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Items: 37

1.

Cystic fibrosis-associated Stenotrophomonas maltophilia strain-specific adaptations and responses to pH.

Gallagher T, Phan J, Oliver A, Chase AB, England WE, Wandro S, Hendrickson C, Riedel SF, Whiteson K.

J Bacteriol. 2019 Jan 14. pii: JB.00478-18. doi: 10.1128/JB.00478-18. [Epub ahead of print]

2.

Minimum Information about an Uncultivated Virus Genome (MIUViG).

Roux S, Adriaenssens EM, Dutilh BE, Koonin EV, Kropinski AM, Krupovic M, Kuhn JH, Lavigne R, Brister JR, Varsani A, Amid C, Aziz RK, Bordenstein SR, Bork P, Breitbart M, Cochrane GR, Daly RA, Desnues C, Duhaime MB, Emerson JB, Enault F, Fuhrman JA, Hingamp P, Hugenholtz P, Hurwitz BL, Ivanova NN, Labonté JM, Lee KB, Malmstrom RR, Martinez-Garcia M, Mizrachi IK, Ogata H, Páez-Espino D, Petit MA, Putonti C, Rattei T, Reyes A, Rodriguez-Valera F, Rosario K, Schriml L, Schulz F, Steward GF, Sullivan MB, Sunagawa S, Suttle CA, Temperton B, Tringe SG, Thurber RV, Webster NS, Whiteson KL, Wilhelm SW, Wommack KE, Woyke T, Wrighton KC, Yilmaz P, Yoshida T, Young MJ, Yutin N, Allen LZ, Kyrpides NC, Eloe-Fadrosh EA.

Nat Biotechnol. 2018 Dec 17. doi: 10.1038/nbt.4306. [Epub ahead of print]

PMID:
30556814
3.

The Phosphate Binder Ferric Citrate Alters the Gut Microbiome in Rats with Chronic Kidney Disease.

Lau WL, Vaziri ND, Nunes ACF, Comeau AM, Langille MGI, England W, Khazaeli M, Suematsu Y, Phan J, Whiteson K.

J Pharmacol Exp Ther. 2018 Dec;367(3):452-460. doi: 10.1124/jpet.118.251389. Epub 2018 Oct 4.

4.

Getting Our Fingers on the Pulse of Slow-Growing Bacteria in Hard-To-Reach Places.

Gallagher T, Phan J, Whiteson K.

J Bacteriol. 2018 Nov 26;200(24). pii: e00540-18. doi: 10.1128/JB.00540-18. Print 2018 Dec 15.

PMID:
30249702
5.

Gut microbial and metabolomic profiles after fecal microbiota transplantation in pediatric ulcerative colitis patients.

Nusbaum DJ, Sun F, Ren J, Zhu Z, Ramsy N, Pervolarakis N, Kunde S, England W, Gao B, Fiehn O, Michail S, Whiteson K.

FEMS Microbiol Ecol. 2018 Sep 1;94(9). doi: 10.1093/femsec/fiy133.

PMID:
30010747
6.

The Microbiome and Metabolome of Preterm Infant Stool Are Personalized and Not Driven by Health Outcomes, Including Necrotizing Enterocolitis and Late-Onset Sepsis.

Wandro S, Osborne S, Enriquez C, Bixby C, Arrieta A, Whiteson K.

mSphere. 2018 Jun 6;3(3). pii: e00104-18. doi: 10.1128/mSphere.00104-18. Print 2018 Jun 27.

7.

Tracking Polymicrobial Metabolism in Cystic Fibrosis Airways: Pseudomonas aeruginosa Metabolism and Physiology Are Influenced by Rothia mucilaginosa-Derived Metabolites.

Gao B, Gallagher T, Zhang Y, Elbadawi-Sidhu M, Lai Z, Fiehn O, Whiteson KL.

mSphere. 2018 Apr 25;3(2). pii: e00151-18. doi: 10.1128/mSphere.00151-18. Print 2018 Apr 25.

8.

Vive la Persistence: Engineering Human Microbiomes in the 21st Century.

Whiteson KL.

mSystems. 2018 Apr 10;3(2). pii: e00166-17. doi: 10.1128/mSystems.00166-17. eCollection 2018 Mar-Apr.

9.

Fermentation products in the cystic fibrosis airways induce aggregation and dormancy-associated expression profiles in a CF clinical isolate of Pseudomonas aeruginosa.

Phan J, Gallagher T, Oliver A, England WE, Whiteson K.

FEMS Microbiol Lett. 2018 May 1;365(10). doi: 10.1093/femsle/fny082.

10.

Longitudinal Monitoring of Biofilm Formation via Robust Surface-Enhanced Raman Scattering Quantification of Pseudomonas aeruginosa-Produced Metabolites.

Nguyen CQ, Thrift WJ, Bhattacharjee A, Ranjbar S, Gallagher T, Darvishzadeh-Varcheie M, Sanderson RN, Capolino F, Whiteson K, Baldi P, Hochbaum AI, Ragan R.

ACS Appl Mater Interfaces. 2018 Apr 18;10(15):12364-12373. doi: 10.1021/acsami.7b18592. Epub 2018 Apr 9.

PMID:
29589446
11.

Making It Last: Storage Time and Temperature Have Differential Impacts on Metabolite Profiles of Airway Samples from Cystic Fibrosis Patients.

Wandro S, Carmody L, Gallagher T, LiPuma JJ, Whiteson K.

mSystems. 2017 Nov 28;2(6). pii: e00100-17. doi: 10.1128/mSystems.00100-17. eCollection 2017 Nov-Dec.

12.

Editorial: Virus Discovery by Metagenomics: The (Im)possibilities.

Dutilh BE, Reyes A, Hall RJ, Whiteson KL.

Front Microbiol. 2017 Sep 8;8:1710. doi: 10.3389/fmicb.2017.01710. eCollection 2017. No abstract available.

13.

Ecological networking of cystic fibrosis lung infections.

Quinn RA, Whiteson K, Lim YW, Zhao J, Conrad D, LiPuma JJ, Rohwer F, Widder S.

NPJ Biofilms Microbiomes. 2016 Dec 2;2:4. doi: 10.1038/s41522-016-0002-1. eCollection 2016.

14.

Differential responses of human dendritic cells to metabolites from the oral/airway microbiome.

Whiteson K, Agrawal S, Agrawal A.

Clin Exp Immunol. 2017 Jun;188(3):371-379. doi: 10.1111/cei.12943. Epub 2017 Mar 21.

15.

Stable isotope profiles reveal active production of VOCs from human-associated microbes.

Phan J, Meinardi S, Barletta B, Blake DR, Whiteson K.

J Breath Res. 2017 Feb 6;11(1):017101. doi: 10.1088/1752-7163/aa5833.

PMID:
28070022
16.

Bacteria in the airways of patients with cystic fibrosis are genetically capable of producing VOCs in breath.

Bos LD, Meinardi S, Blake D, Whiteson K.

J Breath Res. 2016 Dec 17;10(4):047103.

PMID:
27991430
17.

Metabolomics of pulmonary exacerbations reveals the personalized nature of cystic fibrosis disease.

Quinn RA, Lim YW, Mak TD, Whiteson K, Furlan M, Conrad D, Rohwer F, Dorrestein P.

PeerJ. 2016 Aug 11;4:e2174. doi: 10.7717/peerj.2174. eCollection 2016.

18.

Microbial, host and xenobiotic diversity in the cystic fibrosis sputum metabolome.

Quinn RA, Phelan VV, Whiteson KL, Garg N, Bailey BA, Lim YW, Conrad DJ, Dorrestein PC, Rohwer FL.

ISME J. 2016 Jun;10(6):1483-98. doi: 10.1038/ismej.2015.207. Epub 2015 Dec 1.

19.

A Winogradsky-based culture system shows an association between microbial fermentation and cystic fibrosis exacerbation.

Quinn RA, Whiteson K, Lim YW, Salamon P, Bailey B, Mienardi S, Sanchez SE, Blake D, Conrad D, Rohwer F.

ISME J. 2015 Mar 17;9(4):1052. doi: 10.1038/ismej.2014.266. No abstract available.

20.

A Winogradsky-based culture system shows an association between microbial fermentation and cystic fibrosis exacerbation.

Quinn RA, Whiteson K, Lim YW, Salamon P, Bailey B, Mienardi S, Sanchez SE, Blake D, Conrad D, Rohwer F.

ISME J. 2015 Mar 17;9(4):1024-38. doi: 10.1038/ismej.2014.234. Erratum in: ISME J. 2015 Apr;9(4):1052.

21.

Noma affected children from Niger have distinct oral microbial communities based on high-throughput sequencing of 16S rRNA gene fragments.

Whiteson KL, Lazarevic V, Tangomo-Bento M, Girard M, Maughan H, Pittet D, Francois P, Schrenzel J; GESNOMA study group.

PLoS Negl Trop Dis. 2014 Dec 4;8(12):e3240. doi: 10.1371/journal.pntd.0003240. eCollection 2014 Dec.

22.

The upper respiratory tract as a microbial source for pulmonary infections in cystic fibrosis. Parallels from island biogeography.

Whiteson KL, Bailey B, Bergkessel M, Conrad D, Delhaes L, Felts B, Harris JK, Hunter R, Lim YW, Maughan H, Quinn R, Salamon P, Sullivan J, Wagner BD, Rainey PB.

Am J Respir Crit Care Med. 2014 Jun 1;189(11):1309-15. doi: 10.1164/rccm.201312-2129PP.

23.

Biogeochemical forces shape the composition and physiology of polymicrobial communities in the cystic fibrosis lung.

Quinn RA, Lim YW, Maughan H, Conrad D, Rohwer F, Whiteson KL.

MBio. 2014 Mar 18;5(2):e00956-13. doi: 10.1128/mBio.00956-13.

24.

A genomic perspective on a new bacterial genus and species from the Alcaligenaceae family, Basilea psittacipulmonis.

Whiteson KL, Hernandez D, Lazarevic V, Gaia N, Farinelli L, François P, Pilo P, Frey J, Schrenzel J.

BMC Genomics. 2014 Mar 1;15:169. doi: 10.1186/1471-2164-15-169.

25.

Breath gas metabolites and bacterial metagenomes from cystic fibrosis airways indicate active pH neutral 2,3-butanedione fermentation.

Whiteson KL, Meinardi S, Lim YW, Schmieder R, Maughan H, Quinn R, Blake DR, Conrad D, Rohwer F.

ISME J. 2014 Jun;8(6):1247-58. doi: 10.1038/ismej.2013.229. Epub 2014 Jan 9.

26.

Mechanistic model of Rothia mucilaginosa adaptation toward persistence in the CF lung, based on a genome reconstructed from metagenomic data.

Lim YW, Schmieder R, Haynes M, Furlan M, Matthews TD, Whiteson K, Poole SJ, Hayes CS, Low DA, Maughan H, Edwards R, Conrad D, Rohwer F.

PLoS One. 2013 May 30;8(5):e64285. doi: 10.1371/journal.pone.0064285. Print 2013.

27.

Bacteriophage adhering to mucus provide a non-host-derived immunity.

Barr JJ, Auro R, Furlan M, Whiteson KL, Erb ML, Pogliano J, Stotland A, Wolkowicz R, Cutting AS, Doran KS, Salamon P, Youle M, Rohwer F.

Proc Natl Acad Sci U S A. 2013 Jun 25;110(26):10771-6. doi: 10.1073/pnas.1305923110. Epub 2013 May 20.

28.

Effects of amoxicillin treatment on the salivary microbiota in children with acute otitis media.

Lazarevic V, Manzano S, Gaïa N, Girard M, Whiteson K, Hibbs J, François P, Gervaix A, Schrenzel J.

Clin Microbiol Infect. 2013 Aug;19(8):E335-42. doi: 10.1111/1469-0691.12213. Epub 2013 Apr 9.

29.

Going viral: next-generation sequencing applied to phage populations in the human gut.

Reyes A, Semenkovich NP, Whiteson K, Rohwer F, Gordon JI.

Nat Rev Microbiol. 2012 Sep;10(9):607-17. doi: 10.1038/nrmicro2853. Epub 2012 Aug 6. Review.

30.

Bacterial diversity in oral samples of children in niger with acute noma, acute necrotizing gingivitis, and healthy controls.

Bolivar I, Whiteson K, Stadelmann B, Baratti-Mayer D, Gizard Y, Mombelli A, Pittet D, Schrenzel J; Geneva Study Group on Noma (GESNOMA).

PLoS Negl Trop Dis. 2012;6(3):e1556. doi: 10.1371/journal.pntd.0001556. Epub 2012 Mar 6.

31.

Analysis of the salivary microbiome using culture-independent techniques.

Lazarevic V, Whiteson K, Gaïa N, Gizard Y, Hernandez D, Farinelli L, Osterås M, François P, Schrenzel J.

J Clin Bioinforma. 2012 Feb 2;2:4. doi: 10.1186/2043-9113-2-4.

32.

The CodY pleiotropic repressor controls virulence in gram-positive pathogens.

Stenz L, Francois P, Whiteson K, Wolz C, Linder P, Schrenzel J.

FEMS Immunol Med Microbiol. 2011 Jul;62(2):123-39. doi: 10.1111/j.1574-695X.2011.00812.x. Epub 2011 May 27. Review.

33.

Study of inter- and intra-individual variations in the salivary microbiota.

Lazarevic V, Whiteson K, Hernandez D, François P, Schrenzel J.

BMC Genomics. 2010 Sep 28;11:523. doi: 10.1186/1471-2164-11-523.

34.

Metagenomic study of the oral microbiota by Illumina high-throughput sequencing.

Lazarevic V, Whiteson K, Huse S, Hernandez D, Farinelli L, Osterås M, Schrenzel J, François P.

J Microbiol Methods. 2009 Dec;79(3):266-71. doi: 10.1016/j.mimet.2009.09.012. Epub 2009 Sep 29.

35.

Binding and catalytic contributions to site recognition by flp recombinase.

Whiteson KL, Rice PA.

J Biol Chem. 2008 Apr 25;283(17):11414-23. doi: 10.1074/jbc.M800106200. Epub 2008 Feb 13.

36.
37.

Mechanisms of site-specific recombination.

Grindley ND, Whiteson KL, Rice PA.

Annu Rev Biochem. 2006;75:567-605. Review.

PMID:
16756503

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