Welcome to the Song Lab!
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We are in the Department of Microbiology & Immunology at Cornell University.
We have long-time experience studying three medically important pathogens in the Enterobacteriaceae family:
Salmonella enterica, Escherichia coli, and Klebsiella pneumoniae.
Our basic research focuses on three main types of Salmonella virulence factors, benefiting the pathogens: (1) typhoid toxin, (2) Vi capsule variants, and (3) surface proteins, as well as their interactions with the host. To figure out how the host and bacterial pathogens interact, my laboratory uses a multidisciplinary approach that integrates microbiology, biochemistry, cell biology, molecular biology, glycobiology, immunology, structural biology (cryo-EM and X-ray crystallography), and murine models.
Our translational research focuses on finding new classes of antimicrobials and understanding their mechanisms of action against three medically important pathogens in the Enterobacteriaceae family, Salmonella, E. coli, and K. pneumoniae. Our specialized drug discovery prioritization process, integrating the advanced drug screening CED/DED methods, facilitates this research.
Research
Bacterial Virulence
Bacterial Virulence
We study Salmonella Typhi pathogenic mechanisms. We focus on three types of S. Typhi virulence factors: typhoid toxin, Vi capsule variants, and surface proteins.
Bacteria-Host Interaction
Bacteria-Host Interaction
We investigate the interplay between Salmonella Typhi and the host through various infection models, including Cmah null mice infected with hyper Vi capsule S. Typhi strains.
Vaccines and Therapeutics
Vaccines and Therapeutics
We are also interested in the potential application of our basic research findings. We evaluate our rationally designed vaccine and therapeutic candidates against three medically important pathogens in the Enterobacteriaceae family, Salmonella, E. coli, and K. pneumoniae .
Members
Oct 2024
Jan 2023
Feb 2021
Sep 2016
Publications
Song Lab Graduate Student, Postdoctoral Associate, Undergraduate Student
2025
Kim HY, Lee GY, Thompson AJ, McBride R, Fu DJ, Paulson JC, and Song J. Molecular basis of the hepatobiliary tropism of typhoid toxin promoting Salmonella pathogenicity. Science Advances. Accepted.
2024
Lee GY and Song J. Single missense mutations in Vi capsule synthesis genes confer hypervirulence to Salmonella Typhi. Nature Communications. (2024)15:5258.
'Behind the paper' community blog post: '1 in 5 Salmonella Typhi bacteria are Vi capsule variants: insights for future studies on the capsule variants of S. Typhi'
2023
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. 12:e0310223. (*co-first authors).
2022
Neupane D*, Ahn C*, Yang YA, Lee GY, 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).
2021
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.
2020
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
2019
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.
2018
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).
2017
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.
2016
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).
2014
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
Dr. Song's postdoctoral and graduate work (selected)
Song, J*, Gao, X*, and Galán, JE. (2013). Structure and function of the Salmonella Typhi chimaeric A2B5 typhoid toxin. Nature. 499: 350-354. PMCID: PMC4144355. (*co-first authors).
Song, J*, Willinger, T*, Rongvaux, A, Eynon, EE, Stevens, S, Manz, MG, Flavell, RA, Galán, JE. (2010). A mouse model for the human pathogen Salmonella Typhi. Cell Host & Microbe. 8(4): 369-76. PMCID: PMC2972545. (*co-first authors).
Song, J*, Bishop, BL*, Li, G, Grady, R, Stapleton, A, and Abraham, SN. (2009). TLR4-mediated expulsion of E. coli from infected bladder epithelial cells. Proc. Natl. Acad. Sci. USA. 106(35): 14966-71. PMCID: PMC2736405. (*co-first authors).
Song, J, Bishop, BL, Li, G, Duncan, MJ, and Abraham, SN. (2007). TLR4-initiated and cAMP-mediated abrogation of bacterial invasion of the bladder. Cell Host & Microbe. 1(4): 287-298. PMCID: PMC1950120.
Song, J, Duncan, MJ, Li, G, Chan, C, Grady, R, Stapleton, A, and Abraham, SN. (2007). A novel TLR4 mediated signaling pathway leading to IL-6 responses in human bladder epithelial cells. PLOS Pathogens. 3(4): 541-552. PMCID: PMC1857715.
Bishop, BL, Duncan, MJ, Song, J, Li, G, Zaas, D, and Abraham, SN. (2007). Cyclic AMP-regulated exocytosis of E. coli from infected bladder epithelial cells. Nature Medicine. 13(5): 625-630. PMID: 17417648.
Contact
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
Email: js2957@cornell.edu
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