Skip to main content

Publications

2018

  • 65. M Mausz, Y Chen (2018) Microbiology and ecology of methylamine metabolism in the marine environment. In Methylotrophs and Methylotroph Communities. Caister Academic Press, submitted.
  • 64. J Sun, MA Mausz, Y Chen, S Giovannoni (2018) Microbial Trimethylamine Metabolism in Marine Environments. Environmental Microbiology. in press.
  • 63. E Jameson, J Stephenson, H Jones, A Millard, AK Kaster, KJ Purdy, R Airs, JC Murrell, Y Chen*. (2018) Deltaproteobacteria (Pelobacter) and Methanococcides are responsible for choline-dependent methanogenesis in a coastal saltmarsh sediment. ISME Journal, in press.
  • 62. AF Smith, B Rihtman, R Stirrup, E Silvano, M Mausz, DJ Scanlan, Y Chen* (2018) Elucidation of glutamine lipid biosynthesis in marine bacteria reveals its importance under phosphorus deplete growth in Rhodobacteraceae. ISME Journal. In press.
  • 61. T Wei, M Quareshy, Y-Z Zhang, DJ Scanlan, Y Chen* (2018) Manganese is essential for PlcP metallophosphoesterase activity involved in lipid remodelling in abundant marine heterotrophic bacteria. Applied and Environmental Microbiology,84(15):e01109-18
  • 60. AM Howat, J Vollmers, M Taubert, C Grob, JL Dixon, JD Todd, Y Chen, A-K Kaster, JC Murrell (2018) Comparative genomics and mutational analysis reveals a novel XoxF-utilising methylotroph in the Roseobacter group isolated from the marine environment. Frontiers in Microbiology doi: 10.3389/fmicb.2018.00766
  • 59. Jameson E, Quareshy M, Chen Y (2018) Methodological considerations for the identification of choline and carnitine-degrading bacteria in the gut. Methods. 149:42-48.

2017

  • 58. Lidbury I1, Mausz M1, Scanlan DJ, Chen Y*. (2017) Identification of dimethylamine monooxygenase in marine bacteria reveals a metabolic bottleneck in the marine methylated amine degradation pathway.(1equal contribution). The ISME Journal, 11: 1592-1601.
  • 57. M Taubert, C Grob, AM Howat, OJ Burns, J Pratscher, N Jehmlich, M von Bergen, HH Richnow, Y Chen*, JC Murrell *(2017) Methylamine as a Nitrogen Source for Microorganisms from a Coastal Marine Environment Environmental Microbiology, 19(6): 2246–2257. see highlight by L Stein.
  • 56. CY Li, XL Chen, D Zhang, P Wang, Q Sheng, M Peng, BB Xie, QL Qin, PY Li, XY Zhang, HN Su, XY Song, M Shi, BC Zhou, LY Xun, Y Chen, YZ Zhang (2017) Structural mechanisms for bacterial oxidation of oceanic trimethylamine into trimethylamine N-oxide. Molecular Microbiology 103:992–1003.
  • 55. Jameson E, Taubert M, Coyotzi S, Chen Y, Eyice Ö, Schäfer H, Murrell JC, Neufeld JD, Dumont MG. (2017) DNA-, RNA-, and Protein-Based Stable-Isotope Probing for High-Throughput Biomarker Analysis of Active Microorganisms. Methods Mol Biol. 1539:57-74.

2016

  • 54. Zhu Y, Ksibe AZ, Schäfer H, Blindauer CA, Bugg TDH, Chen Y*. (2016) O2-independent demethylation of trimethylamine N-oxide by Tdm of Methylocella silvestris. The FEBS Journal. 283: 3979–3993.
  • 53. Jameson E, Doxey AC, Airs R, Purdy KJ, Murrell JC, Chen Y*. (2016) Metagenomic data-mining reveals contrasting microbial populations responsible for trimethylamine formation in human gut and marine ecosystems. Microbial Geonmics, 2(9): doi:10.1099/mgen.0.000080
  • 52. Lidbury I, Kröber E, Zhang Z, Zhu Y, Murrell JC, Chen Y*, Schäfer H* (2016) A mechanism for bacterial transformations of DMS to DMSO: a missing link in the marine organic sulfur cycle. Environmental Microbiology18(8), 2754–2766. See highlight by P Carini.
  • 51. Jameson E1, Fu T1, Brown IR,Paszkiewicz K, Purdy KJ, Frank S*, Chen Y*. (2016) Anaerobic choline metabolism in microcompartments promotes growth and swarming of Proteus mirabilis. (1equal contribution). Environmental Microbiology, 18(9) 2886-2898.
  • 50. Sibastian M, Smith AF, Gonzalez JM, Fredricks HF, Van Mooy B, Koblizek M, Brandsma J, Koster G, Mestre M, Mostajir B, Pitta P, Postle AD, Sanchez P, Gasol JM, Scanlan DJ, Chen Y. (2016) Lipid remodelling is a widespread strategy in marine heterotrophic bacteria upon phosphorus deficiency. The ISME Journal, 10: 968-978.
  • 49. Taubert, M., Grob, C., Howat, A.M., Burns, O.J., Chen, Y. Neufeld JD, and Murrell, J.C. (2016) Analysis of Active Methylotrophic Communities: When DNA-SIP Meets High-Throughput Technologies. Methods Mol Biol. 2016;1399:235-55.
  • 48. D. Kumaresan, A.M. Hillebrand-Voiculescu, D. Wisher, J. Stephenson, Y. Chen, J.C. Murrell (2016) Microbial life in unusual cave ecosystems sustained by chemosynthetic primary production. In Microbial Life of Cave Systems, Ed. AS Engel P 215-230.
  • 47. Grob, C., Taubert, M., Howat, A.M., Burns, O.J., Chen, Y. and Murrell, J.C. (2016) Chapter: Generating enriched metagenomes from active microorganisms with DNA stable isotope probing. Hydrocarbon and Lipid Microbiology Protocols 163-180.

2015

  • 46. Lidbury, I., Kimberley, G., Scanlan, D.J., Murrell, J.C. Chen, Y. (2015) Comparative genomics and mutagenesis analyses of choline metabolism in the marine Roseobacter clade. Environmental Microbiology, 17(12):5048–5062. See highlight by L Bodrossy.
  • 45. Grob, C., Taubert, M., Howat, A.M., Burns, O.J., Dixon, J.L., Richnow H.H., Jehmlich N., von Bergen M., Chen, Y. and Murrell, J.C. (2015)Combining metagenomics with metaproteomics and stable isotope probing reveals metabolic pathways used by a naturally occurring marine methylotroph. Environmental Microbiology, 17(10):4007-4018.
  • 44. Taubert, M., Grob, C., Howat, A.M., Burns, O.J., Dixon, J.L., Chen, Y. and Murrell, J.C. (2015) XoxF encoding an alternative methanol dehydrogenase is widespread in coastal marine environments. Environmental Microbiology, 17(10):3937-3948.
  • 43. Eyice, O., Namura, M., Chen, Y., Mead, A., Samavedam, S., Schäfer, H. (2015) SIP metagenomics identifies uncultivated Methylophilaceae as dimethylsulphide degrading bacteria in soil and lake sediment. The ISME Journal, 9(11): 2336–2348.
  • 42. Zhang, D., Berry, J., Zhu, D., Wang, Y., Chen, Y., Jiang, Bo., Huang, S., Langford, H., Li, G., Davision, P.A., Xu, J., Aries, E., Huang, W.E. (2015) Magnetic nanoparticle mediated isolation of functional bacteria in a complex microbial community. The ISME Journal,9 (3):603-614.
  • 41. Lidbury, I. Murrell, J.C., Chen, Y.* (2015) 'Trimethylamine and trimethylamine N-oxide are supplementary energy sources for a marine heterotrophic bacterium: implications for marine carbon and nitrogen cycling', The ISME Journal, 9 (3):610-619. (*corresponding author).
  • 40. Wischer, D., Kumaresan, D., Johnston, A., Khawand M. EI., Stephenson, J., Hillebrand-Voiculescu, A.M., Chen, Y., Murrell, J.C. (2015) Bacterial metabolism of methylated amines and identification of novel methylotrophs in Movile Cave. The ISME Journal, 9(1):195–206.

2014

2013

  • 36. Z Huang, F Ye, C Zhang, S Chen, Y Chen J Wu, M Togo, XH Xing (2013) Rational design of a tripartite fusion protein of heparinase I enables one-step affinity purification and real-time activity detection. J Biotech, 163:30¨C 37.
  • 35. S Chen, Z Huang, J Wu, Y Chen, F Ye, C Zhang, R Yatsunami, S Nakamura, X Xing (2013) Combination of site-directed mutagenesis and calcium ion addition for enhanced production of thermostable MBP-fused heparinase I in recombinant Escherichia coli. Appl. Microbiol. Biotechnol. 97(7):2907-16.

2012

  • 34. Y Wang, Y Chen, Q Zhou, S Huang, K Ning, J Xu, RM Kalin, S Rolfe, WE Huang (2012) A culture-independent approach to unravel uncultured bacteria and functional genes in a complex microbial community. PLoS ONE, 7(10): e47530.

  • 33. Y. Chen* (2012) Comparative genomics of methylated amine utilization by marine Roseobacter clade bacteria and development of functional gene markers (tmm, gmaS). Environmental Microbiology. 14(9)2308-2322. (*corresponding author).
  • 32. W-L Hung, W.G. Wade, Y. Chen, D.P. Kelly, A.P. Wood (2012) Design and evaluation of novel primers for the detection of genes encoding diverse enzymes of methylotrophy and autotrophy. Pol. J Microbiol. 61(1):11-22.

2011

  • 31. Chen, Y*. Patel, N.A., Crombie, A. Scrivens, J.H. & Murrell, J.C.* (2011) Bacterial flavin-containing monooxygenase is trimethylamine monooxygenase. Proceedings of the National Academy of Science, 108:17791-17796 (*corresponding author).
  • 30. Md.T Rahman, A Crombie, H Moussard, Y Chen and J C Murrell (2011) 'Acetate represses methane oxidation by Methylocella silvestris in a peat soil microcosm', Applied and Environmental Microbiology, 77:4234-4236.
  • 29. Y Chen*, D Kumaresan, JC Murrell (2011) Stable-isotope probing and its application in soil microbiology. Handbook of Soil Science (2nd Edition). Vol. I 28(3):30-38, Ed. PM Huang, Y Li and ME Sumner. Taylor & Francis Group. (*corresponding author).
  • 28. Md T Rahman, A Crombie, Y Chen, N Stralis-Pavese, L Bodrossy, N P McNamara, J C Murrell. (2011) The distribution and abundance of facultative methanotroph Methylocella. ISME J 5, 1061-1066.
  • 27. Y Chen, MG Dumont, JD Neufeld, JC Murrell (2011) 'Towards 'focused metagenomics': A case study combining DNA stable-isotope probing, multiple displacement amplification and metagenomics', in Handbook of Molecular Microbial Ecology, 491- 496, Editors: F J de Bruijn, John Wiley & Sons, Inc.
  • 26. A Cebron, B Louvel, P Faure, C France-Lanord, Y Chen, J C Murrell, C Leyval.(2011) Root exudates modify the diversity of active phenanthrene-degraders in an aged PAH-contaminated soil as revealed by stable isotope probing. Environmental Microbiology 13(3)722-736.
  • 25. Y Chen*, J C Murrell (2011) DNA-stable isotope probing. In Stable Isotope Probing and Related Technologies. 3-24. ((PDF Document)) Edited by JC Murrell & A Whiteley, ASM press (*corresponding author).