Kuo, Chih-Horng (郭志鴻)

Associate Research Fellow

  • Ph.D. (2008) Genetics, University of Georgia
  • M.S. (2003) Genetics, Iowa State University
  • B.S. (1998) Botany, National Taiwan University
  • +886-2-2787-1044(Lab)
  • +886-2-2787-1127(Office)
  • chk@gate.sinica.edu.tw
  • Evolutionary and Functional Genomics of Symbiotic Bacteria
  • Lab Website
  • Google Scholar

Research Interests: Evolutionary and Functional Genomics of Symbiotic Bacteria

        In microbial evolution, the development of a host-dependent lifestyle often has profound effects on the genome architecture. To better understand the evolutionary processes involved, as well as the functional consequences of changes in the gene content, we utilize genomics and transcriptomics tools to conduct comparative analyses among bacteria with different ecological niches. The recent research projects in our lab are based on two main study systems:

(1) Wall-less bacteria in the class Mollicutes

        The class Mollicutes contains diverse groups of host-associated bacteria with no cell wall, including ‘Candidatus Phytoplasma’ (plant pathogens), Mycoplasma (vertebrate pathogens), and Spiroplasma (mostly insect symbionts, with few plant pathogens). The last group is of particular interest because it contains species that are harmless commensals, beneficial symbionts, or pathogens with varying levels of host-dependence. Thus, comparative studies within this genus can improve our understanding of the evolutionary transitions between different lifestyles and shed light on the evolution of pathogenicity in bacteria. Our short-term goal in this system is to investigate the genetic mechanisms that may explain the phenotypic differences among species with distinct ecological niches. In the long-term, we plan to generate sufficient genomic data in this previously understudied genus such that comprehensive comparisons among different groups within Mollicutes will become possible.

(2) Plant-associated Agrobacterium

        The plant-associated bacteria in the genus Agrobacterium are important because of their biotechnological use in plant transformation and their phytopathogenicity that impacts agriculture. Through collaboration with Dr. Erh-Min Lai in our institute, we are interested in the genetic diversity, genome evolution, and functional characterization across different subgroups within this diverse genus.

All publication list

Selected publication list

  • Chou L#Lin YC#Haryono M, Santos MNM, Cho ST, Weisberg AJ, Wu CF, Chang JH, Lai EM, Kuo CH* (2022) Modular evolution of secretion systems and virulence plasmids in a bacterial species complex. BMC Biology 20:16. DOI: 10.1186/s12915-021-01221-y [bioRxiv preprint DOI: 10.1101/2021.05.20.444927#Equal contribution.
  • Castillo AI#, Tsai CW#, Su CC, Weng LW, Lin YCCho ST, Almeida RPP, Kuo CH* (2021) Genetic differentiation of Xylella fastidiosa following the introduction into Taiwan. Microbial Genomics 7:000727. DOI: 10.1099/mgen.0.000727 [bioRxiv preprint DOI: 10.1101/2021.03.24.436723#Equal contribution.
  • Tan CM#Lin YC#, Li JR, Chien YY, Wang CJ, Chou L, Wang CW, Chiu YC, Kuo CH*, JY Yang* (2021) Accelerating complete phytoplasma genome assembly by immunoprecipitation-based enrichment and MinION-based DNA sequencing for comparative analyses. Frontiers in Microbiology 12:766221. DOI: 10.3389/fmicb.2021.766221 #Equal contribution.
  • Kuo CH, Huang PY, Sheu SY, Sheu DS, Jheng LC, Chen WM* (2021) Zophobihabitans entericus gen. nov., sp. nov., a new member of the family Orbaceae isolated from the gut of a superworm Zophobas morio. International Journal of Systematic and Evolutionary Microbiology 71:005081. DOI: 10.1099/ijsem.0.005081
  • Huang W, MacLean A, Sugio A, Maqbool A, Busscher M, Cho ST, Kamoun S, Kuo CH, Immink RGH, Hogenhout SA* (2021) Parasitic modulation of host development by ubiquitin-independent protein degradation. Cell 184:5201-5214. [Issue Cover] DOI: 10.1016/j.cell.2021.08.029 [bioRxiv preprint DOI: 10.1101/2021.02.15.430920]
  • Wu CF, Weisberg AJ, Davis EW, Chou L, Khan S, Lai EM, Kuo CH, Chang JH* (2021) Diversification of the type VI secretion system in agrobacteria. mBio 12:e01927-21. DOI: 10.1128/mBio.01927-21
  • Hwang HH*, Huang FC, Chien PR, Hung SH, Kuo CH, Deng WL, Chiang EPI, Huang CC* (2021) A plant endophytic bacterium, Burkholderia seminalis strain 869T2, promotes plant growth in Arabidopsis, pai tsai, Chinese amaranth, lettuces and other vegetables. Microorganisms 9:1703. DOI: 10.3390/microorganisms9081703
  • Weng LW#Lin YC#, Su CC, Huang CTCho ST, Chen AP, Chou SJ, Tsai CW*, Kuo CH* (2021) Complete genome sequence of Xylella taiwanensis and comparative analysis of virulence gene content with Xylella fastidiosa. Frontiers in Microbiology 12:684092. DOI: 10.3389/fmicb.2021.684092 [bioRxiv preprint DOI: 10.1101/2021.03.08.434500#Equal contribution.
  • Cho STKung HJ, Huang W, Hogenhout SA, Kuo CH* (2020) Species boundaries and molecular markers for the classification of 16SrI phytoplasmas inferred by genome analysis. Frontiers in Microbiology 11:1531. DOI: 10.3389/fmicb.2020.01531 [bioRxiv preprint DOI: 10.1101/2020.01.31.928135]
  • Weisberg AJ, Davis EW, Tabima J, Belcher MS, Miller M, Kuo CH, Loper JE, Grünwald NJ, Putnam ML, Chang JH* (2020) Unexpected conservation and global transmission of agrobacterial virulence plasmids. Science 368:eaba5256. DOI: 10.1126/science.aba5256
  • Cheng YI#Chou L#, Chiu YF, Hsueh HT, Kuo CH*, Chu HA* (2020) Comparative genomic analysis of a novel strain of Taiwan hot-spring cyanobacterium Thermosynechococcus sp. CL-1. Frontiers in Microbiology 11:82. DOI: 10.3389/fmicb.2020.00082 #Equal contribution.
  • Santos MNM, Cho ST, Wu CF, Chang CJ, Kuo CH, Lai EM* (2020) Redundancy and specificity of type VI secretion vgrG loci in antibacterial activity of Agrobacterium tumefaciens 1D1609 strain. Frontiers in Microbiology 10:3004. DOI: 10.3389/fmicb.2019.03004 [bioRxiv preprint DOI: 10.1101/740209]
  • Cho ST, Lin CP, Kuo CH* (2019) Genomic characterization of the periwinkle leaf yellowing (PLY) phytoplasmas in Taiwan. Frontiers in Microbiology 10: 2194. DOI: 10.3389/fmicb.2019.02194
  • Gasparich GE*, Kuo CH (2019) Genome analysis-based union of the genus Mesoplasma with the genus Entomoplasma. International Journal of Systematic and Evolutionary Microbiology 69: 2735-2738. DOI: 10.1099/ijsem.0.003548
  • Haryono M, Cho ST, Fang MJ, Chen AP, Chou SJ, Lai EM, Kuo CH* (2019) Differentiations in gene content and expression response to virulence induction between two Agrobacterium strains. Frontiers in Microbiology 10: 1554. DOI: 10.3389/fmicb.2019.01554
  • Wu CF, Santos MNM, Cho ST, Chang HH, Tsai YM, Smith DA, Kuo CH*, Chang JH*, Lai EM* (2019) Plant pathogenic Agrobacterium tumefaciens strains have diverse type VI effector-immunity pairs and vary in in planta competitiveness. Molecular Plant-Microbe Interactions 32: 961-971. DOI: 10.1094/MPMI-01-19-0021-R
  • Seruga Music M*, Samarzija I, Hogenhout SA*, Haryono M, Cho ST, Kuo CH* (2019) The genome of 'Candidatus Phytoplasma solani' strain SA-1 is highly dynamic and prone to adopting foreign sequences. Systematic and Applied Microbiology 42: 117-127. DOI: 10.1016/j.syapm.2018.10.008
  • Haryono M, Tsai YM, Lin CT, Huang FC, Ye YC, Deng WL, Hwang HH*, Kuo CH* (2018) Presence of an Agrobacterium-type tumor-inducing plasmid in Neorhizobium sp. NCHU2750 and the link to phytopathogenicity. Genome Biology and Evolution 10: 3188-3195. DOI: 10.1093/gbe/evy249
  • Lo KJ, Lin SS, Lu CW, Kuo CH*, Liu CT* (2018) Whole-genome sequencing and comparative analysis of two plant-associated strains of Rhodopseudomonas palustris (PS3 and YSC3). Scientific Reports 8: 12769. DOI: 10.1038/s41598-018-31128-8
  • Lo WS, Gasparich GE, Kuo CH* (2018) Convergent evolution among ruminant-pathogenic Mycoplasma involved extensive gene content changes. Genome Biology and Evolution 10: 2130-2139. DOI: 10.1093/gbe/evy172
  • Perry BW, Card DC, McGlothlin JW, Pasquesi GIM, Adams RH, Schield DR, Hales NR, Corbin AB, Demuth JP, Hoffmann FG, Vandewege MW, Schott RK, Bhattacharyya N, Chang BSW, Casewell NR, Whiteley G, Reyes-Velasco J, Mackessy SP, Gamble T, Storey KB, Biggar KK, Passow CN, Kuo CH, McGaugh SE, Bronikowski AM, de Koning J, Edwards SV, Pfrender ME, Minx P, Brodie ED, Brodie ED, Warren WC, Castoe TA* (2018)Molecular adaptations for sensing and securing prey and insight into amniote genome diversity from the garter snake genome. Genome Biology and Evolution 10: 2110-2129. DOI: 10.1093/gbe/evy157
  • Tsai YM, Chang A, Kuo CH* (2018) Horizontal gene acquisitions contributed to genome expansion in insect-symbiotic Spiroplasma clarkii. Genome Biology and Evolution 10: 1526-1532. DOI: 10.1093/gbe/evy113
  • Lo WS, Kuo CH* (2017) Horizontal acquisition and transcriptional integration of novel genes in mosquito-associated Spiroplasma. Genome Biology and Evolution 9: 3246-3259. DOI: 10.1093/gbe/evx244
  • Huang YY, Cho ST, Haryono M, Kuo CH* (2017) Complete chloroplast genome sequence of common bermudagrass (Cynodon dactylon (L.) Pers.) and comparative analysis within the family Poaceae. PLOS ONE 12: e0179055. DOI: 10.1371/journal.pone.0179055
  • Orlovskis Z, Canale MC, Haryono M, Lopes JRS, Kuo CH*, Hogenhout S* (2017) A few sequence polymorphisms among isolates of maize bushy stunt phytoplasma associate with organ proliferation symptoms in infected maize plants. Annals of Botany 119: 869-884. DOI: 10.1093/aob/mcw213
Yu-Chen Lin (林宥辰)
Research Assistant

Hung-Jui Kung (龔泓睿)
Research Assistant
Yu Wu (吳宇)
Ph.D. student