Chih-Horng Kuo's Profiles

Publications by Type

Research Articles | Genome Announcements | Reviews | Others

Research Articles

Chen CNN^#, Lin KM^#, Lin YC^#, Chang HY^#, Yong TC, Chiu YF, Kuo CH*, Chu HA* (2025) Comparative genomic analysis of a novel heat-tolerant and euryhaline strain of unicellular marine cyanobacterium Cyanobacterium sp. DS4 from a high-temperature lagoon. [bioRxiv preprint DOI: 10.1101/2025.01.17.633688] ^#Equal contribution.

Lopez-Agudelo JC, Goh FJ, Tchabashvili S, Huang YS, Huang CY, Lee KT, Wang YC, Wu Y, Chang HX, Kuo CH, Lai EM, Wu CH* (2024) Rhizobium rhizogenes A4-derived strains mediate hyper-efficient transient gene expression in Nicotiana benthamiana and other solanaceous plants. [bioRxiv preprint DOI: 10.1101/2024.11.30.626145]

Yang CH*, Huang J, Huyen TNBV, Liu X, Mitra S, Yu M, Zeng Q, Sundin G, Cox K, Förster H, Adaskaveg J, Kuo CH, Yuan X (2024) RejuAgro A: A novel antimicrobial for fire blight control of pome fruits and beyond. [Research Square preprint DOI: 10.21203/rs.3.rs-5050621/v1]

Hung SHW, Yu MY, Liu CH, Huang TC, Peng JH, Jang NY, Kuo CH, Ho YN, Chiang EPI, Hwang HH, Huang CC* (2024) Endophytic pyrroloquinoline quinone enhances banana growth and immunity against Fusarium wilt for plant-microbe mutualisms. [bioRxiv preprint DOI: 10.1101/2024.08.20.608638]

Chang HY, Yen HC, Chu HA, Kuo CH* (2024) Population genomics of a thermophilic cyanobacterium revealed divergence at subspecies level and possible adaptation genes. Botanical Studies 65:35. DOI: 10.1186/s40529-024-00442-y [bioRxiv preprint DOI: 10.1101/2024.08.22.609105]

Yan XH, Pei SC, Yen HC, Blanchard A, Sirand-Pugnet P, Baby V, Gasparich GE, Kuo CH* (2024) Delineating bacterial genera based on gene content analysis: a case study of the Mycoplasmatales–Entomoplasmatales clade within the class Mollicutes. Microbial Genomics 10:001321. DOI: 10.1099/mgen.0.001321 [bioRxiv preprint DOI: 10.1101/2024.08.17.608393]

Hung SHW, Yeh PH, Huang TC, Huang SY, Wu IC, Liu CH, Lin YH, Chien PR, Huang FC, Ho YN, Kuo CH, Hwang HH, Chiang EPI, Huang CC* (2024) A cyclic dipeptide for salinity stress alleviation and the trophic flexibility of endophyte provide insights into saltmarsh plant-microbe interactions. ISME Communications 4:ycae041. DOI: 10.1093/ismeco/ycae041

Fernández FD*, Yan XH, Kuo CH, Marcone C, Conci LR (2024) Improving the comprehension of pathogenicity and phylogeny in ‘Candidatus Phytoplasma meliae’ through genome characterization. Microorgamisms 12:142. DOI: 10.3390/microorganisms12010142

Hung SHW, Huang TC, Lai YC, Wu IC, Liu CH, Huarng YF, Hwang HH, Chiang EPI, Kuo CH, Huang CC* (2023) Endophytic biostimulants for smart agriculture: Burkholderia seminalis 869T2 benefits heading leafy vegetables in-field management in Taiwan. Agronomy 13:967. DOI: 10.3390/agronomy13040967

Wang SC, Chen AP, Chou SJ, Kuo CH*, Lai EM* (2023) Soil inoculation and blocker-mediated sequencing show effects of the antibacterial T6SS on agrobacterial tumorigenesis and gallobiome. mBio 14:e00177-23. DOI: 10.1128/mbio.00177-23 [bioRxiv preprint DOI: 10.1101/2022.10.28.514271] [Featured on Academia Sinica website]

Liu YH, Tseng TS, Wu CR, Cho ST, Kuo CH, Huang XJ, Cheng JY, Hsu KH, Lin KF, Liu CC, Yeh CH* (2023) Rice OsHsp16.9A interacts with OsHsp101 to confer thermotolerance. Plant Science 330:111634. DOI: 10.1016/j.plantsci.2023.111634

Lee SK, Chiang MS, Hseu ZY, Kuo CH*, Liu CT* (2022) A photosynthetic bacterial inoculant exerts beneficial effects on the yield and quality of tomato and affects bacterial community structure in an organic field. Frontiers in Microbiology 13:959080. DOI: 10.3389/fmicb.2022.959080

Cheng YI^#, Lin YC^#, Leu JY, Kuo CH*, Chu HA* (2022) Comparative analysis reveals distinctive genomic features of Taiwan hot-spring cyanobacterium Thermosynechococcus sp. TA-1. Frontiers in Microbiology 13:932840. DOI: 10.3389/fmicb.2022.932840 ^#Equal contribution.

Huang CT, Cho ST, Lin YC, Tan CM, Chiu YC, Yang JY*, Kuo CH* (2022) Comparative genome analysis of 'Candidatus Phytoplasma luffae' reveals the influential roles of potential mobile units in phytoplasma evolution. Frontiers in Microbiology 13:773608. DOI: 10.3389/fmicb.2022.773608 [bioRxiv preprint DOI: 10.1101/2021.09.09.459700]

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] [Featured on Academia Sinica website] ^#Equal contribution.

Castillo AI^#, Tsai CW^#, Su CC, Weng LW, Lin YC, Cho 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*, Yang JY* (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 CT, Cho 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 ST, Kung 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]

Acheampong G, Owusu M, Owusu-Ofori A, Osei I, Sarpong N, Sylverken A, Kung HJ, Cho ST, Kuo CH, Park SE, Marks F, Adu-Sarkodie Y, Owusu-Dabo E* (2019) Chromosomal and plasmid-mediated fluoroquinolone resistance in human Salmonella enterica infection in Ghana. BMC Infectious Diseases 19:898. DOI: 10.1186/s12879-019-4522-1

Pecher P, Moro G, Canale MC, Capdevielle S, Singh A, MacLean A, Sugio A, Kuo CH, Lopes JRS, Hogenhout SA* (2019) Phytoplasma SAP11 effector destabilization of TCP transcription factors differentially impact development and defence of Arabidopsis versus maize. PLOS Pathogens 15:e1008035. DOI: 10.1371/journal.ppat.1008035 [bioRxiv preprint DOI: 10.1101/574319] [Recommendation by Ying-Bo Mao on Faculty Opinions; DOI: 10.3410/f.736671560.793572240]

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 [Recommendation by Vitaly Citovsky on Faculty Opinions; DOI: 10.3410/f.736286615.793563521]

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 [Editor's Pick]

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

Chiu LW, Huang SC, Lee SK, Kuo CH, Lur HS*, Liu CT* (2017) Application of plant growth-promoting rhizobacteria to improve salt stress tolerance in rice (Oryza sativa L. cv. TK9) seedlings. Journal of the Agricultural Association of Taiwan 18:257-274. DOI: 10.6730/JAAT.201712_18(3-4).0004

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 [Recommendation by Alain Filloux on Faculty Opinions; DOI: 10.3410/f.726430927.793522872]

Wu WL, Lai SJ, Yang JT, Chern J. Liang SY, Chou CC, Kuo CH, Lai MC*, Wu SH* (2016) Phosphoproteomic analysis of Methanohalophilus portucalensis FDF1^T 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

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

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

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

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 flava. Biological Bulletin 226:69-80. DOI: 10.1086/BBLv226n1p69 ^#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.

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

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

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.

McGaugh SE*, Bowden RM, Kuo CH, Janzen FJ (2011) Field-measured heritability of the threshold for sex determination in a turtle with temperature dependent sex determination. Evolutionary Ecology Research 13:75-90.

Ochman H*, Worobey M, Kuo CH, Ndjango JB, Peeters M, Hahn B, Hugenholtz P (2010) Evolutionary relationships of wild hominids recapitulated by gut microbial communities. PLOS Biology 8:e1000546. DOI: 10.1371/journal.pbio.1000546 [Recommendation by Sebastian Suerbaum on Faculty Opinions; DOI: 10.3410/f.8771956.9295055]

Kuo CH, Ochman H* (2010) The extinction dynamics of bacterial pseudogenes. PLOS Genetics 6:e1001050. DOI: 10.1371/journal.pgen.1001050

Joseph SJ, Fernandez-Robledo JA, Gardner MJ, El-Sayed NM, Kuo CH, Schott EJ, Wang H, Kissinger JC*, Vasta GR* (2010) The alveolate Perkinsus marinus: biological insights from EST gene discovery. BMC Genomics 11:228. DOI: 10.1186/1471-2164-11-228

Kuo CH, Ochman H* (2009) Inferring clocks when lacking rocks: the variable rates of molecular evolution in bacteria. Biology Direct 4:35. DOI: 10.1186/1745-6150-4-35

Kuo CH, Ochman H* (2009) Deletional bias across the three domains of life. Genome Biology and Evolution 1:145-152. DOI: 10.1093/gbe/evp016

Kuo CH, Moran NA, Ochman H* (2009) The consequences of genetic drift for bacterial genome complexity. Genome Research 19:1450-1454. DOI: 10.1101/gr.091785.109 [Recommendation by Hiroshi Akashi on Faculty Opinions; DOI: 10.3410/f.1163222.623905]

Kuo CH*, Wares JP, Kissinger JC (2008) The apicomplexan whole genome phylogeny: an analysis of incongruence among gene trees. Molecular Biology and Evolution 25:2689-2698. DOI: 10.1093/molbev/msn213

Kuo CH*, Kissinger JC (2008) Consistent and contrasting properties of lineage-specific genes in the apicomplexan parasites Plasmodium and Theileria. BMC Evolutionary Biology 8:108. DOI: 10.1186/1471-2148-8-108

Kuo CH*, Avise JC (2008) Does organismal pedigree impact the magnitude of topological congruence among gene trees for unlinked loci? Genetica 132:219-225. DOI: 10.1007/s10709-007-9167-0

Kuo CH*, Corby-Harris V, Promislow DEL (2008) The unavoidable costs and unexpected benefits of parasitism: population and metapopulation models of parasite-mediated competition. Journal of Theoretical Biology 250:244-256. DOI: 10.1016/j.jtbi.2007.10.004

Kuo CH*, Avise JC (2005) Phylogeographic breaks in low-dispersal species: the emergence of concordance across gene trees. Genetica 124:179-186. DOI: 10.1007/s10709-005-2095-y

Kuo CH*, Janzen FJ (2004) Genetic effects of a persistent bottleneck on a natural population of ornate box turtles (Terrapene ornata). Conservation Genetics 5:425-437. DOI: 10.1023/B:COGE.0000041020.54140.45

Kuo CH*, Janzen FJ (2003) BottleSim: a bottleneck simulation program for long-lived species with overlapping generations. Molecular Ecology Notes 3:669-673. DOI: 10.1046/j.1471-8286.2003.00532.x [Software download at GitHub: https://github.com/chihhorngkuo/BottleSim]

Genome Announcements

Yen HC^#, Wang SC^#, Chen WM, Lai EM*, Kuo CH* (2024) Complete genome sequence of Sphingomonas sp. strain R1, a bacterium isolated from tomato (Solanum lycopersicum). Microbiology Resource Announcements 13:e00242-24. DOI: 10.1128/mra.00242-24 ^#Equal contribution.

Yao RB, Yan XH, Yen HC, Lee S, Chu CC, Hong CF*, Kuo CH* (2024) Complete genome sequence of Agrobacterium pusense Bbcg2-2, a strain isolated from blueberry crown gall in Taiwan. Microbiology Resource Announcements 13:e01083-23. DOI: 10.1128/mra.01083-23

Li NP, Yan XH, Pei SC, Hung TH, Chang TC, Bai QZ, Tai CF*, Kuo CH* (2024) Complete genome sequence of "Candidatus Phytoplasma australasiaticum" WF_GM2021, a plant pathogen associated with soybean witches' broom disease in Taiwan. Microbiology Resource Announcements 13:e00993-23. DOI: 10.1128/mra.00993-23

Hung SHW, Wu IC, Huang CC*, Kuo CH* (2023) Complete genome sequence of Erythrobacteraceae bacterium WH01K, a strain isolated from corals (Acropora sp.) in Taiwan. Microbiology Resource Announcements 12:e00830-23. DOI: 10.1128/mra.00830-23

Salazar JRB, Santos MNM*, Palaad J, Yen HC, Castellano JL, Pena LD, Amar EC, Lai EM, Kuo CH* (2023) Complete genome sequence of Vibrio parahaemolyticus strain PH1273, isolated from the aquacultured shrimp in the Philippines. Microbiology Resource Announcements 12:e00532-23. DOI: 10.1128/mra.00532-23

Cho ST, Chen AP, Chou SJ, Yan XH, Lin CP*, Kuo CH* (2023) Complete genome sequence of "Candidatus Phytoplasma cynodontis" GY2015, a plant pathogen associated with Bermuda grass white leaf disease in Taiwan. Microbiology Resource Announcements 12:e00457-23. DOI: 10.1128/mra.00457-23

Pei SC, Chen AP, Chou SJ, Hung TH*, Kuo CH* (2023) Complete genome sequence of "Candidatus Phytoplasma pruni" PR2021, an uncultivated bacterium associated with poinsettia (Euphorbia pulcherrima). Microbiology Resource Announcements 12:e00443-23. DOI: 10.1128/mra.00443-23

Li Y^#, Yan XH^#, Liu Y, Pei SC, Kuo CH*, Huang W* (2023) Complete genome sequence of "Candidatus Phytoplasma aurantifolia" TB2022, a plant pathogen associated with sweet potato little leaf disease in China. Microbiology Resource Announcements 12:e00308-23. DOI: 10.1128/mra.00308-23 ^#Equal contribution.

Yan XH^#, Lin J^#, Liu Y^#, Huang P, Liu J, Hu Q, Li Y^#, Pei SC, Huang W*, Kuo CH* (2023) Complete genome sequence of "Candidatus Phytoplasma asteris" QS2022, a plant pathogen associated with lettuce chlorotic leaf rot disease in China. Microbiology Resource Announcements 12:e00306-23. DOI: 10.1128/mra.00306-23 ^#Equal contribution.

Hung SHW, Chiu MC, Huang CC*, Kuo CH* (2022) Complete genome sequence of Curtobacterium sp. C1, a beneficial endophyte with the potential for in-plant salinity stress alleviation. Molecular Plant-Microbe Interactions 35:731-735. DOI: 10.1094/MPMI-01-22-0027-A

Cho ST, Zwolińska A, Huang W, Wouters RHM, Mugford ST, Hogenhout SA, Kuo CH* (2020) Complete genome sequence of "Candidatus Phytoplasma asteris" RP166, a plant pathogen associated with the rapeseed phyllody disease in Poland. Microbiology Resource Announcements 9:e00760-20. DOI: 10.1128/MRA.00760-20

Chou L, Lee TY, Tsai YM, Kuo CH* (2019) Complete genome sequence of Spiroplasma alleghenense PLHS-1^T (ATCC 51752), a bacterium isolated from the scorpion fly (Panorpa helena). Microbiology Resource Announcements 8:e00317-19. DOI: 10.1128/MRA.00317-19

Cho ST, Tsai YM, Chen CY*, Kuo CH* (2018) Draft genome sequence of Vibrio vulnificus 86573B, a bacterium isolated from diseased tilapia in Taiwan. Microbiology Resource Announcements 7:e00813-18. DOI: 10.1128/MRA.00813-18

Tsai YM, Lo WS, Wu PS, Cho ST, Kuo CH* (2018) Complete genome sequence of Spiroplasma monobiae MQ-1^T (ATCC 33825), a bacterium isolated from the vespid wasp (Monobia quadridens). Genome Announcements 6:e00347-18. DOI: 10.1128/genomeA.00347-18

Tsai YM, Wu PS, Lo WS, Kuo CH* (2018) Complete genome sequence of Spiroplasma floricola 23-6^T (ATCC 29989), a bacterium isolated from tulip tree (Liriodendron tulipifera L.). Genome Announcements 6:e00302-18. DOI: 10.1128/genomeA.00302-18

Cho ST, Haryono M, Chang HH, Santos MNM, Lai EM, Kuo CH* (2018) Complete genome sequence of Agrobacterium tumefaciens 1D1609. Genome Announcements 6:e00253-18. DOI: 10.1128/genomeA.00253-18

Cho ST, Chen CL, Yang Y, Wang TF*, Kuo CH* (2018) Draft genome sequence of Burkholderia sp. strain WAC0059, a bacterium isolated from the medicinal fungus Antrodia cinnamomea. Genome Announcements 6:e00027-18. DOI: 10.1128/genomeA.00027-18

Tsai YM, Lo WS, Kuo CH* (2017) Complete genome sequence of Spiroplasma corruscae EC-1^T (DSM 19793), a bacterium isolated from a lampyrid beetle (Ellychnia corrusca). Genome Announcements 5:e00964-17. DOI: 10.1128/genomeA.00964-17

Haryono M, Lo WS, Gasparich GE, Kuo CH* (2017) Complete genome sequence of Spiroplasma sp. NBRC 100390. Genome Announcements 5:e00008-17. DOI: 10.1128/genomeA.00008-17

Lo WS, Haryono M, Gasparich GE, Kuo CH* (2017) Complete genome sequence of Spiroplasma sp. TU-14. Genome Announcements 5:e01465-16. DOI: 10.1128/genomeA.01465-16

Shen WY, Lo WS, Lai YC, Kuo CH* (2016) Complete genome sequence of Spiroplasma helicoides TABS-2^T (DSM 22551), a bacterium isolated from a horse fly (Tabanus abactor). Genome Announcements 4:e01201-16. DOI: 10.1128/genomeA.01201-16

Lo WS, Gasparich GE, Kuo CH* (2016) Complete genome sequence of Spiroplasma turonicum Tab4c^T, a bacterium isolated from horse flies (Haematopota sp.). Genome Announcements 4:e01010-16. DOI: 10.1128/genomeA.01010-16

Chang SH, Cho ST, Chen CL, Yang JY*, Kuo CH* (2015) Draft genome sequence of a 16SrII-A subgroup phytoplasma associated with the purple coneflower (Echinacea purpurea) witches’-broom disease in Taiwan. Genome Announcements 3:01398-15. DOI: 10.1128/genomeA.01398-15

Lo WS, Liu PY, Kuo CH* (2015) Complete genome sequence of Spiroplasma cantharicola CC-1^T (DSM 21588), a bacterium isolated from soldier beetle (Cantharis carolinus). Genome Announcements 3:e01253-15. DOI: 10.1128/genomeA.01253-15

Lo WS, Lai YC, Lien YW, Wang TH, Kuo CH* (2015) Complete genome sequence of Spiroplasma litorale TN-1^T (DSM 21781), a bacterium isolated from green-eyed horsefly (Tabanus nigrovittatus). Genome Announcements 3:e01116-15. DOI: 10.1128/genomeA.01116-15

Huang YY, 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

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

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, Chen LL, Kuo CH* (2014) Complete genome sequence of Spiroplasma apis B31^T (ATCC 33834), a bacterium associated with May disease of honeybees (Apis mellifera). Genome Announcements 2:e01151-13. DOI: 10.1128/genomeA.01151-13

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

Reviews

Weisberg AJ*, Wu Y, Chang JH, Lai EM, Kuo CH* (2023) Virulence and ecology of agrobacteria in the context of evolutionary genomics. Annual Review of Phytopathology 61:1-23. DOI: 10.1146/annurev-phyto-021622-125009

Bertaccini A*, Arocha-Rosete Y, Contaldo N, Duduk B, Fiore N, Montano HG, Kube M, Kuo CH, Martini M, Oshima K, Quaglino F, Schneider B, Wei W, Zamorano A (2022) Revision of the 'Candidatus Phytoplasma' species description guidelines. International Journal of Systematic and Evolutionary Microbiology 72:005353. DOI: 10.1099/ijsem.0.005353

Citti C*, Dordet-Frisoni E, Nouvel LX, Kuo CH, Baranowski E (2018) Horizontal gene transfers in mycoplasmas (Mollicutes). Current Issues in Molecular Biology 29:3-22. DOI: 10.21775/cimb.029.003

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

Kuo CH, Ochman H* (2009) The fate of new bacterial genes. FEMS Microbiology Reviews 33:38-43. DOI: 10.1111/j.1574-6976.2008.00140.x

Book Chapters

Huang CT, Pei SC, Kuo CH* (2023) Genomic studies of Asian phytoplasmas. In: Phytoplasma Diseases in Asian Countries Vol III: Characterization, Epidemiology and Management. Eds. Tiwari AK, Oshima K, Yadav A, Esmaeilzadeh-Hosseini S, Hanboonsong Y, Lakhanpaul S. Elsevier. DOI: 10.1016/B978-0-323-91671-4.00002-2. ISBN: 978-0-323-91671-4.

Gasparich GE*, Kuo CH, Foissac X (2020) Spiroplasma. In: Bergey's Manual of Systematics of Archaea and Bacteria. Eds. Trujillo ME, Dedysh S, DeVos P, Hedlund B, Kämpfer P, Rainey FA, Whitman WB. Bergey’s Manual Trust. DOI: 10.1002/9781118960608.gbm01262.pub2a

Kuo CH, Ochman H*, Raghavan R (2011) The genomics of Escherichia coli and beyond. In: The Population Genetics of Bacteria: A Tribute to Thomas S. Whittam. Eds. Walk S, Feng P. American Society for Microbiology Press. ISBN: 978-1-55581-535-6.

Kissinger JC*, Kuo CH (2007) Evolution and comparative genomics of Toxoplasma gondii. In: Toxoplasma: Molecular and Cellular Biology. Eds. Ajioka JW, Soldati D. Horizon Press. ISBN: 978-1-904933-34-2.

Case Reports

Owusu M, Acheampong G, Annan A, Marfo KS, Osei I, Amuasi J, Sarpong N, Im J, Mogeni OD, Chiang HY, Kuo CH, Jeon HJ, Panzner U, Park SE, Marks F, Owusu-Dabo E*, Adu-Sarkodie Y (2019) Ralstonia mannitolilytica sepsis: a case report. Journal of Medical Case Reports 13:318. DOI: 10.1186/s13256-019-2235-0

Owusu M, Marfo KS, Acheampong G, Arthur A, Sarpong N, Im J, Mogeni OD, Annan A, Chiang HY, Kuo CH, Park SE, Marks F, Owusu‐Dabo E*, Adu‐Sarkodie Y (2018) Gonococcal sepsis in a 32-year-old female: a case report. BMC Research Notes 11:253. DOI: 10.1186/s13104-018-3346-1

Owusu M, Owusu-Dabo E*, Acheampong G, Osei I, Amuasi J, Sarpong N, Annan A, Chiang HY, Kuo CH, Park SE, Marks F, Adu-Sarkodie Y (2017) Pseudomonas oryzihabitans sepsis in a 1-year-old child with multiple skin rashes: a case report. Journal of Medical Case Reports 11:77. DOI: 10.1186/s13256-017-1230-6

Conference Proceedings

Weisberg A*, Davis II E, Tabima J, Putnam M, Miller M, Belcher M, Grünwald N, Ream W, Lai EM, Kuo CH, Loper J, Chang J (2022) Evolution and epidemiology of global populations of nursery-associated Agrobacterium. Ecological Genetics 20:26-27. DOI: 10.17816/ecogen112374

Cho ST, Kung HJ, Kuo CH* (2019) Genomic similarities among 16SrI phytoplasmas and implications on species boundaries. Phytopathogenic Mollicutes 9:73-74. DOI: 10.5958/2249-4677.2019.00037.9

卓舒婷, 林長平, 郭志鴻* (2016) 植物菌質體之比較基因體學探討. 重要植物病原細菌與菌質體研討會: pp. 63–80. 國立中興大學植物病理學系.

Commentaries

Balish M, Bertaccini A, Blanchard A, Brown DR*, Browning G, Chalker V, Frey J, Gasparich G, Hoelzle L, Knight T, Knox C, Kuo CH, Manso-Silván L, May M, Pollack JD, Ramirez AS, Spergser J, Taylor-Robinson D, Volokhov D, Zhao Y (2019) Recommended rejection of the names Malacoplasma gen. nov., Mesomycoplasma gen. nov., Metamycoplasma gen. nov., Metamycoplasmataceae fam. nov., Mycoplasmoidaceae fam. nov., Mycoplasmoidales ord. nov., Mycoplasmoides gen. nov., Mycoplasmopsis gen. nov. [Gupta, Sawnani, Adeolu, Alnajar and Oren 2018] and all proposed species comb. nov. therein. International Journal of Systematic and Evolutionary Microbiology 69:3650–3653. DOI: 10.1099/ijsem.0.003632

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

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

Kuo CH*, Janzen FJ (2007) Longevity, overlapping generations, and conservation of turtle populations. Turtle and Tortoise Newsletter 11:18-23.

Editorials

Fukatsu T*, Kakizawa S, Harumoto T, Sugio A, Kuo CH (2024) Editorial: Spiroplasma, mycoplasma, phytoplasma, and other genome-reduced and wall-less Mollicutes: their genetics, genomics, mechanics, interactions and symbiosis with insects, other animals and plants. Frontiers in Microbiology 15:1477536. DOI: 10.3389/fmicb.2024.1477536

Czajkowski R*, Zhu L, Kuo CH, Li Z (2024) Editorial: Insights in microbial symbioses 2022/2023. Frontiers in Microbiology 15:1367452. DOI: 10.3389/fmicb.2024.1367452

Others

Gasparich GE*, Kuo CH, Manso-Silván L, Blanchard A, Balish MF (2024) International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Mollicutes: minutes of the closed meeting, 7 July 2024, Gran Canaria, Spain. International Journal of Systematic and Evolutionary Microbiology 74:006576. DOI: 10.1099/ijsem.0.006576

Popular Science

林婷嫻, 張語辰, 郭志鴻 (2017/10/02) 宛若細菌偵探的演化生物學家郭志鴻. 中央研究院研之有物人物訪談. 中央研究院. [link]

羅文穗, 郭志鴻* (2015/10/29) 蚊科昆蟲共生菌的致病基因演化. 中央研究院週報第1540期知識天地. 中央研究院. [PDF]

Discussions related to microbiology, mostly written in Traditional Chinese (i.e., 中文微生物科普短文), are posted in the Facebook group MiTalk 微生物生態情報網.

Kuo Lab || Evolutionary and Functional Genomics of Symbiotic Bacteria

Institute of Plant and Microbial Biology, Academia Sinica, Taiwan