Daniel Frank, PhD

Frank, D.N. and Robertson, C.E. 2011. The Phyloware Project: A software framework for phylogenomic virtue. In Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches. Ed. F.J. de Bruijns.

Correlation between ATG16L1 and NOD2 Gene Crohn’s Disease-Associated Risk Alleles with Abnormal Ileal Paneth Cell Morphology. W. Cao, E.C. Boedeker, D.N. Frank, K. Cadwell, L. Mayer, T.S. Stappenbeck, R.B. Sartor, E. Li, and N. Harpaz. 2010 US and Canadian Academy of Pathology. Mod. Pathol. 2010; 23(S1):139A

NOD2 genotype is associated with shifts in human ileal mucosa-associated microbial composition. Li, E., Hamm, C.M., Chen, H., Wu, X., Zhang, T., Zhu, W., Robertson, C.E., Pace. N.R., Sartor, R.B., Boedeker, E.C, Harpaz, N., Yuan, J., Sodergren, E., Weinstock, G., Frank, D.N. American Gastroenterological Association Annual Meeting. Chicago, USA. Gastroenterology in press

Ramakrishnan, V.R., Feazel, L.M., Abrass, L.J., and Frank, D.N. 2012. Prevalence and abundance of Staphylococcus aureus in the middle meatus of patients with chronic rhinosinusitis, nasal polyps, and asthma. Intl Forum Allergy Rhinol. In Press

Nelson, A.W., Feazel, L.M., Robertson, C.E., Spear, J.R. and Frank, D.N. 2012. Microbiological water quality monitoring in a resource-limited urban area: a study in Kumbo, Cameroon. J. Pub. Health in Africa. 3(2):e19.

DiBaise, J.K., Frank, D.N., and Mathur, R. 2012. Impact of the Gut Microbiota on the Development of Obesity: Current Concepts. Am J Gastroenterol Suppl 1:22-27

Hara, N., Alkanani, A.K., Ir, D., Robertson, C.E., Wagner, B., Frank, D.N., and D. Zipris. 2012. Prevention of Virus-Induced Type 1 Diabetes with Antibiotic Therapy. J. Immunol. 189(8): 3805-3814

Janoff, E.N., Gustafson, C., and Frank, D.N. 2012. The world within: Living with our microbial guests and guides. Transl. Res. 160(4):239-245

• Neville, M.C. Anderson, S.M. McManaman, J.L., Badger T.M., Contractor, N. Crume, T., Dabelea, D., Sharon Donovan, Nicole Forman, Frank, D.N., Friedman, J., Bruce German, Armand Goldman, Darryl Hadsell, Michael Hambidge, Katherine Hinde, Russell C. Hovey, Nelson D. Horseman, Edward Janoff, Nancy Krebs, Carlito Lebrilla, Danielle LeMay, Paul MacLean, Paula Meier, Ardythe Morrow, Joseph Neu, Laurie A. Nommsen-Rivers, Monique Rijnkels, Victoria Seewaldt, Joshua Van Houten, Williamson, P. 2012. Lactation and Neonatal Nutrition: The Public Health Implications of Human Milk. J. Mammary Gland Biology and Neoplasia. 17(2):167-188

Lozupone, C., Faust, K., Raes, J., Faith, J., Frank, D.N., Zaneveld, J., Gordon, J.E., and Knight, R. 2012. Identifying genomic and metabolic features that underlie the early successional and opportunistic lifestyles of human gut symbionts. Genome Research. 22(10):1974-1984

Frank, D.N., Manigart, O., Van de Perre, P., Meda, N., Leroy, V., Valea, D., Zhang, W., Dabis, F., Pace, N.R., and Janoff, E.N. 2012. Altered Vaginal Microbiota in African Women with HIV Infection from Burkina Faso is Associated with Risk of Perinatal Mother-to-Child HIV Transmission. J. AIDS. 60(3):299-306

Kelley, C.J., Colgan, S.P. and Frank, D.N. 2012. Of Microbes and Meals: The Health Consequences of Dietary Endotoxemia. Nutr Clin Pract. 27(2):215-225

Zhang, T, DeSimone, R.A., Jiao, X., Rohlf, F.J., Zhu, W, Gong, Q.Q., Hunt, S.R., Dassopoulos, T., Newberry, R.D., Sodergren, E., Weinstock, G.M., Robertson, C.E., Frank, D.N., Li, E. 2012. Host genes related to Paneth cells and xenobiotic metabolism are associated with shifts in human ileum-associated microbial composition. PLoS ONE. 7(6):e30044

Li, E., Hamm, C.M., Gulati, A., Sartor, R.B., Chen, H., Wu, X., Zhang, Tianyi Z., Rohlf, F.J., Zhu, W., Gu, C., Robertson, C.E., Pace, N.R., Sartor, R.B., Boedeker, E.C., Harpaz, N., Yuan, J., Weinstock, G.M., Sodergren, E., and Frank, D.N. 2012. Inflammatory Bowel Disease Phenotype, C. difficile, and NOD2 Genotype are Associated with Shifts in Human Ileum Associated Microbial Composition. PLoS ONE. 7(6)e26284

Xiong, X., Frank, D.N., Robertson, C.E., Hung, S., Markle, J., Canty, A., McCoy, K.D., Macpherson, A.J., Poussier, P., Danska, J., and Parkinson, J. 2012. Generation and Analysis of A Mouse Model Metatranscriptome Through Illumina Based RNA-Sequencing. PLoS ONE. 7(4):e36009

Feazel, L.M., Robertson, C.E., Ramakrishnan, V.R., and Frank, D.N. 2012. Microbiome complexity and Staphylococcus aureus in chronic rhinosinusitis. The Laryngoscope. 122(2):467-472

Ramakrishnan VR, Feazel LM, Gitomer SA, Ir D, Robertson CE, Frank DN. The microbiome of the middle meatus in healthy adults. PLoS One. 2013;8(12):e85507. PubMed PMID: 24386477

Tong M, Li X, Wegener Parfrey L, Roth B, Ippoliti A, Wei B, Borneman J, McGovern DP, Frank DN, Li E, Horvath S, Knight R, Braun J. A modular organization of the human intestinal mucosal microbiota and its association with inflammatory bowel disease. PLoS One. 2013;8(11):e80702. PubMed PMID: 24260458

Robertson CE, Harris JK, Wagner BD, Granger D, Browne K, Tatem B, Feazel LM, Park K, Pace NR, Frank DN. Explicet: graphical user interface software for metadata-driven management, analysis and visualization of microbiome data. Bioinformatics. 2013 Dec 1;29(23):3100-1. PubMed PMID: 24021386

Khailova L, Frank DN, Dominguez JA, Wischmeyer PE. Probiotic administration reduces mortality and improves intestinal epithelial homeostasis in experimental sepsis. Anesthesiology. 2013 Jul;119(1):166-77. PubMed PMID: 23571641

Robertson CE, Baumgartner LK, Harris JK, Peterson KL, Stevens MJ, Frank DN, Pace NR. Culture-independent analysis of aerosol microbiology in a metropolitan subway system. Appl Environ Microbiol. 2013 Jun;79(11):3485-93. PubMed PMID: 23542619

Wu X, Berkow K, Frank DN, Li E, Gulati AS, Zhu W. Comparative analysis of microbiome measurement platforms using latent variable structural equation modeling. BMC Bioinformatics. 2013 Mar 5;14:79. PubMed PMID: 23497007

Markle JG, Frank DN, Adeli K, von Bergen M, Danska JS. Microbiome manipulation modifies sex-specific risk for autoimmunity. Gut Microbes. 2014 Jul 1;5(4):485-93. PubMed PMID: 25007153

Ward EK, Schuster DP, Stowers KH, Royse AK, Ir D, Robertson CE, Frank DN, Austin GL. The effect of PPI use on human gut microbiota and weight loss in patients undergoing laparoscopic Roux-en-Y gastric bypass. Obes Surg. 2014 Sep;24(9):1567-71. PubMed PMID: 24849914

Krebs NF, Sherlock LG, Westcott J, Culbertson D, Hambidge KM, Feazel LM, Robertson CE, Frank DN. Effects of different complementary feeding regimens on iron status and enteric microbiota in breastfed infants. J Pediatr. 2013 Aug;163(2):416-23. PubMed PMID: 23452586

Ling AL, Robertson CE, Harris JK, Frank DN, Kotter CV, Stevens MJ, Pace NR, Hernandez MT. Carbon dioxide and hydrogen sulfide associations with regional bacterial diversity patterns in microbially induced concrete corrosion. Environ Sci Technol. 2014 Jul 1;48(13):7357-64. PubMed PMID: 24842376

Dominguez SR, Dolan SA, West K, Dantes RB, Epson E, Friedman D, Littlehorn CA, Arms LE, Walton K, Servetar E, Frank DN, Kotter CV, Dowell E, Gould CV, Hilden JM, Todd JK. High colonization rate and prolonged shedding of Clostridium difficile in pediatric oncology patients. Clin Infect Dis. 2014 Aug;59(3):401-3. PubMed PMID: 24785235

Markle JG, Frank DN, Mortin-Toth S, Robertson CE, Feazel LM, Rolle-Kampczyk U, von Bergen M, McCoy KD, Macpherson AJ, Danska JS. Sex differences in the gut microbiome drive hormone-dependent regulation of autoimmunity. Science. 2013 Mar 1;339(6123):1084-8. PubMed PMID: 23328391

Hambidge KM, Krebs NF, Westcott JE, Garces A, Goudar SS, Kodkany BS, Pasha O, Tshefu A, Bose CL, Figueroa L, Goldenberg RL, Derman RJ, Friedman JE, Frank DN, McClure EM, Stolka K, Das A, Koso-Thomas M, Sundberg S, Preconception Trial Group. Preconception maternal nutrition: a multi-site randomized controlled trial. BMC Pregnancy Childbirth. 2014 Mar 20;14:111. PubMed PMID: 24650219

Hara N, Alkanani AK, Ir D, Robertson CE, Wagner BD, Frank DN, Zipris D. The role of the intestinal microbiota in type 1 diabetes. Clin Immunol. 2013 Feb;146(2):112-9. PubMed PMID: 23314185

Dillon SM, Lee EJ, Kotter CV, Austin GL, Dong Z, Hecht DK, Gianella S, Siewe B, Smith DM, Landay AL, Robertson CE, Frank DN, Wilson CC. An altered intestinal mucosal microbiome in HIV-1 infection is associated with mucosal and systemic immune activation and endotoxemia. Mucosal Immunol. 2014 Jul;7(4):983-94. PubMed PMID: 24399150

Ramakrishnan VR, Feazel LM, Abrass LJ, Frank DN. Prevalence and abundance of Staphylococcus aureus in the middle meatus of patients with chronic rhinosinusitis, nasal polyps, and asthma. Int Forum Allergy Rhinol. 2013 Apr;3(4):267-71. PubMed PMID: 23055295

Rodriguez de Evgrafov, M. Frank, D.N., Koll, P., Baumgartner, L.K., Hernandez, M.T., and Pace, N.R. 2013. Culture-Independent Microbiological Analysis of Bioaerosols in Concentrated Animal Feeding Operations. Aer. Sci. Technol. 47:755-766

Frank, D.N. and Li, E. 2013. Tension at the Border: How Host Genetics and the Enteric Microbiota Conspire in Crohn’s Disease. In The Human Microbiota: How Microbial Communities Affect Health and Disease. Ed. D. Fredricks.

Li E., Frank D.N., Sartor R. 2013. Effect of Crohn's Disease Risk Alleles on Enteric Microbiota. In: Nelson K. (Ed.) Encyclopedia of Metagenomics: SpringerReference (www.springerreference.com). Springer-Verlag Berlin Heidelberg.

Alkanani AK, Hara N, Lien E, Ir D, Kotter CV, Robertson CE, Wagner BD, Frank DN, Zipris D. Induction of diabetes in the RIP-B7.1 mouse model is critically dependent on TLR3 and MyD88 pathways and is associated with alterations in the intestinal microbiome. Diabetes. 2014 Feb;63(2):619-31. PubMed PMID: 24353176

Hauser LJ, Feazel LM, Ir D, Fang R, Wagner BD, Robertson CE, Frank DN, Ramakrishnan VR. Sinus culture poorly predicts resident microbiota. Int Forum Allergy Rhinol. 2015 Jan;5(1):3-9. PubMed PMID: 25278448

Hull NM, Reens AL, Robertson CE, Stanish LF, Harris JK, Stevens MJ, Frank DN, Kotter C, Pace NR. Molecular analysis of single room humidifier bacteriology. Water Res. 2015 Feb 1;69:318-27. PubMed PMID: 25574772

Gitomer SA, Ramakrishnan VR, Malcolm KC, Kofonow JM, Ir D, Frank DN. Initial investigation of small colony variants of Staphylococcus aureus in chronic rhinosinusitis. Am J Rhinol Allergy. 2015 Jan-Feb;29(1):29-34. PubMed PMID: 25590313

Flass T, Tong S, Frank DN, Wagner BD, Robertson CE, Kotter CV, Sokol RJ, Zemanick E, Accurso F, Hoffenberg EJ, Narkewicz MR. Intestinal lesions are associated with altered intestinal microbiome and are more frequent in children and young adults with cystic fibrosis and cirrhosis. PLoS One. 2015;10(2):e0116967. PubMed PMID: 25658710

Dillon SM, Frank DN, Wilson CC. The gut microbiome and HIV-1 pathogenesis: a two-way street. AIDS. 2016 Nov 28;30(18):2737-2751. PubMed PMID: 27755100

Lee JT, Frank DN, Ramakrishnan V. Microbiome of the paranasal sinuses: Update and literature review. Am J Rhinol Allergy. 2016 Jan;30(1):3-16. PubMed PMID: 26867525

McCollister B, Kotter CV, Frank DN, Washburn T, Jobling MG. Whole-Genome Sequencing Identifies In Vivo Acquisition of a blaCTX-M-27-Carrying IncFII Transmissible Plasmid as the Cause of Ceftriaxone Treatment Failure for an Invasive Salmonella enterica Serovar Typhimurium Infection. Antimicrob Agents Chemother. 2016 Dec;60(12):7224-7235. PubMed PMID: 27671066

Barron MA, Frank DN, Claypool D, Ir D, Ning MF, Curtis D, Weinberg A. Antibody responses to influenza a H1N1 vaccine compared to the circulating strain in influenza vaccine recipients during the 2013/2014 season in North America. J Clin Virol. 2016 Oct;83:56-60. PubMed PMID: 27591557

Pandrea I, Xu C, Stock JL, Frank DN, Ma D, Policicchio BB, He T, Kristoff J, Cornell E, Haret-Richter GS, Trichel A, Ribeiro RM, Tracy R, Wilson C, Landay AL, Apetrei C. Antibiotic and Antiinflammatory Therapy Transiently Reduces Inflammation and Hypercoagulation in Acutely SIV-Infected Pigtailed Macaques. PLoS Pathog. 2016 Jan;12(1):e1005384. PubMed PMID: 26764484

Shukla SK, Cook D, Meyer J, Vernon SD, Le T, Clevidence D, Robertson CE, Schrodi SJ, Yale S, Frank DN. Changes in Gut and Plasma Microbiome following Exercise Challenge in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS). PLoS One. 2015;10(12):e0145453. PubMed PMID: 26683192

Ramakrishnan VR, Hauser LJ, Frank DN. The sinonasal bacterial microbiome in health and disease. Curr Opin Otolaryngol Head Neck Surg. 2016 Feb;24(1):20-5. PubMed PMID: 26575518

Son JS, Zheng LJ, Rowehl LM, Tian X, Zhang Y, Zhu W, Litcher-Kelly L, Gadow KD, Gathungu G, Robertson CE, Ir D, Frank DN, Li E. Comparison of Fecal Microbiota in Children with Autism Spectrum Disorders and Neurotypical Siblings in the Simons Simplex Collection. PLoS One. 2015;10(10):e0137725. PubMed PMID: 26427004

Dominguez SR, Anderson LJ, Kotter CV, Littlehorn CA, Arms LE, Dowell E, Todd JK, Frank DN. Comparison of Whole-Genome Sequencing and Molecular-Epidemiological Techniques for Clostridium difficile Strain Typing. J Pediatric Infect Dis Soc. 2015 Apr 23. [Epub ahead of print] PubMed PMID: 26407257

Tang M, Frank DN, Sherlock L, Ir D, Robertson CE, Krebs NF. Effect of Vitamin E With Therapeutic Iron Supplementation on Iron Repletion and Gut Microbiome in US Iron Deficient Infants and Toddlers. J Pediatr Gastroenterol Nutr. 2016 Sep;63(3):379-85. PubMed PMID: 27548249

Jobling MG, Raleigh EA, Frank DN. Complete Genome Sequence of Escherichia coli ER1821R, a Laboratory K-12 Derivative Engineered To Be Deficient in All Methylcytosine and Methyladenine Restriction Systems. Genome Announc. 2016 Aug 11;4(4). PubMed PMID: 27516504

Jarrett MJ, Vázquez-Torres A, Frank DN, McCollister BD, Henthorn PK, Ir D, Sheeder J, Guy MS, Anwar HQ, Behbakht K. Influence of Gelatin-Thrombin Matrix Tissue Sealant on Bacterial Colony Formation and Risk of Pelvic Infection. Infect Dis Obstet Gynecol. 2016;2016:2649708. PubMed PMID: 27199534

Weinberg A, Curtis D, Ning MF, Claypool DJ, Jalbert E, Patterson J, Frank DN, Ir D, Armon C. Immune Responses to Circulating and Vaccine Viral Strains in HIV-Infected and Uninfected Children and Youth Who Received the 2013/2014 Quadrivalent Live-Attenuated Influenza Vaccine. Front Immunol. 2016 Apr 15;7:142. PubMed PMID: 27148262

Wagner BD, Frank DN, Zipris D. Response to Comment on Alkanani et al. Alterations in Intestinal Microbiota Correlate With Susceptibility to Type 1 Diabetes. Diabetes 2015;64:3510-3520. Diabetes. 2015 Oct;64(10):e41. PubMed PMID: 26405282

Lemas DJ, Young BE, Baker PR 2nd, Tomczik AC, Soderborg TK, Hernandez TL, de la Houssaye BA, Robertson CE, Rudolph MC, Ir D, Patinkin ZW, Krebs NF, Santorico SA, Weir T, Barbour LA, Frank DN, Friedman JE. Alterations in human milk leptin and insulin are associated with early changes in the infant intestinal microbiome. Am J Clin Nutr. 2016 May;103(5):1291-300. PubMed PMID: 27140533

Hauser LJ, Ir D, Kingdom TT, Robertson CE, Frank DN, Ramakrishnan VR. Investigation of bacterial repopulation after sinus surgery and perioperative antibiotics. Int Forum Allergy Rhinol. 2016 Jan;6(1):34-40. PubMed PMID: 26388320

Brumbaugh DE, Arruda J, Robbins K, Ir D, Santorico SA, Robertson CE, Frank DN. Mode of Delivery Determines Neonatal Pharyngeal Bacterial Composition and Early Intestinal Colonization. J Pediatr Gastroenterol Nutr. 2016 Sep;63(3):320-8. PubMed PMID: 27035381

Bessesen MT, Kotter CV, Wagner BD, Adams JC, Kingery S, Benoit JB, Robertson CE, Janoff EN, Frank DN. MRSA colonization and the nasal microbiome in adults at high risk of colonization and infection. J Infect. 2015 Dec;71(6):649-57. PubMed PMID: 26335708

Hauser LJ, Ir D, Kingdom TT, Robertson CE, Frank DN, Ramakrishnan VR. Evaluation of bacterial transmission to the paranasal sinuses through sinus irrigation. Int Forum Allergy Rhinol. 2016 Aug;6(8):800-6. PubMed PMID: 26990369

Wieland A, Frank DN, Harnke B, Bambha K. Systematic review: microbial dysbiosis and nonalcoholic fatty liver disease. Aliment Pharmacol Ther. 2015 Nov;42(9):1051-63. PubMed PMID: 26304302

Ramakrishnan VR, Frank DN. Impact of cigarette smoking on the middle meatus microbiome in health and chronic rhinosinusitis. Int Forum Allergy Rhinol. 2015 Nov;5(11):981-9. PubMed PMID: 26272413

Lee JT, Frank DN, Ramakrishnan V. Microbiome of the paranasal sinuses: Update and literature review. Am J Rhinol Allergy. 2016 Jan-Feb;30(1):3-16. PubMed PMID: 26867525

Pandrea I, Xu C, Stock JL, Frank DN, Ma D, Policicchio BB, He T, Kristoff J, Cornell E, Haret-Richter GS, Trichel A, Ribeiro RM, Tracy R, Wilson C, Landay AL, Apetrei C. Antibiotic and Antiinflammatory Therapy Transiently Reduces Inflammation and Hypercoagulation in Acutely SIV-Infected Pigtailed Macaques. PLoS Pathog. 2016 Jan 14;12(1):e1005384. PubMed PMID: 26764484

Dillon SM, Lee EJ, Donovan AM, Guo K, Harper MS, Frank DN, McCarter MD, Santiago ML, Wilson CC. Enhancement of HIV-1 infection and intestinal CD4 T cell depletion ex vivo by gut microbes altered during chronic HIV-1 infection. Retrovirology. 2016 Jan 14;13:5. PubMed PMID: 26762145

Ramakrishnan VR, Hauser LJ, Frank DN. The sinonasal bacterial microbiome in health and disease. Curr Opin Otolaryngol Head Neck Surg. 2016 Feb;24(1):20-5. PubMed PMID: 26575518

Dominguez SR, Anderson LJ, Kotter CV, Littlehorn CA, Arms LE, Dowell E, Todd JK, Frank DN. Comparison of Whole-Genome Sequencing and Molecular-Epidemiological Techniques for Clostridium difficile Strain Typing. J Pediatric Infect Dis Soc. 2016 Sep;5(3):329-32. PubMed PMID: 26407257

Yi J, Slaughter A, Kotter CV, Moore EE, Hauser CJ, Itagaki K, Wohlauer M, Frank DN, Silliman C, Banerjee A, Peltz E. A "CLEAN CASE" OF SYSTEMIC INJURY: MESENTERIC LYMPH AFTER HEMORRHAGIC SHOCK ELICITS A STERILE INFLAMMATORY RESPONSE. Shock. 2015 Oct;44(4):336-40. PubMed PMID: 26196840

Hauser LJ, Ir D, Kingdom TT, Robertson CE, Frank DN, Ramakrishnan VR. Investigation of bacterial repopulation after sinus surgery and perioperative antibiotics. Int Forum Allergy Rhinol. 2016 Jan;6(1):34-40. PubMed PMID: 26388320

Dillon SM, Lee EJ, Kotter CV, Austin GL, Gianella S, Siewe B, Smith DM, Landay AL, McManus MC, Robertson CE, Frank DN, McCarter MD, Wilson CC. Gut dendritic cell activation links an altered colonic microbiome to mucosal and systemic T-cell activation in untreated HIV-1 infection. Mucosal Immunol. 2016 Jan;9(1):24-37. PubMed PMID: 25921339

Frank DN, Bales ES, Monks J, Jackman MJ, MacLean PS, Ir D, Robertson CE, Orlicky DJ, McManaman JL. Perilipin-2 Modulates Lipid Absorption and Microbiome Responses in the Mouse Intestine. PLoS One. 2015;10(7):e0131944. PubMed PMID: 26147095

Zhang Y, Rowehl L, Krumsiek JM, Orner EP, Shaikh N, Tarr PI, Sodergren E, Weinstock GM, Boedeker EC, Xiong X, Parkinson J, Frank DN, Li E, Gathungu G. Identification of Candidate Adherent-Invasive E. coli Signature Transcripts by Genomic/Transcriptomic Analysis. PLoS One. 2015;10(6):e0130902. PubMed PMID: 26125937

Son JS, Khair S, Pettet DW 3rd, Ouyang N, Tian X, Zhang Y, Zhu W, Mackenzie GG, Robertson CE, Ir D, Frank DN, Rigas B, Li E. Altered Interactions between the Gut Microbiome and Colonic Mucosa Precede Polyposis in APCMin/ Mice. PLoS One. 2015;10(6):e0127985. PubMed PMID: 26121046

Feazel LM, Santorico SA, Robertson CE, Bashraheil M, Scott JA, Frank DN, Hammitt LL. Effects of Vaccination with 10-Valent Pneumococcal Non-Typeable Haemophilus influenza Protein D Conjugate Vaccine (PHiD-CV) on the Nasopharyngeal Microbiome of Kenyan Toddlers. PLoS One. 2015;10(6):e0128064. PubMed PMID: 26083474

Alkanani AK, Hara N, Gottlieb PA, Ir D, Robertson CE, Wagner BD, Frank DN, Zipris D. Alterations in Intestinal Microbiota Correlate With Susceptibility to Type 1 Diabetes. Diabetes. 2015 Oct;64(10):3510-20. PubMed PMID: 26068542

Dillon SM, Lee EJ, Kotter CV, Austin GL, Gianella S, Siewe B, Smith DM, Landay AL, McManus MC, Robertson CE, Frank DN, McCarter MD, Wilson CC. Gut dendritic cell activation links an altered colonic microbiome to mucosal and systemic T-cell activation in untreated HIV-1 infection. Mucosal Immunol. 2016 Jan;9(1):24-37. PubMed PMID: 25921339

Ramakrishnan VR, Hauser LJ, Feazel LM, Ir D, Robertson CE, Frank DN. Sinus microbiota varies among chronic rhinosinusitis phenotypes and predicts surgical outcome. J Allergy Clin Immunol. 2015 Aug;136(2):334-42.e1. PubMed PMID: 25819063

Ling AL, Robertson CE, Harris JK, Frank DN, Kotter CV, Stevens MJ, Pace NR, Hernandez MT. High-resolution microbial community succession of microbially induced concrete corrosion in working sanitary manholes. PLoS One. 2015;10(3):e0116400. PubMed PMID: 25748024

Wang M, Frasch SC, Li G, Feng D, Gao B, Xu L, Ir D, Frank DN, Bratton DL, Ju C. Role of gp91(phox) in hepatic macrophage programming and alcoholic liver disease. Hepatol Commun. 2017 Oct;1(8):765-779. PubMed PMID: 29404493

Orlandi RR, Kingdom TT, Hwang PH, Smith TL, Alt JA, Baroody FM, Batra PS, Bernal-Sprekelsen M, Bhattacharyya N, Chandra RK, Chiu A, Citardi MJ, Cohen NA, DelGaudio J, Desrosiers M, Dhong HJ, Douglas R, Ferguson B, Fokkens WJ, Georgalas C, Goldberg A, Gosepath J, Hamilos DL, Han JK, Harvey R, Hellings P, Hopkins C, Jankowski R, Javer AR, Kern R, Kountakis S, Kowalski ML, Lane A, Lanza DC, Lebowitz R, Lee HM, Lin SY, Lund V, Luong A, Mann W, Marple BF, McMains KC, Metson R, Naclerio R, Nayak JV, Otori N, Palmer JN, Parikh SR, Passali D, Peters A, Piccirillo J, Poetker DM, Psaltis AJ, Ramadan HH, Ramakrishnan VR, Riechelmann H, Roh HJ, Rudmik L, Sacks R, Schlosser RJ, Senior BA, Sindwani R, Stankiewicz JA, Stewart M, Tan BK, Toskala E, Voegels R, Wang de Y, Weitzel EK, Wise S, Woodworth BA, Wormald PJ, Wright ED, Zhou B, Kennedy DW. International Consensus Statement on Allergy and Rhinology: Rhinosinusitis. Int Forum Allergy Rhinol. 2016 Feb;6 Suppl 1:S22-S209. PubMed PMID: 26889651

Handorean A, Robertson CE, Harris JK, Frank D, Hull N, Kotter C, Stevens MJ, Baumgardner D, Pace NR, Hernandez M. Microbial aerosol liberation from soiled textiles isolated during routine residuals handling in a modern health care setting. Microbiome. 2015 Dec 9;3:72. PubMed PMID: 26646166

Nash MJ, Frank DN, Friedman JE. Early Microbes Modify Immune System Development and Metabolic Homeostasis-The "Restaurant" Hypothesis Revisited. Front Endocrinol (Lausanne). 2017;8:349. PubMed PMID: 29326657

Liu C, Frank DN, Horch M, Chau S, Ir D, Horch EA, Tretina K, van Besien K, Lozupone CA, Nguyen VH. Associations between acute gastrointestinal GvHD and the baseline gut microbiota of allogeneic hematopoietic stem cell transplant recipients and donors. Bone Marrow Transplant. 2017 Dec;52(12):1643-1650. PubMed PMID: 28967895

Sokoya M, Ramakrishnan VR, Frank DN, Rahkola J, Getz A, Kingdom TT, Kofonow JM, Nguyen Q, Janoff EN. Expression of immunoglobulin D is increased in chronic rhinosinusitis. Ann Allergy Asthma Immunol. 2017 Oct;119(4):317-323.e1. PubMed PMID: 28958373

Needell JC, Ir D, Robertson CE, Kroehl ME, Frank DN, Zipris D. Maternal treatment with short-chain fatty acids modulates the intestinal microbiota and immunity and ameliorates type 1 diabetes in the offspring. PLoS One. 2017;12(9):e0183786. PubMed PMID: 28886045

Xiong X, Bales ES, Ir D, Robertson CE, McManaman JL, Frank DN, Parkinson J. Perilipin-2 modulates dietary fat-induced microbial global gene expression profiles in the mouse intestine. Microbiome. 2017 Sep 6;5(1):117. PubMed PMID: 28877764

Dillon SM, Castleman MJ, Frank DN, Austin GL, Gianella S, Cogswell AC, Landay AL, Barker E, Wilson CC. Brief Report: Inflammatory Colonic Innate Lymphoid Cells Are Increased During Untreated HIV-1 Infection and Associated With Markers of Gut Dysbiosis and Mucosal Immune Activation. J Acquir Immune Defic Syndr. 2017 Dec 1;76(4):431-437. PubMed PMID: 28825942

Kuhn KA, Schulz HM, Regner EH, Severs EL, Hendrickson JD, Mehta G, Whitney AK, Ir D, Ohri N, Robertson CE, Frank DN, Campbell EL, Colgan SP. Bacteroidales recruit IL-6-producing intraepithelial lymphocytes in the colon to promote barrier integrity. Mucosal Immunol. 2017 Aug 16. [Epub ahead of print] PubMed PMID: 28812548

Tang M, Frank DN, Hendricks AE, Ir D, Esamai F, Liechty E, Hambidge KM, Krebs NF. Iron in Micronutrient Powder Promotes an Unfavorable Gut Microbiota in Kenyan Infants. Nutrients. 2017 Jul 19;9(7). PubMed PMID: 28753958

Rick AM, Aguilar A, Cortes R, Gordillo R, Melgar M, Samayoa-Reyes G, Frank DN, Asturias EJ. Group B Streptococci Colonization in Pregnant Guatemalan Women: Prevalence, Risk Factors, and Vaginal Microbiome. Open Forum Infect Dis. 2017 Winter;4(1):ofx020. PubMed PMID: 28480290

Needell JC, Dinarello CA, Ir D, Robertson CE, Ryan SM, Kroehl ME, Frank DN, Zipris D. Implication of the intestinal microbiome as a potential surrogate marker of immune responsiveness to experimental therapies in autoimmune diabetes. PLoS One. 2017;12(3):e0173968. PubMed PMID: 28301545

McCollister B, Kotter CV, Frank DN, Washburn T, Jobling MG. Erratum for McCollister et al., Whole-Genome Sequencing Identifies In Vivo Acquisition of a bla (CTX-M-27)-Carrying IncFII Transmissible Plasmid as the Cause of Ceftriaxone Treatment Failure for an Invasive Salmonella enterica Serovar Typhimurium Infection. Antimicrob Agents Chemother. 2017 Mar;61(3). PubMed PMID: 28232307

Friedman JE, Young BE, Lemas DJ, Barbour LA, Frank DN, Santorico SA. Reply to M Gotteland and F Magne. Am J Clin Nutr. 2017 Jan;105(1):234-236. PubMed PMID: 28049665

Dillon SM, Kibbie J, Lee EJ, Guo K, Santiago ML, Austin GL, Gianella S, Landay AL, Donovan AM, Frank DN, McCARTER MD, Wilson CC. Low abundance of colonic butyrate-producing bacteria in HIV infection is associated with microbial translocation and immune activation. AIDS. 2017 Feb 20;31(4):511-521. PubMed PMID: 28002063

Ramakrishnan VR, Gitomer S, Kofonow JM, Robertson CE, Frank DN. Investigation of sinonasal microbiome spatial organization in chronic rhinosinusitis. Int Forum Allergy Rhinol. 2017 Jan;7(1):16-23. PubMed PMID: 27627048

Santos-Cortez RLP, Chiong CM, Frank DN, Ryan AF, Giese APJ, Bootpetch Roberts T, Daly KA, Steritz MJ, Szeremeta W, Pedro M, Pine H, Yarza TKL, Scholes MA, Llanes EGDV, Yousaf S, Friedman N, Tantoco MLC, Wine TM, Labra PJ, Benoit J, Ruiz AG, de la Cruz RAR, Greenlee C, Yousaf A, Cardwell J, Nonato RMA, Ray D, Ong KMC, So E, Robertson CE, Dinwiddie J, Lagrana-Villagracia SM, Gubbels SP, Shaikh RS, Cass SP, Einarsdottir E, Lee NR, Schwartz DA, Gloria-Cruz TLI, Bamshad MJ, Yang IV, Kere J, Abes GT, Prager JD, Riazuddin S, Chan AL, Yoon PJ, Nickerson DA, Cutiongco-de la Paz EM, Streubel SO, Reyes-Quintos MRT, Jenkins HA, Mattila P, Chan KH, Mohlke KL, Leal SM, Hafrén L, Chonmaitree T, Sale MM, Ahmed ZM. FUT2 Variants Confer Susceptibility to Familial Otitis Media. Am J Hum Genet. 2018 Nov 1;103(5):679-690. PubMed PMID: 30401457

Soderborg TK, Clark SE, Mulligan CE, Janssen RC, Babcock L, Ir D, Lemas DJ, Johnson LK, Weir T, Lenz LL, Frank DN, Hernandez TL, Kuhn KA, D'Alessandro A, Barbour LA, El Kasmi KC, Friedman JE. The gut microbiota in infants of obese mothers increases inflammation and susceptibility to NAFLD. Nat Commun. 2018 Oct 26;9(1):4462. PubMed PMID: 30367045

García-Arroyo FE, Gonzaga G, Muñoz-Jiménez I, Blas-Marron MG, Silverio O, Tapia E, Soto V, Ranganathan N, Ranganathan P, Vyas U, Irvin A, Ir D, Robertson CE, Frank DN, Johnson RJ, Sánchez-Lozada LG. Probiotic supplements prevented oxonic acid-induced hyperuricemia and renal damage. PLoS One. 2018;13(8):e0202901. PubMed PMID: 30142173

Ramakrishnan VR, Holt J, Nelson LF, Ir D, Robertson CE, Frank DN. Determinants of the Nasal Microbiome: Pilot Study of Effects of Intranasal Medication Use. Allergy Rhinol (Providence). 2018 Jan-Dec;9:2152656718789519. PubMed PMID: 30128169

Regner EH, Ohri N, Stahly A, Gerich ME, Fennimore BP, Ir D, Jubair WK, Görg C, Siebert J, Robertson CE, Caplan L, Frank DN, Kuhn KA. Functional intraepithelial lymphocyte changes in inflammatory bowel disease and spondyloarthritis have disease specific correlations with intestinal microbiota. Arthritis Res Ther. 2018 Jul 20;20(1):149. PubMed PMID: 30029674

Ramakrishnan VR, Frank DN. Microbiome in patients with upper airway disease: Moving from taxonomic findings to mechanisms and causality. J Allergy Clin Immunol. 2018 Jul;142(1):73-75. PubMed PMID: 29803801

Nycz BT, Dominguez SR, Friedman D, Hilden JM, Ir D, Robertson CE, Frank DN. Correction: Evaluation of bloodstream infections, Clostridium difficile infections, and gut microbiota in pediatric oncology patients. PLoS One. 2018;13(5):e0197530. PubMed PMID: 29746574

Benoit JB, Frank DN, Bessesen MT. Genomic evolution of Staphylococcus aureus isolates colonizing the nares and progressing to bacteremia. PLoS One. 2018;13(5):e0195860. PubMed PMID: 29723202

Jubair WK, Hendrickson JD, Severs EL, Schulz HM, Adhikari S, Ir D, Pagan JD, Anthony RM, Robertson CE, Frank DN, Banda NK, Kuhn KA. Modulation of Inflammatory Arthritis in Mice by Gut Microbiota Through Mucosal Inflammation and Autoantibody Generation. Arthritis Rheumatol. 2018 Aug;70(8):1220-1233. PubMed PMID: 29534332

Jenkins TC, Haukoos JS, Cotton E, Weitzenkamp D, Frank DN, Burman WJ. Time Course of C-Reactive Protein and Procalcitonin Levels During the Treatment of Acute Bacterial Skin Infections. Open Forum Infect Dis. 2018 Mar;5(3):ofy029. PubMed PMID: 29516022

Friedman JE, Dobrinskikh E, Alfonso-Garcia A, Fast A, Janssen RC, Soderborg TK, Anderson AL, Reisz JA, D'Alessandro A, Frank DN, Robertson CE, de la Houssaye BA, Johnson LK, Orlicky DJ, Wang XX, Levi M, Potma EO, El Kasmi KC, Jonscher KR. Pyrroloquinoline quinone prevents developmental programming of microbial dysbiosis and macrophage polarization to attenuate liver fibrosis in offspring of obese mice. Hepatol Commun. 2018 Mar;2(3):313-328. PubMed PMID: 29507905

Mintz M, Khair S, Grewal S, LaComb JF, Park J, Channer B, Rajapakse R, Bucobo JC, Buscaglia JM, Monzur F, Chawla A, Yang J, Robertson CE, Frank DN, Li E. Longitudinal microbiome analysis of single donor fecal microbiota transplantation in patients with recurrent Clostridium difficile infection and/or ulcerative colitis. PLoS One. 2018;13(1):e0190997. PubMed PMID: 29385143

Nycz BT, Dominguez SR, Friedman D, Hilden JM, Ir D, Robertson CE, Frank DN. Evaluation of bloodstream infections, Clostridium difficile infections, and gut microbiota in pediatric oncology patients. PLoS One. 2018;13(1):e0191232. PubMed PMID: 29329346

Kuhn KA, Schulz HM, Regner EH, Severs EL, Hendrickson JD, Mehta G, Whitney AK, Ir D, Ohri N, Robertson CE, Frank DN, Campbell EL, Colgan SP. Bacteroidales recruit IL-6-producing intraepithelial lymphocytes in the colon to promote barrier integrity. Mucosal Immunol. 2018 Mar;11(2):357-368. PubMed PMID: 28812548

He T, Xu C, Krampe N, Dillon SM, Sette P, Falwell E, Haret-Richter GS, Butterfield T, Dunsmore TL, McFadden WM Jr, Martin KJ, Policicchio BB, Raehtz KD, Penn EP, Tracy RP, Ribeiro RM, Frank DN, Wilson CC, Landay AL, Apetrei C, Pandrea I. High-fat diet exacerbates SIV pathogenesis and accelerates disease progression. J Clin Invest. 2019 Dec 2;129(12):5474-5488. PubMed PMID: 31710311

Tang M, Frank DN, Tshefu A, Lokangaka A, Goudar SS, Dhaded SM, Somannavar MS, Hendricks AE, Ir D, Robertson CE, Kemp JF, Lander RL, Westcott JE, Hambidge KM, Krebs NF. Different Gut Microbial Profiles in Sub-Saharan African and South Asian Women of Childbearing Age Are Primarily Associated With Dietary Intakes. Front Microbiol. 2019;10:1848. PubMed PMID: 31474951

Soderborg TK, Carpenter CM, Janssen RC, Weir TL, Robertson CE, Ir D, Young BE, Krebs NF, Hernandez TL, Barbour LA, Frank DN, Kroehl M, Friedman JE. Gestational Diabetes Is Uniquely Associated With Altered Early Seeding of the Infant Gut Microbiota. Front Endocrinol (Lausanne). 2020;11:603021. PubMed PMID: 33329403

Bootpetch TC, Hafrén L, Elling CL, Baschal EE, Manichaikul AW, Pine HS, Szeremeta W, Scholes MA, Cass SP, Larson ED, Chan KH, Ishaq R, Prager JD, Shaikh RS, Gubbels SP, Yousaf A, Wine TM, Bamshad MJ, Yoon PJ, Jenkins HA, Nickerson DA, Streubel SO, Friedman NR, Frank DN, Einarsdottir E, Kere J, Riazuddin S, Daly KA, Leal SM, Ryan AF, Mattila PS, Ahmed ZM, Sale MM, Chonmaitree T, Santos-Cortez RLP. Multi-omic studies on missense PLG variants in families with otitis media. Sci Rep. 2020 Sep 14;10(1):15035. PubMed PMID: 32929111

Frank DN, Giese APJ, Hafren L, Bootpetch TC, Yarza TKL, Steritz MJ, Pedro M, Labra PJ, Daly KA, Tantoco MLC, Szeremeta W, Reyes-Quintos MRT, Ahankoob N, Llanes EGDV, Pine HS, Yousaf S, Ir D, Einarsdottir E, de la Cruz RAR, Lee NR, Nonato RMA, Robertson CE, Ong KMC, Magno JPM, Chiong ANE, Espiritu-Chiong MC, San Agustin ML, Cruz TLG, Abes GT, Bamshad MJ, Cutiongco-de la Paz EM, Kere J, Nickerson DA, Mohlke KL, Riazuddin S, Chan A, Mattila PS, Leal SM, Ryan AF, Ahmed ZM, Chonmaitree T, Sale MM, Chiong CM, Santos-Cortez RLP. Otitis media susceptibility and shifts in the head and neck microbiome due to SPINK5 variants. J Med Genet. 2020 Jul 24. [Epub ahead of print] PubMed PMID: 32709676

Soderborg TK, Clark SE, Mulligan CE, Janssen RC, Babcock L, Ir D, Young B, Krebs NF, Lemas DJ, Johnson LK, Weir T, Lenz LL, Frank DN, Hernandez TL, Kuhn KA, D'Alessandro A, Barbour LA, El Kasmi KC, Friedman JE. Author Correction: The gut microbiota in infants of obese mothers increases inflammation and susceptibility to NAFLD. Nat Commun. 2019 Jul 1;10(1):2965. PubMed PMID: 31263097

Shahir NM, Wang JR, Wolber EA, Schaner MS, Frank DN, Ir D, Robertson CE, Chaumont N, Sadiq TS, Koruda MJ, Rahbar R, Nix BD, Newberry RD, Sartor RB, Sheikh SZ, Furey TS. Crohn's Disease Differentially Affects Region-Specific Composition and Aerotolerance Profiles of Mucosally Adherent Bacteria. Inflamm Bowel Dis. 2020 Nov 19;26(12):1843-1855. PubMed PMID: 32469069

Chen J, Larson ED, Anderson CB, Agarwal P, Frank DN, Kinnamon SC, Ramakrishnan VR. Expression of Bitter Taste Receptors and Solitary Chemosensory Cell Markers in the Human Sinonasal Cavity. Chem Senses. 2019 Sep 7;44(7):483-495. PubMed PMID: 31231752

Olli KE, Rapp C, O'Connell L, Collins CB, McNamee EN, Jensen O, Jedlicka P, Allison KC, Goldberg MS, Gerich ME, Frank DN, Ir D, Robertson CE, Evans CM, Aherne CM. Muc5ac Expression Protects the Colonic Barrier in Experimental Colitis. Inflamm Bowel Dis. 2020 Aug 20;26(9):1353-1367. PubMed PMID: 32385500

Kelly CJ, Alexeev EE, Farb L, Vickery TW, Zheng L, Eric L C, Kitzenberg DA, Battista KD, Kominsky DJ, Robertson CE, Frank DN, Stabler SP, Colgan SP. Oral vitamin B(12) supplement is delivered to the distal gut, altering the corrinoid profile and selectively depleting Bacteroides in C57BL/6 mice. Gut Microbes. 2019;10(6):654-662. PubMed PMID: 31062653

Takahashi S, Luo Y, Ranjit S, Xie C, Libby AE, Orlicky DJ, Dvornikov A, Wang XX, Myakala K, Jones BA, Bhasin K, Wang D, McManaman JL, Krausz KW, Gratton E, Ir D, Robertson CE, Frank DN, Gonzalez FJ, Levi M. Bile acid sequestration reverses liver injury and prevents progression of nonalcoholic steatohepatitis in Western diet-fed mice. J Biol Chem. 2020 Apr 3;295(14):4733-4747. PubMed PMID: 32075905

Reisdorph NA, Hendricks AE, Tang M, Doenges KA, Reisdorph RM, Tooker BC, Quinn K, Borengasser SJ, Nkrumah-Elie Y, Frank DN, Campbell WW, Krebs NF. Nutrimetabolomics reveals food-specific compounds in urine of adults consuming a DASH-style diet. Sci Rep. 2020 Jan 24;10(1):1157. PubMed PMID: 31980691

Li E, Zhang Y, Tian X, Wang X, Gathungu G, Wolber A, Shiekh SS, Sartor RB, Davidson NO, Ciorba MA, Zhu W, Nelson LM, Robertson CE, Frank DN. Influence of Crohn's disease related polymorphisms in innate immune function on ileal microbiome. PLoS One. 2019;14(2):e0213108. PubMed PMID: 30818349

Liu J, Johnson R, Dillon S, Kroehl M, Frank DN, Tuncil YE, Zhang X, Ir D, Robertson CE, Seifert S, Higgins J, Hamaker B, Wilson CC, Erlandson KM. Among older adults, age-related changes in the stool microbiome differ by HIV-1 serostatus. EBioMedicine. 2019 Feb;40:583-594. PubMed PMID: 30685386

MacLaren R, Radcliffe RA, Van Matre ET, Robertson CE, Ir D, Frank DN. The Acute Influence of Acid Suppression with Esomeprazole on Gastrointestinal Microbiota and Brain Gene Expression Profiles in a Murine Model of Restraint Stress. Neuroscience. 2019 Feb 1;398:206-217. PubMed PMID: 30557653

Baschal EE, Larson ED, Bootpetch Roberts TC, Pathak S, Frank G, Handley E, Dinwiddie J, Moloney M, Yoon PJ, Gubbels SP, Scholes MA, Cass SP, Jenkins HA, Frank DN, Yang IV, Schwartz DA, Ramakrishnan VR, Santos-Cortez RLP. Identification of Novel Genes and Biological Pathways That Overlap in Infectious and Nonallergic Diseases of the Upper and Lower Airways Using Network Analyses. Front Genet. 2019;10:1352. PubMed PMID: 32010199

Jobira B, Frank DN, Pyle L, Silveira LJ, Kelsey MM, Garcia-Reyes Y, Robertson CE, Ir D, Nadeau KJ, Cree-Green M. Obese Adolescents With PCOS Have Altered Biodiversity and Relative Abundance in Gastrointestinal Microbiota. J Clin Endocrinol Metab. 2020 Jun 1;105(6). PubMed PMID: 31970418

Wheatley EG, Curtis BJ, Hulsebus HJ, Boe DM, Najarro K, Ir D, Robertson CE, Choudhry MA, Frank DN, Kovacs EJ. Advanced Age Impairs Intestinal Antimicrobial Peptide Response and Worsens Fecal Microbiome Dysbiosis Following Burn Injury in Mice. Shock. 2020 Jan;53(1):71-77. PubMed PMID: 30672882

Nakayama T, Lee IT, Le W, Tsunemi Y, Borchard NA, Zarabanda D, Dholakia SS, Gall PA, Yang A, Kim D, Akutsu M, Kashiwagi T, Patel ZM, Hwang PH, Frank DN, Haruna SI, Ramakrishnan VR, Nolan GP, Jiang S, Nayak JV. Inflammatory molecular endotypes of nasal polyps derived from Caucasian and Japanese populations. J Allergy Clin Immunol. 2021 Dec 1. [Epub ahead of print] PubMed PMID: 34863854

Stanislawski MA, Frank DN, Borengasser SJ, Ostendorf DM, Ir D, Jambal P, Bing K, Wayland L, Siebert JC, Bessesen DH, MacLean PS, Melanson EL, Catenacci VA. The Gut Microbiota during a Behavioral Weight Loss Intervention. Nutrients. 2021 Sep 18;13(9). PubMed PMID: 34579125

Karoor V, Strassheim D, Sullivan T, Verin A, Umapathy NS, Dempsey EC, Frank DN, Stenmark KR, Gerasimovskaya E. The Short-Chain Fatty Acid Butyrate Attenuates Pulmonary Vascular Remodeling and Inflammation in Hypoxia-Induced Pulmonary Hypertension. Int J Mol Sci. 2021 Sep 14;22(18). PubMed PMID: 34576081

Hirsch SD, Elling CL, Bootpetch TC, Scholes MA, Hafrén L, Streubel SO, Pine HS, Wine TM, Szeremeta W, Prager JD, Einarsdottir E, Yousaf A, Baschal EE, Rehman S, Bamshad MJ, Nickerson DA, Riazuddin S, Leal SM, Ahmed ZM, Yoon PJ, Kere J, Chan KH, Mattila PS, Friedman NR, Chonmaitree T, Frank DN, Ryan AF, Santos-Cortez RLP. The role of CDHR3 in susceptibility to otitis media. J Mol Med (Berl). 2021 Nov;99(11):1571-1583. PubMed PMID: 34322716

Erlandson KM, Liu J, Johnson R, Dillon S, Jankowski CM, Kroehl M, Robertson CE, Frank DN, Tuncil Y, Higgins J, Hamaker B, Wilson CC. An exercise intervention alters stool microbiota and metabolites among older, sedentary adults. Ther Adv Infect Dis. 2021 Jan-Dec;8:20499361211027067. PubMed PMID: 34262758

Vickery TW, Armstrong M, Kofonow JM, Robertson CE, Kroehl ME, Reisdorph NA, Ramakrishnan VR, Frank DN. Specialized pro-resolving mediator lipidome and 16S rRNA bacterial microbiome data associated with human chronic rhinosinusitis. Data Brief. 2021 Jun;36:107023. PubMed PMID: 33937456

Malik SA, Zhu C, Li J, LaComb JF, Denoya PI, Kravets I, Miller JD, Yang J, Kramer M, McCombie WR, Robertson CE, Frank DN, Li E. Impact of preoperative antibiotics and other variables on integrated microbiome-host transcriptomic data generated from colorectal cancer resections. World J Gastroenterol. 2021 Apr 14;27(14):1465-1482. PubMed PMID: 33911468

Siebert JC, Stanislawski MA, Zaman A, Ostendorf DM, Konigsberg IR, Jambal P, Ir D, Bing K, Wayland L, Scorsone JJ, Lozupone CA, Görg C, Frank DN, Bessesen D, MacLean PS, Melanson EL, Catenacci VA, Borengasser SJ. Multiomic Predictors of Short-Term Weight Loss and Clinical Outcomes During a Behavioral-Based Weight Loss Intervention. Obesity (Silver Spring). 2021 May;29(5):859-869. PubMed PMID: 33811477

Dillon SM, Abdo MH, Wilson MP, Liu J, Jankowski CM, Robertson CE, Tuncil Y, Hamaker B, Frank DN, MaWhinney S, Wilson CC, Erlandson KM. A Unique Gut Microbiome-Physical Function Axis Exists in Older People with HIV: An Exploratory Study. AIDS Res Hum Retroviruses. 2021 Jul;37(7):542-550. PubMed PMID: 33787299

Carpenter CM, Frank DN, Williamson K, Arbet J, Wagner BD, Kechris K, Kroehl ME. tidyMicro: a pipeline for microbiome data analysis and visualization using the tidyverse in R. BMC Bioinformatics. 2021 Feb 1;22(1):41. PubMed PMID: 33526006

Jobira B, Frank DN, Silveira LJ, Pyle L, Kelsey MM, Garcia-Reyes Y, Robertson CE, Ir D, Nadeau KJ, Cree-Green M. Hepatic steatosis relates to gastrointestinal microbiota changes in obese girls with polycystic ovary syndrome. PLoS One. 2021;16(1):e0245219. PubMed PMID: 33465100

Vickery TW, Armstrong M, Kofonow JM, Robertson CE, Kroehl ME, Reisdorph NA, Ramakrishnan VR, Frank DN. Altered tissue specialized pro-resolving mediators in chronic rhinosinusitis. Prostaglandins Leukot Essent Fatty Acids. 2021 Jan;164:102218. PubMed PMID: 33338738

Frank DN, Giese APJ, Hafren L, Bootpetch TC, Yarza TKL, Steritz MJ, Pedro M, Labra PJ, Daly KA, Tantoco MLC, Szeremeta W, Reyes-Quintos MRT, Ahankoob N, Llanes EGDV, Pine HS, Yousaf S, Ir D, Einarsdottir E, de la Cruz RAR, Lee NR, Nonato RMA, Robertson CE, Ong KMC, Magno JPM, Chiong ANE, Espiritu-Chiong MC, San Agustin ML, Cruz TLG, Abes GT, Bamshad MJ, Cutiongco-de la Paz EM, Kere J, Nickerson DA, Mohlke KL, Riazuddin S, Chan A, Mattila PS, Leal SM, Ryan AF, Ahmed ZM, Chonmaitree T, Sale MM, Chiong CM, Santos-Cortez RLP. Otitis media susceptibility and shifts in the head and neck microbiome due to SPINK5 variants. J Med Genet. 2021 Jul;58(7):442-452. PubMed PMID: 32709676

Tang M, Matz KL, Berman LM, Davis KN, Melanson EL, Frank DN, Hendricks AE, Krebs NF. Effects of Complementary Feeding With Different Protein-Rich Foods on Infant Growth and Gut Health: Study Protocol. Front Pediatr. 2021;9:793215. PubMed PMID: 35096709

Elling CL, Scholes MA, Streubel SO, Larson ED, Wine TM, Bootpetch TC, Yoon PJ, Kofonow JM, Gubbels SP, Cass SP, Robertson CE, Jenkins HA, Prager JD, Frank DN, Chan KH, Friedman NR, Ryan AF, Santos-Cortez RLP. The FUT2 Variant c.461G>A (p.Trp154*) Is Associated With Differentially Expressed Genes and Nasopharyngeal Microbiota Shifts in Patients With Otitis Media. Front Cell Infect Microbiol. 2021;11:798246. PubMed PMID: 35096646

Tang M, Ma C, Weinheimer-Haus EM, Robertson CE, Kofonow JM, Berman LM, Waljee A, Zhu J, Frank DN, Krebs NF. Different gut microbiota in U.S. formula-fed infants consuming a meat vs. dairy-based complementary foods: A randomized controlled trial. Front Nutr. 2022;9:1063518. PubMed PMID: 36778973

Ramos RJ, Zhu C, Joseph DF, Thaker S, Lacomb JF, Markarian K, Lee HJ, Petrov JC, Monzur F, Buscaglia JM, Chawla A, Small-Harary L, Gathungu G, Morganstern JA, Yang J, Li J, Pamer EG, Robertson CE, Frank DN, Cross JR, Li E. Metagenomic and bile acid metabolomic analysis of fecal microbiota transplantation for recurrent Clostridiodes difficile and/or inflammatory bowel diseases. Med Res Arch. 2022 Oct 31;10(10). PubMed PMID: 36618438

Chriswell ME, Lefferts AR, Clay MR, Hsu AR, Seifert J, Feser ML, Rims C, Bloom MS, Bemis EA, Liu S, Maerz MD, Frank DN, Demoruelle MK, Deane KD, James EA, Buckner JH, Robinson WH, Holers VM, Kuhn KA. Clonal IgA and IgG autoantibodies from individuals at risk for rheumatoid arthritis identify an arthritogenic strain of Subdoligranulum. Sci Transl Med. 2022 Oct 26;14(668):eabn5166. PubMed PMID: 36288282

Wang XX, Xie C, Libby AE, Ranjit S, Levi J, Myakala K, Bhasin K, Jones BA, Orlicky DJ, Takahashi S, Dvornikov A, Kleiner DE, Hewitt SM, Adorini L, Kopp JB, Krausz KW, Rosenberg A, McManaman JL, Robertson CE, Ir D, Frank DN, Luo Y, Gonzalez FJ, Gratton E, Levi M. The role of FXR and TGR5 in reversing and preventing progression of Western diet-induced hepatic steatosis, inflammation, and fibrosis in mice. J Biol Chem. 2022 Nov;298(11):102530. PubMed PMID: 36209823

McMahan RH, Hulsebus HJ, Najarro KM, Giesy LE, Frank DN, Kovacs EJ. Changes in gut microbiome correlate with intestinal barrier dysfunction and inflammation following a 3-day ethanol exposure in aged mice. Alcohol. 2022 Sep 20. [Epub ahead of print] PubMed PMID: 36150609

Jackson CL, Frank DN, Robertson CE, Ir D, Kofonow JM, Montlha MP, Mutsaerts EAML, Nunes MC, Madhi SA, Ghosh D, Weinberg A. Evolution of the Gut Microbiome in HIV-Exposed Uninfected and Unexposed Infants during the First Year of Life. mBio. 2022 Oct 26;13(5):e0122922. PubMed PMID: 36073815

Tang M, Weaver NE, Frank DN, Ir D, Robertson CE, Kemp JF, Westcott J, Shankar K, Garces AL, Figueroa L, Tshefu AK, Lokangaka AL, Goudar SS, Somannavar M, Aziz S, Saleem S, McClure EM, Hambidge KM, Hendricks AE, Krebs NF. Longitudinal Reduction in Diversity of Maternal Gut Microbiota During Pregnancy Is Observed in Multiple Low-Resource Settings: Results From the Women First Trial. Front Microbiol. 2022;13:823757. PubMed PMID: 35979501

Sugino KY, Hernandez TL, Barbour LA, Kofonow JM, Frank DN, Friedman JE. A maternal higher-complex carbohydrate diet increases bifidobacteria and alters early life acquisition of the infant microbiome in women with gestational diabetes mellitus. Front Endocrinol (Lausanne). 2022;13:921464. PubMed PMID: 35966074

Jones ST, Guo K, Cooper EH, Dillon SM, Wood C, Nguyen DH, Shen G, Barrett BS, Frank DN, Kroehl M, Janoff EN, Kechris K, Wilson CC, Santiago ML. Altered Immunoglobulin Repertoire and Decreased IgA Somatic Hypermutation in the Gut during Chronic HIV-1 Infection. J Virol. 2022 Sep 14;96(17):e0097622. PubMed PMID: 35938870

Ramakrishnan VR, Larson E, Holt J, Frank DN. Infection and inflammation in chronic rhinosinusitis: Gene ontology/pathway analysis perspective. Int Forum Allergy Rhinol. 2022 Dec;12(12):1566-1569. PubMed PMID: 35829680

Tayachew B, Vanden Brink H, Garcia-Reyes Y, Rahat H, D'Alessandro A, Frank DN, Robertson CE, Silveira L, Kelsey M, Pyle L, Cree-Green M. Combined Oral Contraceptive Treatment Does Not Alter the Gut Microbiome but Affects Amino Acid Metabolism in Sera of Obese Girls With Polycystic Ovary Syndrome. Front Physiol. 2022;13:887077. PubMed PMID: 35800349

Frank DN, Magno JPM, Velasco KJS, Bootpetch TC, Salud JED, David KJV, Miller AL, Yee EC, Dulnuan HP, Pyles RB, Lacuata JAC, Arbizo JL, Kofonow JM, Guce B, Mendoza KMD, Robertson CE, Ilustre GMS, Chiong ANE, Lu SL, Tongol EA, Sacayan ND, Yarza TKL, Chiong CM, Santos-Cortez RLP. Microbiota Associated With Cholesteatoma Tissue in Chronic Suppurative Otitis Media. Front Cell Infect Microbiol. 2022;12:746428. PubMed PMID: 35521215

McMahan RH, Hulsebus HJ, Najarro KM, Giesy LE, Frank DN, Orlicky DJ, Kovacs EJ. Age-Related Intestinal Dysbiosis and Enrichment of Gut-specific Bacteria in the Lung Are Associated With Increased Susceptibility to Streptococcus pneumoniae Infection in Mice. Front Aging. 2022;3. PubMed PMID: 35392033

Manuel CA, Johnson LK, Pugazhenthi U, Fong DL, Fink M, Habenicht LM, Leszczynski JK, Diana IR, Schurr MJ, Frank DN. Effect of Antimicrobial Prophylaxis on Corynebacterium bovis Infection and the Skin Microbiome of Immunodeficient Mice. Comp Med. 2022 Apr 1;72(2):78-89. PubMed PMID: 35379380

Diaz Del Valle F, Zakrajsek JK, Min SJ, Koff PB, Bell HW, Kincaid KA, Frank DN, Ramakrishnan V, Ghosh M, Vandivier RW. Impact of Airline Secondhand Tobacco Smoke Exposure on Respiratory Health and Lung Function Decades After Exposure Cessation. Chest. 2022 Sep;162(3):556-568. PubMed PMID: 35271841

Dillon SM, Mickens KL, Thompson TA, Cooper EH, Nesladek S, Christians AJ, Castleman M, Guo K, Wood C, Frank DN, Kechris K, Santiago ML, Wilson CC. Granzyme B( ) CD4 T cells accumulate in the colon during chronic HIV-1 infection. Gut Microbes. 2022 Jan-Dec;14(1):2045852. PubMed PMID: 35258402

Frank DN, Qiu Y, Cao Y, Zhang S, Lu L, Kofonow JM, Robertson CE, Liu Y, Wang H, Levens CL, Kuhn KA, Song J, Ramakrishnan VR, Lu SL. A dysbiotic microbiome promotes head and neck squamous cell carcinoma. Oncogene. 2022 Feb;41(9):1269-1280. PubMed PMID: 35087236

Dyamenahalli K, Choy K, Frank DN, Najarro K, Boe D, Colborn KL, Idrovo JP, Wagner AL, Wiktor AJ, Afshar M, Burnham EL, McMahan RH, Kovacs EJ. Age and Injury Size Influence the Magnitude of Fecal Dysbiosis in Adult Burn Patients. J Burn Care Res. 2022 Sep 1;43(5):1145-1153. PubMed PMID: 35020913

Nakayama T, Lee IT, Le W, Tsunemi Y, Borchard NA, Zarabanda D, Dholakia SS, Gall PA, Yang A, Kim D, Akutsu M, Kashiwagi T, Patel ZM, Hwang PH, Frank DN, Haruna SI, Ramakrishnan VR, Nolan GP, Jiang S, Nayak JV. Inflammatory molecular endotypes of nasal polyps derived from White and Japanese populations. J Allergy Clin Immunol. 2022 Apr;149(4):1296-1308.e6. PubMed PMID: 34863854

Seymour BJ, Trent B, Allen BE, Berlinberg AJ, Tangchittsumran J, Jubair WK, Chriswell ME, Liu S, Ornelas A, Stahly A, Alexeev EE, Dowdell AS, Sneed SL, Fechtner S, Kofonow JM, Robertson CE, Dillon SM, Wilson CC, Anthony RM, Frank DN, Colgan SP, Kuhn KA. Microbiota-dependent indole production stimulates the development of collagen-induced arthritis in mice. J Clin Invest. 2023 Dec 19. [Epub ahead of print] PubMed PMID: 38113112

Francis D, Chawla A, LaComb JF, Markarian K, Robertson CE, Frank DN, Gathungu GN. Gastroesophageal reflux and PPI exposure alter gut microbiota in very young infants. Front Pediatr. 2023;11:1254329. PubMed PMID: 38027267

Hill EB, Reisdorph RM, Rasolofomanana-Rajery S, Michel C, Khajeh-Sharafabadi M, Doenges KA, Weaver N, Quinn K, Sutliff AK, Tang M, Borengasser SJ, Frank DN, O'Connor LE, Campbell WW, Krebs NF, Hendricks AE, Reisdorph NA. Salmon Food-Specific Compounds and Their Metabolites Increase in Human Plasma and Are Associated with Cardiometabolic Health Indicators Following a Mediterranean-Style Diet Intervention. J Nutr. 2024 Jan;154(1):26-40. PubMed PMID: 37918675

Born SEM, Reichlen MJ, Bartek IL, Benoit JB, Frank DN, Voskuil MI. Population heterogeneity in Mycobacterium smegmatis and Mycobacterium abscessus. Microbiology (Reading). 2023 Oct;169(10). PubMed PMID: 37862100

Fechtner S, Allen BE, Chriswell ME, Jubair WK, Robertson CE, Kofonow JN, Frank DN, Holers VM, Kuhn KA. 3,3-dimethyl-1-butanol and its metabolite 3,3-dimethylbutyrate ameliorate collagen-induced arthritis independent of choline trimethylamine lyase activity. Res Sq. 2023 Sep 5. PubMed PMID: 37720032

Hill EB, Konigsberg IR, Ir D, Frank DN, Jambal P, Litkowski EM, Lange EM, Lange LA, Ostendorf DM, Scorsone JJ, Wayland L, Bing K, MacLean PS, Melanson EL, Bessesen DH, Catenacci VA, Stanislawski MA, Borengasser SJ. The Microbiome, Epigenome, and Diet in Adults with Obesity during Behavioral Weight Loss. Nutrients. 2023 Aug 16;15(16). PubMed PMID: 37630778

Walrath T, Najarro KM, Giesy LE, Khair S, Frank DN, Robertson CE, Orlicky DJ, Quillinan N, Idrovo JP, McMahan RH, Kovacs EJ. REMOTE BURN INJURY IN AGED MICE INDUCES COLONIC LYMPHOID AGGREGATE EXPANSION AND DYSBIOSIS OF THE FECAL MICROBIOME WHICH CORRELATES WITH NEUROINFLAMMATION. Shock. 2023 Oct 1;60(4):585-593. PubMed PMID: 37548929

Elling CL, Goff SH, Hirsch SD, Tholen K, Kofonow JM, Curtis D, Robertson CE, Prager JD, Yoon PJ, Wine TM, Chan KH, Scholes MA, Friedman NR, Frank DN, Herrmann BW, Santos-Cortez RLP. Otitis Media in Children with Down Syndrome Is Associated with Shifts in the Nasopharyngeal and Middle Ear Microbiotas. Genet Test Mol Biomarkers. 2023 Jul;27(7):221-228. PubMed PMID: 37522794

Odiase E, Frank DN, Young BE, Robertson CE, Kofonow JM, Davis KN, Berman LM, Krebs NF, Tang M. The Gut Microbiota Differ in Exclusively Breastfed and Formula-Fed United States Infants and are Associated with Growth Status. J Nutr. 2023 Sep;153(9):2612-2621. PubMed PMID: 37506974

Robinson PZ, Frank DN, Ramakrishnan VR. Inflammation resolution and specialized pro-resolving lipid mediators in chronic rhinosinusitis. Expert Rev Clin Immunol. 2023 Jul-Dec;19(8):969-979. PubMed PMID: 37392068

Morton JT, Jin DM, Mills RH, Shao Y, Rahman G, McDonald D, Zhu Q, Balaban M, Jiang Y, Cantrell K, Gonzalez A, Carmel J, Frankiensztajn LM, Martin-Brevet S, Berding K, Needham BD, Zurita MF, David M, Averina OV, Kovtun AS, Noto A, Mussap M, Wang M, Frank DN, Li E, Zhou W, Fanos V, Danilenko VN, Wall DP, Cárdenas P, Baldeón ME, Jacquemont S, Koren O, Elliott E, Xavier RJ, Mazmanian SK, Knight R, Gilbert JA, Donovan SM, Lawley TD, Carpenter B, Bonneau R, Taroncher-Oldenburg G. Multi-level analysis of the gut-brain axis shows autism spectrum disorder-associated molecular and microbial profiles. Nat Neurosci. 2023 Jul;26(7):1208-1217. PubMed PMID: 37365313

Colbert JF, Kirsch JM, Erzen CL, Langouët-Astrié CJ, Thompson GE, McMurtry SA, Kofonow JM, Robertson CE, Kovacs EJ, Sullivan RC, Hippensteel JA, Sawant NV, De Nisco NJ, McCollister BD, Schwartz RS, Horswill AR, Frank DN, Duerkop BA, Schmidt EP. Aging-Associated Augmentation of Gut Microbiome Virulence Capability Drives Sepsis Severity. mBio. 2023 Jun 27;14(3):e0005223. PubMed PMID: 37102874

Taylor JZ, Fong DL, Habenicht LM, Fink MK, Leszczynski JK, Frank DN, Kofonow JM, Robertson CE, Nicklawsky AG, Schurr MJ, Manuel CA. Effects of Extended Cage Component Sanitation Interval on the Microenvironment, Health, and Gastrointestinal Microbiome of Rats (Rattus norvegicus). J Am Assoc Lab Anim Sci. 2023 May 1;62(3):212-221. PubMed PMID: 37072181

Biswas K, Ramakrishnan VR, Hollemann E, Lorenz K, Wagner Mackenzie B, Frank DN, Douglas RG, Hummel T. Bacterial communities in the nasal passage of postviral olfactory dysfunction patients. Int Forum Allergy Rhinol. 2023 Oct;13(10):1962-1965. PubMed PMID: 36846913

O'Connor JB, Wagner BD, Harris JK, Frank DN, Clabots DE, Laguna TA. Detection and identification of fungi in the lower airway of children with and without cystic fibrosis. Front Microbiol. 2023;14:1119703. PubMed PMID: 36846802

McMahan RH, Hulsebus HJ, Najarro KM, Giesy LE, Frank DN, Kovacs EJ. Changes in gut microbiome correlate with intestinal barrier dysfunction and inflammation following a 3-day ethanol exposure in aged mice. Alcohol. 2023 Mar;107:136-143. PubMed PMID: 36150609

Gathungu, G.N., Frank, D.N., Chawla, A., Robertson, C.E., LaComb, J.F., Markarian, K., Burghard, B.M., and Woroniecki, R. (2023). Gut Microbiota Profiles of Children with Obesity or Metabolic Syndrome: Body Mass Index Is a Lead Actor. Obesities 3, 253-264.

Associate Professor, Medicine-Infectious Disease

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