Research and Testing microbial Diversity with pyrosequencing

Microbial Diversity Studies: Our specialty is bacterial and fungal / yeast diversity evaluation using the bTEFAP and fTEFAP approach..

We offer competative rates and low cost collaborative rates for researchers moving rapidly toward publications.

All pricing is based upon quotes!! Here we will provide general estimates but actual cost may vary.

LOOK BELOW FOR SOME OF THE WORK WE HAVE SPONSORED AND COLLABORATED ON WITH AMAZING SCIENTISTS AROUND THE WORLD

Tag-encoded FLX amplicon pyrosequencing for the elucidation of microbial and functional gene diversity in any environment.

Sun Y, Wolcott RD, Dowd SE.

Methods Mol Biol. 2011;733:129-41.

PMID:: 21431767

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 Mar 24. [Epub ahead of print]

PMID:: 21430786

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 Mar 2. doi: 10.1111/j.1574-6941.2011.01079.x. [Epub ahead of print]

PMID:: 21366628

Black Box Chimera Check (B2C2): a Windows-Based Software for Batch Depletion of Chimeras from Bacterial 16S rRNA Gene Datasets.

Gontcharova V, Youn E, Wolcott RD, Hollister EB, Gentry TJ, Dowd SE.

Open Microbiol J. 2010 Aug 11;4:47-52.

PMID:: 21339894; [PubMed - in process]

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Maternal methyl-donor supplementation induces prolonged murine offspring colitis susceptibility in association with mucosal epigenetic and microbiomic changes.

Schaible TD, Harris RA, Dowd SE, Smith CW, Kellermayer R.

Hum Mol Genet. 2011 May 1;20(9):1687-96. Epub 2011 Feb 4.

PMID:: 21296867

Genome-wide polymorphism and comparative analyses in the white-tailed deer (Odocoileus virginianus): a model for conservation genomics.

Seabury CM, Bhattarai EK, Taylor JF, Viswanathan GG, Cooper SM, Davis DS, Dowd SE, Lockwood ML, Seabury PM.

PLoS One. 2011 Jan 19;6(1):e15811.

PMID:: 21283515; [PubMed - in process]

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Massive parallel 16S rRNA gene pyrosequencing reveals highly diverse fecal bacterial and fungal communities in healthy dogs and cats.

Handl S, Dowd SE, Garcia-Mazcorro JF, Steiner JM, Suchodolski JS.

FEMS Microbiol Ecol. 2011 May;76(2):301-10. doi: 10.1111/j.1574-6941.2011.01058.x. Epub 2011 Feb 14.

PMID:: 21261668

Bacterial Diversity in Solenopsis invicta and Solenopsis geminata Ant Colonies Characterized by 16S amplicon 454 Pyrosequencing.

Ishak HD, Plowes R, Sen R, Kellner K, Meyer E, Estrada DA, Dowd SE, Mueller UG.

Microb Ecol. 2011 Jan 18. [Epub ahead of print]

PMID:: 21243351

Colonic mucosal DNA methylation, immune response, and microbiome patterns in Toll-like receptor 2-knockout mice.

Kellermayer R, Dowd SE, Harris RA, Balasa A, Schaible TD, Wolcott RD, Tatevian N, Szigeti R, Li Z, Versalovic J, Smith CW.

FASEB J. 2011 May;25(5):1449-60. Epub 2011 Jan 12.

PMID:: 21228220; [PubMed - in process]

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10.

Assessment of bacterial diversity in the cattle tick Rhipicephalus (Boophilus) microplus through tag-encoded pyrosequencing.

Andreotti R, Pérez de León AA, Dowd SE, Guerrero FD, Bendele KG, Scoles GA.

BMC Microbiol. 2011 Jan 6;11(1):6.

PMID:: 21211038; [PubMed - in process]

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11.

Culture-independent characterization of bacteria and fungi in a poultry bioaerosol using pyrosequencing: a new approach.

Nonnenmann MW, Bextine B, Dowd SE, Gilmore K, Levin JL.

J Occup Environ Hyg. 2010 Dec;7(12):693-9.

PMID:: 21058154

12.

Exposure to a social stressor alters the structure of the intestinal microbiota: implications for stressor-induced immunomodulation.

Bailey MT, Dowd SE, Galley JD, Hufnagle AR, Allen RG, Lyte M.

Brain Behav Immun. 2011 Mar;25(3):397-407. Epub 2010 Oct 30.

PMID:: 21040780

13.

Phylogenetic and gene-centric metagenomics of the canine intestinal microbiome reveals similarities with humans and mice.

Swanson KS, Dowd SE, Suchodolski JS, Middelbos IS, Vester BM, Barry KA, Nelson KE, Torralba M, Henrissat B, Coutinho PM, Cann IK, White BA, Fahey GC Jr.

ISME J. 2011 Apr;5(4):639-49. Epub 2010 Oct 21.

PMID:: 20962874; [PubMed - in process]

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14.

Evaluation of in vitro gas production and rumen bacterial populations fermenting corn milling (co)products.

Williams WL, Tedeschi LO, Kononoff PJ, Callaway TR, Dowd SE, Karges K, Gibson ML.

J Dairy Sci. 2010 Oct;93(10):4735-43.

PMID:: 20855008

15.

Evaluation of the bacterial diversity of pressure ulcers using bTEFAP pyrosequencing.

Smith DM, Snow DE, Rees E, Zischkau AM, Hanson JD, Wolcott RD, Sun Y, White J, Kumar S, Dowd SE.

BMC Med Genomics. 2010 Sep 21;3:41.

PMID:: 20854691; [PubMed - indexed for MEDLINE]

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16.

Evaluation of bacterial diversity in the rumen and feces of cattle fed different levels of dried distillers grains plus solubles using bacterial tag-encoded FLX amplicon pyrosequencing.

Callaway TR, Dowd SE, Edrington TS, Anderson RC, Krueger N, Bauer N, Kononoff PJ, Nisbet DJ.

J Anim Sci. 2010 Dec;88(12):3977-83. Epub 2010 Aug 20.

PMID:: 20729286

17.

Pyrosequencing study of fecal microflora of autistic and control children.

Finegold SM, Dowd SE, Gontcharova V, Liu C, Henley KE, Wolcott RD, Youn E, Summanen PH, Granpeesheh D, Dixon D, Liu M, Molitoris DR, Green JA 3rd.

Anaerobe. 2010 Aug;16(4):444-53. Epub 2010 Jul 9.

PMID:: 20603222

18.

Analysis of expressed sequence tags from a significant livestock pest, the stable fly (Stomoxys calcitrans), identifies transcripts with a putative role in chemosensation and sex determination.

Olafson PU, Lohmeyer KH, Dowd SE.

Arch Insect Biochem Physiol. 2010 Jul;74(3):179-204.

PMID:: 20572127

19.

A comparison of bacterial composition in diabetic ulcers and contralateral intact skin.

Gontcharova V, Youn E, Sun Y, Wolcott RD, Dowd SE.

Open Microbiol J. 2010 Mar 17;4:8-19.

PMID:: 20461221; [PubMed - in process]

20.

Molecular characterization of the polymicrobial flora in chronic rhinosinusitis.

Stephenson MF, Mfuna L, Dowd SE, Wolcott RD, Barbeau J, Poisson M, James G, Desrosiers M.

J Otolaryngol Head Neck Surg. 2010 Apr;39(2):182-7.

PMID:: 20211106

21.

Stressor exposure disrupts commensal microbial populations in the intestines and leads to increased colonization by Citrobacter rodentium.

Bailey MT, Dowd SE, Parry NM, Galley JD, Schauer DB, Lyte M.

Infect Immun. 2010 Apr;78(4):1509-19. Epub 2010 Feb 9.

PMID:: 20145094

22.

Photoperiod modulates gut bacteria composition in male Siberian hamsters (Phodopus sungorus).

Bailey MT, Walton JC, Dowd SE, Weil ZM, Nelson RJ.

Brain Behav Immun. 2010 May;24(4):577-84. Epub 2010 Jan 4.

PMID:: 20045457

23.

Rumen bacterial diversity dynamics associated with changing from bermudagrass hay to grazed winter wheat diets.

Pitta DW, Pinchak E, Dowd SE, Osterstock J, Gontcharova V, Youn E, Dorton K, Yoon I, Min BR, Fulford JD, Wickersham TA, Malinowski DP.

Microb Ecol. 2010 Apr;59(3):511-22.

PMID:: 20037795

24.

Bacterial diversity in surgical site infections: not just aerobic cocci any more.

Wolcott RD, Gontcharova V, Sun Y, Zischakau A, Dowd SE.

J Wound Care. 2009 Aug;18(8):317-23.

PMID:: 19862869

25.

Evaluation of the bacterial diversity among and within individual venous leg ulcers using bacterial tag-encoded FLX and titanium amplicon pyrosequencing and metagenomic approaches.

Wolcott RD, Gontcharova V, Sun Y, Dowd SE.

BMC Microbiol. 2009 Oct 27;9:226.

PMID:: 19860898

26.

Generalized antifungal activity and 454-screening of Pseudonocardia and Amycolatopsis bacteria in nests of fungus-growing ants.

Sen R, Ishak HD, Estrada D, Dowd SE, Hong E, Mueller UG.

Proc Natl Acad Sci U S A. 2009 Oct 20;106(42):17805-10. Epub 2009 Sep 22.

PMID:: 19805175

27.

The effect of the macrolide antibiotic tylosin on microbial diversity in the canine small intestine as demonstrated by massive parallel 16S rRNA gene sequencing.

Suchodolski JS, Dowd SE, Westermarck E, Steiner JM, Wolcott RD, Spillmann T, Harmoinen JA.

BMC Microbiol. 2009 Oct 2;9:210.

PMID:: 19799792

28.

A database of expressed genes from Cochliomyia hominivorax (Diptera: Calliphoridae).

Guerrero FD, Dowd SE, Djikeng A, Wiley G, Macmil S, Saldivar L, Najar F, Roe BA.

J Med Entomol. 2009 Sep;46(5):1109-16.

PMID:: 19769042

29.

Microarray analysis of female- and larval-specific gene expression in the horn fly (Diptera: Muscidae).

Guerrero FD, Dowd SE, Sun Y, Saldivar L, Wiley GB, Macmil SL, Najar F, Roe BA, Foil LD.

J Med Entomol. 2009 Mar;46(2):257-70.

PMID:: 19351076

30.

Identification of yeast in chronic wounds using new pathogen-detection technologies.

Leake JL, Dowd SE, Wolcott RD, Zischkau AM.

J Wound Care. 2009 Mar;18(3):103-4, 106, 108.

PMID:: 19247230

31.

Evaluation of the bacterial diversity in cecal contents of laying hens fed various molting diets by using bacterial tag-encoded FLX amplicon pyrosequencing.

Callaway TR, Dowd SE, Wolcott RD, Sun Y, McReynolds JL, Edrington TS, Byrd JA, Anderson RC, Krueger N, Nisbet DJ.

Poult Sci. 2009 Feb;88(2):298-302.

PMID:: 19151343

32.

Memory and learning behavior in mice is temporally associated with diet-induced alterations in gut bacteria.

Li W, Dowd SE, Scurlock B, Acosta-Martinez V, Lyte M.

Physiol Behav. 2009 Mar 23;96(4-5):557-67. Epub 2008 Dec 24.

PMID:: 19135464

33.

Polymicrobial nature of chronic diabetic foot ulcer biofilm infections determined using bacterial tag encoded FLX amplicon pyrosequencing (bTEFAP).

Dowd SE, Wolcott RD, Sun Y, McKeehan T, Smith E, Rhoads D.

PLoS One. 2008 Oct 3;3(10):e3326.

PMID:: 18833331

34.

Bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP) for microbiome studies: bacterial diversity in the ileum of newly weaned Salmonella-infected pigs.

Dowd SE, Sun Y, Wolcott RD, Domingo A, Carroll JA.

Foodborne Pathog Dis. 2008 Aug;5(4):459-72.

PMID:: 18713063

35.

Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP).

Dowd SE, Callaway TR, Wolcott RD, Sun Y, McKeehan T, Hagevoort RG, Edrington TS.

BMC Microbiol. 2008 Jul 24;8:125.

PMID:: 18652685

36.

Survey of bacterial diversity in chronic wounds using pyrosequencing, DGGE, and full ribosome shotgun sequencing.

Dowd SE, Sun Y, Secor PR, Rhoads DD, Wolcott BM, James GA, Wolcott RD.

BMC Microbiol. 2008 Mar 6;8:43.

PMID:: 18325110

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