strain 2886-75, Associated with the First Reported Case of Human Infection in the United States.

Sanjar F, Hazen TH, Shah SM, Koenig SS, Agrawal S, Daugherty S, Sadzewicz L, Tallon LJ, Mammel MK, Feng P, Soderlund R, Tarr PI, Debroy C, Dudley EG, Cebula TA, Ravel J, Fraser CM, Rasko DA, Eppinger M.

Genome Announc. 2014 Jan 9;2(1). pii: e01120-13. doi: 10.1128/genomeA.01120-13.

40.

Genetic variation in vitro and in vivo of an attenuated Lassa vaccine candidate.

Zapata JC, Goicochea M, Nadai Y, Eyzaguirre LM, Carr JK, Tallon LJ, Sadzewicz L, Myers G, Fraser CM, Su Q, Djavani M, Lukashevich IS, Salvato MS.

J Virol. 2014 Mar;88(6):3058-66. doi: 10.1128/JVI.03035-13. Epub 2013 Dec 11.

41.

Simultaneous transcriptional profiling of bacteria and their host cells.

Humphrys MS, Creasy T, Sun Y, Shetty AC, Chibucos MC, Drabek EF, Fraser CM, Farooq U, Sengamalay N, Ott S, Shou H, Bavoil PM, Mahurkar A, Myers GS.

PLoS One. 2013 Dec 4;8(12):e80597. doi: 10.1371/journal.pone.0080597. eCollection 2013.

42.

Science and regulation. Probiotics: finding the right regulatory balance.

Hoffmann DE, Fraser CM, Palumbo FB, Ravel J, Rothenberg K, Rowthorn V, Schwartz J.

Science. 2013 Oct 18;342(6156):314-5. doi: 10.1126/science.1244656. No abstract available. Erratum in: Science. 2013 Nov 8;342(6159):693.

PMID:
24136953
43.

Inter- and intra-specific pan-genomes of Borrelia burgdorferi sensu lato: genome stability and adaptive radiation.

Mongodin EF, Casjens SR, Bruno JF, Xu Y, Drabek EF, Riley DR, Cantarel BL, Pagan PE, Hernandez YA, Vargas LC, Dunn JJ, Schutzer SE, Fraser CM, Qiu WG, Luft BJ.

BMC Genomics. 2013 Oct 10;14:693. doi: 10.1186/1471-2164-14-693.

44.

Trying to fit in: are patterns of orientation of a keystone grazer set by behavioural responses to ecosystem engineers or wave action?

Fraser CM, Coleman RA, Seebacher F.

Oecologia. 2014 Jan;174(1):67-75. doi: 10.1007/s00442-013-2743-3. Epub 2013 Aug 31.

PMID:
23996227
45.

Draft Genome Sequences of Three O157 Enteropathogenic Escherichia coli Isolates.

Hazen TH, Sahl JW, Fraser CM, Donnenberg MS, Scheutz F, Rasko DA.

Genome Announc. 2013 Jul 18;1(4). pii: e00516-13. doi: 10.1128/genomeA.00516-13.

46.

Refining the pathovar paradigm via phylogenomics of the attaching and effacing Escherichia coli.

Hazen TH, Sahl JW, Fraser CM, Donnenberg MS, Scheutz F, Rasko DA.

Proc Natl Acad Sci U S A. 2013 Jul 30;110(31):12810-5. doi: 10.1073/pnas.1306836110. Epub 2013 Jul 15.

47.

Differential response of the cynomolgus macaque gut microbiota to Shigella infection.

Seekatz AM, Panda A, Rasko DA, Toapanta FR, Eloe-Fadrosh EA, Khan AQ, Liu Z, Shipley ST, Detolla LJ, Sztein MB, Fraser CM.

PLoS One. 2013 Jun 5;8(6):e64212. doi: 10.1371/journal.pone.0064212. Print 2013.

48.

Genome sequences of 65 Helicobacter pylori strains isolated from asymptomatic individuals and patients with gastric cancer, peptic ulcer disease, or gastritis.

Blanchard TG, Czinn SJ, Correa P, Nakazawa T, Keelan M, Morningstar L, Santana-Cruz I, Maroo A, McCracken C, Shefchek K, Daugherty S, Song Y, Fraser CM, Fricke WF.

Pathog Dis. 2013 Jul;68(2):39-43. doi: 10.1111/2049-632X.12045. Epub 2013 May 23.

49.

Impact of oral typhoid vaccination on the human gut microbiota and correlations with s. Typhi-specific immunological responses.

Eloe-Fadrosh EA, McArthur MA, Seekatz AM, Drabek EF, Rasko DA, Sztein MB, Fraser CM.

PLoS One. 2013 Apr 24;8(4):e62026. doi: 10.1371/journal.pone.0062026. Print 2013.

50.

Whole-Genome Draft Sequences of 26 Enterohemorrhagic Escherichia coli O157:H7 Strains.

Eppinger M, Daugherty S, Agrawal S, Galens K, Sengamalay N, Sadzewicz L, Tallon L, Cebula TA, Mammel MK, Feng P, Soderlund R, Tarr PI, Debroy C, Dudley EG, Fraser CM, Ravel J.

Genome Announc. 2013 Feb 28;1(2):e0013412. doi: 10.1128/genomeA.00134-12.

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