Book chapter

1. Ju F, Fang, HHP, Zhang T*. Application of Metagenomics in Environmental Anaerobic Technology. Book chapter V of “Anaerobic Biotechnology: Environmental Protection and ResourceRecovery”, Imperial College Press, October, 2015. ISBN: 978-1-78326-790-3

2. Zhang HL, Zhou NJ, Ju F*. Immunoreaction-based Sensors to Improve Bacterial Detection. Book chapter of “Handbook of BiochipsSpringerMay 2020. ISBN: 978-1-4614-6623-9

3. Huang XY, Zhang L, Yuan L, Ju F*. (2021). Quantitative Metagenomics and MetatranscriptomicsMethods of Microbiome. Bio-101: e2003693. DOI: 10.21769/BioProtoc. 2003693

4. Zhang L, Ju F*. (2021). RNA-Stable Isotope Probing for Microbial Communities. Bio-101:e2003692. DOI: 10.21769/BioProtoc. 2003692

5. Zhao Z, Ju F*. (2020). Isolation and Extraction of IntracellularAbsorbed-extracellular and Free-extracellular Environmental DNA from AquaticMicrobial Community. Bio-101: e2003587. DOI: 10.21769/BioProtoc. 2003587

Journal Papers

Journal name (no. of articles): Microbiome (1), Water Research (7), The ISME Journal (4), Environmental Science & Technology (9), Science of the Total Environment (5), Applied Microbiology and Biotechnology (6), Environmental Microbiology (2), Journal of Hazardous Materials (2), Scientific Reports (2) and other journals.

1. Zhang ZG, Zhang GQ Ju F*. 2022. Using Culture-Enriched Phenotypic Metagenomics for Targeted High-Throughput Monitoring of Clinically-Important Fraction of Beta-Lactam Resistome. Environmental Science & Technology. 56: 11429-11439

2. Gao H, Zhao Z, Zhang L, Ju F*. 2022. Cyanopeptides restriction and degradation co-mediate microbiota assembly during a freshwater cyanobacterial harmful algal bloom (CyanoHAB) . Water Research. 220: 118674

3. Yang XY# , Zhang L# , Chen Y, He Q, Liu T, Zhang GQ, Yuan L, Peng HR, Wang H, Ju F*. 2022. Micro(nano)plastic size and concentration co-differentiate nitrogen transformation, microbiota dynamics, and assembly patterns in constructed wetlands. Water Research.118636

4. He LQ#, Huang XY#, Zhang GQ, Yuan L, Shen EH, Zhang L, Zhang XH, Zhang T, Tao L*, Ju F*. 2022. Distinctive signatures of pathogenic and antibiotic resistant potentials in the hadal microbiome. Environmental Microbiome

5. Shuai M L, Zhang G Q, Zeng FF, Fu YQ, Liang XX, Yuan L, Xu FZ, Gou WL, Miao ZL, Jiang ZL, Wang JT, Zhuo LB, Chen YM, Ju F*, Zheng JS* .2022.   Human Gut Antibiotic Resistome and Progression of Diabetes. Advanced Science.   e2104965

6. He YZ , Jin H, Gao H, Zhang GQ, Ju F*. 2021. Prevalence, production, and ecotoxicity of chlorination-derived metformin byproducts in Chinese urban water systems. Science of the Total Environment. 151665

7. Zhang L, Yin W, Wang C, Zhang A, Zhang H, Zhang T, Ju F*. 2021. Untangling Microbiota Diversity and Assembly Patterns in the World's Largest Water Diversion Canal. Water Research. 117617

8. Zhang HL, Yao Y, Hui Y, Zhou NJ*, Ju F*. 2021. A 3D-Printed Microfluidic Gradient Concentration Chip for Rapid Antibiotic Susceptibility Testing. Bio-Design and Manufacturing.174: 1-10

9. Yuan L, Wang YB, Zhang L, Alejandro P, Zhou JZ, Smets BF, Bürgmann H, Ju F*. 2021. Pathogenic and indigenous denitrifying bacteria are transcriptionally active and key multi-antibiotic resistant players in wastewater treatment plants. Environmental Science & Technology. 55(15): 10862-10874

10. Yang XY, Wang H,   Zhang L, Kong LW, Chen Y*,   He Q,   Li L, Grossart H-P, Ju F*. 2021. Marine algae facilitate transfer of microplastics and associated pollutants into food webs.Science of the Total Environment. (787): 147535

11. Zhang RS#, He YZ#, Yao LX#, Chen J, Zhu SH, Rao XX, Tang PY, You J, Hua GQ, Zhang L, Ju F*, Wu LF* . 2021. Metformin chlorination byproducts in drinking water exhibit marked toxicities of a potential health concern. Environment International. (146): 106244

12. Gao CH, Cao H, Ju F, Xiao KQ, Cai P, Wu Y, Huang Q. 2021. Emergent transcriptional adaption facilitates convergent succession within a synthetic community. ISME Communications. 1(1): 1-5

13. Lee J, Ju F, Maile-Moskowitz A, Beck K, Maccagna A,  McArdell C, Molin MD, Fenicia F, Vikesland P, Pruden A, Stamm, C, Buergmann H. 2021. Unraveling the riverine antibiotic resistome: the downstream fate of anthropogenic inputs. Water Research. (197): 117050

14. Wang Y, Qin W, Jiang X, Ju F, Mao Y, Zhang A, Stahl DA, Zhang T. 2021. Seasonal Prevalence of Ammonia-Oxidizing Archaea in a Full-Scale Municipal Wastewater Treatment Plant Treating Saline Wastewater Revealed by a 6-Year Time-Series Analysis. Environmental Science & Technology. 55(4): 2662-2673

15. CaoY, Yu X, Ju F, Zhan H, Jiang B, Kang H, Xie Z. 2020. Airborne Bacterial Community Diversity, Source and Function along the Antarctic Coast. Science of The Total Environment. 142700

16. Hu WC, Liang JS, Ju F, Wang QJ, Liu RP, Bai YH*, Liu HJ, Qu JH, 2020. Metagenomics unravels differential microbiome composition and metabolic potential in rapid sandfilters purifying surface water versus groundwater. Environmental Science &Technology. 54(8): 5197-5206

17. Ju F, Zhang T. 2019. Advances in meta-omics research on activated sludge microbial community. Microbiology China. 46(8): 2038-2052

18. Ju F, Beck K, Yin X, McArdell Christa, 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

19. Zhao FZ#, Ju F#, Huang K, Mao Y, Zhang XX*., Ren H, Zhang T*. 2019. Comprehensive insights into the key components of bacterial assemblages in pharmaceutical wastewater treatment plants. Science of The Total Environment. 651, 2148-2157

20. Guo F, Zhang T, Li B, Wang Z, Ju F, Liang Y, 2019. Mycobacterial species and their contribution to cholesterol degradation in wastewater treatment plants. Scientific reports. 9(1): 836

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

22. Jiang XT, Ye L, Ju F, Wang YL, Zhang T*. 2018. Toward an intensive longitudinal understanding of activated sludge bacterial assembly and dynamics. Environmental Science & Technology. 52(15): 8224-8232

23. Jiang XT, Ye L, Ju F, Li B, Ma LP, ZhangT*. 2018. Temporal dynamics of activated sludge bacterial communities in twodiversity variant full-scale sewage treatment plants.Applied microbiology and biotechnology. 1-10

24. Huang K, Mao Y, Zhao F, Zhang XX, Ju F, Ye L, Wang Y, Li B, Ren H, Zhang T. 2018. Free-living bacteria and potential bacterial pathogens in sewage treatment plants. Applied microbiology and biotechnology. 102 (5): 2455-2464

25. 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

26. Hu A, Ju F, Hou L, Li J, Yang X, Wang H,Mulla SI, Sun Q, Bürgmann H*, Yu CP*. 2017. Strong impact of anthropogenic contamination on the cooccurrence patterns of a riverine microbial community. Environmental Microbiology. 19(12): 4993-5009

27. Ju F, Li B, Ma LP, Wang YB, Huang DP,Zhang T*. 2016. Antibiotic resistance genes and human bacterial pathogens:co-occurrence, removal, and enrichment in municipal sewage sludge digesters. Water Research. 91, 1-10   

28. Ju F, Wang YB, Lau FTK, Fung WC, Huang DP, Xia Y, Zhang T*. 2016. Anaerobic digestion of chemically enhanced primarytreatment (CEPT) sludge and the microbial community structure. Applied Microbiology and Biotechnology. 100 (20): 8975-8982

29. 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

30. Li B, Yang Y, Ma LP, Ju F, Guo F, TiedjeJ. Zhang T*. 2015. Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes. The ISME Journal. 9(11): 2490-2502

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

32. 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

33. 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

34. Wang YB, Xia Y, Ju F, Zhang T*. 2015. Metagenome approaches revealed a biological prospect for improvement on mesophilic cellulose degradation. Applied Microbiology and Biotechnology. 99(24): 10871-10879

35. Chao YQ, Ma LP, Yang Y, Ju F, Zhang XX,Wu, WM, Zhang T*. 2014. Metagenomic analysis reveals significant changes ofmicrobial compositions and protective functions during drinking watertreatment. Scientific Reports. srep03550

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

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

38. Peng XX, Guo F, Ju F, Zhang T*. 2014. Shifts in the microbial community, nitrifiers and denitrifiers in the biofilmin a full-scale rotating biological contactor. Environmental Science &Technology. 48(14): 8044-8052

39. 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