1. Lee, DH., Bu, JH., Kim, M., Cha
CJ. 2026. The prevalence and diversity of carbapenem-hydrolyzing
bacteria and β-lactamases in the aquatic environment
of the Han River, South Korea. J Hazard Mater. Vol. 21., page 101078.,
https://doi.org/10.1016/j.hazadv.2026.101078
2. Kim, ST., Kim, M., Cha CJ. 2026.
Sphingomonas degradans sp. nov. and Sphingomonas paludis sp. nov.,
isolated from the Han River and a wetland in South Korea. J Microbiol. Vol.
64(1): e2510010. https://doi.org/10.71150/jm.2510010
3. Geeta Chhetri, Jong-Min Jeon, Gayeon
Hwang, Tae-Rim Choi, Baeksoo Park, Yung-Hun Yang, Sang-Hyoun Kim, Chang-Jun
Cha, Jeong-Jun Yoon. 2026. First Report of bio-plastic degradation
by a newly isolated Aquincola sp. From the eggplant rhizosphere. Int
J Biol Macromol. Vol. 344, Part 1, Page 150516, https://doi.org/10.1016/j.ijbiomac.2026.150516
4. Kim, YS., Yerang Yang., Kim, M.,
Lee, DH., Cha, CJ. 2025. Genome-based classification of Paraniabella
aurantiaca gen. nov., sp. Nov., isolated from soil and taxonomic
reclassification of five species within the genus Niabella. J
Microbiol. Vol. 63, No. 10, e2505005, https://doi.org/10.71150/jm.2505005
5. Li L., Li B., Yin X., Xia Y., Yang
Y., Xu X., Lam TTY., Leung KMY., Xu F., Zhang X., Guo J., Schmitt H., Wright
GD., Midega J., Bezuidenhout C., Picão RC., Ahammad SZ., Smalla K., Djordjevic
SP., Pruden A., Vikesland P., Frigon D., Walsh F., Berendonk TU., Corno G.,
Fatta-Kassinos D., Cha, CJ., Ashbolt N., Ying G., Luo Y., Wang Y., Shen
J., Zhang Y., Yang M., Li X., Hu B., Zhu L., Wu Y., Tang S., Kan B., Zhu YG.,
Smets BF., Graham D., Honda R., Cytryn E., Donner E., Nielsen PH., van
Loosdrecht M., Gillings MR., Gaze W., Manaia CM., Alvarez PJJ., Blaser MJ.,
Topp E., Zhang T. 2025. Assessing antimicrobial resistance connectivity
across One Health sectors. Nat Water. 16(1):7319. https://doi.org/10.1038/s41467-025-62455-w.
6. Geeta Chhetri, Jeon JM., Hwang, G.,
Choi, TR., Yang, YH., Cha, CJ., Yoon, JJ. 2025. Biodegradation of
PCL, PBS, and PBAT at low temperatures by Aeromicrobium sp. JJY06: A
newly isolated strain for cold-environment plastic cleanup. J Hazard
Mater. 495:138896. https://doi.org/10.1016/j.jhazmat.2025.138896.
7. Kim, YJ., Kim, YS. & Cha, CJ.
2024. Taxonomic and genomic characterization of a siderophore-producing
bacterium, Rhodoligotrophos ferricapiens sp. nov isolated from
lettuce cultivation soil. Antonie van Leeuwenhoek 118, 43.
https://doi.org/10.1007/s10482-024-02052-xs
8. Lee, DH., Lee, K., Kim, YS., Cha
CJ. 2024. Comprehensive genomic landscape of antibiotic resistance
in Staphylococcus epidermidis. mSystems 0:e00226-24.
https://doi.org/10.1128/msystems.00226-24
9. Kim, YS., Hwang, EM., Jeong, CM., Cha
CJ. 2023. Flavobacterium psychrotrophum sp. nov. and
Flavobacterium panacagri sp. nov., Isolated from Freshwater and
Soil. J Microbiol. 61:891–901.
https://doi.org/10.1007/s12275-023-00081-1
10. Yin X, Chen X, Jiang XT, Yang Y, Li B,
Shum MH, Lam TTY, Leung GM, Rose J, Sanchez-Cid C, Vogel TM, Walsh F, Berendonk
TU, Midega J, Uchea C, Frigon D, Wright GD, Bezuidenhout C, Picão RC, Ahammad
SZ, Nielsen PH, Hugenholtz P, Ashbolt NJ, Corno G, Fatta-Kassinos D, Bürgmann
H, Schmitt H, Cha CJ, Pruden A, Smalla K, Cytryn E, Zhang Y, Yang M, Zhu
YG, Dechesne A, Smets BF, Graham DW, Gillings MR, Gaze WH, Manaia CM, van
Loosdrecht MCM, Alvarez PJJ, Blaser MJ, Tiedje JM, Topp E, Zhang T. 2023.
Toward a Universal Unit for Quantification of Antibiotic Resistance Genes in
Environmental Samples. Environ Sci Technol. doi:
10.1021/acs.est.3c00159.
11. Kim JJ, Seong HJ, Johnson TA, Cha
CJ, Sul WJ, Chae JC. 2023. Persistence of antibiotic resistance
from animal agricultural effluents to surface water revealed by genome-centric
metagenomics. J Hazard Mater. 457:131761. doi:
10.1016/j.jhazmat.2023.131761.
12. Lee, K., Raguideau, S., Sirén,
K. Asnicar F, Cumbo F, Hildebrand F, Segata N, Cha CJ*, Quince
C*. 2023. Population-level impacts of antibiotic usage on the
human gut microbiome. Nat Commun 14:1191.
doi:10.1038/s41467-023-36633-7. *Co-corresponding author
13. Kim, M., Kim, YS. & Cha CJ. 2023. Chryseobacterium
paludis sp. nov. and Chryseobacterium foetidum sp. nov. Isolated
from the Aquatic Environment, South Korea. J Microbiol. 61:37–47.
doi:10.1007/s12275-022-00008-2.
14. Kim DW,
Ahn JH, Cha CJ. 2022. Biodegradation of plastics:
mining of plastic-degrading microorganisms and enzymes using metagenomics
approaches. J Microbiol. 60(10):969-976. doi:
10.1007/s12275-022-2313-7.
15. Lee DH,
Cha JH, Kim DW, Lee K, Kim YS, Oh HY, Cho YH, Cha CJ. 2022. Colistin-degrading
proteases confer collective resistance to microbial communities during
polymicrobial infections. Microbiome. 10(1):129. doi: 10.1186/s40168-022-01315-x.
16. Oh S, Kim
Y, Choi D, Park JW, Chung SY, Maeng SK, Cha CJ. 2022.
Effects of biochar addition on the fate of ciprofloxacin an its associated
antibiotic tolerance in an activated sludge microbiome. Environ
Pollut. 1;1306:119407. doi: 10.1016/j.envpol.2022.119407.
17. Park EH,
Kim YS, Cha CJ. 2022. Commamonas fluminis sp.
nov., isolated from the Han River, Republic of korea. Int J Syst Evol
Microbiol. 72(3). doi: 10.1099/ijsem.0.005287.
18. Chau LTT,
Kim YS, Cha CJ. 2022. Pedobacter qauae sp.
nov., a multi-drug resistant bacterium isolated from fresh water. Antonie
Van Leeuwenhoek. 115(3):445-457. doi:
10.1007/s10482-022-01708-w
19. Cha JH,
Hong M and Cha CJ. 2021. Fungal β-Glycosidase Belonging
to Subfamily 4 of Glycoside Hydrolase Family 30 with Transglycosylation
Activity. J Agric Food Chem. 69(50):15261-15267. doi:
10.1021/acs.jafc.1c05197.
20. Borsetto
C, Raguideau S, Travis E, Kim DW, Lee DH,
Bottrill A, Stark R, Song L, Cha CJ, Pearson J, Quince C, Singer
AC, Wellington EMH. 2021. Impact of sulfamethoxazole on a riverine
microbiome. Water Res. 1;201:117382. doi:
10.1016/j.waters.2021.117382.
21. Kim DW
and Cha CJ. 2021. Antibiotic resistome from the
One-Health perspective: understanding and controlling antimicrobial resistance
transmission. Exp Mol Med. 53(3):301-309.
doi: 10.1038/s12276-021-00569-z.
22. Lee k, Kim
DW and Cha CJ. 2021. Overview of bioinformatic methods
for analysis of antibiotic resistome from genome and metagenome data. J
Microbiol. 59(3):270-280. doi: 10.1007/s12275-021-0652-4.
23. Kim YS,
Jang SH, and Cha CJ. 2021. Myroides fluvii sp.
nov., isolated from the Han River. Int J Syst Evol Microbiol. 71(2).
doi: 10.1099/ijsem.0.004623.
24. Redhead S,
Nieuwland J, Esteves S, Lee DH, Kim DW, Mathias J, Cha CJ, Toleman
M, Dinsdale R, Guwy A, Hayhurst E. 2020. Fate of antibiotic
resistant E. coli and antibiotic resistance genes during full
scale conventional and advanced anaerobic digestion of sewage sludge. PLoS
One. 15(12):e0237283. doi: 10.1371/journal.pone.0237283.
25. Moon K,
Jeon JH, Kang I, Park KS, Lee K, Cha CJ, Lee SH, Cho JC. 2020.
Freshwater viral metagenome reveals novel and functional phage-borne antibiotic
resistance genes. Microbiome. 8(1):75. doi:
10.1186/s40168-020-00863-4.
26. Lee, K.,
D.-W. Kim, D.-H. Lee, Y.-S. Kim, J.-H. Bu, J.-H. Cha, C. N. Thawng,
E.-M. Hwang, H. J. Seong, W. J. Sul, E. M. H. Wellington, C. Quince
and C.-J. Cha. 2020. Mobile resistome of human gut and
pathogen drives anthropogenic bloom of antibiotic resistance. Microbiome. 8(1):2.
doi: 10.1186/s40168-019-0774-7.
27. Lee, J.
Y., H. Lee, M. Park, C.-J. Cha, D. Shin and K. S. Ko. 2019. Lytic
transglycosylase contributes to the survival of lipooligosaccharide-deficient,
colistin-dependent Acinetobacter baumannii. Clin. Microbiol.
Infect. S1198-743X(19): 30050-3. doi: 10.1016/j.cmi.2019.02.004
28. Kim,
D.-W., C. N. Thawng, K. Lee, E. M. H. Wellington and C.-J. Cha. 2019.
A novel sulfonamide resistance mechanism by two-component flavin-dependent
monooxygenase system in sulfonamide-degrading actinobacteria. Environ.
Int. 127:206-215
29. Oh, S., D.
Choi and C.-J. Cha. 2019. Ecological processes underpinning
microbial community structure during exposure to subinhibitory level of
triclosan. Sci. Rep. 9(1):4598
30. Kim,
D.-W., K. Lee, D.-H. Lee and C.-J. Cha. 2018. Comparative genomic
analysis of pyrene-degrading Mycobacterium species: Genomic islands
and ring-hydroxylating dioxygenases involved in the pyrene degradation. J.
Microbiol. 56(11):798-804
31. Cha,
J.-H., J. J. Yoon and C.-J. Cha. 2018. Functional characterization
of a thermostable endoglucanase belonging to glycoside hydrolase family 45
from Fomitopsis palustris. Appl. Microbiol. Biotechnol. 102(15):
6515-6523
32. Kim,
D.-W., C. N. Thawng, K. Lee and C.-J. Cha. 2018. Revisiting
Polymorphic Diversity of Aminoglycoside N-Acetyltransferase AAC(6’)-Ib Based on
Bacterial Genomes of Human, Animal, and Environmental Origins. Front.
Microbiol. doi:10.3389/fmicb.2018.01831
33. Choi,
J.-H, K. Lee, D.-W. Kim, D. Y. Kil, G.-B. Kim and C.-J. Cha. 2018.
Influence of dietary avilamycin on ileal and cecal microbiota in broiler
chickens. Poult. Sci. 97(3): 970-979
34. Kim, Y.-S.
and C.-J. Cha. 2018. Paenibacillus translucens sp. nov.,
isolated from tidal flat sediment. Int. J. Sys. Evol.
Microbiol. 68(3): 936-941
35. Bu, J.-H.
and C.-J. Cha. 2018. Flavobacterium foetidum sp. nov.,
isolated from ginseng soil. Int. J. Sys. Evol. Microbiol. 68(2):
616-622
36. Nahar, S.
and C.-J. Cha. 2018. Paenibacillus limicola sp. nov.,
isolated from tidal flat sediment. Int. J. Sys. Evol.
Microbiol. 68(1): 423-426
37. Kim,
D.-W., C. N. Thawng, J.-H Choi, K. Lee and C.-J. Cha. 2018.
Polymorphism of antibiotic-inactivating enzyme driven by ecology expands the
environmental resistome. ISME J. 12: 267-276
38. Lee, CR,
JH Lee, KS Park, JH Jeon, YB Kim, C.-J. Cha, BC Jeong and SH Lee.
2017. Antimicrobial Resistance of Hypervirulent Klebsiella pneumoniae:
Epidemiology, Hypervirulence-Associated Determinants, and Resistance
Mechanisms. Front. Cell. Infect. Microbiol. 7:483. doi:
10.3389/fcimb.2017.00483
39. Lee, D.-H.
and C.-J. Cha. 2017. Ramlibacter alkalitolerans sp. nov.,
alkali-tolerant bacterium isolated from soil of ginseng. Int. J. Sys.
Evol. Microbiol. 67(11): 4619-4623
40. Kim,
D.-W., C. N. Thawng, S. H. Lee and C.-J. Cha. 2017. Unique Features
of Aeromonas Plasmid pAC3 and Expression of the Plasmid-Mediated
Quinolone Resistance Genes. mSphere. 2(3): e00203-17
41. Lee, CR,
JH Lee, M Park, KS Park, IK Bae, YB Kim, C.-J. Cha, BC Jeong and SH
Lee. 2017. Biology of Acinetobacter baumannii: Pathogenesis, Antibiotic
Resistance Mechanisms, and Prospective Treatment Options. Front. Cell.
Infect. Microbiol. 7:55. doi: 10.3389/fcimb.2017.00055
42. Lee, D.-H.
and C.-J. Cha. 2016. Flavihumibacter sediminis sp. nov.,
isolated from tidal flat sediment. Int. J. Sys. Evol.
Microbiol. 66(11): 4310–4314
43. Choi,
J.-H., J.-H. Seok, H.-J. Jang, J.-H. Cha and C.-J. Cha.
2016. Cohnella saccharovorans sp. nov., isolated from ginseng
soil. Int. J. Sys. Evol. Microbiol. 66(4): 1713–1717
44. Song, K.,
J. Lee, C.-J. Cha and H. Kang. 2015. Effects of Phragmites
invasion on soil microbial activity and structure in a brackish
marsh. Plant Soil. 392(1): 45–56
45. Unno, T.,
J.-H. Choi, H.-G. Hur, M. J. Sadowsky, Y.-T. Ahn, C.-S. Huh, G. B. Kim
and C.-J. Cha. 2015. Changes in human gut microbiota influenced by
probiotic fermented milk ingestion. J. Dairy Sci. 98(6): 3568-3576
46. Choi,
J.-H., K. M. Lee, M. K. Lee, C.-J. Cha. And G. B. Kim.
2014. Bifidobacterium faecale sp. nov., isolated from human
feces. Int. J. Sys. Evol. Microbiol. 64(9): 3134-3139
47. Choi, J.
H., G. B. Kim and C.-J. Cha. 2014. Spatial heterogeneity and
stability of bacterial community in the gastrointestinal tracts of broiler
chickens. Poult. Sci. 93(8): 1942-1950
48. Choi,
J.-H., J.-H. Seok, J.-H. Cha and C.-J. Cha. 2014. Lysobacter
panacisoli sp. nov., isolated from ginseng soil. Int. J. Sys. Evol.
Microbiol. 64(7): 2193–2197
49. Kim,
B.-S., H. Yi, J. Chun and C.-J. Cha. 2014. Genome sequence of type
strain of Staphylococcus aureus subsp. aureus. Gut
Pathogens. 6(1): 6
50. Choi,
J.-H., and C.-J. Cha. 2014. Bacillus panacisoli sp. nov.,
isolated from ginseng soil. Int. J. Sys. Evol. Microbiol. 64(3):
901–906
51. Yi, H, J.
Chun and C.-J. Cha. 2014. Genomic insights into the taxonomic
status of the three subspecies of Bacillus subtilis. Sys. Appl.
Microbiol. 37(2): 95-9
52. Rahman, M.
M., and C.-J. Cha. 2013. Ferrimonas gelatinilytica sp.
nov., isolated from tidal flat sediment. Int. J. Sys. Evol.
Microbiol. 63(11): 4309-4314
53. Park, S.
J., J.-H. Choi, C.-J. Cha. 2013. Chryseobacterium
aestuarii sp. nov., isolated from the wetland of Han River,
Korea. Int. J. Sys. Evol. Microbiol. 63(3): 1062-1068
54. Thawng, C.
N., S. J. Park, Cha JH, C.-J. Cha. 2013. Stakelama
sediminis sp. nov., isolated from tidal flat sediment. Int. J. Sys.
Evol. Microbiol. 63(2): 560 - 564
55. Kim,
Y.-H., W.-S. Song, H. Go, C.-J. Cha, C. Lee, M.-H. Yu, P. C. K.
Lau, K. Lee. 2013. 2-Nitrobenzoate 2-nitroreductase (NbaA) switches its
substrate specificity from 2-nitrobenzoic acid to 2,4-dinitrobenzoic acid under
oxidizing conditions. J. Bacteriol. 195(2): 180-192.
56. Cha,
J.-H., C.-J. Cha. 2013. Gordonia alkaliphila sp. nov., an
actinomycete isolated from tidal flat sediment from the Yellow Sea,
Korea. Int. J. Sys. Evol. Microbiol. 63(1): 327 - 331
57. Park,
E.J., J. Chun, C.-J. Cha, W. S. Park, C. O. Jeon and J. W. Bae.
2012. Bacterial community analysis during fermentation of ten representative
kinds of kimchi with barcoded pyrosequencing. Food Microbiol. 30(1):
197-204.
58. Yeo, I.
C., N. K. Lee, C.-J. Cha and Y. T. Hahm. 2012. Interspecies
Interaction of Signal Peptide PapR Secreted by Bacillus cereus and
Its Effect on Production of Antimicrobial Peptide. Appl. Biochem.
Biotechnol. 66(3): 700-710.
59. Go, H., C.
J. Moore, M. Lee, E. Shin, C. O. Jeon, C.-J. Cha, S. H. Han, S.-J.
Kim, S.-W. Lee, Y. Lee, N.-C. Ha, Y.-H. Kim, S. N. Cohen and K. Lee. 2011.
Upregulation of RNase E activity by mutation of a site that uncompetitively
interferes with RNA binding. RNA Biology. 8(6): 1022-1034.
60. Kim,
H.-J., H.-J., S.-J. Eom, S.-J. Park,