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Items: 1 to 50 of 58

1.

What is new and relevant for sequencing-based microbiome research? A mini-review.

Fricker AM, Podlesny D, Fricke WF.

J Adv Res. 2019 Mar 23;19:105-112. doi: 10.1016/j.jare.2019.03.006. eCollection 2019 Sep. Review.

2.

Global phylogenomics of multidrug-resistant Salmonella enterica serotype Kentucky ST198.

Hawkey J, Le Hello S, Doublet B, Granier SA, Hendriksen RS, Fricke WF, Ceyssens PJ, Gomart C, Billman-Jacobe H, Holt KE, Weill FX.

Microb Genom. 2019 Jul;5(7). doi: 10.1099/mgen.0.000269. Epub 2019 May 20.

3.

Qualitative and Quantitative DNA- and RNA-Based Analysis of the Bacterial Stomach Microbiota in Humans, Mice, and Gerbils.

Wurm P, Dörner E, Kremer C, Spranger J, Maddox C, Halwachs B, Harrison U, Blanchard T, Haas R, Högenauer C, Gorkiewicz G, Fricke WF.

mSystems. 2018 Nov 20;3(6). pii: e00262-18. doi: 10.1128/mSystems.00262-18. eCollection 2018 Nov-Dec.

4.

Gut microbiota-dependent modulation of innate immunity and lymph node remodeling affects cardiac allograft outcomes.

Bromberg JS, Hittle L, Xiong Y, Saxena V, Smyth EM, Li L, Zhang T, Wagner C, Fricke WF, Simon T, Brinkman CC, Mongodin EF.

JCI Insight. 2018 Oct 4;3(19). pii: 121045. doi: 10.1172/jci.insight.121045.

5.

Salmonella Activation of STAT3 Signaling by SarA Effector Promotes Intracellular Replication and Production of IL-10.

Jaslow SL, Gibbs KD, Fricke WF, Wang L, Pittman KJ, Mammel MK, Thaden JT, Fowler VG Jr, Hammer GE, Elfenbein JR, Ko DC.

Cell Rep. 2018 Jun 19;23(12):3525-3536. doi: 10.1016/j.celrep.2018.05.072.

6.

High intake of orange juice and cola differently affects metabolic risk in healthy subjects.

Büsing F, Hägele FA, Nas A, Döbert LV, Fricker A, Dörner E, Podlesny D, Aschoff J, Pöhnl T, Schweiggert R, Fricke WF, Carle R, Bosy-Westphal A.

Clin Nutr. 2019 Apr;38(2):812-819. doi: 10.1016/j.clnu.2018.02.028. Epub 2018 Mar 3.

PMID:
29571566
7.

"Available upon request": not good enough for microbiome data!

Langille MGI, Ravel J, Fricke WF.

Microbiome. 2018 Jan 10;6(1):8. doi: 10.1186/s40168-017-0394-z. No abstract available.

8.

Corrigendum: Allelic variation contributes to bacterial host specificity.

Yue M, Han X, De Masi L, Zhu C, Ma X, Zhang J, Wu R, Schmieder R, Kaushik RS, Fraser GP, Zhao S, McDermott PF, Weill FX, Mainil JG, Arze C, Fricke WF, Edwards RA, Brisson D, Zhang NR, Rankin SC, Schifferli DM.

Nat Commun. 2017 Aug 8;8:15229. doi: 10.1038/ncomms15229.

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.

Checks and Balances-Microbiota Shifts in Immunosuppressed Mice.

Fricke WF, Bromberg JS.

Transplantation. 2017 Jan;101(1):26-27. doi: 10.1097/TP.0000000000001493. No abstract available.

PMID:
28005697
11.

Erratum to: Type 2 immunity-dependent reduction of segmented filamentous bacteria in mice infected with the helminthic parasite Nippostrongylus brasiliensis.

Fricke WF, Song Y, Wang AJ, Smith A, Grinchuk V, Pei C, Ma B, Lu N, Urban JF Jr, Shea-Donohue T, Zhao A.

Microbiome. 2015 Dec 21;3:77. doi: 10.1186/s40168-015-0142-1. No abstract available.

12.

Allelic variation contributes to bacterial host specificity.

Yue M, Han X, De Masi L, Zhu C, Ma X, Zhang J, Wu R, Schmieder R, Kaushik RS, Fraser GP, Zhao S, McDermott PF, Weill FX, Mainil JG, Arze C, Fricke WF, Edwards RA, Brisson D, Zhang NR, Rankin SC, Schifferli DM.

Nat Commun. 2015 Oct 30;6:8754. doi: 10.1038/ncomms9754. Erratum in: Nat Commun. 2017 Aug 08;8:15229.

13.

Type 2 immunity-dependent reduction of segmented filamentous bacteria in mice infected with the helminthic parasite Nippostrongylus brasiliensis.

Fricke WF, Song Y, Wang AJ, Smith A, Grinchuk V, Mongodin E, Pei C, Ma B, Lu N, Urban JF Jr, Shea-Donohue T, Zhao A.

Microbiome. 2015 Sep 17;3:40. doi: 10.1186/s40168-015-0103-8. Erratum in: Microbiome. 2015;3:77. Mongodin, Emmanuel [Added].

14.

Microbiota—implications for immunity and transplantation.

Bromberg JS, Fricke WF, Brinkman CC, Simon T, Mongodin EF.

Nat Rev Nephrol. 2015 Jun;11(6):342-53. doi: 10.1038/nrneph.2015.70. Epub 2015 May 12. Review.

PMID:
25963591
15.

Gastric LTi cells promote lymphoid follicle formation but are limited by IRAK-M and do not alter microbial growth.

Shiu J, Piazuelo MB, Ding H, Czinn SJ, Drakes ML, Banerjee A, Basappa N, Kobayashi KS, Fricke WF, Blanchard TG.

Mucosal Immunol. 2015 Sep;8(5):1047-59. doi: 10.1038/mi.2014.132. Epub 2015 Jan 21.

16.

Efficacy of fecal microbiota transplantation in 2 children with recurrent Clostridium difficile infection and its impact on their growth and gut microbiome.

Walia R, Garg S, Song Y, Girotra M, Cuffari C, Fricke WF, Dutta SK.

J Pediatr Gastroenterol Nutr. 2014 Nov;59(5):565-70. doi: 10.1097/MPG.0000000000000495.

PMID:
25023578
17.

Standardized metadata for human pathogen/vector genomic sequences.

Dugan VG, Emrich SJ, Giraldo-Calderón GI, Harb OS, Newman RM, Pickett BE, Schriml LM, Stockwell TB, Stoeckert CJ Jr, Sullivan DE, Singh I, Ward DV, Yao A, Zheng J, Barrett T, Birren B, Brinkac L, Bruno VM, Caler E, Chapman S, Collins FH, Cuomo CA, Di Francesco V, Durkin S, Eppinger M, Feldgarden M, Fraser C, Fricke WF, Giovanni M, Henn MR, Hine E, Hotopp JD, Karsch-Mizrachi I, Kissinger JC, Lee EM, Mathur P, Mongodin EF, Murphy CI, Myers G, Neafsey DE, Nelson KE, Nierman WC, Puzak J, Rasko D, Roos DS, Sadzewicz L, Silva JC, Sobral B, Squires RB, Stevens RL, Tallon L, Tettelin H, Wentworth D, White O, Will R, Wortman J, Zhang Y, Scheuermann RH.

PLoS One. 2014 Jun 17;9(6):e99979. doi: 10.1371/journal.pone.0099979. eCollection 2014.

18.

The more the merrier? Reduced fecal microbiota diversity in preterm infants treated with antibiotics.

Fricke WF.

J Pediatr. 2014 Jul;165(1):8-10. doi: 10.1016/j.jpeds.2014.03.022. Epub 2014 Apr 21. No abstract available.

PMID:
24750805
19.

A physicians' wish list for the clinical application of intestinal metagenomics.

Klymiuk I, Högenauer C, Halwachs B, Thallinger GG, Fricke WF, Steininger C.

PLoS Med. 2014 Apr 15;11(4):e1001627. doi: 10.1371/journal.pmed.1001627. eCollection 2014 Apr.

20.

CloVR-ITS: Automated internal transcribed spacer amplicon sequence analysis pipeline for the characterization of fungal microbiota.

White JR, Maddox C, White O, Angiuoli SV, Fricke WF.

Microbiome. 2013 Feb 4;1(1):6. doi: 10.1186/2049-2618-1-6.

21.

Colonization patterns of soil microbial communities in the Atacama Desert.

Crits-Christoph A, Robinson CK, Barnum T, Fricke WF, Davila AF, Jedynak B, McKay CP, Diruggiero J.

Microbiome. 2013 Nov 20;1(1):28. doi: 10.1186/2049-2618-1-28.

22.

Efficacy of combined jejunal and colonic fecal microbiota transplantation for recurrent Clostridium difficile Infection.

Dutta SK, Girotra M, Garg S, Dutta A, von Rosenvinge EC, Maddox C, Song Y, Bartlett JG, Vinayek R, Fricke WF.

Clin Gastroenterol Hepatol. 2014 Sep;12(9):1572-6. doi: 10.1016/j.cgh.2013.12.032. Epub 2014 Jan 16.

PMID:
24440222
23.

Human microbiota characterization in the course of renal transplantation.

Fricke WF, Maddox C, Song Y, Bromberg JS.

Am J Transplant. 2014 Feb;14(2):416-27. doi: 10.1111/ajt.12588. Epub 2013 Dec 26.

24.

Microbiota dynamics in patients treated with fecal microbiota transplantation for recurrent Clostridium difficile infection.

Song Y, Garg S, Girotra M, Maddox C, von Rosenvinge EC, Dutta A, Dutta S, Fricke WF.

PLoS One. 2013 Nov 26;8(11):e81330. doi: 10.1371/journal.pone.0081330. eCollection 2013. Erratum in: PLoS One. 2014;9(7):e104471.

25.

Bacterial genome sequencing in the clinic: bioinformatic challenges and solutions.

Fricke WF, Rasko DA.

Nat Rev Genet. 2014 Jan;15(1):49-55. doi: 10.1038/nrg3624. Epub 2013 Nov 26. Review.

PMID:
24281148
26.

Characterization of the bacterial community of the chemically defended Hawaiian sacoglossan Elysia rufescens.

Davis J, Fricke WF, Hamann MT, Esquenazi E, Dorrestein PC, Hill RT.

Appl Environ Microbiol. 2013 Nov;79(22):7073-81. doi: 10.1128/AEM.01568-13. Epub 2013 Sep 6.

27.

Genome Sequence of Salmonella enterica Serotype Tennessee Strain CDC07-0191, Implicated in the 2006-2007 Multistate Food-Borne Outbreak Linked to Peanut Butter in the United States.

Deng X, Salazar JK, Frezet S, Maccannell D, Ribot EM, Fields PI, Fricke WF, Zhang W.

Genome Announc. 2013 May 23;1(3). pii: e00260-13. doi: 10.1128/genomeA.00260-13.

28.

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.

29.

Immune status, antibiotic medication and pH are associated with changes in the stomach fluid microbiota.

von Rosenvinge EC, Song Y, White JR, Maddox C, Blanchard T, Fricke WF.

ISME J. 2013 Jul;7(7):1354-66. doi: 10.1038/ismej.2013.33. Epub 2013 Mar 7.

30.

Natural transformation facilitates transfer of transposons, integrons and gene cassettes between bacterial species.

Domingues S, Harms K, Fricke WF, Johnsen PJ, da Silva GJ, Nielsen KM.

PLoS Pathog. 2012;8(8):e1002837. doi: 10.1371/journal.ppat.1002837. Epub 2012 Aug 2.

31.

Whole-genome sequences of Bacillus subtilis and close relatives.

Earl AM, Eppinger M, Fricke WF, Rosovitz MJ, Rasko DA, Daugherty S, Losick R, Kolter R, Ravel J.

J Bacteriol. 2012 May;194(9):2378-9. doi: 10.1128/JB.05675-11.

32.

Proof of concept of microbiome-metabolome analysis and delayed gluten exposure on celiac disease autoimmunity in genetically at-risk infants.

Sellitto M, Bai G, Serena G, Fricke WF, Sturgeon C, Gajer P, White JR, Koenig SS, Sakamoto J, Boothe D, Gicquelais R, Kryszak D, Puppa E, Catassi C, Ravel J, Fasano A.

PLoS One. 2012;7(3):e33387. doi: 10.1371/journal.pone.0033387. Epub 2012 Mar 14.

33.

Origin and variation of tunicate secondary metabolites.

Schmidt EW, Donia MS, McIntosh JA, Fricke WF, Ravel J.

J Nat Prod. 2012 Feb 24;75(2):295-304. doi: 10.1021/np200665k. Epub 2012 Jan 10. Review.

34.

Complex microbiome underlying secondary and primary metabolism in the tunicate-Prochloron symbiosis.

Donia MS, Fricke WF, Partensky F, Cox J, Elshahawi SI, White JR, Phillippy AM, Schatz MC, Piel J, Haygood MG, Ravel J, Schmidt EW.

Proc Natl Acad Sci U S A. 2011 Dec 20;108(51):E1423-32. doi: 10.1073/pnas.1111712108. Epub 2011 Nov 28.

35.

Resources and costs for microbial sequence analysis evaluated using virtual machines and cloud computing.

Angiuoli SV, White JR, Matalka M, White O, Fricke WF.

PLoS One. 2011;6(10):e26624. doi: 10.1371/journal.pone.0026624. Epub 2011 Oct 19.

36.

CloVR: a virtual machine for automated and portable sequence analysis from the desktop using cloud computing.

Angiuoli SV, Matalka M, Gussman A, Galens K, Vangala M, Riley DR, Arze C, White JR, White O, Fricke WF.

BMC Bioinformatics. 2011 Aug 30;12:356. doi: 10.1186/1471-2105-12-356.

37.

Genome sequence of Ruegeria sp. strain KLH11, an N-acylhomoserine lactone-producing bacterium isolated from the marine sponge Mycale laxissima.

Zan J, Fricke WF, Fuqua C, Ravel J, Hill RT.

J Bacteriol. 2011 Sep;193(18):5011-2. doi: 10.1128/JB.05556-11. Epub 2011 Jul 8.

38.

Comparative genomics of 28 Salmonella enterica isolates: evidence for CRISPR-mediated adaptive sublineage evolution.

Fricke WF, Mammel MK, McDermott PF, Tartera C, White DG, Leclerc JE, Ravel J, Cebula TA.

J Bacteriol. 2011 Jul;193(14):3556-68. doi: 10.1128/JB.00297-11. Epub 2011 May 20.

39.

Variation in tropical reef symbiont metagenomes defined by secondary metabolism.

Donia MS, Fricke WF, Ravel J, Schmidt EW.

PLoS One. 2011 Mar 22;6(3):e17897. doi: 10.1371/journal.pone.0017897.

40.

Horizontal gene transfer of a ColV plasmid has resulted in a dominant avian clonal type of Salmonella enterica serovar Kentucky.

Johnson TJ, Thorsness JL, Anderson CP, Lynne AM, Foley SL, Han J, Fricke WF, McDermott PF, White DG, Khatri M, Stell AL, Flores C, Singer RS.

PLoS One. 2010 Dec 22;5(12):e15524. doi: 10.1371/journal.pone.0015524.

41.

No resistance plasmid in Yersinia pestis, North America.

Wagner DM, Runberg J, Vogler AJ, Lee J, Driebe E, Price LB, Engelthaler DM, Fricke WF, Ravel J, Keim P.

Emerg Infect Dis. 2010 May;16(5):885-7. doi: 10.3201/eid1605.090892. No abstract available.

42.

The role of genomics in the identification, prediction, and prevention of biological threats.

Fricke WF, Rasko DA, Ravel J.

PLoS Biol. 2009 Oct;7(10):e1000217. doi: 10.1371/journal.pbio.1000217. Epub 2009 Oct 26.

43.

Antimicrobial resistance-conferring plasmids with similarity to virulence plasmids from avian pathogenic Escherichia coli strains in Salmonella enterica serovar Kentucky isolates from poultry.

Fricke WF, McDermott PF, Mammel MK, Zhao S, Johnson TJ, Rasko DA, Fedorka-Cray PJ, Pedroso A, Whichard JM, Leclerc JE, White DG, Cebula TA, Ravel J.

Appl Environ Microbiol. 2009 Sep;75(18):5963-71. doi: 10.1128/AEM.00786-09. Epub 2009 Jul 31.

44.

Comparative genomics of the IncA/C multidrug resistance plasmid family.

Fricke WF, Welch TJ, McDermott PF, Mammel MK, LeClerc JE, White DG, Cebula TA, Ravel J.

J Bacteriol. 2009 Aug;191(15):4750-7. doi: 10.1128/JB.00189-09. Epub 2009 May 29.

45.

Genome sequence of Desulfobacterium autotrophicum HRM2, a marine sulfate reducer oxidizing organic carbon completely to carbon dioxide.

Strittmatter AW, Liesegang H, Rabus R, Decker I, Amann J, Andres S, Henne A, Fricke WF, Martinez-Arias R, Bartels D, Goesmann A, Krause L, Pühler A, Klenk HP, Richter M, Schüler M, Glöckner FO, Meyerdierks A, Gottschalk G, Amann R.

Environ Microbiol. 2009 May;11(5):1038-55. doi: 10.1111/j.1462-2920.2008.01825.x. Epub 2009 Jan 14.

46.

The genome organization of Ralstonia eutropha strain H16 and related species of the Burkholderiaceae.

Fricke WF, Kusian B, Bowien B.

J Mol Microbiol Biotechnol. 2009;16(1-2):124-35. doi: 10.1159/000142899. Epub 2008 Oct 29.

PMID:
18957867
47.

Insights into the environmental resistance gene pool from the genome sequence of the multidrug-resistant environmental isolate Escherichia coli SMS-3-5.

Fricke WF, Wright MS, Lindell AH, Harkins DM, Baker-Austin C, Ravel J, Stepanauskas R.

J Bacteriol. 2008 Oct;190(20):6779-94. doi: 10.1128/JB.00661-08. Epub 2008 Aug 15.

48.

The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates.

Rasko DA, Rosovitz MJ, Myers GS, Mongodin EF, Fricke WF, Gajer P, Crabtree J, Sebaihia M, Thomson NR, Chaudhuri R, Henderson IR, Sperandio V, Ravel J.

J Bacteriol. 2008 Oct;190(20):6881-93. doi: 10.1128/JB.00619-08. Epub 2008 Aug 1.

49.

Ralstonia eutropha H16 flagellation changes according to nutrient supply and state of poly(3-hydroxybutyrate) accumulation.

Raberg M, Reinecke F, Reichelt R, Malkus U, König S, Pötter M, Fricke WF, Pohlmann A, Voigt B, Hecker M, Friedrich B, Bowien B, Steinbüchel A.

Appl Environ Microbiol. 2008 Jul;74(14):4477-90. doi: 10.1128/AEM.00440-08. Epub 2008 May 23.

50.

The genome of Clostridium kluyveri, a strict anaerobe with unique metabolic features.

Seedorf H, Fricke WF, Veith B, Brüggemann H, Liesegang H, Strittmatter A, Miethke M, Buckel W, Hinderberger J, Li F, Hagemeier C, Thauer RK, Gottschalk G.

Proc Natl Acad Sci U S A. 2008 Feb 12;105(6):2128-33. doi: 10.1073/pnas.0711093105. Epub 2008 Jan 24.

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