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Comparative metagenomic analysis of microbial taxonomic and functional variations in untreated surface and reclaimed waters used in irrigation applications.

Chopyk J, Nasko DJ, Allard S, Bui A, Treangen T, Pop M, Mongodin EF, Sapkota AR.

Water Res. 2019 Oct 31;169:115250. doi: 10.1016/j.watres.2019.115250. [Epub ahead of print]


The Bacterial Communities of Little Cigars and Cigarillos Are Dynamic Over Time and Varying Storage Conditions.

Smyth EM, Chattopadhyay S, Babik K, Reid M, Chopyk J, Malayil L, Kulkarni P, Hittle LE, Clark PI, Sapkota AR, Mongodin EF.

Front Microbiol. 2019 Oct 25;10:2371. doi: 10.3389/fmicb.2019.02371. eCollection 2019.


Current State of and Future Opportunities for Prediction in Microbiome Research: Report from the Mid-Atlantic Microbiome Meet-up in Baltimore on 9 January 2019.

Sakowski E, Uritskiy G, Cooper R, Gomes M, McLaren MR, Meisel JS, Mickol RL, Mintz CD, Mongodin EF, Pop M, Rahman MA, Sanchez A, Timp W, Vela JD, Wolz CM, Zackular JP, Chopyk J, Commichaux S, Davis M, Dluzen D, Ganesan SM, Haruna M, Nasko D, Regan MJ, Sarria S, Shah N, Stacy B, Taylor D, DiRuggiero J, Preheim SP.

mSystems. 2019 Oct 8;4(5). pii: e00392-19. doi: 10.1128/mSystems.00392-19.


Characterization and Analysis of the Skin Microbiota in Rosacea: A Case-Control Study.

Rainer BM, Thompson KG, Antonescu C, Florea L, Mongodin EF, Bui J, Fischer AH, Pasieka HB, Garza LA, Kang S, Chien AL.

Am J Clin Dermatol. 2019 Sep 9. doi: 10.1007/s40257-019-00471-5. [Epub ahead of print]


It's complicated!

Husson J, Mongodin EF, Bromberg JS.

Am J Transplant. 2019 Oct;19(10):2673-2674. doi: 10.1111/ajt.15563. Epub 2019 Sep 9. No abstract available.


Unique and specific Proteobacteria diversity in urinary microbiota of tolerant kidney transplanted recipients.

Colas L, Mongodin EF, Montassier E, Chesneau M, Guerif P, Hittle L, Giral M, Bromberg JS, Brouard S; DIVAT Consortium.

Am J Transplant. 2019 Aug 2. doi: 10.1111/ajt.15549. [Epub ahead of print]


De-bugging the system: could antibiotics improve liver transplant outcomes?

Bromberg JS, Scalea JR, Mongodin EF.

J Clin Invest. 2019 Jul 22;129(8):3054-3057. doi: 10.1172/JCI130314. eCollection 2019 Jul 22.


The bacterial communities of the small intestine and stool in children with short bowel syndrome.

Zeichner SL, Mongodin EF, Hittle L, Huang SH, Torres C.

PLoS One. 2019 May 16;14(5):e0215351. doi: 10.1371/journal.pone.0215351. eCollection 2019.


The Association Between the Developing Nasal Microbiota of Hospitalized Neonates and Staphylococcus aureus Colonization.

Khamash DF, Mongodin EF, White JR, Voskertchian A, Hittle L, Colantuoni E, Milstone AM.

Open Forum Infect Dis. 2019 Mar 21;6(4):ofz062. doi: 10.1093/ofid/ofz062. eCollection 2019 Apr.


The respiratory tract microbiome and its relationship to lung cancer and environmental exposures found in rural china.

Hosgood HD 3rd, Mongodin EF, Wan Y, Hua X, Rothman N, Hu W, Vermeulen R, Seow WJ, Rohan T, Xu J, Li J, He J, Huang Y, Yang K, Wu G, Wei F, Shi J, Sapkota AR, Lan Q.

Environ Mol Mutagen. 2019 Aug;60(7):617-623. doi: 10.1002/em.22291. Epub 2019 May 8.


Quenching by sodium thiosulfate does not influence 16S rRNA gene sequencing profiles of reclaimed water from three sites in the Mid-Atlantic, United States.

Allard SM, Solaiman S, Callahan MT, Bui A, Craddock H, Haymaker J, Foust D, Duncan R, Smyth E, Mongodin EF, Hashem F, May E, Micallef SA, Sapkota AR.

Environ Res. 2019 May;172:296-300. doi: 10.1016/j.envres.2019.02.022. Epub 2019 Feb 15.


Creek to Table: Tracking fecal indicator bacteria, bacterial pathogens, and total bacterial communities from irrigation water to kale and radish crops.

Allard SM, Callahan MT, Bui A, Ferelli AMC, Chopyk J, Chattopadhyay S, Mongodin EF, Micallef SA, Sapkota AR.

Sci Total Environ. 2019 May 20;666:461-471. doi: 10.1016/j.scitotenv.2019.02.179. Epub 2019 Feb 12.


Little cigars and cigarillos harbor diverse bacterial communities that differ between the tobacco and the wrapper.

Chattopadhyay S, Smyth EM, Kulkarni P, Babik KR, Reid M, Hittle LE, Clark PI, Mongodin EF, Sapkota AR.

PLoS One. 2019 Feb 22;14(2):e0211705. doi: 10.1371/journal.pone.0211705. eCollection 2019.


Association of Systemic Antibiotic Treatment of Acne With Skin Microbiota Characteristics.

Chien AL, Tsai J, Leung S, Mongodin EF, Nelson AM, Kang S, Garza LA.

JAMA Dermatol. 2019 Apr 1;155(4):425-434. doi: 10.1001/jamadermatol.2018.5221.


Erratum: Author Correction: High-resolution bacterial 16S rRNA gene profile meta-analysis and biofilm status reveal common colorectal cancer consortia.

Drewes JL, White JR, Dejea CM, Fathi P, Iyadorai T, Vadivelu J, Roslani AC, Wick EC, Mongodin EF, Loke MF, Thulasi K, Gan HM, Goh KL, Chong HY, Kumar S, Wanyiri JW, Sears CL.

NPJ Biofilms Microbiomes. 2019 Jan 9;5:2. doi: 10.1038/s41522-018-0078-x. eCollection 2019.


Direct Diagnostic Tests for Lyme Disease.

Schutzer SE, Body BA, Boyle J, Branson BM, Dattwyler RJ, Fikrig E, Gerald NJ, Gomes-Solecki M, Kintrup M, Ledizet M, Levin AE, Lewinski M, Liotta LA, Marques A, Mead PS, Mongodin EF, Pillai S, Rao P, Robinson WH, Roth KM, Schriefer ME, Slezak T, Snyder JL, Steere AC, Witkowski J, Wong SJ, Branda JA.

Clin Infect Dis. 2019 Mar 5;68(6):1052-1057. doi: 10.1093/cid/ciy614.


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.


Temporal instability of the post-surgical maxillary sinus microbiota.

Koutsourelakis I, Halderman A, Khalil S, Hittle LE, Mongodin EF, Lane AP.

BMC Infect Dis. 2018 Aug 30;18(1):441. doi: 10.1186/s12879-018-3272-9.


Conventional wastewater treatment and reuse site practices modify bacterial community structure but do not eliminate some opportunistic pathogens in reclaimed water.

Kulkarni P, Olson ND, Paulson JN, Pop M, Maddox C, Claye E, Rosenberg Goldstein RE, Sharma M, Gibbs SG, Mongodin EF, Sapkota AR.

Sci Total Environ. 2018 Oct 15;639:1126-1137. doi: 10.1016/j.scitotenv.2018.05.178. Epub 2018 May 26.


Agricultural Freshwater Pond Supports Diverse and Dynamic Bacterial and Viral Populations.

Chopyk J, Allard S, Nasko DJ, Bui A, Mongodin EF, Sapkota AR.

Front Microbiol. 2018 Apr 24;9:792. doi: 10.3389/fmicb.2018.00792. eCollection 2018.


Plasticity in early immune evasion strategies of a bacterial pathogen.

Bernard Q, Smith AA, Yang X, Koci J, Foor SD, Cramer SD, Zhuang X, Dwyer JE, Lin YP, Mongodin EF, Marques A, Leong JM, Anguita J, Pal U.

Proc Natl Acad Sci U S A. 2018 Apr 17;115(16):E3788-E3797. doi: 10.1073/pnas.1718595115. Epub 2018 Apr 2.


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.


Advances in Serodiagnostic Testing for Lyme Disease Are at Hand.

Branda JA, Body BA, Boyle J, Branson BM, Dattwyler RJ, Fikrig E, Gerald NJ, Gomes-Solecki M, Kintrup M, Ledizet M, Levin AE, Lewinski M, Liotta LA, Marques A, Mead PS, Mongodin EF, Pillai S, Rao P, Robinson WH, Roth KM, Schriefer ME, Slezak T, Snyder J, Steere AC, Witkowski J, Wong SJ, Schutzer SE.

Clin Infect Dis. 2018 Mar 19;66(7):1133-1139. doi: 10.1093/cid/cix943.


High-resolution bacterial 16S rRNA gene profile meta-analysis and biofilm status reveal common colorectal cancer consortia.

Drewes JL, White JR, Dejea CM, Fathi P, Iyadorai T, Vadivelu J, Roslani AC, Wick EC, Mongodin EF, Loke MF, Thulasi K, Gan HM, Goh KL, Chong HY, Kumar S, Wanyiri JW, Sears CL.

NPJ Biofilms Microbiomes. 2017 Nov 29;3:34. doi: 10.1038/s41522-017-0040-3. eCollection 2017. Erratum in: NPJ Biofilms Microbiomes. 2019 Jan 9;5:2.


Complete Genome Sequence of a Strain of Bifidobacterium pseudolongum Isolated from Mouse Feces and Associated with Improved Organ Transplant Outcome.

Mongodin EF, Hittle LL, Nadendla S, Brinkman CC, Xiong Y, Bromberg JS.

Genome Announc. 2017 Oct 5;5(40). pii: e01089-17. doi: 10.1128/genomeA.01089-17.


Changes in the microbiota cause genetically modified Anopheles to spread in a population.

Pike A, Dong Y, Dizaji NB, Gacita A, Mongodin EF, Dimopoulos G.

Science. 2017 Sep 29;357(6358):1396-1399. doi: 10.1126/science.aak9691. Epub 2017 Sep 28.


Comparison of the Microbiota of Older Adults Living in Nursing Homes and the Community.

Roghmann MC, Lydecker AD, Hittle L, DeBoy RT, Nowak RG, Johnson JK, Mongodin EF.

mSphere. 2017 Sep 13;2(5). pii: e00210-17. doi: 10.1128/mSphere.00210-17. eCollection 2017 Sep-Oct.


Amino acid metabolic signaling influences Aedes aegypti midgut microbiome variability.

Short SM, Mongodin EF, MacLeod HJ, Talyuli OAC, Dimopoulos G.

PLoS Negl Trop Dis. 2017 Jul 28;11(7):e0005677. doi: 10.1371/journal.pntd.0005677. eCollection 2017 Jul.


A robust in vitro model for trans-lymphatic endothelial migration.

Xiong Y, Brinkman CC, Famulski KS, Mongodin EF, Lord CJ, Hippen KL, Blazar BR, Bromberg JS.

Sci Rep. 2017 May 9;7(1):1633. doi: 10.1038/s41598-017-01575-w.


Smokeless tobacco products harbor diverse bacterial microbiota that differ across products and brands.

Smyth EM, Kulkarni P, Claye E, Stanfill S, Tyx R, Maddox C, Mongodin EF, Sapkota AR.

Appl Microbiol Biotechnol. 2017 Jul;101(13):5391-5403. doi: 10.1007/s00253-017-8282-9. Epub 2017 Apr 22.


Temporal Variations in Cigarette Tobacco Bacterial Community Composition and Tobacco-Specific Nitrosamine Content Are Influenced by Brand and Storage Conditions.

Chopyk J, Chattopadhyay S, Kulkarni P, Smyth EM, Hittle LE, Paulson JN, Pop M, Buehler SS, Clark PI, Mongodin EF, Sapkota AR.

Front Microbiol. 2017 Mar 7;8:358. doi: 10.3389/fmicb.2017.00358. eCollection 2017.


Microbiological effect of mupirocin and chlorhexidine for Staphylococcus aureus decolonization in community and nursing home based adults.

Roghmann MC, Lydecker AD, Langenberg P, Mongodin EF, Johnson JK.

Diagn Microbiol Infect Dis. 2017 May;88(1):53-57. doi: 10.1016/j.diagmicrobio.2017.02.005. Epub 2017 Feb 13.


Mentholation affects the cigarette microbiota by selecting for bacteria resistant to harsh environmental conditions and selecting against potential bacterial pathogens.

Chopyk J, Chattopadhyay S, Kulkarni P, Claye E, Babik KR, Reid MC, Smyth EM, Hittle LE, Paulson JN, Cruz-Cano R, Pop M, Buehler SS, Clark PI, Sapkota AR, Mongodin EF.

Microbiome. 2017 Feb 15;5(1):22. doi: 10.1186/s40168-017-0235-0.


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.


Global Analysis and Comparison of the Transcriptomes and Proteomes of Group A Streptococcus Biofilms.

Freiberg JA, Le Breton Y, Tran BQ, Scott AJ, Harro JM, Ernst RK, Goo YA, Mongodin EF, Goodlett DR, McIver KS, Shirtliff ME.

mSystems. 2016 Dec 6;1(6). pii: e00149-16. eCollection 2016 Nov-Dec.


Functional genomic analyses of Enterobacter, Anopheles and Plasmodium reciprocal interactions that impact vector competence.

Dennison NJ, Saraiva RG, Cirimotich CM, Mlambo G, Mongodin EF, Dimopoulos G.

Malar J. 2016 Aug 22;15(1):425. doi: 10.1186/s12936-016-1468-2.


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.


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.


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.


Complete Genome Sequence of ER2796, a DNA Methyltransferase-Deficient Strain of Escherichia coli K-12.

Anton BP, Mongodin EF, Agrawal S, Fomenkov A, Byrd DR, Roberts RJ, Raleigh EA.

PLoS One. 2015 May 26;10(5):e0127446. doi: 10.1371/journal.pone.0127446. eCollection 2015.


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.


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].


Association between cigarette smoking and the vaginal microbiota: a pilot study.

Brotman RM, He X, Gajer P, Fadrosh D, Sharma E, Mongodin EF, Ravel J, Glover ED, Rath JM.

BMC Infect Dis. 2014 Aug 28;14:471. doi: 10.1186/1471-2334-14-471.


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.


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.


The potential role of lung microbiota in lung cancer attributed to household coal burning exposures.

Hosgood HD 3rd, Sapkota AR, Rothman N, Rohan T, Hu W, Xu J, Vermeulen R, He X, White JR, Wu G, Wei F, Mongodin EF, Lan Q.

Environ Mol Mutagen. 2014 Oct;55(8):643-51. doi: 10.1002/em.21878. Epub 2014 Jun 3.


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.


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.


Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn's disease.

Erickson AR, Cantarel BL, Lamendella R, Darzi Y, Mongodin EF, Pan C, Shah M, Halfvarson J, Tysk C, Henrissat B, Raes J, Verberkmoes NC, Fraser CM, Hettich RL, Jansson JK.

PLoS One. 2012;7(11):e49138. doi: 10.1371/journal.pone.0049138. Epub 2012 Nov 28.


Analysis of the gut microbiota in the old order Amish and its relation to the metabolic syndrome.

Zupancic ML, Cantarel BL, Liu Z, Drabek EF, Ryan KA, Cirimotich S, Jones C, Knight R, Walters WA, Knights D, Mongodin EF, Horenstein RB, Mitchell BD, Steinle N, Snitker S, Shuldiner AR, Fraser CM.

PLoS One. 2012;7(8):e43052. doi: 10.1371/journal.pone.0043052. Epub 2012 Aug 15.

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