Research

The Claesen group aims to functionally characterize molecular mechanisms that control bacterial interspecies and microbe-host interactions in the human microbiome. Bacteria use small molecule chemicals to mediate these interactions and the genetic information required for their production is typically encoded in one physical location of the bacterial chromosome, in biosynthetic gene clusters (BGCs). Using in silico techniques, we identified several widespread families of BGCs that we are now characterizing experimentally, prioritizing on the BGCs predicted to be involved in modulation of community composition or interaction with the host immune system. Our research will contribute to a better mechanistic understanding of the microbes that live in our gut and skin, leading to the discovery of druggable small molecules, new targets for antibacterial therapy and beneficial bacterial strains that can be employed for intervention therapies. The areas of expertise in the Claesen group include microbiology, bacterial genetics and synthetic biology, small molecule biosynthesis and biochemistry, and animal models for microbiome studies of metabolic disease and cancer development.

Claesen group publications:

18. Ozcam M, JH Oh, R Tocmo, D Acharya, S Zhang, S Ruiz-Ramírez, F Li, CC Cheng, E Vivas, FE Rey, J Claesen, T Bugni, J Walter, and JP van Pijkeren. A secondary metabolite drives intraspecies antagonism in a gut symbiont that is inhibited by peptidoglycan acetylation. bioRxiv, doi.org/10.1101/2021.06.11.448121 (preprint)

17. Chambers LM, EL Esakov, C Braley, L Trestan, Z Alali, D Bayik, JD Lathia, N Sangwan, P Bazeley, AS Joehlin-Price, M Dwidar, A Hajjar, PP Ahern, J Claesen, P Rose, R Vargas, C Michener, and O Reizes. Disruption of the gut microbiota attenuates epithelial ovarian cancer sensitivity to cisplatin therapy. bioRxiv, doi.org/10.1101/2020.06.16.155226 (preprint)

16. Johnston I, LJ Osborn*, RL Markley*, EA McManus, A Kadam, KB Schultz, N Nagajothi, PP Ahern, JM Brown, and J Claesen (2021). Identification of essential genes for Escherichia coli aryl polyene biosynthesis and function in biofilm formation. NPJ Biofilms Microbiomes, 7: 56. (*equal contribution)

15. Orabi D*, LJ Osborn*, K Fung, W Massey, AJ Horak III, F Aucejo, I Choucair, B DeLucia, Z Wang, J Claesen, and JM Brown (2021). A surgical method for continuous intraportal infusion of gut microbial metabolites in mice. JCI Insight, 6(9): e145607. (*equal contribution)

14. Claesen J, JB Spagnolo, S Flores Ramos, KL Kurita, AL Byrd, AA Aksenov, AV Melnik, WR Wong, S Wang, RD Hernandez, MS Donia, PC Dorrestein, HH Kong, JA Segre, RG Linington, MA Fischbach, and KP Lemon (2020). A Cutibacterium acnes antibiotic modulates human skin microbiota composition in hair follicles. Sci Transl Med, 12(570): eaay5445.

13. Bell A, J Brunt, E Crost, L Vaux, R Nepravishta, CD Owen, D Latousakis, A Xiao, W Li, X Chen, MA Walsh, J Claesen, J Angulo, GH Thomas, and N Juge (2019). Elucidation of a sialic acid metabolism pathway in mucus-foraging Ruminococcus gnavus unravels mechanisms of bacterial adaptation to the gutNat Microbiol, 4(12): 2393-2404.

12. Ozcam M, R Tocmo, JH Oh, A Afrazi, JD Mezrich, S Roos, J Claesen, and JP van Pijkeren (2019). The gut symbionts Lactobacillus reuteri R2lc and 2010 encode a polyketide synthase cluster that activates the mammalian aryl-hydrocarbon receptorAppl Environ Microbiol, 85(10): e01661-18.

11. Claesen J (2018). Topical antiseptics and the skin microbiotaJ Investig Dermatol, 138(10):2106-2107. (commentary)


Prior publications:

10. Ridaura V, N Bouladoux, J Claesen, E Chen, AL Byrd, M Constantinides, S Tamoutounour, MA Fischbach, and Y Belkaid (2018). Contextual control of skin immunity and inflammation by CorynebacteriumJ Exp Med, 215(3): 785-799.

9. Smanski MJ, H Zhou, J Claesen, B Shen, MA Fischbach, and CA Voigt (2016). Synthetic biology to access and expand nature’s chemical diversityNat Rev Microbiol, 14(3): 135-149. (review)

8. Thanapipatsiri A, J Claesen, JP Gomez-Escribano, M Bibb, and A Thamchaipenet (2015). A Streptomyces coelicolor host for the heterologous expression of Type III polyketide synthase genesMicrob Cell Fact, 14(1): 145.

7. Medema MH, R Kottmann, P Yilmaz, M Cummings, JB Biggins, K Blin, I de Bruijn, YH Chooi, J Claesen, RC Coates, et al. (2015). Minimum information about a biosynthetic gene clusterNat Chem Biol, 11(9): 625-631.

6. Claesen J, and MA Fischbach (2015). Synthetic microbes as drug delivery systemsACS Synth Biol, 4(4): 358-364. (review)

5. Wollenberg MS*, J Claesen*, IF Escapa, KL Aldridge, MA Fischbach, and KP Lemon (2014). Propionibacterium-produced coproporphyrin III induces Staphylococcus aureus aggregation and biofilm formationmBio, 5(4): e01286-01214. (*equal contribution)

4. Cimermancic P*, MH Medema*, J Claesen*, K Kurita, LC Wieland Brown, K Mavrommatis, A Pati, PA Godfrey, M Koehrsen, J Clardy, BW Birren, E Takano, A Sali, RG Linington, and MA Fischbach (2014). Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clustersCell, 158(2): 412-421. (*equal contribution)

3. Claesen J, and MJ Bibb (2011). Biosynthesis and regulation of grisemycin, a new member of the linaridin family of ribosomally synthesized peptides produced by Streptomyces griseus IFO 13350J Bacteriol, 193(10): 2510-2516.

2. Claesen J, and M Bibb (2010). Genome mining and genetic analysis of cypemycin biosynthesis reveal an unusual class of posttranslationally modified peptidesProc Natl Acad Sci USA, 107(37): 16297-16302.

1. Goto Y, B Li, J Claesen, Y Shi, MJ Bibb, and WA van der Donk (2010). Discovery of unique lanthionine synthetases reveals new mechanistic and evolutionary insightsPLoS Biol, 8(3): e1000339.