Faculty Information

Deepak Saxena, MS, PhD

Molecular Pathobiology
345 E. 24th Street, room 921-B, New York, NY 10010
Phone: 212-998-9256
Fax: 212-995-4087
E-mail: ds100@nyu.edu

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Postdoc, New York University 1999-2005
PhD, Microbiology, MS University of Baroda, India 1999
PGDBM, Business Management, NM Institute of Management Studies, Mumbai, India 1996
MS, Microbiology, MS University of Baroda, India 1990
BS, Zoology, Physiology, MS University of Baroda, India 1988

Research Interests / Professional Overview

We are trying to establish the association between the Human Microbiome, chronic inflammation, metabolism and carcinogenesis. We use metabolomics, microbiome, and metagenomics sequencing methods to follow the functional genomics and relative abundance of microbes in a community over time. These microbial communities’ exhibit rich ecological dynamics and our goal is to understand how microbes interact with host to promote metabolic health.

Current Research Projects:


Pancreatic ductal adenocarcinoma (PDA) carries an enormous human toll. We have preliminary data suggesting that elements of the gut microbiome promote pancreatic oncogenesis in genetically susceptible hosts by inducing myeloid cell immune-suppression. We expect to find that one’s microbiotic profile can serve as a biomarker of risk and that targeting the microbiome holds therapeutic promise in PDA.


E-cigs have been marketed as a safer alternative to tobacco smoke. E-cigs aerosol contain nicotine and other toxic compounds which is harmful to the body and is associated with toxicity and addiction. Currently, little is known to evaluate the safety of E-cigarette on public health. Our application will improve the understanding of adverse health effects of E-cigarette aerosol and advance our ability to develop reliable guidelines for marketing and educating public on the danger of E-cigarette use.


A large market opportunity exists for an efficient and consumer friendly gum health therapy because of the critical and longstanding problem of periodontal diseases worldwide. The proposed project is the first step in development of a superhydrophobic surface (SHS) photodynamic therapy (PDT) that will add to the tools we have at present to treat anaerobic bacteria in perio pockets in general. The device is capable of delivering singlet oxygen in a highly localized and controllable fashion without the sensitizer coming in direct contact with the tissue. The objective of this proposal is to design superhydrophobic device tips and validate their use in vitro with mixed cultures (anaerobic P. gingivalis, B. forsythus, and F. nucleatum) and human saliva biofilms on hydroxyapatite discs.


To determine the difference in the genomic composition of bacteria. These patterns of genomic variation across virulent bacteria or the differences between virulent and non-virulent strains are used in interpreting both the genomic history of an organism and the functional interpretation of the genomic organization. Further, we utilize microfluidics, systems biology, and machine learning approaches to classify bacterial strains involved in human health and disease.

Current Funding

NIH: NCI R01CA206105 and NIDCR R01DE025992, R41DE026083.

NIH: Clinical and Translational Science Center, Weill Cornell Medical Center

Lustgarten Foundation

NYU Mega Funds

Representative Publications

Complete listing available on the NYU Health Sciences Library site.

Search PubMed for articles.

Yuqi Guo, Chengzhi Xie, Xiyan Li, Jian Yang, Tao Yu, Ruohan Zhang, Tianqing Zhang, Deepak Saxena, Michael Snyder, Yingjie Wu & Xin Li. 2017. Succinate and its G-protein-coupled receptor stimulates osteoclastogenesis. Nat Commun 8, 15621 doi: 10.1038/ncomms15621.

Saxena D, Li Y, Devota A, Pushalkar S, Abrams W, Barber C, Corby P, Poles M, Phelan J, and Malamud D, 2016. Modulation of the orodigestive tract microbiome in HIV-infected patients. Oral Dis 1:73-8.

Moyes DL, Saxena D, John MD, Malamud D. 2016 The gut and oral microbiome in HIV disease: a workshop report. Oral Dis 1:166-70.

Kamer AR, Fortea JO, Videla S, Mayoral A, Janal M, Carmona-Iragui M, Benejam B, Craig RG6, Saxena D, Corby P, Glodzik L, Annam KR, Robbins M, de Leon MJ. 2016 Periodontal disease's contribution to Alzheimer's disease progression in Down syndrome. Alzheimers Dement 4:49-57.

Zambirinis C, Levie E, Nguy S, Avanzi A, Barilla R, Xu Y, Tomkötter L, Daley D, Greco S, Deutsch M, Jonnadula S, Torres-Hernandez A, Tippens D, Pushalkar S, Eisenthal A, Saxena D, Ahn J, Hajdu C, Engle D, Tuveson D, Miller G. 2015. TLR9 Ligation in Pancreatic Stellate Cells Promotes Tumorigenesis. Journal of Experimental Medicine 212:2077-94.

Pushalkar S, Li X, Kurago Z, Ramanathapuram L, Matsumura S, Fleisher K, Glickman R, Yan W, Li Y, Saxena S. 2014. Oral Microbiota and Host Innate Immune Response in Bisphosphonate-Related Osteonecrosis of the Jaw. International Journal of Oral Science, Nature Publish Group. 1-8.

Contantinos P. Zambirinis, Smruti Pushalkar, George Miller and Deepak Saxena. 2014 Pancreatic Cancer, Inflammation and Microbiome Cancer Journal: The Journal of Principles & Practice of Oncology 20:195-202.

Liu L, Pushalkar S, Saxena D, LeGeros RZ, Zhang, Y. 2014. Antibacterial property expressed by a novel calcium phosphate glass. JBMR Appl Biomater 102:423-9

Fleisher KE, Jolly A, Chippada-Venkata UD, Norman RG, Saxena D, Glickman RS. 2013. Osteonecrosis of the Jaw Onset Times are Based on the Route of Bisphosphonate Therapy. Journal of Oral and Maxillofacial Surgery 71: 513-519.

Kenneth E. Fleisher, Anu Jolly, Robert G. Norman, Deepak Saxena, Robert S. Glickman, 2012. Duration of bisphosphonate therapy and association with osteonecrosis of the jaw. Journal of Oral and Maxillofacial Surgery 71:513-9

Liu G, Saxena D, Chen Z, Norman RG, Phelan JA, Laverty M, Fisch GS, Corby PM, Abrams W, Malamud D, Li Y. 2012. HIV infection affects Streptococcus mutans levels, but not genotypes. J Dent Res 91:834-40. Cover image for the September issue of the Journal of Dental Research

Smruti Pushalkar, Xiaojie Ji, Yihong Li, Cherry Estilo and Deepak Saxena 2012. Characterizing oral microflora associated with squamous cell carcinoma tissues. BMC Microbiology 20:12:144.

Teixeira AH, Pereira ES, Rodrigues LKA, Saxena D, Duarte S, Zanin ICJ. 2012. The photodynamic antimicrobial chemotherapy effect on in vitro and in situ biofilms. Caries Research 46:549-554

Xi Wei, Smruti Pushalkar, Cherry Estilo, Choyi Wong, Azeez Farooki, Monica Fornier, George Bohle, Joseph Huryn, Yihong Li, Stephen Doty and Deepak Saxena 2012. Molecular Profiling of Oral Microbiota in Jaw Bone Samples of Bisphosphonate Related Osteonecrosis of the Jaw. Oral Disease 18:602-12

Saxena, D., Li, Y., Pei, Z, Poles, M, Abrams, WR, Malamud, D. 2012. Human microbiome and HIV/AIDS. Curr HIV.AIDS Rep 9:44-51

Xiaojie Ji, , Smruti Pushalkar, Yihong Li, Robert Glickman, Kenneth Fleisher, and Deepak Saxena. 2012. Antibiotic effects on bacterial profile in osteonecrosis of the jaw. Oral Disease 18:85-95

Chen Z, Trivedi HM, Chhun N, Varnes MV, Saxena D, Xu T, Li Y*. Using DGGE and 16S rRNA gene sequence analysis to evaluate changes in oral bacterial composition. Chinese Journal of Dental Research 2011;14:95-103.

Duarte S, Kuo SP, Murata RM, Chen CY, Saxena D, Huang KJ, and Popovic S. 2011. Air plasma effect on dental disinfection. Physics of Plasmas 2011;18(7):073503

Pushalkar S, Mane SP, Ji X, Li Y, Evans C, Crasta OR, Morse D, Meagher R, Singh A, Saxena D. 2011. Microbial diversity in saliva of oral squamous cell carcinoma. FEMS Immunol Med Microbiol 61:269-77 PMCID: PMC3078631

Fleisher KE, Welch G, Kottal S, Craig RG, Saxena D, Glickman RS. 2010. Predicting Risk for Bisphosphonate-Related Osteonecrosis of the Jaws: CTX vs. Radiographic Markers. Oral Surgery, Oral Medicine, Oral Pathology, Oral Radiology and Endodontology 110:509-516. PMID: 20674404

Liu G, Saxena D, Deng H, Norman RG, Chen Z, Abrams WR, Malamud D, Li Y. 2010. Effect of protease inhibitors on the quantitative and qualitative assessment of oral microorganisms. FEMS Microbiol Lett 312:63-70. PMCID: PMC3018767

Saxena D, Caufield PW, Li Y, Brown S, Song J, and Norman R. 2008. Genetic Classification of Severe Early Childhood Caries Using Subtracted DNA Fragments from Streptococcus mutans. J Clin Microbiol 46:2868-73.

Li Y, Ge Y, Saxena D, Caufield PW. 2007. Genetic profiling of the oral microbiota associated with severe early childhood caries. J Clin Microbiol 45:81-7.

Chen Z, Saxena D, Ge Y, Caufield PW, and Li Y. 2007. Species-specific primers for detection and quantification of Streptococcus mutans in clinical samples. FEMS Microbiol 272:154-62.

Caufield PW, Saxena D, Fitch D, Li Y. 2007. Population Structure of Plasmid-Containing Strains of Streptococcus mutans, a Member of the Human Indigenous Biota. J Bacteriol 189:1238-43.

Li Y, Saxena D, Barnes VM, Trivedi HM, Ge Y, and Xu T. 2006. PCR-based denaturing gradient gel electrophoresis in the evaluation of oral microbiota. Oral Microbiol Immunol 21:333-339.

Saxena D, Li Y, Caufield PW. 2005. Unique Bacterial Gene Segments from Streptococcus mutans with Potential Relevance to Dental Caries Identified by Subtraction DNA Hybridization. J Clin Microbiol 43:3508-3511.

Saxena D, Stotzky G. 2001. Bt corn has a higher lignin content than non-Bt corn. Am J Bot 88:1704-1706.

Saxena D, Stotzky, G. 2001. Bt toxin is not taken up from soil by plants. Nature Biotech 19: 199.

Saxena D, Flores S, Stotzky G. 1999. Insecticidal toxin in root exudates from Bt corn. Nature 402:480.