Environmental Microbiome &

Biotechnology Lab (EMBLab)

Publications at Westlake (* Denotes corresponding author)

53.Zhu, X., Angelidaki, I., Zhang, T., & Ju F*. 2024. Metagenomics Disentangles Differential Resistome Traits and Risks in FullScale Anaerobic Digestion Plants under Ambient, Mesophilic, and Thermophilic Conditions. ACS Environmental Au.

52.Zhang G, Wang H, Zhang Z, Zhang L, Guo G, Yang J, Yuan F,Ju F*. 2024. Highly accurate classification and discovery of microbial protein-coding gene functions using FunGeneTyper: an extensible deep learning framework. Briefings in Bioinformatics. 25 (4).

51.Zhu X, Li P, Ju F*. 2024. Microbiome dynamics and products profiles of biowaste fermentation under different organic loads and additives. Eng Life Sci. 24:e2300216.

50.Ju F*, Zhai Q, Luo G, Tang H, Dai L. 2024. Microbiome research for advancing engineering in life science. Engineering in Life Sciences. 24 (5).

49.Yuan L, Yu P, Huang X, Zhao Z, Chen L, Ju F*. 2024. Seasonal succession, host associations, and biochemical roles of aquatic viruses in a eutrophic lake plagued by cyanobacterial blooms. Environ Int.

48.Zhao Z, Qin W, Li L, Zhao H, Ju F*. 2024. Discovery of Candidatus Nitrosomaritimum as a new genus of ammonia-oxidizing archaea widespread in anoxic saltmarsh intertidal aquifers. Environmental Science & Technology.

47.Zhang, Y., & Ju   F*. 2024. Uninheritable but Widespread Bacterial Symbiont Enterococcus casseliflavus Mediates Detoxification of the Insecticide Chlorantraniliprole in the Agricultural Invasive Pest Spodoptera frugiperda. Journal of agricultural and food chemistry.

46.Zhang Z, Zhu X, Su JQ, Zhu S, Zhang L, Ju F*. 2024. Metagenomic insights into potential impacts of antibacterial biosynthesis and anthropogenic activity on nationwide soil resistome. Journal of Hazardous Materials. 473: 134677.

45.Zhang Z, Zhang L, Zhang L, Chu H, Zhou J, Ju F*. 2024. Diversity and distribution of biosynthetic gene clusters in agricultural soil microbiomes. mSystems. 9 (4): e01263-23.

44.Lu Zhang, Lingyun Guo, Zhongli Cui, Ju F*.2024.Exploiting predatory bacteria as biocontrol agents across ecosystems,Trends in Microbiology.

43.Yang X, Chen Y, Liu T, Zhang L, Wang H, Chen M, He Q, Liu G, Ju F* .2024. Plastic particles affect N2O release via altering core microbial metabolisms in constructed wetlands. Water Research.

42.Zhang Y, Mao K, Chen K, Zhao Z,Ju F*. 2024. Symbiont community assembly shaped by insecticide exposure and feedback on insecticide resistance of Spodoptera frugiperda. Commun Biol.

41.Yuan L, Ju F*. 2023. Potential auxiliary metabolic capabilities andactivities reveal biochemical impacts of viruses in municipal wastewater treatment plants. Environmental Science & Technology. 57(13):5485-5498

40.Zhang, H., Wang, L., Zhang, Z., Lin, J., & Ju F*. 2023. Cost-Efficient Micro-Well Array-Based Colorimetric Antibiotic Susceptibility Testing (MacAST) for Bacteria from Culture or Community. Biosensors, 13(12), 1028.

39.Xinyu Zhu, Songmei Zhu, Ze Zhao, Xiaoxi Kang,   Ju F*,2023.Microbiome dynamics during anaerobic digestion of food waste and the genetic potential for poly (lactic acid) co-digestion,Chemical Engineering Journal,145194.

38.Hui Wang, Yubo Wang, Guoqing Zhang, Ze Zhao, Ju F*,2023. Temporal Dynamics and Performance Association of the Tetrasphaera-Enriched Microbiome for Enhanced Biological Phosphorus Removal. Engineering.

37.Hui Wang, Limin Lin, Lu Zhang, Ping Han, Ju F*,2023. Microbiome assembly mechanism and functional potential in enhanced biological phosphorus removal system enriched with Tetrasphaera-related polyphosphate accumulating organisms,Environmental Research.

36.Lin L, Ju F*,2023. Evaluation of different 16S rRNA gene hypervariable regions and reference databases for profiling engineered microbiota structure and functional guilds in a swine wastewater treatment plant. Interface Focus.

35.Zhang L, Huang X, Zhou J, Ju F*. 2023.Active predation, phylogenetic diversity, and global prevalence of myxobacteria in wastewater treatment plants. ISME J.

34.Lee, J., Ju F*, 2023. Beck, K. et al. Differential effects of wastewater treatment plant effluents on the antibiotic resistomes of diverse river habitats. ISME J .

33.Moran Tang, Qian Chen, Haohui Zhong, Ju F*, Yang Wu, Jingrun Hu, Si Li, Weiling Sun,2023.

Exploring diversity patterns and driving mechanisms of the antibiotic resistome and microbiome in saline groundwater,Journal of Hazardous Materials.

32.Zhang Z, Zhang L, Zhang G, Zhao Z, Wang H, Ju F*. 2023. Deduplication Improves Cost-Efficiency and Yields of De Novo Assembly and Binning of Shotgun Metagenomes in Microbiome Research. Microbiol Spectr.

31.Yuanzhen He, Hui Jin, Ju F*,2023. Toxicological effects and underlying mechanisms of chlorination-derived metformin byproducts in Escherichia coli,Science of The Total Environment,167281.

30.Lin Zhu, Ling Yuan, Xin-Yi Shuai, Ze-Jun Lin, Yu-Jie Sun, Zhen-Chao Zhou, Ling-Xuan Meng, Ju F*, Hong Chen,2023. Deciphering basic and key traits of antibiotic resistome in influent and effluent of hospital wastewater treatment systems,Water Research,119614.

29.Ze Zhao, Lu Zhang, Guoqing Zhang, Han Gao, Xiaogang Chen, Ling Li, Ju F*, 2023. Hydrodynamic and anthropogenic disturbances co-shape microbiota rhythmicity and community assembly within intertidal groundwater-surface water continuum, Water Research,120236.

28. Shuai M, Zhang G, Zeng F, Fu Y, Ju F*, Ju-Sheng Zheng*, et al. 2022. Human gut antibiotic resistome andprogression of diabetes. Advanced Science. e2104965

27. Zhang, Huilin & Yao, Yuan & Hui, Yue & Zhang, Lu & Zhou, Nanjia & Ju F*. 2021. A 3D-printed microfluidic gradient concentration chip for rapid antibiotic-susceptibility testing. Bio-Design and Manufacturing.

26. He L*,Huang X*, Zhang G, Yuan L, Shen E, Zhang L, Zhang X, Zhang T, Tao L*, Ju F*. 2022. Distinctive signatures of pathogenic and antibiotic resistant potentials in thehadal microbiome. Environmental Microbiome. 25.17(1): 19

25. He Y, Zhang Y, Ju F*. 2022. Metformin contamination in global waters: biotic and abiotic transformation, byproduct generation and toxicity, and evaluation as a pharmaceutical indicator. Environmental Science & Technology. 56(19):13528-13545.

24. Zhang Z, Zhang G, Ju F*. 2022. Using Culture-Enriched Phenotypic Metagenomics for Targeted High-Throughput Monitoring of Clinically-Important Fraction of Beta-Lactam Resistome. bioRxiv.

23. Zhang Z, Peng H, Yang D, Zhang G, Zhang J, Ju F*. 2022. Polyvinyl chloride degradation by a bacterium isolated fromthe gut of insect larvae. Nature Communication. 13: 5360.

22.He Y, Jin H, Gao H, Zhang G, Ju F*. 2022. Prevalence, production, and ecotoxicity ofchlorination-derived metformin byproducts in Chinese urban water systems. Science of the Total Environment. 151665

21.Gao H, Zhao Z, Zhang L, Ju F*. 2022.Cyanopeptides restriction and degradation co-mediate microbiota assembly duringa freshwater cyanobacterial harmful algal bloom (CyanoHAB). Water Research. 220.118674

20.Yang X, Zhang L, Chen Y *, He Q, Liu T, Zhang G, Yuan L, Peng H, Wang H, Ju F*. 2022. Micro(nano)plasticsize and concentration co-differentiate nitrogen transformation, microbiotadynamics, and assembly patterns in constructed wetlands. Water Research. 220:118636

19.Zhang R, He Y, Yao L, Chen J, Zhu S, Rao X, Tang P, You J, Hua G, Zhang L, Ju F*, Wu L*. 2021. Metformin chlorination byproducts in drinking water exhibit markedtoxicities of a potential health concern. Environment International. 146:106244

18.Yuan L, Wang Y, Zhang L, Alejandro P, Zhou J, Smets B, Bürgmann H, Ju F*. 2021. Pathogenic andindigenous denitrifying bacteria are transcriptionally active and key multi-antibioticresistant players in wastewater treatment plants. Environmental Science& Technology. 55(15):10862-10874.

17.Yang X, Wang H, Zhang L, Kong L, Chen Y, He Q, Li L, Grossart HP, Ju F*. Marine algae facilitate transfer of microplastics and associated pollutants into food webs. Sci Total Environ. 2021

16.Zhang L, Yin W, Wang C, Zhang A, Zhang H, Ju F*. 2021. Untangling microbiota diversity and assembly patterns in the world's largest waterdiversion canal. Water Research. 117617.

Publications Prior to Westlake University‍

15.Ju F, Beck K, Yin X, McArdell C, Singer H, Johnson D, Zhang T, Buergmann H. 2019. Wastewater treatment plant resistomes are shaped by bacterial composition,genetic exchange and upregulated expression in the effluent. The ISME Journal. 13(2):346-360

14.Zhao F*, Ju F*, Huang K, Mao Y, Zhang X, Ren H, Zhang T. 2019. Comprehensive insights into the key components of bacterial assemblages inpharmaceutical wastewater treatment plants. Science of The Total Environment. 651:2148-2157.

13.Ju F, Wang Y, Zhang T. 2018. Bioreactor microbial ecosystems with differentiated methanogenic phenol biodegradation and competitive metabolic pathways unraveledwith genome-resolved metagenomics. Biotechnology for Biofuels. 11(1):135

12. Ju F, Lau F, Zhang T. 2017. Linking microbial community, environmental variables and methanogenesis in anaerobic biogas digesters of chemically enhanced primary treatment sludge. Environmental Science & Technology. 51(7):3982-3992

11.Ju F, Wang Y, Lau F, Fung W, Huang D, Xia Y, Zhang T. 2016. Anaerobic digestion of chemically enhanced primary treatment (CEPT) sludge and themicrobial community structure. Applied Microbiology and Biotechnology. 100(20):8975-8982

10.Ju F*, Li B*, Ma L, Wang Y, Huang D, Zhang T. 2016. Antibiotic resistance genes and human bacterial pathogens: co-occurrence, removal, and enrichmentin municipal sewage sludge digesters. Water Research. 91:1-10 (^#equal contribution)

9.Ju F, Zhang T. 2015. 16S rRNA gene high-throughput sequencing data mining of microbial diversity and interactions. Applied Microbiology and Biotechnology. 99(10):4119-4129

8. Ju F, Zhang T. 2015. Experimental design and bioinformatics analysis for the application of metagenomics in environmental sciences and biotechnology. Environmental Science & Technology. 49(21):12628-12640

7. Li B*, Ju F*, Cai L, Zhang T. 2015. Profile and fate of bacterial pathogens in sewage treatment plants revealed by high-throughput metagenomic approach. Environmental Science & Technology. 49(17):10492–10502 (^#equalcontribution)

6.Ju F, Zhang T. 2015. Bacterial assembly and temporal dynamics in activated sludge of a full-scale municipal wastewater treatment plant. The ISME Journal. 9:683-695

5.Ju F, Xia Y, Guo F, Wang Z, Zhang T. 2014. Taxonomic relatedness shapes bacterial assembly in activated sludge of globally distributed wastewater treatment plants. Environmental Microbiology. 16(8):2421-2432

4.Ju F, Guo F, Ye L, Xia Y, Zhang T. 2014. Metagenomic analysis on seasonal microbial variations of activated sludge from a full-scale wastewater treatment plant over four years. Environmental Microbiology Reports. 6(1):80-89

3.Ju F, Zhang T. 2014. Novel microbial populations in ambient and mesophilic biogas-producing and phenol-degrading consortia unraveled by high-throughput sequencing. Microbial Ecology. 68(2):235-246.

2. Ju F, Hu Y, Cheng J. 2011. Removal of chelatedCu (II) from aqueous solution by adsorption–coprecipitation with ironhydroxides prepared from microelectrolysis process. Desalination. 274(1):130-135   

1. Ju F, Hu Y. 2011. Removal of EDTA-chelatedcopper from aqueous solution by interior microelectrolysis. Separation and Purification Technology. 78(1):33-41