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Research Introduction

Bacteria span a broad spectrum, from beneficial commensals to opportunistic and obligate pathogens, and their interactions with the human host are complex, dynamic, and medically significant. While bacterial infections remain among the leading causes of morbidity and mortality worldwide, numerous commensal species play vital roles in shaping host immunity, metabolism, and resistance to pathogen colonization. Moreover, certain commensal isolates have shown promise as next-generation probiotics.

At the same time, opportunistic pathogens such as Klebsiella pneumoniae, Streptococcus pneumoniae, and Pseudomonas aeruginosa can transition from harmless colonizers to life-threatening invaders, particularly in vulnerable patient populations.

Our group aims to understand the genetic and molecular basis of how bacteria adapt to and affect their host environment, whether as pathogens, commensals, or beneficial symbionts. We are a bacterial genetics lab specializing in the development and application of high-throughput functional genomic tools, particularly CRISPRi-based screening platforms, to systematically explore gene function in both model and non-model bacterial species.

By integrating genetic screens with mechanistic studies and in vivo infection models, we strive to translate fundamental discoveries into new strategies for infection control, antimicrobial therapy, and microbiome engineering.

High-Throughput Genetic Screening Platforms

We develop and apply forward genetic screening strategies, mainly CRISPR interference sequencing (CRISPRi-seq), to map bacterial gene function under diverse conditions.

Related Publications

  1. Liu, X., Gallay, C., Kjos, M., Domenech, A., Slager, J., Kessel, S.P. van, Knoops, K., Sorg, R.A., Zhang, J.-R., and Veening, J.-W. (2017). High‐throughput CRISPRi phenotyping identifies new essential genes in Streptococcus pneumoniae. Molecular Systems Biology 13, 931. https://doi.org/10.15252/msb.20167449. (cover paper) (CRISPRi phenotyping)
  2. de Bakker, V., Liu, X., Bravo, A.M., and Veening, J.-W. (2022). CRISPRi-seq for genome-wide fitness quantification in bacteria. Nat Protoc 17, 252–281. https://doi.org/10.1038/s41596-021-00639-6. (CRISPRi-seq)
  3. Dénéréaz, J., Eray, E., Jana, B., De Bakker, V., Todor, H., Van Opijnen, T., Liu, X., and Veening, J.-W. (2024). Dual CRISPRi-Seq for genome-wide genetic interaction studies identifies key genes involved in the pneumococcal cell cycle. Preprint, https://doi.org/10.1101/2024.08.14.607739. (Dual CRISPRi-seq)
  4. Jana, B., Liu, X., Dénéréaz, J., Park, H., Leshchiner, D., Liu, B., Gallay, C., Zhu, J., Veening, J.-W., and van Opijnen, T. (2024). CRISPRi-TnSeq maps genome-wide interactions between essential and non-essential genes in bacteria. Nat Microbiol 9, 2395–2409. https://doi.org/10.1038/s41564-024-01759-x. (CRISPRi-Tn-seq)
  5. Zhou, Y., Song, Y., Zhang, Y., Liu, X., Liu, L., Bao, Y., Wang, J., and Yang, L. (2024). Azalomycin F4a targets peptidoglycan synthesis of Gram-positive bacteria revealed by high-throughput CRISPRi-seq analysis. Microbiol Res 280, 127584. https://doi.org/10.1016/j.micres.2023.127584. (CRISPRi-seq)

Efficient Genetic Toolkits

We build CRISPRi and genome-editing tools tailored to genetically intractable bacteria, enabling scalable, precise functional analysis across a broad range of bacteria.

Related Publications

  1. Rengifo-Gonzalez, M., Mazzuoli, M.-V., Janssen, A.B., Rueff, A.-S., Burnier, J., Liu, X., and Veening, J.-W. (2025). Make-or-break prime editing for genome engineering in Streptococcus pneumoniae. Nat Commun 16, 3796. https://doi.org/10.1038/s41467-025-59068-8 (Prime Editing in Streptococcus pneumoniae)
  2. Liu, L., He, Y., Zhang, T., Geng, R., Hu, Y., Luo, M., Zhou, H., and Liu, X. (2024). Equip Fusobacterium nucleatum genetic tool kits with compatible shuttle vectors and engineered intermediatory E. coli strains for enhanced transformation efficiency. Preprint, https://doi.org/10.1101/2024.07.17.603877 (Genetic tools for Fn) (Resources: https://wekwikgene.wllsb.edu.cn/labs/9da86538-e3e9-4138-b775-6c4405a947b8)

Antibiotic Resistance and Therapeutic Target Discovery

We investigate the molecular mechanisms underlying antibiotic resistance and identify genetic vulnerabilities that can be exploited to reverse resistance or enhance antibiotic efficacy.

Related Publications

  1. Zhang, Y., Zhang, T., Xiao, X., Wang, Y., Kawalek, A., Ou, J., Ren, A., Sun, W., de Bakker, V., Liu, Y., et al. Xue Liu (2025). CRISPRi screen identifies FprB as a synergistic target for gallium therapy in Pseudomonas aeruginosa. Nat Commun 16, 5870. https://doi.org/10.1038/s41467-025-61208-z.
  2. Liu, X., de Bakker, V., Heggenhougen, M.V., Mårli, M.T., Frøynes, A.H., Salehian, Z., Porcellato, D., Morales Angeles, D., Veening, J.-W., and Kjos, M. (2024). Genome-wide CRISPRi screens for high-throughput fitness quantification and identification of determinants for dalbavancin susceptibility in Staphylococcus aureus. mSystems 9, e01289-23. https://doi.org/10.1128/msystems.01289-23.
  3. Liu, X., Li, J.-W., Feng, Z., Luo, Y., Veening, J.-W., and Zhang, J.-R. (2017). Transcriptional Repressor PtvR Regulates Phenotypic Tolerance to Vancomycin in Streptococcus pneumoniae. J Bacteriol 199. https://doi.org/10.1128/JB.00054-17.
  4. Zhang, H., Li, X., Liu, X., Ji, X., Ma, X., Chen, J., Bao, Y., Zhang, Y., Xu, L., Yang, L., et al. (2023). The usnic acid derivative peziculone targets cell walls of Gram-positive bacteria revealed by high-throughput CRISPRi-seq analysis. Int J Antimicrob Agents 62, 106876. https://doi.org/10.1016/j.ijantimicag.2023.106876.
  5. Dewachter, L., Dénéréaz, J., Liu, X., de Bakker, V., Costa, C., Baldry, M., Sirard, J.-C., and Veening, J.-W. (2022). Amoxicillin-resistant Streptococcus pneumoniae can be resensitized by targeting the mevalonate pathway as indicated by sCRilecs-seq. Elife 11, e75607. https://doi.org/10.7554/eLife.75607.
  6. Dong, N., Zeng, Y., Wang, Y., Liu, C., Lu, J., Cai, C., Liu, X., Chen, Y., Wu, Y., Fang, Y., et al. (2022). Distribution and spread of the mobilised RND efflux pump gene cluster tmexCD-toprJ in clinical Gram-negative bacteria: a molecular epidemiological study. Lancet Microbe 3, e846–e856. https://doi.org/10.1016/S2666-5247(22)00221-X.
  7. Wang, X., Zeng, Y., Sheng, L., Larson, P., Liu, X., Zou, X., Wang, S., Guo, K., Ma, C., Zhang, G., et al. (2019). A Cinchona Alkaloid Antibiotic That Appears To Target ATP Synthase in Streptococcus pneumoniae. J. Med. Chem. 62, 2305–2332. https://doi.org/10.1021/acs.jmedchem.8b01353.
  8. Yang, H., Liu, X., Li, Q., Li, L., Zhang, J.-R., and Tang, Y. (2016). Total synthesis and preliminary SAR study of (±)-merochlorins A and B. Org Biomol Chem 14, 198–205. https://doi.org/10.1039/c5ob01946j.

Bacterial Pathogenesis and Host Adaptation

We employ CRISPRi-seq and complementary approaches to uncover key virulence factors and regulatory networks that drive infection and host adaptation in pathogens such as K. pneumoniae, S. pneumoniae, S. aureus and P. aeruginosa.

Related Publications

  1. Liu, X., Kimmey, J.M., Matarazzo, L., de Bakker, V., Van Maele, L., Sirard, J.-C., Nizet, V., and Veening, J.-W. (2021). Exploration of Bacterial Bottlenecks and Streptococcus pneumoniae Pathogenesis by CRISPRi-Seq. Cell Host & Microbe 29, 107-120.e6. https://doi.org/10.1016/j.chom.2020.10.001
  2. Liu, X., Van Maele, L., Matarazzo, L., Soulard, D., Alves Duarte da Silva, V., de Bakker, V., Dénéréaz, J., Bock, F.P., Taschner, M., Ou, J., et al. (2024). A conserved antigen induces respiratory Th17-mediated broad serotype protection against pneumococcal superinfection. Cell Host Microbe 32, 304-314.e8. https://doi.org/10.1016/j.chom.2024.02.002
  3. Zhang, B., Liu, X., Lambert, E., Mas, G., Hiller, S., Veening, J.-W., and Perez, C. (2020). Structure of a proton-dependent lipid transporter involved in lipoteichoic acids biosynthesis. Nat Struct Mol Biol 27, 561–569. https://doi.org/10.1038/s41594-020-0425-5
  4. De Bakker, V., Liu, X., Tang, J., Barbisan, M., Baker, J.L., and Veening, J.-W. (2025). Multi-omics profiling reveals atypical sugar utilization and identifies a key membrane composition regulator in Streptococcus pneumoniae. Preprint, https://doi.org/10.1101/2025.06.13.659575
  5. Barbuti, M.D., Lambert, E., Myrbråten, I.S., Ducret, A., Stamsås, G.A., Wilhelm, L., Liu, X., Salehian, Z., Veening, J.-W., Straume, D., et al. (2024). The function of CozE proteins is linked to lipoteichoic acid biosynthesis in Staphylococcus aureus. mBio 15, e0115724. https://doi.org/10.1128/mbio.01157-24
  6. Minhas, V., Domenech, A., Synefiaridou, D., Straume, D., Brendel, M., Cebrero, G., Liu, X., Costa, C., Baldry, M., Sirard, J.-C., et al. (2023). Competence remodels the pneumococcal cell wall exposing key surface virulence factors that mediate increased host adherence. PLoS Biol 21, e3001990. https://doi.org/10.1371/journal.pbio.3001990
  7. Zhu, D., Wang, L., Shang, G., Liu, X., Zhu, J., Lu, D., Wang, L., Kan, B., Zhang, J.-R., and Xiang, Y. (2014). Structural biochemistry of a Vibrio cholerae dinucleotide cyclase reveals cyclase activity regulation by folates. Mol Cell 55, 931–937. https://doi.org/10.1016/j.molcel.2014.08.001
  8. He, L., Nair, M.K.M., Chen, Y., Liu, X., Zhang, M., Hazlett, K.R.O., Deng, H., and Zhang, J.-R. (2016). The Protease Locus of Francisella tularensis LVS Is Required for Stress Tolerance and Infection in the Mammalian Host. Infect Immun 84, 1387–1402. https://doi.org/10.1128/IAI.00076-16
  9. Wen, Z., Sertil, O., Cheng, Y., Zhang, S., Liu, X., Wang, W.-C., and Zhang, J.-R. (2015). Sequence elements upstream of the core promoter are necessary for full transcription of the capsule gene operon in Streptococcus pneumoniae strain D39. Infect Immun 83, 1957–1972. https://doi.org/10.1128/IAI.02944-14

Collaborators

Related Publications

  1. Rengifo-Gonzalez, M., Mazzuoli, M.-V., Janssen, A.B., Rueff, A.-S., Burnier, J., Liu, X., and Veening, J.-W. (2025). Make-or-break prime editing for genome engineering in Streptococcus pneumoniae. Nat Commun 16, 3796. https://doi.org/10.1038/s41467-025-59068-8 (Prime Editing in Streptococcus pneumoniae)
  2. Liu, L., He, Y., Zhang, T., Geng, R., Hu, Y., Luo, M., Zhou, H., and Liu, X. (2024). Equip Fusobacterium nucleatum genetic tool kits with compatible shuttle vectors and engineered intermediatory E. coli strains for enhanced transformation efficiency. Preprint, https://doi.org/10.1101/2024.07.17.603877 (Genetic tools for Fn) (Resources: https://wekwikgene.wllsb.edu.cn/labs/9da86538-e3e9-4138-b775-6c4405a947b8)