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

  • 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
  • Bondage DD, Lin JS, Ma LS, Kuo CH, Lai EM* (2016) VgrG C terminus confers the type VI effector transport specificity and is required for binding with PAAR and adaptor–effector complex. Proceedings of the National Academy of Sciences of the United States of America 113: E3931-E3940. DOI: 10.1073/pnas.1600428113
  • Wu WL, Lai SJ, Yang JT, Chern J. Liang SY, Chou CC, Kuo CH, Lai MC*, Wu SH* (2016) Phosphoproteomic analysis of Methanohalophilus portucalensis FDF1T identified the role of protein phosphorylation in methanogenesis and osmoregulation. Scientific Reports 6: 29013. DOI: 10.1038/srep29013
  • Chang CLT, Chung CY, Kuo CH, Kuo TF, Yang CW*, Yang WC* (2016) Beneficial effect of Bidens pilosa on body weight gain, food conversion ratio, gut bacteria and coccidiosis in chickens. PLOS ONE 11: e0146141. DOI: 10.1371/journal.pone.0146141
  • Lo WS, Huang YY, Kuo CH* (2016) Winding paths to simplicity: genome evolution in facultative insect symbionts. FEMS Microbiology Reviews 40: 855-874. DOI: 10.1093/femsre/fuw028
  • Cho ST, Chang HH, Egamberdieva D, Kamilova F, Lugtenberg B, Kuo CH* (2015) Genome analysis of Pseudomonas fluorescens PCL1751: a rhizobacterium that controls root diseases and alleviates salt stress for its plant host. PLOS ONE 10: e0140231. DOI: 10.1371/journal.pone.0140231
  • Lo WS, Gasparich GE, Kuo CH* (2015) Found and lost: the fates of horizontally acquired genes in arthropod-symbiotic Spiroplasma. Genome Biology and Evolution 7: 2458-2472. DOI: 10.1093/gbe/evv160
  • Kuo CH* (2015) Scrambled and not-so-tiny genomes of fungal endosymbionts. Proceedings of the National Academy of Sciences of the United States of America 112: 7622-7623. DOI: 10.1073/pnas.1508360112
  • Huang HH, Cho ST, Lo WS, Wang YC, Lai EM, Kuo CH* (2015) Complete genome sequence of Agrobacterium tumefaciens Ach5. Genome Announcements 3: e00570-15. DOI: 10.1128/genomeA.00570-15
  • McGaugh SE*, Bronikowski AM*, Kuo CH*, Reding DM, Addis EA, Flagel LE, Janzen FJ, Schwartz TS* (2015) Rapid molecular evolution across amniotes of the IIS/TOR network. Proceedings of the National Academy of Sciences of the United States of America 112: 7055-7060. DOI: 10.1073/pnas.1419659112
  • Paredes JC, Herren JK, Schüpfer F, Marin R, Clavero S, Kuo CH, Lemaitre B*, Béven L* (2015) Genome sequence of the Drosophila melanogaster male-killing Spiroplasma MSRO endosymbionts. mBio 6: e02437-14. DOI: 10.1128/mBio.02437-14
  • Chang HH, Cho ST, Canale MC, Mugford ST, Lopes JRS, Hogenhout SA, Kuo CH* (2015) Complete genome sequence of "Candidatus Sulcia muelleri" ML, an obligate nutritional symbiont of maize leafhopper (Dalbulus maidis). Genome Announcements 3: e01483-14. DOI: 10.1128/genomeA.01483-14
  • Liu AC, Chou CY, Chen LL, Kuo CH* (2015) Bacterial community dynamics in a swine wastewater anaerobic reactor revealed by 16S rDNA sequence analysis. Journal of Biotechnology 194: 124-131. DOI: 10.1016/j.jbiotec.2014.11.026
  • Su HJ, Hogenhout SA, Al-Sadi AM, Kuo CH* (2014) Complete chloroplast genome sequence of Omani lime (Citrus aurantiifolia) and comparative analysis within the rosids. PLoS ONE 9: e113049. DOI: 10.1371/journal.pone.0113049
  • Lo WS, Chen HJ, Chen CY, Kuo CH* (2014) Complete genome sequence of Vibrio vulnificus 93U204, a bacterium isolated from diseased tilapia in Taiwan. Genome Announcements 2: e01005-14. DOI: 10.1128/genomeA.01005-14
  • Ku C, Lo WS, Kuo CH* (2014) Molecular evolution of the actin-like MreB protein gene family in wall-less bacteria. Biochemical and Biophysical Research Communications 446: 927-932. DOI: 10.1016/j.bbrc.2014.03.039
  • Radjacommare R, Usharani R, Kuo CH, Fu H* (2014) Distinct phylogenetic relationships and biochemical properties of Arabidopsis ovarian tumor-related deubiquitinases support their functional differentiation. Frontiers in Plant Science 5: 84. DOI: 10.3389/fpls.2014.00084
  • Tung CH#, Cheng YR#, Lin CY, Ho JS, Kuo CH, Yu JK*, Su YH* (2014) A new copepod with transformed body plan and unique phylogenetic position parasitic in the acorn worm Ptychodera flavaBiological Bulletin 226: 69-80#Equal contribution.
  • Chang TH#, Lo WS#, Ku C, Chen LL, Kuo CH* (2014) Molecular evolution of the substrate utilization strategies and putative virulence factors in mosquito-associated Spiroplasma species. Genome Biology and Evolution 6: 500-509. DOI: 10.1093/gbe/evu033 #Equal contribution.
  • Ku C, Lo WS, Chen LL, Kuo CH* (2014) Complete genome sequence of Spiroplasma apis B31T (ATCC 33834), a bacterium associated with May disease of honeybees (Apis mellifera). Genome Announcements 2: e01151-13. DOI: 10.1128/genomeA.01151-13
  • Lo WS, Ku C, Chen LL, Chang TH, Kuo CH* (2013) Comparison of metabolic capacities and inference of gene content evolution in mosquito-associated Spiroplasma diminutum and S. taiwanense. Genome Biology and Evolution 5: 1512-1523. DOI: 10.1093/gbe/evt108
  • Ku C, Lo WS, Chen LL, Kuo CH* (2013) Complete genomes of two dipteran-associated spiroplasmas provided insights into the origin, dynamics, and impacts of viral invasion in Spiroplasma. Genome Biology and Evolution 5: 1151-1164. DOI: 10.1093/gbe/evt084
  • Lo WS, Chen LL, Chung WC, Gasparich GE, Kuo CH* (2013) Comparative genome analysis of Spiroplasma melliferum IPMB4A, a honeybee-associated bacterium. BMC Genomics 14: 22. DOI: 10.1186/1471-2164-14-22
  • Shelomi M, Lo WS, Kimsey LS, Kuo CH* (2013) Analysis of the gut microbiota of walking sticks (Phasmatodea). BMC Research Notes 6: 368. DOI: 10.1186/1756-0500-6-368
  • Ku C, Chung WC, Chen LL, Kuo CH* (2013) The complete plastid genome sequence of Madagascar periwinkle Catharanthus roseus (L.) G. Don: plastid genome evolution, molecular marker identification, and phylogenetic implications in asterids. PLoS ONE 8: e68518. DOI: 10.1371/journal.pone.0068518
  • Ku C, Hu JM, Kuo CH* (2013) Complete plastid genome sequence of the basal asterid Ardisia polysticta Miq. and comparative analyses of asterid plastid genomes. PLoS ONE 8: e62548. DOI: 10.1371/journal.pone.0062548
  • Chung WC, Chen LL, Lo WS, Kuo PA, Tu J, Kuo CH* (2013) Complete genome sequence of Serratia marcescens WW4. Genome Announcements 1: e00126-13. DOI: 10.1128/genomeA.00126-13
  • Kuo PA, Kuo CH, Lai YK, Graumann P, Tu J* (2013) Phosphate limitation induces the intergeneric inhibition of Pseudomonas aeruginosa by Serratia marcescens isolated from paper machines. FEMS Microbiology Ecology 84: 577-587. DOI: 10.1111/1574-6941.12086
  • Ku C, Lo WS, Kuo CH* (2013) Horizontal transfer of potential mobile units in phytoplasmas. Mobile Genetic Elements 3: e26145. DOI: 10.4161/mge.26145
  • Chung WC#, Chen LL#, Lo WS, Lin CP, Kuo CH* (2013) Comparative analysis of the peanut witches’-broom phytoplasma genome reveals horizontal transfer of potential mobile units and effectors. PLoS ONE 8: e62770. DOI: 10.1371/journal.pone.0062770 #Equal contribution.
  • Chen LL#, Chung WC#, Lin CP, Kuo CH* (2012) Comparative analysis of gene content evolution in phytoplasmas and mycoplasmas. PLoS ONE 7: e34407. DOI: 10.1371/journal.pone.0034407 #Equal contribution.
Shu-Ting Cho (卓舒婷)
Project Manager
Yu-Chen Lin (林宥辰)
Research Assistant

Hung-Jui Kung (龔泓睿)
Research Assistant
Lin Chou (周林)
Research Assistant
Ting-Yi Lee (李庭儀)
M.S. student