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Items: 43

1.

Microbial-derived products as potential new antimicrobials.

Seal BS, Drider D, Oakley BB, Brüssow H, Bikard D, Rich JO, Miller S, Devillard E, Kwan J, Bertin G, Reeves S, Swift SM, Raicek M, Gay CG.

Vet Res. 2018 Jul 31;49(1):66. doi: 10.1186/s13567-018-0563-5. Review.

2.

The cecal microbiome of commercial broiler chickens varies significantly by season.

Oakley BB, Vasconcelos EJR, Diniz PPVP, Calloway KN, Richardson E, Meinersmann RJ, Cox NA, Berrang ME.

Poult Sci. 2018 Oct 1;97(10):3635-3644. doi: 10.3382/ps/pey214.

PMID:
30016503
3.

Characterization of two glycosyl hydrolases, putative prophage endolysins, that target Clostridium perfringens.

Swift SM, Waters JJ, Rowley DT, Oakley BB, Donovan DM.

FEMS Microbiol Lett. 2018 Aug 1;365(16). pii: fny179. doi: 10.1093/femsle/fny179.

PMID:
30010898
4.

Assessing Cat Flea Microbiomes in Northern and Southern California by 16S rRNA Next-Generation Sequencing.

Vasconcelos EJR, Billeter SA, Jett LA, Meinersmann RJ, Barr MC, Diniz PPVP, Oakley BB.

Vector Borne Zoonotic Dis. 2018 Sep;18(9):491-499. doi: 10.1089/vbz.2018.2282. Epub 2018 Jun 12.

PMID:
29893631
5.

Environmental reservoirs of pathogenic mycobacteria across the Ethiopian biogeographical landscape.

King HC, Khera-Butler T, James P, Oakley BB, Erenso G, Aseffa A, Knight R, Wellington EM, Courtenay O.

PLoS One. 2017 Mar 23;12(3):e0173811. doi: 10.1371/journal.pone.0173811. eCollection 2017.

6.

Variation in Campylobacter Multilocus Sequence Typing Subtypes from Chickens as Detected on Three Plating Media.

Berrang ME, Ladely SR, Meinersmann RJ, Line JE, Oakley BB, Cox NA.

J Food Prot. 2016 Nov;79(11):1986-1989. doi: 10.4315/0362-028X.JFP-16-188.

PMID:
28221919
7.
8.

Genome Sequence of a Urease-Positive Campylobacter lari Strain.

Meinersmann RJ, Bono JL, Lindsey RL, Genzlinger LL, Loparev VN, Oakley BB.

Genome Announc. 2015 Oct 15;3(5). pii: e01191-15. doi: 10.1128/genomeA.01191-15.

9.

A Thermophilic Phage Endolysin Fusion to a Clostridium perfringens-Specific Cell Wall Binding Domain Creates an Anti-Clostridium Antimicrobial with Improved Thermostability.

Swift SM, Seal BS, Garrish JK, Oakley BB, Hiett K, Yeh HY, Woolsey R, Schegg KM, Line JE, Donovan DM.

Viruses. 2015 Jun 12;7(6):3019-34. doi: 10.3390/v7062758.

10.

Comparative analysis of the intestinal bacterial and RNA viral communities from sentinel birds placed on selected broiler chicken farms.

Day JM, Oakley BB, Seal BS, Zsak L.

PLoS One. 2015 Jan 30;10(1):e0117210. doi: 10.1371/journal.pone.0117210. eCollection 2015.

11.

Successional changes in the chicken cecal microbiome during 42 days of growth are independent of organic acid feed additives.

Oakley BB, Buhr RJ, Ritz CW, Kiepper BH, Berrang ME, Seal BS, Cox NA.

BMC Vet Res. 2014 Nov 27;10:282. doi: 10.1186/s12917-014-0282-8.

12.

The chicken gastrointestinal microbiome.

Oakley BB, Lillehoj HS, Kogut MH, Kim WK, Maurer JJ, Pedroso A, Lee MD, Collett SR, Johnson TJ, Cox NA.

FEMS Microbiol Lett. 2014 Nov;360(2):100-12. doi: 10.1111/1574-6968.12608. Epub 2014 Oct 13. Review.

13.

Sampling by sponge wipe or skin excision for recovery of inoculated Salmonella and Campylobacter from defeathered broiler carcasses.

Berrang ME, Cox NA, Oakley BB.

J Food Prot. 2014 May;77(5):824-7. doi: 10.4315/0362-028X.JFP-13-403.

PMID:
24780339
14.

Metabolic flexibility as a major predictor of spatial distribution in microbial communities.

Carbonero F, Oakley BB, Purdy KJ.

PLoS One. 2014 Jan 21;9(1):e85105. doi: 10.1371/journal.pone.0085105. eCollection 2014.

15.

Can probiotics improve the environmental microbiome and resistome of commercial poultry production?

Pedroso AA, Hurley-Bacon AL, Zedek AS, Kwan TW, Jordan AP, Avellaneda G, Hofacre CL, Oakley BB, Collett SR, Maurer JJ, Lee MD.

Int J Environ Res Public Health. 2013 Sep 25;10(10):4534-59. doi: 10.3390/ijerph10104534.

16.

Prospecting environmental mycobacteria: combined molecular approaches reveal unprecedented diversity.

Pontiroli A, Khera TT, Oakley BB, Mason S, Dowd SE, Travis ER, Erenso G, Aseffa A, Courtenay O, Wellington EM.

PLoS One. 2013 Jul 18;8(7):e68648. doi: 10.1371/journal.pone.0068648. Print 2013.

17.

Proposed model for the high rate of rearrangement and rapid migration observed in some IncA/C plasmid lineages.

Meinersmann RJ, Lindsey RL, Bono JL, Smith TP, Oakley BB.

Appl Environ Microbiol. 2013 Aug;79(16):4806-14. doi: 10.1128/AEM.01259-13. Epub 2013 Jun 7.

18.

The poultry-associated microbiome: network analysis and farm-to-fork characterizations.

Oakley BB, Morales CA, Line J, Berrang ME, Meinersmann RJ, Tillman GE, Wise MG, Siragusa GR, Hiett KL, Seal BS.

PLoS One. 2013;8(2):e57190. doi: 10.1371/journal.pone.0057190. Epub 2013 Feb 27.

19.

Construction, expression, purification and antigenicity of recombinant Campylobacter jejuni flagellar proteins.

Yeh HY, Hiett KL, Line JE, Oakley BB, Seal BS.

Microbiol Res. 2013 May 6;168(4):192-8. doi: 10.1016/j.micres.2012.11.010. Epub 2013 Jan 9.

21.

Isolation of Shiga toxin-producing Escherichia coli serogroups O26, O45, O103, O111, O121, and O145 from ground beef using modified rainbow agar and post-immunomagnetic separation acid treatment.

Tillman GE, Wasilenko JL, Simmons M, Lauze TA, Minicozzi J, Oakley BB, Narang N, Fratamico P, Cray AC Jr.

J Food Prot. 2012 Sep;75(9):1548-54. doi: 10.4315/0362-028X.JFP-12-110.

PMID:
22947460
22.

Molecular characterization of podoviral bacteriophages virulent for Clostridium perfringens and their comparison with members of the Picovirinae.

Volozhantsev NV, Oakley BB, Morales CA, Verevkin VV, Bannov VA, Krasilnikova VM, Popova AV, Zhilenkov EL, Garrish JK, Schegg KM, Woolsey R, Quilici DR, Line JE, Hiett KL, Siragusa GR, Svetoch EA, Seal BS.

PLoS One. 2012;7(5):e38283. doi: 10.1371/journal.pone.0038283. Epub 2012 May 29.

23.

Recombinant Expression of a Putative Amidase Cloned from the Genome of Listeria monocytogenes that Lyses the Bacterium and its Monolayer in Conjunction with a Protease.

Simmons M, Morales CA, Oakley BB, Seal BS.

Probiotics Antimicrob Proteins. 2012 Mar;4(1):1-10. doi: 10.1007/s12602-011-9084-5.

PMID:
26781731
24.

Free-living and aggregate-associated Planctomycetes in the Black Sea.

Fuchsman CA, Staley JT, Oakley BB, Kirkpatrick JB, Murray JW.

FEMS Microbiol Ecol. 2012 May;80(2):402-16. doi: 10.1111/j.1574-6941.2012.01306.x. Epub 2012 Feb 7.

25.

Pyrosequencing-based validation of a simple cell-suspension polymerase chain reaction assay for Campylobacter with application of high-processivity polymerase and novel internal amplification controls for rapid and specific detection.

Oakley BB, Line JE, Berrang ME, Johnson JM, Buhr RJ, Cox NA, Hiett KL, Seal BS.

Diagn Microbiol Infect Dis. 2012 Feb;72(2):131-8. doi: 10.1016/j.diagmicrobio.2011.11.001.

PMID:
22248734
26.

Complete genome sequence of the podoviral bacteriophage ΦCP24R, which is virulent for Clostridium perfringens.

Morales CA, Oakley BB, Garrish JK, Siragusa GR, Ard MB, Seal BS.

Arch Virol. 2012 Apr;157(4):769-72. doi: 10.1007/s00705-011-1218-2. Epub 2012 Jan 5.

PMID:
22218967
27.

Genotypic distribution of a specialist model microorganism, Methanosaeta, along an estuarine gradient: does metabolic restriction limit niche differentiation potential?

Carbonero F, Oakley BB, Hawkins RJ, Purdy KJ.

Microb Ecol. 2012 May;63(4):856-64. doi: 10.1007/s00248-011-9993-6. Epub 2011 Dec 20.

PMID:
22183047
28.

Contrasting patterns of niche partitioning between two anaerobic terminal oxidizers of organic matter.

Oakley BB, Carbonero F, Dowd SE, Hawkins RJ, Purdy KJ.

ISME J. 2012 May;6(5):905-14. doi: 10.1038/ismej.2011.165. Epub 2011 Nov 24.

29.

Application of high-throughput sequencing to measure the performance of commonly used selective cultivation methods for the foodborne pathogen Campylobacter.

Oakley BB, Morales CA, Line JE, Seal BS, Hiett KL.

FEMS Microbiol Ecol. 2012 Feb;79(2):327-36. doi: 10.1111/j.1574-6941.2011.01219.x. Epub 2011 Nov 1.

31.

The complete genome sequence and genetic analysis of ΦCA82 a novel uncultured microphage from the turkey gastrointestinal system.

Zsak L, Day JM, Oakley BB, Seal BS.

Virol J. 2011 Jun 29;8:331. doi: 10.1186/1743-422X-8-331.

32.

Comparative genomics of four closely related Clostridium perfringens bacteriophages reveals variable evolution among core genes with therapeutic potential.

Oakley BB, Talundzic E, Morales CA, Hiett KL, Siragusa GR, Volozhantsev NV, Seal BS.

BMC Genomics. 2011 Jun 1;12(1):282. doi: 10.1186/1471-2164-12-282.

33.

Ovine pedomics: the first study of the ovine foot 16S rRNA-based microbiome.

Calvo-Bado LA, Oakley BB, Dowd SE, Green LE, Medley GF, Ul-Hassan A, Bateman V, Gaze W, Witcomb L, Grogono-Thomas R, Kaler J, Russell CL, Wellington EM.

ISME J. 2011 Sep;5(9):1426-37. doi: 10.1038/ismej.2011.25. Epub 2011 Mar 24.

34.

ThermoPhyl: a software tool for selecting phylogenetically optimized conventional and quantitative-PCR taxon-targeted assays for use with complex samples.

Oakley BB, Dowd SE, Purdy KJ.

FEMS Microbiol Ecol. 2011 Jul;77(1):17-27. doi: 10.1111/j.1574-6941.2011.01079.x. Epub 2011 Mar 21.

35.

The genome sequence and proteome of bacteriophage ΦCPV1 virulent for Clostridium perfringens.

Volozhantsev NV, Verevkin VV, Bannov VA, Krasilnikova VM, Myakinina VP, Zhilenkov EL, Svetoch EA, Stern NJ, Oakley BB, Seal BS.

Virus Res. 2011 Feb;155(2):433-9. doi: 10.1016/j.virusres.2010.11.012. Epub 2010 Dec 7.

PMID:
21144870
36.

Evolutionary divergence and biogeography of sympatric niche-differentiated bacterial populations.

Oakley BB, Carbonero F, van der Gast CJ, Hawkins RJ, Purdy KJ.

ISME J. 2010 Apr;4(4):488-97. doi: 10.1038/ismej.2009.146. Epub 2010 Jan 7.

PMID:
20054357
37.
38.

Improving the isolation of anaerobes on solid media: the example of the fastidious Methanosaeta.

Carbonero F, Oakley BB, Purdy KJ.

J Microbiol Methods. 2010 Feb;80(2):203-5. doi: 10.1016/j.mimet.2009.11.013. Epub 2009 Dec 4. Erratum in: J Microbiol Methods. 2010 Jul;82(1):112.

PMID:
19969029
39.

Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities.

Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF.

Appl Environ Microbiol. 2009 Dec;75(23):7537-41. doi: 10.1128/AEM.01541-09. Epub 2009 Oct 2.

40.

Diversity of human vaginal bacterial communities and associations with clinically defined bacterial vaginosis.

Oakley BB, Fiedler TL, Marrazzo JM, Fredricks DN.

Appl Environ Microbiol. 2008 Aug;74(15):4898-909. doi: 10.1128/AEM.02884-07. Epub 2008 May 16.

41.

Targeted PCR for detection of vaginal bacteria associated with bacterial vaginosis.

Fredricks DN, Fiedler TL, Thomas KK, Oakley BB, Marrazzo JM.

J Clin Microbiol. 2007 Oct;45(10):3270-6. Epub 2007 Aug 8.

42.

Analysis of nitrite reductase (nirK and nirS) genes and cultivation reveal depauperate community of denitrifying bacteria in the Black Sea suboxic zone.

Oakley BB, Francis CA, Roberts KJ, Fuchsman CA, Srinivasan S, Staley JT.

Environ Microbiol. 2007 Jan;9(1):118-30.

PMID:
17227417
43.

Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean.

Francis CA, Roberts KJ, Beman JM, Santoro AE, Oakley BB.

Proc Natl Acad Sci U S A. 2005 Oct 11;102(41):14683-8. Epub 2005 Sep 26.

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