Publications

All publications in PubMed

2024

Transkingdom Network Analysis (TkNA): A Systems Framework for Inferring Causal Factors Underlying Host-Microbiota and Other Multi-Omic Interactions. Newman NK, Macovsky MS, Rodrigues RR, Bruce AM, Pederson JW, Padiadpu J, Shan J, Williams J, Patil SS, Dzutsev AK, Shulzhenko N, Trinchieri G, Brown K, Morgun A. Transkingdom Network Analysis (TkNA): a systems framework for inferring causal factors underlying host-microbiota and other multi-omic interactions. Nature Protocols. 2024 Mar 12. doi: 10.1038/s41596-024-00960-w. Epub ahead of print. PMID: 38472495.

Intestinal IL-22RA1 signaling regulates intrinsic and systemic lipid and glucose metabolism to alleviate obesity-associated disorders. Gaudino SJ, Singh A, Huang H, Padiadpu J, Jean-Pierre M, Kempen C, Bahadur T, Shiomitsu K, Blumberg R, Shroyer KR, Beyaz S, Shulzhenko N, Morgun A, Kumar P. Nat Commun. 2024 Feb 21;15(1):1597. doi: 10.1038/s41467-024-45568-6.PMID: 38383607

2023

Reducing gut microbiome-driven adipose tissue inflammation alleviates metabolic syndrome. Newman NK, Zhang Y, Padiadpu J, Miranda CL, Magana AA, Wong CP, Hioki KA, Pederson JW, Li Z, Gurung M, Bruce AM, Brown K, Bobe G, Sharpton TJ, Shulzhenko N, Maier CS, Stevens JF, Gombart AF, Morgun A. Reducing gut microbiome-driven adipose tissue inflammation alleviates metabolic syndrome. Microbiome. 2023 Sep 21;11(1):208. doi: 10.1186/s40168-023-01637-4. PMID: 37735685; PMCID: PMC10512512.

Multi-omic network analysis identified betacellulin as a novel target of omega-3 fatty acid attenuation of western diet-induced nonalcoholic steatohepatitis. Padiadpu J, Garcia-Jaramillo M, Newman NK, Pederson JW, Rodrigues R, Li Z, Singh S, Monnier P, Trinchieri G, Brown K, Dzutsev AK, Shulzhenko N, Jump DB, Morgun A. Multi-omic network analysis identified betacellulin as a novel target of omega-3 fatty acid attenuation of western diet-induced nonalcoholic steatohepatitis. EMBO Mol Med. 2023 Nov 8;15(11):e18367. doi: 10.15252/emmm.202318367. Epub 2023 Oct 20. PMID: 37859621; PMCID: PMC10630881.

Early transcriptome changes associated with western diet induced NASH in Ldlr-/- mice points to activation of hepatic macrophages and an acute phase response. Padiadpu J, Spooner MH, Li Z, Newman N, Löhr CV, Apperson KD, Dzutsev A, Trinchieri G, Shulzhenko N, Morgun A, Jump DB. Front Nutr. 2023 Aug 7;10:1147602. doi: 10.3389/fnut.2023.1147602. eCollection 2023.PMID: 37609485

GATA4 controls regionalization of tissue immunity and commensal-driven immunopathology. Earley ZM, Lisicka W, Sifakis JJ, Aguirre-Gamboa R, Kowalczyk A, Barlow JT, Shaw DG, Discepolo V, Tan IL, Gona S, Ernest JD, Matzinger P, Barreiro LB, Morgun A, Bendelac A, Ismagilov RF, Shulzhenko N, Riesenfeld SJ, Jabri B. GATA4 controls regionalization of tissue immunity and commensal-driven immunopathology. Immunity. 2023 Jan 10;56(1):43-57.e10. doi: 10.1016/j.immuni.2022.12.009. PMID: 36630917; PMCID: PMC10262782.

2022

Microbiota and adipocyte mitochondrial damage in type 2 diabetes are linked by Mmp12+ macrophages. Zhipeng Li, Manoj Gurung, Richard R. Rodrigues, Jyothi Padiadpu, Nolan K. Newman, Nathan P. Manes, Jacob W. Pederson, Renee L. Greer, Stephany Vasquez-Perez, Hyekyoung You, Kaito A. Hioki, Zoe Moulton, Anna Fel, Dominic De Nardo, Amiran K. Dzutsev, Aleksandra Nita-Lazar, Giorgio Trinchieri, Natalia Shulzhenko, Andrey Morgun; Microbiota and adipocyte mitochondrial damage in type 2 diabetes are linked by Mmp12+ macrophages. J Exp Med 4 July 2022; 219 (7): e20220017. doi: https://doi.org/10.1084/jem.20220017

Intestinal microbiota signatures of clinical response and immune-related adverse events in melanoma patients treated with anti-PD-1. John A. McCulloch, Diwakar Davar, Richard R. Rodrigues, Jonathan H. Badger, Jennifer R. Fang, Alicia M. Cole, Ascharya K. Balaji, Marie Vetizou, Stephanie M. Prescott, Miriam R. Fernandes, Raquel G. F. Costa, Wuxing Yuan, Rosalba Salcedo, Erol Bahadiroglu, Soumen Roy, Richelle N. DeBlasio, Robert M. Morrison, Joe-Marc Chauvin, Quanquan Ding, Bochra Zidi, Ava Lowin, Saranya Chakka, Wentao Gao, Ornella Pagliano, Scarlett J. Ernst, Amy Rose, Nolan K. Newman, Andrey Morgun, Hassane M. Zarour, Giorgio Trinchieri & Amiran K. Dzutsev. Nature Medicine. 2022 Feb 28 https://doi.org/10.1038/s41591-022-01698-2

Fecal Implants From App NL–G–F and App NL–G–F/E4 Donor Mice Sufficient to Induce Behavioral Phenotypes in Germ-Free Mice. Kundu P, Stagaman K, Kasschau K, Holden S, Shulzhenko N, Sharpton TJ, Raber J.Front Behav Neurosci. 2022 Feb 8;16:791128. doi: 10.3389/fnbeh.2022.791128. eCollection 2022.PMID: 35210996 Free PMC article.

Enriched dietary saturated fatty acids induce trained immunity via ceramide production that enhances severity of endotoxemia and clearance of infection. Seufert AL, Hickman JW, Traxler SK, Peterson RM, Waugh TA, Lashley SJ, Shulzhenko N, Napier RJ, Napier BA. Enriched dietary saturated fatty acids induce trained immunity via ceramide production that enhances severity of endotoxemia and clearance of infection. Elife. 2022 Oct 20;11:e76744. doi: 10.7554/eLife.76744. PMID: 36264059.

2021

Fecal microbiota transplant overcomes resistance to anti-PD-1 therapy in melanoma patients. Davar D, Dzutsev AK, McCulloch JA, Rodrigues RR, Chauvin JM, Morrison RM, Deblasio RN, Menna C, Ding Q, Pagliano O, Zidi B, Zhang S, Badger JH, Vetizou M, Cole AM, Fernandes MR, Prescott S, Costa RGF, Balaji AK, Morgun A, Vujkovic-Cvijin I, Wang H, Borhani AA, Schwartz MB, Dubner HM, Ernst SJ, Rose A, Najjar YG, Belkaid Y, Kirkwood JM, Trinchieri G, Zarour HM. Science. 2021 Feb 5;371(6529):595-602. doi: 10.1126/science.abf3363. PMID: 33542131

Dietary Indole-3-Carbinol Activates AhR in the Gut, Alters Th17-Microbe Interactions, and Exacerbates Insulitis in NOD Mice. Kahalehili HM, Newman NK, Pennington JM, Kolluri SK, Kerkvliet NI, Shulzhenko N, Morgun A, Ehrlich AK. Front Immunol. 2021 Jan 21;11:606441. doi: 10.3389/fimmu.2020.606441. eCollection 2020.PMID: 33552063 https://www.frontiersin.org/articles/10.3389/fimmu.2020.606441/full

Transkingdom interactions between Lactobacilli and hepatic mitochondria attenuate western diet-induced diabetes. Rodrigues RR, Gurung M, Li Z, García-Jaramillo M, Greer R, Gaulke C, Bauchinger F, You H, Pederson JW, Vasquez-Perez S, White KD, Frink B, Philmus B, Jump DB, Trinchieri G, Berry D, Sharpton TJ, Dzutsev A, Morgun A, Shulzhenko N. Nat Commun. 2021 Jan 4;12(1):101. doi: 10.1038/s41467-020-20313-x.PMID: 33397942

2020

Gut-resident CX3CR1hi macrophages induce tertiary lymphoid structures and IgA response in situ. Koscsó B, Kurapati S, Rodrigues RR, Nedjic J, Gowda K, Shin C, Soni C, Ashraf AZ, Purushothaman I, Palisoc M, Xu S, Sun H, Chodisetti SB, Lin E, Mack M, Kawasawa YI, He P, Rahman ZSM, Aifantis I, Shulzhenko N, Morgun A, Bogunovic M. Sci Immunol. 2020 Apr 10;5(46). pii: eaax0062. doi: 10.1126/sciimmunol.aax0062. PMID: 32276965

Germ-Free Swiss Webster Mice on a High-Fat Diet Develop Obesity, Hyperglycemia, and Dyslipidemia. Logan IE, Bobe G, Miranda CL, Vasquez-Perez S, Choi J, Lowry MB, Sharpton TJ, Morgun A, Maier CS, Stevens JF, Shulzhenko N, Gombart AF. Microorganisms. 2020 Apr 5;8(4). pii: E520. doi: 10.3390/microorganisms8040520. PMID: 32260528

Role of gut microbiota in type 2 diabetes pathophysiology. Gurung M, Li Z, You H, Rodrigues R, Jump DB, Morgun A, Shulzhenko N. EBioMedicine. 2020 Jan 2;51:102590. doi: 10.1016/j.ebiom.2019.11.051. [Epub ahead of print] Review. PMID: 31901868

Improvements in Metabolic Syndrome by Xanthohumol Derivatives Are Linked to Altered Gut Microbiota and Bile Acid Metabolism. Zhang Y, Bobe G, Revel JS, Rodrigues RR, Sharpton TJ, Fantacone ML, Raslan K, Miranda CL, Lowry MB, Blakemore PR, Morgun A, Shulzhenko N, Maier CS, Stevens JF, Gombart AF. Mol Nutr Food Res. 2020 Jan;64(1):e1900789. doi: 10.1002/mnfr.201900789. Epub 2019 Dec 15. PMID: 31755244

2019

Effect of temperature and time on the thanatomicrobiome of the cecum, ileum, kidney, and lung of domestic rabbits. Lawrence KE, Lam KC, Morgun A, Shulzhenko N, Löhr CV. Journal of Veterinary Diagnostic Investigation. 2019 Mar;31(2):155-163. doi: 10.1177/1040638719828412. Epub 2019 Feb 10. PMID: 30741115

2018

Commensal bacteria contribute to insulin resistance in aging by activating innate B1a cells. Bodogai M, O’Connell J, Kim K, Kim Y, Moritoh K, Chen C, Gusev F, Vaughan K, Shulzhenko N, Mattison JA, Lee-Chang C, Chen W, Carlson O, Becker KG, Gurung M, Morgun A, White J, Meade T, Perdue K, Mack M, Ferrucci L, Trinchieri G, de Cabo R, Rogaev E, Egan J, Wu J, Biragyn A. Sci Transl Med. 2018 Nov 14;10(467). pii: eaat4271. doi: 10.1126/scitranslmed.aat4271. PMID: 30429354

CVID enteropathy is characterized by exceeding low mucosal IgA levels and interferon-driven inflammation possibly related to the presence of a pathobiont. Shulzhenko N, Dong X, Vyshenska D, Greer RL, Gurung M, Vasquez-Perez S, Peremyslova E, Sosnovtsev S, Quezado M, Yao M, Montgomery-Recht K, Strober W, Fuss IJ, Morgun A. Clin Immunol. 2018 Sep 19;197:139-153. doi: 10.1016/j.clim.2018.09.008 [CVID-PDF]

Transkingdom network reveals bacterial players associated with cervical cancer gene expression program. Lam KC, Vyshenska D, Hu J, Rodrigues RR, Nilsen A, Zielke RA, Brown NS, Aarnes E, Sikora AE, Shulzhenko N, Lyng H, Morgun A. PeerJ 6:e5590 https://doi.org/10.7717/peerj.5590

Transkingdom Networks: A Systems Biology Approach to Identify Causal Members of Host–Microbiota Interactions. Richard R. Rodrigues, Natalia Shulzhenko, and Andrey Morgun in Robert Beiko et al. (eds.), Microbiome Analysis: Methods and Protocols, Methods in Molecular Biology, 2018, vol. 1849, https://doi.org/10.1007/978-1-4939-8728-3_15. [Buy here]

2017

Antibiotic-Induced Alterations in Gut Microbiota Are Associated with Changes in Glucose Metabolism in Healthy Mice. Richard R. Rodrigues, Renee L. Greer, Xiaoxi Dong, Karen N. DSouza, Manoj Gurung, Jia Y. Wu, Andrey Morgun and Natalia Shulzhenko. Front. Microbiol., 22 November 2017 | doi: 10.3389/fmicb.2017.02306

Arsenic exposure and intestinal microbiota in children from Sirajdikhan, Bangladesh. Xiaoxi Dong, Natalia Shulzhenko, Julien Lemaitre, Renee L. Greer, Kate Peremyslova, Quazi Quamruzzaman, Mahmudar Rahman, Omar Sharif Ibn Hasan, Sakila Afroz Joya, Mostofa Golam, David C. Christiani, Andriy Morgun, Molly L. Kile. PLoS ONE 12(12): e0188487. | doi: 10.1371/journal.pone.0188487

Multi-omics Comparative Analysis Reveals Multiple Layers of Host Signaling Pathway Regulation by the Gut Microbiota. Manes NP, Shulzhenko N, Nuccio AG, Azeem S, Morgun A, Nita-Lazar A.  mSystems. 2017 Oct 24;2(5). pii: e00107-17. doi: 10.1128/mSystems.00107-17

Interplay between viruses and bacterial microbiota in cancer development. Vyshenska D, Lam KC, Shulzhenko N, Morgun A. Semin Immunol. 2017 Jun 9. pii: S1044-5323(16)30082-3. doi: 10.1016/j.smim.2017.05.003. PMID: 28602713

Mycobacterium tuberculosis Proteome Response to Antituberculosis Compounds Reveals Metabolic “Escape” Pathways That Prolong Bacterial Survival. Danelishvili L, Shulzhenko N, Chinison JJJ, Babrak L, Hu J, Morgun A, Burrows G, Bermudez LE. Antimicrob Agents Chemother. 2017 Jun 27;61(7). pii: e00430-17. doi: 10.1128/AAC.00430-17. Print 2017 Jul.PMID: 28416555

2016

Differentially co-expressed edges are essential signal transmitters in regulatory networks; Thomas L., Vyshenska D., Shulzhenko N., Yambartsev A, Morgun A. F1000Research 22 Nov 2016, 5:2740 (doi: 10.12688/f1000research.9708.1.

Akkermansia muciniphila mediates negative effects of IFNγ on glucose metabolism. Greer RL, Dong X, Moraes AC, Zielke RA, Fernandes GR, Peremyslova E, Vasquez-Perez S, Schoenborn AA, Gomes EP, Pereira AC, Ferreira SR, Yao M, Fuss IJ, Strober W, Sikora AE, Taylor GA, Gulati AS, Morgun A, Shulzhenko N. Nat Commun. 2016 Nov 14;7:13329. doi: 10.1038/ncomms13329

Unexpected links reflect the noise in networks. Yambartsev A, Perlin MA, Kovchegov Y, Shulzhenko N, Mine KL, Dong X, Morgun A. Biol Direct. 2016 Oct 13;11(1):52. PMID: 27737689

Investigating a holobiont: Microbiota perturbations and transkingdom networks. Greer R, Dong X, Morgun A, Shulzhenko N. Gut Microbes. 2016 Mar 3;7(2):126-35. doi: 10.1080/19490976.2015.1128625. Epub 2016 Mar 16. PMID:26979110  Investigating a holobiont- Microbiota perturbations and transkingdom networks

2015

Uncovering effects of antibiotics on the host and microbiota using transkingdom gene networks Morgun A, Dzutsev A, Dong X, Greer RL, Sexton DJ, Ravel J, Schuster M, Hsiao W, Matzinger P, Shulzhenko N. Gut. 2015 Nov;64(11):1732-43. doi: 10.1136/gutjnl-2014-308820. Epub 2015 Jan 22 Uncovering effects of antibiotics on the host and microbiota using transkingdom gene networks-Morgun-et-al_Supplemental material: Gut2015-SUPPLEM-MATERIAL-ALL121214 Gut_2015-Supplem tables S1-4 tables S1-4_08-20-14_1.xlsx

Reverse enGENEering of Regulatory Networks from Big Data: A Roadmap for Biologists. Dong X, Yambartsev A, Ramsey SA, Thomas LD, Shulzhenko N, Morgun A. Bioinform Biol Insights. 2015 Apr 29;9:61-74. doi: 10.4137/BBI.S12467. eCollection 2015. Review. PubMed PMID: 25983554 ;article pdf

High pre-transplant TREC levels indicate good prognosis after hematopoietic stem cell transplantation Adriano de Moraes Arantes1,2, Kharen Kawemura1, Adriana Seber3, José Salvador Rodrigues de Oliveira2,4, Maria Gerbase-DeLima1, Natalia Shulzhenko1,5, Andrey Morgun1,6  F1000Research 2015,4:1458 (doi: 10.12688/f1000research.7330.1); full text

2014

Ménage à trois: an evolutionary interplay between human papillomavirus, a tumor, and a woman. Shulzhenko N,  Lyng H, Sanson GF,  Morgun A. Trends Microbiol. 2014 Jun;22(6):345-53. doi: 10.1016/j.tim.2014.02.009. Epub 2014 Mar 24. Review.PMID: 24674660.

2013

Bridging immunity and lipid metabolism by gut microbiota. Greer RL, Morgun A, Shulzhenko N.   J Allergy Clin Immunol. 2013 Aug;132(2):253-62; quiz 263. doi: 10.1016/j.jaci.2013.06.025. Review. PMID: 23905915

Gene network reconstruction reveals cell cycle and antiviral genes as major drivers of cervical cancer. Mine KL,Shulzhenko N, Yambartsev A, Rochman M, Sanson GF, Lando M, Varma S, Skinner J, Volfovsky N, Deng T, Brenna SM, Carvalho CR, Ribalta JC, Bustin M, Matzinger P, Silva ID, Lyng H, Gerbase-DeLima M, Morgun  A. Nat Commun. 2013;4:1806. PMID: 23651994

2011

Crosstalk between B lymphocytes, microbiota and the intestinal epithelium governs immunity versus metabolism in the gut.  Shulzhenko N, Morgun A, Hsiao W, Battle M, Yao M, Gavrilova O, Orandle M, Mayer L, Macpherson AJ, McCoy KD, Fraser-Liggett C, Matzinger P. Nat Med. 2011 Nov 20;17(12):1585-93. doi: 10.1038/nm.2505. PMID: 22101768

Construct and Compare Gene Coexpression Networks with DAPfinder and DAPview.  Skinner J, Kotliarov Y, Varma S, Mine KL, Yambartsev A, Simon R, Huyen Y, Morgun A. BMC Bioinformatics. 2011 Jul 14;12:286. doi: 10.1186/1471-2105-12-286. PMID: 21756334