Song Lab@Cornell

Welcome to the Song Lab!

We are in the Department of Microbiology & Immunology at Cornell University. 

We study bacterial pathogens with a primary focus on the human-exclusive Gram-negative pathogen, Salmonella enterica serovar Typhi (Salmonella Typhi or S. Typhi)

Antimicrobial resistance is an urgent global public health threat. Similar to other bacterial pathogens, multi-drug resistant (MDR) and even extensively drug-resistant (XDR) S. Typhi strains are spreading globally, which are anticipated to worsen the morbidity and mortality of typhoid fever if new interventions are not implemented. The historical adaptability and persistence of typhoid fever underscore the need for research providing critical insights into new intervention strategies against S. Typhi.

The unifying themes of our ongoing research program are seeking to understand the underlying mechanisms that control the pathogenesis and disease associated with Salmonella Typhi, as well as develop intervention strategies against the bacteria and/or its associated disease. The research program is continuously evolving based on the current public health demand. We use a multidisciplinary approach integrating data & computational science, cell biology, molecular biology, microbiology, biochemistry, glycobiology, immunology, structural biology (cryo-EM and X-ray crystallography), and murine models to decipher the interactions between the host and (drug-resistant) bacterial pathogens. 


Bacterial Virulence

We study Salmonella Typhi pathogenic mechanisms using various infection models. Our focus is on two S. Typhi's virulence factors, typhoid toxin and Vi capsular polysaccharide (CPS).

Bacteria-Host Interaction

We study the interplay between Salmonella Typhi and the host using various infection models. 

Vaccines and Therapeutics

We develop and characterize experimental typhoid vaccines and therapeutics.


Song lab member caricature (Jan 2023)


Song Lab Graduate Student, Postdoctoral Associate, Undergraduate Student


Lee GY and Song J. Single missense mutations in Vi capsule synthesis genes confer hypervirulence to Salmonella Typhi. Preprint available at BioRxiv.


Kwon RS*, Lee GY*, Lee S, and Song J. Antimicrobial properties of tomato juice and peptides against typhoidal Salmonella. Microbiology Spectrum. In press. (*co-first authors).


Lee S, Lee GY, and Song J. PltA regulates the export of typhoid toxin vesicle carriers by coopting the coat protein complex II. Preprint available at SSRN. 


Neupane D*, Ahn C*, Yang YA, Lee G, and Song J. Malnutrition and maternal vaccinations against typhoid toxin. PLOS Pathogens. 18(8):e1010731. PMCID: PMC9401117. (*co-first authors).


Du L and Song J. Delivery, structure, and function of bacterial genotoxins. Virulence. 13(1):1199-1215. PMCID: PMC9341358.


Song J. Bacterial AB toxins and host-microbe interactions. Advances in Microbial Physiology. 81:67-109. PMID: 36167443.


Lee S*, Inzerillo S*, Lee GY, Bosire EM, Mahato SK, and Song J. Glycan-Mediated Molecular Interactions in Bacterial Pathogenesis. Trends in Microbiology. 30(3):254-267. PMCID: PMC875896. (* co-first authors).


Dulal HP*, Vance DJ*, Neupane DP*, Chen X, Tremblay JM, Shoemaker CB, Mantis NJ#, and Song J#. Neutralization of typhoid toxin by alpaca-derived, single-domain antibodies targeting the PltB and CdtB subunits. Infection & Immunity. 90(2):e0051521. PMCID: PMC8852740. (* co-first authors, # co-senior authors).

  Highlighted in Spotlight (Infection & Immunity 2022).



Lee GY and Song J. Complete genome sequence of Salmonella enterica serovar Typhi strain ISP2825. Microbiology Resource Announcements. 10(41):e0080421. PMCID: PMC8515888.


  NCBI Reference Sequence: NZ_CP080960.1


Kim C*, Latif I* (*, co-first author), Neupane DP, Lee GY, Kwon RS, Batool A, Ahmed Q, Qamar MU# (# co-senior author), and Song J#. The molecular basis of extensively drug-resistant Salmonella Typhi isolates from pediatric septicemia patients. PLOS One. 16(9): e0257744. PMCID: PMC8478237.


Nguyen T and Song J. Direct IgG epitope mapping on bacterial AB toxins by cryo-EM. STAR Protocols. 2(4):100852. PMCID: PMC8496303.


Nguyen T*, Richards AF*, Sim JH, Feathers JR, Neupane DP, Yang Y-A, Byun HM, Lee SH, Slyke GV, Fromme JC, Mantis NJ, and Song J. The structural basis of Salmonella A2B5 neutralization by antibodies targeting the glycan-receptor binding subunits. Cell Reports. 36(10): 109654. PMCID: PMC8459933. (* co-first authors).


Structure of TyTx1 (anti-PltB IgG) bound to typhoid toxin: PDB 7K7H and EMDB-22699

Structure of TyTx4 (anti-PltB IgG) bound to typhoid toxin: PDB 7K7I and EMDB-22700


Ahn C*, Yang Y-A*, Neupane DP, Nguyen T, Richards AF, Sim JH, Mantis NJ, and Song J. Mechanisms of typhoid toxin neutralization by antibodies targeting glycan receptor binding and nuclease subunits. iScience. 24(5):102454. PMCID: PMC8169802. (* co-first author).


Structure of TyTx11 (anti-CdtB IgG) bound to typhoid toxin: PDB 6VX4 and EMDB-21429


Neupane DP, Dulal HP, and Song J. Enteric fever diagnosis: current challenges and future directions. Pathogens. 10(4):410. PMCID: PMC8065732.



Lee S*, Yang Y-A*, Milano SK, Nguyen T, Ahn C, Sim JH, Thompson AJ, Hillpot EC, Yoo G, Paulson JC, and Song J. Salmonella typhoid toxin PltB subunit and its non-typhoidal Salmonella ortholog confer differential host adaptation and virulence. Cell Host & Microbe. 27(6):937-949. PMCID: PMC7292776. (* co-first author).

Highlighted in Previews (Cell Host & Microbe 2020, 27(6): 851-853).


Structure of typhoid toxin PltB+α2-3 glycan(Neu5Ac-α2-3-Gal-β1-4-GlcNAc): PDB 6P4M

Structure of typhoid toxin PltB+α2-6 glycan (Neu5Ac-α2-6-Gal-β1-4-GlcNAc): PDB 6P4N

Structure of PltBN29K: PDB 6P4P

Structure of PltBN29K+α2-3 glycan (Neu5Ac-α2-3-Gal-β1-4-GlcNAc): PDB 6P4Q

Structure of PltBN29K+α2-6 glycan (Neu5Ac-α2-6-Gal-β1-4-GlcNAc): PDB 6P4R

Structure of PltBT65I: PDB 6P4S

Structure of PltBT65I+α2-3 glycan (Neu5Ac-α2-3-Gal-β1-4-GlcNAc): PDB 6P4T


Nguyen T*, Lee S*, Yang Y-A, Ahn C, Sim JH, Kei TG, Barnard KN, Yu H, Millano SK, Chen X, Parrish CR, and Song J. The role of 9-O-acetylated glycan receptor moieties in the typhoid toxin binding and intoxication. PLOS Pathogens. 16(2): e1008336. PMCID: PMC7055914. (* co-first author).


Structure of typhoid toxin PltB+9OAc-α2-3 glycan (Neu5,9Ac2α2-3Galβ1-4GlcNAc): PDB 6TYN

Structure of typhoid toxin PltB+4OAc-α2-3 glycan (Neu4,5Ac2α2-3Galβ1-4GlcNAc): PDB 6TYO

Structure of typhoid toxin PltB+9OAc-α2-6 glycan Neu5,9Ac2α2-6Galβ1-4GlcNAc): PDB 6TYQ



Yang Y, Higgins CH, Rehman I, Galvao KN, Brito IL, Bicalho ML, Song J, Wang H, and Bicalho RC. (2019). The genomic diversity, virulence, and antimicrobial resistance of Klebsiella pneumoniae from cows and humans. Applied and Environmental Microbiology. 85(6): e02654-18. PMCID: PMC6414388.



Yang Y-A*, Chong A*, and Song J. (2018). Why is eradicating typhoid fever so challenging: implications for vaccine and therapeutic design. Vaccines. 6(3):45. PMCID: PMC6160957. (* co-first author).


Yang Y-A, Lee S, Zhao J, Thompson AJ, McBride R, Tsogtbaatar B, Paulson JC, Nussinov R, Deng L, and Song J. (2018). In vivo tropism of Salmonella Typhi toxin to cells expressing a multiantennal glycan receptor. Nature Microbiology. 3(2): 155-163. PMCID: PMC6045816.

         Highlighted in News and Views (Nature Microbiology 2018, 3(2): 124-126). 


Liu Y, Qi L, Qi L, Ding T, Wang Z, Fu J, Hu M, Li M, Song J# , and Liu X#. Temporal regulation of a Salmonella Typhimurium virulence factor by the transcriptional regulator YdcR. Molecular & Cellular Proteomics. 16(9):1683-1693.


Chong, A, Lee, S, Yang, Y-A, and Song J. The role of typhoid toxin in Salmonella Typhi virulence. Yale Journal of Biology & Medicine. 90(2):283-290. Review article.



Chang S-J, Song J, and Galán JE. Receptor-mediated sorting of typhoid toxin during its export from Salmonella Typhi-infected cells. Cell Host Microbe. 20(5):682-689.


Song J*, Wilhelm CL*, Wangdi T, Maira-Litran T, Lee S-J, Raetz M, Sturge CR, Mirpuri J, Pei J, Grishin NV, McSorley SJ, Gewirtz AT, Baumler AJ, Pier GB, Galán JE#, and Yarovinsky F#. Absence of TLR11 in mice does not confer susceptibility to Salmonella Typhi. Cell. 164(5):827-8. (* co-first authors, # co-senior authors).



Deng L*, Song J*, Gao X*, Wang J, Yu H, Chen X, Varki N, Naito-Matsui Y, Galán JE, and Varki A. Host adaptation of a bacterial toxin from the human pathogen Salmonella Typhi. Cell. 159(6):1290-9. (* co-first authors).


Structure of typhoid toxin PltB+GD2 glycan: PDB 4RHS


The Laboratory of Jeongmin Song

Department of Microbiology & Immunology, Cornell University. 

Veterinary Medical Center, Room C4109 (Dr. Song) or Room C4108 (Lab). 

930 Campus Road, Ithaca, NY 14853

If you are interested in joining the Song Lab, please contact PI, Jeongmin Song (js2957 at with your CV. 

Graduate students: Dr. Song is affiliated with the following graduate programs at Cornell University: the Biomedical & Biological Sciences program (BBS), the Biochemistry, Molecular Cellular Biology program (BMCB), and the Microbiology program. 

Postdoctoral Associates: Applicants must have a Ph.D. in Biomedical Sciences and/or related fields (Microbiology, Biochemistry, etc.) to be considered for a postdoctoral associate position.