Honors & Awards

  • Dean's Postdoctoral Fellowship, School of Medicine, Stanford University, USA (2021)
  • JEDI Champion Award, Stanford University, USA (2021)
  • Austin Hooey Graduate Research Excellence Recognition Award, Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, USA (2019)
  • Cornelia Ye Outstanding Teaching Assistant Award, Center for Teaching Innovation, Cornell University, USA (2018)
  • Inductee, Edward A. Bouchet Honor Society, Howard and Yale Universities, USA (2018)
  • Procter & Gamble Award, Procter & Gamble, USA (2018)
  • Excellence in Leadership Award, Graduate School, Cornell University, USA (2017)
  • Outstanding Graduate or Professional Student, Cornell Asian Pacific Islander Student Union, Cornell University, USA (2017)
  • Second place, Biotechnology Entrepreneurship Students Team, Department of Biotechnology (Government of India) and ABLE (Association for Biotech Led Enterprises) (2010)
  • Summer Research Fellowship, Indian Academy of Sciences, Indian National Science Academy, and National Academy of Sciences, India (2008)

Boards, Advisory Committees, Professional Organizations

  • Advisor, Telling Our Stories: A Public History of Belonging at Cornell, Cornell University, USA (2020 - Present)
  • Co-Lead, Diversity and Inclusion Program, Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, USA (2018 - 2019)
  • Founder, Science Blender Podcast, Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, USA (2017 - Present)

Professional Education

  • Doctor of Philosophy, Cornell University, Microbiology (2019)
  • Master of Science, Madurai Kamaraj University, Genomics (2011)
  • Bachelor of Science, Madras University, Biochemistry (2009)

Stanford Advisors

Community and International Work

  • ARISE: Amplifying Role models as Inspiration for STEM Education, New York



    Ongoing Project


    Opportunities for Student Involvement


  • Women's Outreach in Materials, Energy and Nanobiotechnology (W.O.M.E.N), Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, USA



    Ongoing Project


    Opportunities for Student Involvement



  • Matthew P. Delisa, Aravind Natarajan. "United StatesBacterial system for producing human O-glycoproteins", Cornell University, Oct 28, 2021

Lab Affiliations

All Publications

  • Gastrointestinal symptoms and fecal shedding of SARS-CoV-2 RNA suggest prolonged gastrointestinal infection. Med (New York, N.Y.) Natarajan, A., Zlitni, S., Brooks, E. F., Vance, S. E., Dahlen, A., Hedlin, H., Park, R. M., Han, A., Schmidtke, D. T., Verma, R., Jacobson, K. B., Parsonnet, J., Bonilla, H. F., Singh, U., Pinsky, B. A., Andrews, J. R., Jagannathan, P., Bhatt, A. S. 2022


    COVID-19 manifests with respiratory, systemic, and gastrointestinal (GI) symptoms.1,2 SARS-CoV-2 RNA is detected in respiratory and fecal samples, and recent reports demonstrate viral replication in both the lung and intestinal tissue.3-5 Although much is known about early fecal RNA shedding, little is known about the long term shedding, especially in those with mild COVID-19. Furthermore, most reports of fecal RNA shedding do not correlate these findings with GI symptoms.6.We analyze the dynamics of fecal RNA shedding up to 10 months after COVID-19 diagnosis in 113 individuals with mild to moderate disease. We also correlate shedding with disease symptoms.Fecal SARS-CoV-2 RNA is detected in 49.2% [95% Confidence interval = 38.2%-60.3%] of participants within the first week after diagnosis. Whereas there was no ongoing oropharyngeal SARS-CoV-2 RNA shedding in subjects at and after 4 months, 12.7% [8.5%-18.4%] of participants continued to shed SARS-CoV-2 RNA in the feces at 4 months after diagnosis and 3.8% [2.0%-7.3%] shed at 7 months. Finally, we find that GI symptoms (abdominal pain, nausea, vomiting) are associated with fecal shedding of SARS-CoV-2 RNA.The extended presence of viral RNA in feces, but not respiratory samples, along with the association of fecal viral RNA shedding with GI symptoms suggest that SARS-CoV-2 infects the GI tract, and that this infection can be prolonged in a subset of individuals with COVID-19.

    View details for DOI 10.1016/j.medj.2022.04.001

    View details for PubMedID 35434682

    View details for PubMedCentralID PMC9005383

  • Standardized preservation, extraction and quantification techniques for detection of fecal SARS-CoV-2 RNA. Nature communications Natarajan, A., Han, A., Zlitni, S., Brooks, E. F., Vance, S. E., Wolfe, M., Singh, U., Jagannathan, P., Pinsky, B. A., Boehm, A., Bhatt, A. S. 2021; 12 (1): 5753


    Patients with COVID-19 shed SARS-CoV-2 RNA in stool, sometimes well after their respiratory infection has cleared. This may be significant for patient health, epidemiology, and diagnosis. However, methods to preserve stool, and to extract and quantify viral RNA are not standardized. We test the performance of three preservative approaches at yielding detectable SARS-CoV-2 RNA: the OMNIgene-GUT kit, Zymo DNA/RNA shield kit, and the most commonly applied, storage without preservative. We test these in combination with three extraction kits: QIAamp Viral RNA Mini Kit, Zymo Quick-RNA Viral Kit, and MagMAX Viral/Pathogen Kit. We also test the utility of ddPCR and RT-qPCR for the reliable quantification of SARS-CoV-2 RNA from stool. We identify that the Zymo DNA/RNA preservative and the QiaAMP extraction kit yield more detectable RNA than the others, using both ddPCR and RT-qPCR. Taken together, we recommend a comprehensive methodology for preservation, extraction and detection of RNA from SARS-CoV-2 and other coronaviruses in stool.

    View details for DOI 10.1038/s41467-021-25576-6

    View details for PubMedID 34599164

  • Engineering orthogonal human O-linked glycoprotein biosynthesis in bacteria. Nature chemical biology Natarajan, A. n., Jaroentomeechai, T. n., Cabrera-Sánchez, M. n., Mohammed, J. C., Cox, E. C., Young, O. n., Shajahan, A. n., Vilkhovoy, M. n., Vadhin, S. n., Varner, J. D., Azadi, P. n., DeLisa, M. P. 2020


    A major objective of synthetic glycobiology is to re-engineer existing cellular glycosylation pathways from the top down or construct non-natural ones from the bottom up for new and useful purposes. Here, we have developed a set of orthogonal pathways for eukaryotic O-linked protein glycosylation in Escherichia coli that installed the cancer-associated mucin-type glycans Tn, T, sialyl-Tn and sialyl-T onto serine residues in acceptor motifs derived from different human O-glycoproteins. These same glycoengineered bacteria were used to supply crude cell extracts enriched with glycosylation machinery that permitted cell-free construction of O-glycoproteins in a one-pot reaction. In addition, O-glycosylation-competent bacteria were able to generate an antigenically authentic Tn-MUC1 glycoform that exhibited reactivity with antibody 5E5, which specifically recognizes cancer-associated glycoforms of MUC1. We anticipate that the orthogonal glycoprotein biosynthesis pathways developed here will provide facile access to structurally diverse O-glycoforms for a range of important scientific and therapeutic applications.

    View details for DOI 10.1038/s41589-020-0595-9

    View details for PubMedID 32719555

  • Microbes and microbiomes in 2020 and beyond. Nature communications Natarajan, A. n., Bhatt, A. S. 2020; 11 (1): 4988

    View details for DOI 10.1038/s41467-020-18850-6

    View details for PubMedID 33020496

  • Glyco-recoded Escherichia coli: Recombineering-based genome editing of native polysaccharide biosynthesis gene clusters METABOLIC ENGINEERING Yates, L. E., Natarajan, A., Li, M., Hale, M. E., Mills, D. C., DeLisa, M. P. 2019; 53: 59–68


    Recombineering-based redesign of bacterial genomes by adding, removing or editing large segments of genomic DNA is emerging as a powerful technique for expanding the range of functions that an organism can perform. Here, we describe a glyco-recoding strategy whereby major non-essential polysaccharide gene clusters in K-12 Escherichia coli are replaced with orthogonal glycosylation components for both biosynthesis of heterologous glycan structures and site-specific glycan conjugation to target proteins. Specifically, the native enterobacterial common antigen (ECA) and O-polysaccharide (O-PS) antigen loci were systematically replaced with ∼9-10 kbp of synthetic DNA encoding Campylobacter jejuni enzymes required for asparagine-linked (N-linked) protein glycosylation. Compared to E. coli cells carrying the same glycosylation machinery on extrachromosomal plasmids, glyco-recoded strains attached glycans to acceptor protein targets with equal or greater efficiency while exhibiting markedly better growth phenotypes and higher glycoprotein titers. Overall, our results define a convenient and reliable framework for bacterial glycome editing that provides a more stable route for chemical diversification of proteins in vivo and effectively expands the bacterial glycoengineering toolkit.

    View details for DOI 10.1016/j.ymben.2019.02.002

    View details for Web of Science ID 000459953300006

    View details for PubMedID 30772453

  • A cell-free biosynthesis platform for modular construction of protein glycosylation pathways. Nature communications Kightlinger, W. n., Duncker, K. E., Ramesh, A. n., Thames, A. H., Natarajan, A. n., Stark, J. C., Yang, A. n., Lin, L. n., Mrksich, M. n., DeLisa, M. P., Jewett, M. C. 2019; 10 (1): 5404


    Glycosylation plays important roles in cellular function and endows protein therapeutics with beneficial properties. However, constructing biosynthetic pathways to study and engineer precise glycan structures on proteins remains a bottleneck. Here, we report a modular, versatile cell-free platform for glycosylation pathway assembly by rapid in vitro mixing and expression (GlycoPRIME). In GlycoPRIME, glycosylation pathways are assembled by mixing-and-matching cell-free synthesized glycosyltransferases that can elaborate a glucose primer installed onto protein targets by an N-glycosyltransferase. We demonstrate GlycoPRIME by constructing 37 putative protein glycosylation pathways, creating 23 unique glycan motifs, 18 of which have not yet been synthesized on proteins. We use selected pathways to synthesize a protein vaccine candidate with an α-galactose adjuvant motif in a one-pot cell-free system and human antibody constant regions with minimal sialic acid motifs in glycoengineered Escherichia coli. We anticipate that these methods and pathways will facilitate glycoscience and make possible new glycoengineering applications.

    View details for DOI 10.1038/s41467-019-12024-9

    View details for PubMedID 31776339

  • Metabolic engineering of glycoprotein biosynthesis in bacteria. Emerging topics in life sciences Natarajan, A., Jaroentomeechai, T., Li, M., Glasscock, C. J., DeLisa, M. P. 2018; 2 (3): 419-432


    The demonstration more than a decade ago that glycoproteins could be produced in Escherichia coli cells equipped with the N-linked protein glycosylation machinery from Campylobacter jejuni opened the door to using simple bacteria for the expression and engineering of complex glycoproteins. Since that time, metabolic engineering has played an increasingly important role in developing and optimizing microbial cell glyco-factories for the production of diverse glycoproteins and other glycoconjugates. It is becoming clear that future progress in creating efficient glycoprotein expression platforms in bacteria will depend on the adoption of advanced strain engineering strategies such as rational design and assembly of orthogonal glycosylation pathways, genome-wide identification of metabolic engineering targets, and evolutionary engineering of pathway performance. Here, we highlight recent advances in the deployment of metabolic engineering tools and strategies to develop microbial cell glyco-factories for the production of high-value glycoprotein targets with applications in research and medicine.

    View details for DOI 10.1042/ETLS20180004

    View details for PubMedID 33525794

  • Single-pot glycoprotein biosynthesis using a cell-free transcription-translation system enriched with glycosylation machinery (vol 9, 2018) NATURE COMMUNICATIONS Jaroentomeechai, T., Stark, J. C., Natarajan, A., Glasscock, C. J., Yates, L. E., Hsu, K. J., Mrksich, M., Jewett, M. C., DeLisa, M. P. 2018; 9: 3396


    The original version of this Article contained an error in Figure 2, wherein the bottom right western blot panel in Figure 2a was blank. This has now been corrected in both the PDF and HTML versions of the Article.

    View details for DOI 10.1038/s41467-018-05620-8

    View details for Web of Science ID 000442126800002

    View details for PubMedID 30127449

    View details for PubMedCentralID PMC6102295

  • A cell-free platform for rapid synthesis and testing of active oligosaccharyltransferases BIOTECHNOLOGY AND BIOENGINEERING Schoborg, J. A., Hershewe, J. M., Stark, J. C., Kightlinger, W., Kath, J. E., Jaroentomeechai, T., Natarajan, A., DeLisa, M. P., Jewett, M. C. 2018; 115 (3): 739–50


    Protein glycosylation, or the attachment of sugar moieties (glycans) to proteins, is important for protein stability, activity, and immunogenicity. However, understanding the roles and regulations of site-specific glycosylation events remains a significant challenge due to several technological limitations. These limitations include a lack of available tools for biochemical characterization of enzymes involved in glycosylation. A particular challenge is the synthesis of oligosaccharyltransferases (OSTs), which catalyze the attachment of glycans to specific amino acid residues in target proteins. The difficulty arises from the fact that canonical OSTs are large (>70 kDa) and possess multiple transmembrane helices, making them difficult to overexpress in living cells. Here, we address this challenge by establishing a bacterial cell-free protein synthesis platform that enables rapid production of a variety of OSTs in their active conformations. Specifically, by using lipid nanodiscs as cellular membrane mimics, we obtained yields of up to 420 μg/ml for the single-subunit OST enzyme, "Protein glycosylation B" (PglB) from Campylobacter jejuni, as well as for three additional PglB homologs from Campylobacter coli, Campylobacter lari, and Desulfovibrio gigas. Importantly, all of these enzymes catalyzed N-glycosylation reactions in vitro with no purification or processing needed. Furthermore, we demonstrate the ability of cell-free synthesized OSTs to glycosylate multiple target proteins with varying N-glycosylation acceptor sequons. We anticipate that this broadly applicable production method will advance glycoengineering efforts by enabling preparative expression of membrane-embedded OSTs from all kingdoms of life.

    View details for DOI 10.1002/bit.26502

    View details for Web of Science ID 000423672800020

    View details for PubMedID 29178580

  • An Engineered Survival-Selection Assay for Extracellular Protein Expression Uncovers Hypersecretory Phenotypes in Escherichia coli ACS SYNTHETIC BIOLOGY Natarajan, A., Haitjema, C. H., Lee, R., Boock, J. T., DeLisa, M. P. 2017; 6 (5): 875–83


    The extracellular expression of recombinant proteins using laboratory strains of Escherichia coli is now routinely achieved using naturally secreted substrates, such as YebF or the osmotically inducible protein Y (OsmY), as carrier molecules. However, secretion efficiency through these pathways needs to be improved for most synthetic biology and metabolic engineering applications. To address this challenge, we developed a generalizable survival-based selection strategy that effectively couples extracellular protein secretion to antibiotic resistance and enables facile isolation of rare mutants from very large populations (i.e., 1010-12 clones) based simply on cell growth. Using this strategy in the context of the YebF pathway, a comprehensive library of E. coli single-gene knockout mutants was screened and several gain-of-function mutations were isolated that increased the efficiency of extracellular expression without compromising the integrity of the outer membrane. We anticipate that this user-friendly strategy could be leveraged to better understand the YebF pathway and other secretory mechanisms-enabling the exploration of protein secretion in pathogenesis as well as the creation of designer E. coli strains with greatly expanded secretomes-all without the need for expensive exogenous reagents, assay instruments, or robotic automation.

    View details for DOI 10.1021/acssynbio.6b00366

    View details for Web of Science ID 000402026600013

    View details for PubMedID 28182400

  • Substitute sweeteners: diverse bacterial oligosaccharyltransferases with unique N-glycosylation site preferences SCIENTIFIC REPORTS Ollis, A. A., Chai, Y., Natarajan, A., Perregaux, E., Jaroentomeechai, T., Guarino, C., Smith, J., Zhang, S., DeLisa, M. P. 2015; 5: 15237


    The central enzyme in the Campylobacter jejuni asparagine-linked glycosylation pathway is the oligosaccharyltransferase (OST), PglB, which transfers preassembled glycans to specific asparagine residues in target proteins. While C. jejuni PglB (CjPglB) can transfer many diverse glycan structures, the acceptor sites that it recognizes are restricted predominantly to those having a negatively charged residue in the -2 position relative to the asparagine. Here, we investigated the acceptor-site preferences for 23 homologs with natural sequence variation compared to CjPglB. Using an ectopic trans-complementation assay for CjPglB function in glycosylation-competent Escherichia coli, we demonstrated in vivo activity for 16 of the candidate OSTs. Interestingly, the OSTs from Campylobacter coli, Campylobacter upsaliensis, Desulfovibrio desulfuricans, Desulfovibrio gigas, and Desulfovibrio vulgaris, exhibited significantly relaxed specificity towards the -2 position compared to CjPglB. These enzymes glycosylated minimal N-X-T motifs in multiple targets and each followed unique, as yet unknown, rules governing acceptor-site preferences. One notable example is D. gigas PglB, which was the only bacterial OST to glycosylate the Fc domain of human immunoglobulin G at its native 'QYNST' sequon. Overall, we find that a subset of bacterial OSTs follow their own rules for acceptor-site specificity, thereby expanding the glycoengineering toolbox with previously unavailable biocatalytic diversity.

    View details for DOI 10.1038/srep15237

    View details for Web of Science ID 000363029800001

    View details for PubMedID 26482295

    View details for PubMedCentralID PMC4894442

  • Universal Genetic Assay for Engineering Extracellular Protein Expression ACS SYNTHETIC BIOLOGY Haitjema, C. H., Boock, J. T., Natarajan, A., Dominguez, M. A., Gardner, J. G., Keating, D. H., Withers, S. T., DeLisa, M. P. 2014; 3 (2): 74–82


    A variety of strategies now exist for the extracellular expression of recombinant proteins using laboratory strains of Escherichia coli . However, secreted proteins often accumulate in the culture medium at levels that are too low to be practically useful for most synthetic biology and metabolic engineering applications. The situation is compounded by the lack of generalized screening tools for optimizing the secretion process. To address this challenge, we developed a genetic approach for studying and engineering protein-secretion pathways in E. coli . Using the YebF pathway as a model, we demonstrate that direct fluorescent labeling of tetracysteine-motif-tagged secretory proteins with the biarsenical compound FlAsH is possible in situ without the need to recover the cell-free supernatant. High-throughput screening of a bacterial strain library yielded superior YebF expression hosts capable of secreting higher titers of YebF and YebF-fusion proteins into the culture medium. We also show that the method can be easily extended to other secretory pathways, including type II and type III secretion, directly in E. coli . Thus, our FlAsH-tetracysteine-based genetic assay provides a convenient, high-throughput tool that can be applied generally to diverse secretory pathways. This platform should help to shed light on poorly understood aspects of these processes as well as to further assist in the construction of engineered E. coli strains for efficient secretory-protein production.

    View details for DOI 10.1021/sb400142b

    View details for Web of Science ID 000331927100003

    View details for PubMedID 24200127