Dr LI, Liguan    李麗觀 博士
Assistant Professor
Department of Science and Environmental Studies
Contact
ORCiD
0000-0003-4349-0532
Phone
(852) 2948 7520
Email
lilig@eduhk.hk
Address
10 Lo Ping Road, Tai Po, New Territories, Hong Kong
Website
https://pappl.eduhk.hk/rich/web/person.xhtml?pid=312560&name=LI, Liguan
Scopus ID
57040130600
Research Interests
My overarching research interests revolve around environmental microbiome – microbial communities and their interactions with the environment. I use a combination of modern experimental methods (molecular methods, bacteria culture, etc.) and advanced bioinformatic approaches (metagenomics, big-data mining, etc.) to answer fundamental and applied microbial ecological questions in the environment.
 
More specifically, I am interested in exploring the potential of environmental microbiology research for public health management, elucidating effect of environmental pollutants on the development of antibiotic resistance, deciphering the behaviour of antibiotic resistance genes in the human related environment,. Under current One Health Initiative, I firmly believe pursuing environmental microbiology research in the context of human health and sustainable environment will largely facilitate tackling grand challenges facing humanity today like infectious disease, antibiotic resistance and climate change.
Teaching Interests

Microbiology

Environmental science

Environmental engineering

STEM education

External Appointments

Editorial board of Frontiers in Environmental Science

Editorial board Frontiers in Microbiology

Personal Profile

I received my BSc and MSc in Environmental Science, got PhD in Environmental Engineering from The University of Hong Kong (HKU) in 2016. After that, I went to the Denmark to pursue Postdoc research in microbial ecology in the Technical University of Denmark (DTU). In 2021, I came back to Hong Kong and joined HKU as Research Assistant Professor in Department of Civil Engineering. In July 2024, I joined Department of Science and Environmental Studies (SES), EdUHK.


I am committed to delivering teaching and research excellence, believe that the vibrant teaching and research environment at EdUHK will foster numerous productive collaborations in near future.

Research Interests
My overarching research interests revolve around environmental microbiome – microbial communities and their interactions with the environment. I use a combination of modern experimental methods (molecular methods, bacteria culture, etc.) and advanced bioinformatic approaches (metagenomics, big-data mining, etc.) to answer fundamental and applied microbial ecological questions in the environment.
 
More specifically, I am interested in exploring the potential of environmental microbiology research for public health management, elucidating effect of environmental pollutants on the development of antibiotic resistance, deciphering the behaviour of antibiotic resistance genes in the human related environment,. Under current One Health Initiative, I firmly believe pursuing environmental microbiology research in the context of human health and sustainable environment will largely facilitate tackling grand challenges facing humanity today like infectious disease, antibiotic resistance and climate change.
Teaching Interests

Microbiology

Environmental science

Environmental engineering

STEM education

External Appointments

Editorial board of Frontiers in Environmental Science

Editorial board Frontiers in Microbiology

Research Outputs
Journal Publications
Mao X, Yin X, Yang Y, Gao F, Li S, Shi X, Deng Y, Li L, Leung KMY, Zhang, T. (2025). Longitudinal metagenomic analysis on antibiotic resistome, mobilome, and microbiome of river ecosystems in a sub-tropical metropolitan city. Water Research, 274, Article 123102. https://doi.org/10.1016/j.watres.2025.123102
SDGs infomation: 3 - Good Health and Well-Being, 6 - Clean Water and Sanitation, 11 - Sustainable Cities and Communities, 14 - Life Below Water
Li Q, Li H, Tian L, Wang Y, Ouyang Z, Li LG, Mao Y. (2025). Genomic insights and metabolic pathways of an enriched bacterial community capable of degrading polyethylene. Environmental International, 197, Article 109334. https://doi.org/10.1016/j.envint.2025.109334
SDGs infomation: 3 - Good Health and Well-Being, 6 - Clean Water and Sanitation, 11 - Sustainable Cities and Communities, 14 - Life Below Water, 15 - Life on Land
Wang C, Yang Y, Xu X, Wang D, Shi X, Liu L, Deng Y, Li L, Zhang T. (2025). The quest for environmental analytical microbiology: Absolute quantitative microbiome using cellular internal standards. Microbiome, 13, Article 26. https://doi.org/10.1186/s40168-024-02009-2
SDGs infomation: 3 - Good Health and Well-Being, 6 - Clean Water and Sanitation, 11 - Sustainable Cities and Communities, 14 - Life Below Water, 15 - Life on Land
Tian L, Fang G, Li G, L Li LG, Zhang T, Mao Y (2024). Metagenomic approach revealed the mobility and co-occurrence of antibiotic resistomes between non-intensive aquaculture environment and human. Microbiome, 12, Article 107. https://doi.org/10.1186/s40168-024-01824-x
Tian L, Fang G, Li LG, Zhang T, Mao Y. (2024). Metagenomic approach revealed the mobility and co-occurrence of antibiotic resistomes between non-intensive aquaculture environment and human. Microbiome, 12, 107.
SDGs infomation: 3 - Good Health and Well-Being, 6 - Clean Water and Sanitation, 11 - Sustainable Cities and Communities, 14 - Life Below Water
Mao X, Yin X, Yang Y, Che Y, Xu X, Deng Y, Li LG, Zhang T (2024). Standardization in global environmental antibiotic resistance genes (ARGs) surveillance. Critical Reviews in Environmental Science and Technology. https://doi.org/10.1080/10643389.2024.2344453
Manaia CM, Aga DS, Cytryn E, Gaze WH, Graham DW, Guo J, Leonard AFC, Li LG, Murray AK, Nunes OC, Rodriguez‐Mozaz S, Topp E, Zhang T (2024). The complex interplay between antibiotic resistance and pharmaceutical and personal care products in the environment. Environmental Toxicology and Chemistry, 43(3), 637-652. https://doi.org/10.1002/etc.5555
Zheng Q, Li LG, Yin X, Che Y, Zhang T. (2023). Is ICE hot? A genomic comparative study reveals integrative and conjugative elements as “hot” vectors for the dissemination of antibiotic resistance genes. mSystems, 8(6), Article e00178-23. https://doi.org/10.1128/msystems.00178-23
Li LG, Zhang T (2023). Roadmap to tackle antibiotic resistance in the environment under the One Health framework. mLife, 2(3), 224-228. https://doi.org/10.1002/mlf2.12078
Li LG, Zhang T (2023). Plasmid-mediated antibiotic resistance gene transfer under environmental stresses: Insights from laboratory-based studies. Science of the Total Environment, 887, Article 163870. https://doi.org/10.1016/j.scitotenv.2023.163870
Yin X, Zheng X, Li LG, Zhang AN, Jiang XT, Zhang T (2023). ARGs-OAP v3.0: Antibiotic-resistance gene database curation and analysis pipeline optimization. Engineering, 27, 234-241. https://doi.org/10.1016/j.eng.2022.10.011
Moradigaravand D, Li LG, Dechesne A, Nesme J, Cruz R, Ahmad H, Banzhaf M, Sørensen SJ, Smets BF, Kreft JU (2023). Plasmid permissiveness of wastewater microbiomes can be predicted from 16S rRNA sequences by machine learning. Bioinformatics, 39(7), Article btad400. https://doi.org/10.1093/bioinformatics/btad400
Yin X, Li LG, Chen X, Liu YY, Lam TTY, Topp E, Zhang T (2023). Global environmental resistome: Distinction and connectivity across diverse habitats benchmarked by metagenomic analyses. Water Research, 235, Article 119875. https://doi.org/10.1016/j.watres.2023.119875
Huang Y, Li LG, Yin X, Zhang T (2023). Polycyclic aromatic hydrocarbon (PAH) biodegradation capacity revealed by a genome-function relationship approach. Environmental Microbiome, 18, Article 39. https://doi.org/10.1186/s40793-023-00497-7
Wang CX, Yang Y, Wang, Y, Wang D, Xu X, Wang Y, Li LG, Yang C, Zhang T (2022). Absolute quantification and genome-centric analyses elucidate the dynamics of microbial populations in anaerobic digesters. Water Research, 224, Article 119049. https://doi.org/10.1016/j.watres.2022.119049
Wang Y, Li LG, Xia Y, Zhang T (2022). Reliable and scalable identification and prioritization of putative cellulolytic anaerobes with large genome data. Frontiers in Bioinformatics, 2, Article 813771. https://doi.org/10.3389/fbinf.2022.813771
Yin X, Yang Y, Deng Y, Huang Y, Li LG, Chan LYL, Zhang T (2022). An assessment of resistome and mobilome in wastewater treatment plants through temporal and spatial metagenomic analysis. Water Research, 209, Article 117885. https://doi.org/10.1016/j.watres.2021.117885
Zhang AN, Gaston JM, Dai CL, Zhao S, Poyet M, Groussin M, Yin X, Li LG, Loosdrecht MCM, Topp E, Gillings MR, Hanage WP, Tiedje JM, Moniz K, Alm EJ, Zhang T (2021). An omics-based framework for assessing the health risk of antimicrobial resistance genes. Nature Communications, 12, Article 4765. https://doi.org/10.1038/s41467-021-25096-3
Li LG, Nesme J, Quintela-Baluja M, Balboa S, Hashsham SA, Williams M, Yu Z, Sorensen S, Graham D, Romalde J, Dechesne A, Smets BF (2021). Extended-spectrum β-lactamase and carbapenemase genes are substantially and sequentially reduced during conveyance and treatment of urban sewage. Environmental Science & Technology, 55(9), 5939-5949. https://doi.org/10.1021/acs.est.0c08548
Li LG, Huang Q, Yin X, Zhang T (2020). Source tracking of antibiotic resistance genes in the environment: Challenges, progress, and prospects. Water Research, 185, Article 116127. https://doi.org/10.1016/j.watres.2020.116127
Zhang AN, Hou CJ, Negi M, Li LG, Zhang T (2020). Online searching platform for the antibiotic resistome in bacterial tree of life and global habitats. FEMS Microbiology Ecology, 96(7), Article fiaa107. https://doi.org/10.1093/femsec/fiaa107
Pan Y, Zeng J, Li LG, Yang J, Tang Z, Xiong W, Li Y, Chen S, Zeng Z (2020). Coexistence of antibiotic resistance genes and virulence factors deciphered by large-scale complete genome analysis. mSystems, 5(3), Article e00821-19. https://doi.org/10.1128/mSystems.00821-19
Zhai W, Qin T, Li LG, Guo T, Yin X, Khan MI, Hashmi MZ, Liu X, Tang X, Xu J (2020). Abundance and diversity of microbial arsenic biotransformation genes in the sludge of full-scale anaerobic digesters from a municipal wastewater treatment plant. Environmental International, 138, Article 105535. https://doi.org/10.1016/j.envint.2020.105535
Li LG, Dechesne A, Madsen JS, Nesme J, Sørensen SJ, Smets BF (2020). Plasmids persist in a microbial community by providing fitness benefit to multiple phylotypes. The ISME Journal, 14(5), 1170-1181. https://doi.org/10.1038/s41396-020-0596-4
Guo T, Li LG, Zhai W, Xu B, Xiaole Yin, He Y, Xu J, Zhang T, Tang X (2019). Distribution of arsenic and its biotransformation genes in sediments from the East China Sea. Environmental Pollution, 253, 949-958. https://doi.org/10.1016/j.envpol.2019.07.091
Xu JX, Li XM, Sun GX, Cui L, Ding LJ, He C, Li LG, Shi Q, Smets BF, Zhu YG (2019). Fate of labile organic carbon in paddy soil is regulated by microbial ferric iron reduction. Environmental Science & Technology, 53(15), 8533-8542. https://doi.org/10.1021/acs.est.9b01323
Li LG, Yin X, Zhang, T (2018). Tracking antibiotic resistance gene pollution from different sources using machine-learning classification. Microbiome, 6, Article 93. https://doi.org/10.1186/s40168-018-0480-x
Yin X, Jiang XT, Chai B, Li LG, Yang Y, Cole JR, Tiedje JM and Zhang T (2018). ARGs-OAP v2.0 with an expanded SARG database and Hidden Markov Models for enhancement characterization and quantification of antibiotic resistance genes in environmental metagenomes. Bioinformatics, 34(13), 2263-2270. https://doi.org/10.1093/bioinformatics/bty053
Zhang AN, Li LG, Ma L, Gillings MR, Tiedje JM and Zhang T (2018). Conserved phylogenetic distribution and limited antibiotic resistance of class 1 integrons revealed by assessing the bacterial genome and plasmid collection. Microbiome, 6, Article 130. https://doi.org/10.1186/s40168-018-0516-2
Li LG, Dechesne A, He Z, Madsen JS, Nesme J, Sørensen SJ, and Smets BF (2018). Estimating the transfer range of plasmids encoding antimicrobial resistance in a wastewater treatment plant microbial community. Environmental Science and Technology Letters, 5(5), 260-265. https://doi.org/10.1021/acs.estlett.8b00105
Xia Y, Li AD, Deng Y, Jiang X, Li LG, Zhang T (2017). MinION Nanopore sequencing enables correlation between resistome phenotype and genotype of coliform bacteria in municipal sewage. Frontiers in Microbiology, 8, Article 2105. https://doi.org/10.3389/fmicb.2017.02105
Yang C, Yang Y, Che Y, Xia Y, Li LG, Xiong W, Zhang T (2017). Bioprospecting for β-lactam resistance genes using a metagenomics-guided strategy. Applied Microbiology and Biotechnology, 101, 6253-6260. https://doi.org/10.1007/s00253-017-8343-0
Luo G, Li B, Li LG, Zhang T, Irini Angelidaki (2017). Antibiotic resistance genes and correlations with microbial community and metal resistance genes in full-scale biogas reactors as revealed by metagenomic analysis. Environmental Science & Technology, 51(7), 4069-4080. https://doi.org/10.1021/acs.est.6b05100
Li LG, Xia Y, Zhang T (2017). Co-occurrence of antibiotic and metal resistance genes revealed in complete genome collection. The ISME Journal, 11(3), 651-662. https://doi.org/10.1038/ismej.2016.155
Xiao KQ, Li LG, Ma LP, Zhang SY, Bao P, Zhang T, Zhu YG (2016). Metagenomic analysis revealed highly diverse microbial arsenic metabolism genes in paddy soils with low-arsenic contents. Environmental Pollution, 211, 1-8. https://doi.org/10.1016/j.envpol.2015.12.023
Mao YP, Wang ZP, Li LG, Jiang XT, Zhang XX, Ren HQ, Zhang T (2016). Exploring the shift in structure and function of microbial communities performing biological phosphorus removal. PLoS One, 11(8), Article e0161506. https://doi.org/10.1371/journal.pone.0161506
Ma LP, Xia Y, Li B, Yang Y, Li LG, Tiedje J, Zhang T (2016). Metagenomic assembly reveals hosts of antibiotic resistance genes and the shared resistome in pig, chicken, and human feces. Environmental Science & Technology, 50(1), 420-427. https://doi.org/10.1021/acs.est.5b03522
Li AD, Li LG, Zhang T (2015). Exploring antibiotic resistance genes and metal resistance genes in plasmid metagenomes from wastewater treatment plants. Frontiers in Microbiology, 6, Article 1025. https://doi.org/10.3389/fmicb.2015.01025
Li LG, Cai L, Zhang XX, Zhang T (2014). Potentially novel copper resistance genes in copper-enriched activated sludge revealed by metagenomic analysis. Applied Microbiology and Biotechnology, 98, 10255-10266. https://doi.org/10.1007/s00253-014-5939-5
Li LG, Cai L, Zhang, T (2013). Genome of Cupriavidus sp. HMR-1, a heavy metal-resistant bacterium. Genome Announcements, 1(1), Article e00202-12. https://doi.org/10.1128/genomeA.00202-12

Conference Papers
Li LG (2024, December). Plasmid transfer and maintenance in microbial communities of urban wastewater environment. The 1st International Conference on Health, Environment, Education and Research 2024 (CHEER2024) & The 10th International Conference on Water Resource and Environment 2024 (WRE2024), Hong Kong.
SDGs infomation: 3 - Good Health and Well-Being, 6 - Clean Water and Sanitation, 11 - Sustainable Cities and Communities, 14 - Life Below Water, 15 - Life on Land
Li Liguan, Zhao Yuxiang, Zhu Dong, Zhang Tong. (2024, September). Distribution profile and health risk of antibiotic resistance genes in soil at national and global scales. SETAC Asia-Pacific 14th Biennial Meeting 2024, Tianjin, China. https://www.setac.org/discover-events/global-meetings/setac-asia-pacific-14th-biennial-meeting.html
SDGs infomation: 3 - Good Health and Well-Being, 6 - Clean Water and Sanitation, 11 - Sustainable Cities and Communities, 12 - Responsible Consumption and Production, 15 - Life on Land

Projects
Carbon emissions from China’s inland waters and coastal ecosystems under global change
Aquatic ecosystems, including inland waters and coastal waters, are important components of the global carbon (C) cycle. Inland waters are significant sources of C emissions for the atmosphere whereas coastal ecosystems are typically C sinks. Globally, carbon dioxide (CO2) and methane (CH4) emissions from inland waters are estimated to be 2.33.9 PgC yr1, which is comparable in magnitude to that of the terrestrial C sink. Coastal ecosystems can partially offset these emissions through C sequestration in coastal vegetation and sediments. Thus, carbon emissions from inland waters and C burial in coastal ecosystems collectively regulate global/regional C budgets. Nevertheless, due to the lack of spatially resolved sampling and the abundance of diverse aquatic ecosystems, the estimated emission fluxes remain largely uncertain. Furthermore, the environmental and anthropogenic controls on C emissions and their response to global change remain poorly studied. Such knowledge gaps form barriers to projecting future C budgets and formulating effective strategies for addressing climate change. We need to mechanistically understand the sources of these greenhouse gases and predict how the fluxes might change in the future, which is critical for climate change modelling and mitigation.

This proposed project aims to conduct a comprehensive assessment of C emissions from Chinese inland waters and coastal ecosystems by combining field-based in-situ measurements across China and computer-based modelling. Particularly, field surveys will be conducted in representative aquatic ecosystems with contrasting settings of climate, hydrology, geology, and human disturbance. We will quantitatively investigate the sources of CO2 and CH4 emissions from China’s aquatic ecosystems and examine the taxonomic composition of microbial community that governs the biogeochemical cycling of organic C and the resulting emission. This project will also explore environmental and anthropogenic controls
Project Start Year: 2025, Principal Investigator(s): Ran, Lishan (LI, Liguan as Co-Principal Investigator)

 
Conjugative Transfer of Plasmid-borne Antibiotic Resistance Genes to Environmental Bacteria in Crop Production Systems Irrigated with Municipal Wastewater Effluents
Climate change is constraining the availability of water for irrigating crops in many parts of the world, threatening global food security. In response, the use of municipal wastewater effluent for irrigation is becoming a necessity. Wastewater effluent contains residues of antibiotics and other micropollutants, antibiotic resistant bacteria excreted by humans, and the antibiotic-resistance genes and mobile genetic elements that they carry. There is very little knowledge about what impact wastewater effluent might have on the reservoir of antimicrobial resistance in irrigated crop production systems. Likewise, what if any risk of transmission of antibiotic resistance genes from the effluent microbiome to the microbiome in the soil or on crops is largely unknown. This knowledge is required to identify if this practice will contribute to the transmission of antimicrobial resistance transmission from effluent back to to humans via the food chain or the environment. Should this be the case, the information gained would be used to inform policies and practices governing the acceptable quality of water used in various irrigation scenarios. The proposed research will characterize the complement of plasmids (the plasmidome) of municipal effluent. Long read metagenomic sequencing will be used to close plasmids, and provide genetic context for plasmid associated antibiotic resistance genes. Plasmid-host associations will be established using Hi-C approach. Associations between plasmid composition and community structure will be searched using machine learning. In vitro, the presence of quite low antibiotic concentrations can increase the frequency of conjugation. This will be explored in soil and in phyllosphere communities. The Hong Kong group will contribute extensive experience with bioinformatics tools deployed on long read and metagenomic sequencing. The France group will undertake experiments with irrigation on crops, and has extensive experience in bacteriology.
Project Start Year: 2025, Principal Investigator(s): Zhang, Tong, Fabrice, Martin-Laurent (LI, Liguan as Co-Principal Investigator)
SDGs Information: 2 - Zero Hunger, 3 - Good Health and Well-Being, 6 - Clean Water and Sanitation, 7 - Affordable and Clean Energy, 8 - Decent Work and Economic Growth, 11 - Sustainable Cities and Communities, 12 - Responsible Consumption and Production, 15 - Life on Land
 
Air and Surface Contamination Patterns of Antibiotic Resistance Bacteria and Genes of in Hospital Environment
In this proposed project, we will combine culture-dependent and -independent methods to examine environmental microbiome and resistome in Intensive Care Units and Accident & Emergency Departments of hospitals. Through collaboration with the Affiliated Hospital of Zhejiang University, we will collect surface and air samples to examine and compare antibiotic resistance patterns at the sites. The results delivered will give a comprehensive overview of antibiotic resistance in the hospital environment, which may help establish priorities to control the spread of nosocomial antibiotic resistance.
Project Start Year: 2025, Principal Investigator(s): LI, Liguan

 
Deciphering plasmid mediated antibiotic resistance gene transmission through urban wastewater system
Antibiotic resistance has been one of the greatest challenges facing humanity today. Numerous cases of antibiotic resistance have rendered treatment failure, posing a great threat to human health. Besides clinical setting, the environment has been recognized as an important reservoir of antibiotic resistance genes (ARGs). As the interaction interface between bacteria originating from the human gut and the environment, the urban wastewater system (UWS) has particularly been suggested as a pathway for ARG dissemination. Indeed, the UWS borne antibiotic resistance has been largely attributed to plasmid-mediated ARG transmission. Plasmids — extrachromosomal replicons, can efficiently shuttle genes across diverse taxa — a process known as horizontal gene transfer. It is therefore essential to evaluate to what extent and in which way the plasmid behaviour in UWS contribute to ARG transmission in the environment. Coupling cutting-edge sequencing technologies and experimental tools, we here propose the integrated research project to decipher plasmid-mediated ARG transmission in UWSs, and explore novel control strategies. The efforts of all the five tasks in the project will identify options of science and technique which should be prioritized to tackle the plasmid-mediated ARG transmission in UWSs. The project will have significant impacts, both short-term and long-term, on multiple aspects of scientific research, technology development and public health. The knowledge generated in this project will fill several research gaps in environmental dimension of antibiotic resistance. We believe the project will facilitate setting up an integrated ‘One Health’ framework by providing comprehensive knowledge of the environmental dimension of plasmid-mediated ARG transmission.
Project Start Year: 2023, Principal Investigator(s): LI, Liguan
SDGs Information: 3 - Good Health and Well-Being, 6 - Clean Water and Sanitation, 11 - Sustainable Cities and Communities, 12 - Responsible Consumption and Production, 15 - Life on Land
 
Co-selection of antibiotic resistance genes by environmental pollutants
Antibiotic resistance is a global crisis of public health facing humanity today. The environment has been recognized as the key element in mediating enrichment and transmission of antibiotic resistance genes (ARGs). Current complicated pollution status has been the essential selection pressure for ARG enrichment and transfer, thus largely deteriorating ARG development in the environment. In this project, we will carry out systematic surveillance of ARG profile in key economic regions in China, including Greater Bay Area, Yangtze River Delta, etc. Through large scale metagenomic analysis, we will map the ARG profile across the regions, which will be correlated with social economic and environmental geographical parameters to decipher the contributing factors for ARG development. Based on the regional environmental surveillance, we will design microcosms to investigate the role of environmental pollutants (including antibiotic/non-antibiotic pharmaceuticals, metals,etc.) in long-term ARG co-selection. Metagenomics, metatranscriptomics and metaproteomics will be integrated to examine to what extent and in which way the environmental pollutants facilitating ARG selection and transmission, as well as regulating ARG expression. To further evaluate the risk of environmental pollutants in promoting ARG transmission, we will combine conjugation, transformation experiments and multi-omics to assess transfer frequency and disentangle the molecular mechanisms. Altogether, the project will form a comprehensive understanding of ARG co-selection driving by complicated pollution in the environment. It will be the basis for controlling ARG transmission in the environment and for reducing the risk of population ARG exposure.
Project Start Year: 2022, Principal Investigator(s): Zhang, Tong (LI, Liguan as Co-Investigator)
SDGs Information: 3 - Good Health and Well-Being, 6 - Clean Water and Sanitation, 11 - Sustainable Cities and Communities, 12 - Responsible Consumption and Production, 15 - Life on Land