[1]

Song X, Fredj Z, Zheng Y, Zhang H, Rong G, et al. 2023. Biosensors for waterborne virus detection: challenges and strategies. Journal of Pharmaceutical Analysis 13:1252−1268

doi: 10.1016/j.jpha.2023.08.020
[2]

Wang A, Huang F, Wang W, Zhao Y, Su Y, et al. 2025. GWPD: a multifunctional platform to unravel biological risk factors in global engineered water systems. Engineering 51:254−262

doi: 10.1016/j.eng.2024.04.022
[3]

Zhao Y, Fan L, Gao SH, Huang F, Lei Z, et al. 2024. Strain-level multidrug-resistant pathogenic bacteria in urban wastewater treatment plants: transmission, source tracking and evolution. Water Research 267:122538

doi: 10.1016/j.watres.2024.122538
[4]

Zhao Y, Huang F, Wang W, Gao R, Fan L, et al. 2023. Application of high-throughput sequencing technologies and analytical tools for pathogen detection in urban water systems: progress and future perspectives. Science of The Total Environment 900:165867

doi: 10.1016/j.scitotenv.2023.165867
[5]

Zhang Y, Huo J, Zheng X. 2021. Wastewater: China's next water source. Science 374:1332

doi: 10.1126/science.abm6738
[6]

Hwang Y, Roux S, Coclet C, Krause SJE, Girguis PR. 2023. Viruses interact with hosts that span distantly related microbial domains in dense hydrothermal mats. Nature Microbiology 8:946−957

doi: 10.1038/s41564-023-01347-5
[7]

Chen Y, Wang Y, Paez-Espino D, Polz MF, Zhang T. 2021. Prokaryotic viruses impact functional microorganisms in nutrient removal and carbon cycle in wastewater treatment plants. Nature Communications 12:5398

doi: 10.1038/s41467-021-25678-1
[8]

Luo XQ, Wang P, Li JL, Ahmad M, Duan L, et al. 2022. Viral community-wide auxiliary metabolic genes differ by lifestyles, habitats, and hosts. Microbiome 10:190

doi: 10.1186/s40168-022-01384-y
[9]

Chen ML, An XL, Liao H, Yang K, Su JQ, et al. 2021. Viral community and virus-associated antibiotic resistance genes in soils amended with organic fertilizers. Environmental Science & Technology 55:13881−13890

doi: 10.1021/acs.est.1c03847
[10]

Diamond MB, Keshaviah A, Bento AI, Conroy-Ben O, Driver EM, et al. 2022. Wastewater surveillance of pathogens can inform public health responses. Nature Medicine 28:1992−1995

doi: 10.1038/s41591-022-01940-x
[11]

Farkas K, Hillary LS, Malham SK, McDonald JE, Jones DL. 2020. Wastewater and public health: the potential of wastewater surveillance for monitoring COVID-19. Current Opinion in Environmental Science & Health 17:14−20

doi: 10.1016/j.coesh.2020.06.001
[12]

Singer AC, Thompson JR, Filho CRM, Street R, Li X, et al. 2023. A world of wastewater-based epidemiology. Nature Water 1:408−415

doi: 10.1038/s44221-023-00083-8
[13]

Jo EK. 2019. Interplay between host and pathogen: immune defense and beyond. Experimental & Molecular Medicine 51:1−3

doi: 10.1038/s12276-019-0281-8
[14]

Chen YT, Lohia GK, Chen S, Liu Z, Wong Fok Lung T, et al. 2025. A host-pathogen metabolic synchrony that facilitates disease tolerance. Nature Communications 16:3729

doi: 10.1038/s41467-025-59134-1
[15]

Wu LY, Wijesekara Y, Piedade GJ, Pappas N, Brussaard CPD, et al. 2024. Benchmarking bioinformatic virus identification tools using real-world metagenomic data across biomes. Genome Biology 25:97

doi: 10.1186/s13059-024-03236-4
[16]

Tang A, Zhang J, Huang J, Deng Y, Wang D, et al. 2024. Decrypting the viral community in aerobic activated sludge reactors treating antibiotic production wastewater. Water Research 265:122253

doi: 10.1016/j.watres.2024.122253
[17]

Shi Z, Long X, Zhang C, Chen Z, Usman M, et al. 2024. Viral and bacterial community dynamics in food waste and digestate from full-scale biogas plants. Environmental Science & Technology 58:13010−13022

doi: 10.1021/acs.est.4c04109
[18]

Zhang J, Tang A, Jin T, Sun D, Guo F, et al. 2024. A panoramic view of the virosphere in three wastewater treatment plants by integrating viral-like particle-concentrated and traditional non-concentrated metagenomic approaches. iMeta 3:e188

doi: 10.1002/imt2.188
[19]

Yuan L, Ju F. 2023. Potential auxiliary metabolic capabilities and activities reveal biochemical impacts of viruses in municipal wastewater treatment plants. Environmental Science & Technology 57:5485−5498

doi: 10.1021/acs.est.2c07800
[20]

Lehto KM, Länsivaara A, Hyder R, Luomala O, Lipponen A, et al. 2024. Wastewater-based surveillance is an efficient monitoring tool for tracking influenza A in the community. Water Research 257:121650

doi: 10.1016/j.watres.2024.121650
[21]

Tisza M, Javornik Cregeen S, Avadhanula V, Zhang P, Ayvaz T, et al. 2023. Wastewater sequencing reveals community and variant dynamics of the collective human virome. Nature Communications 14:6878

doi: 10.1038/s41467-023-42064-1
[22]

Zhang N, Zhu D, Yao Z, Zhu DZ. 2025. Virus-prokaryote interactions assist pollutant removal in constructed wetlands. Bioresource Technology 416:131791

doi: 10.1016/j.biortech.2024.131791
[23]

Ng C, Tan B, Jiang XT, Gu X, Chen H, et al. 2019. Metagenomic and resistome analysis of a full-scale municipal wastewater treatment plant in Singapore containing membrane bioreactors. Frontiers in Microbiology 10:172

doi: 10.3389/fmicb.2019.00172
[24]

Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114−2120

doi: 10.1093/bioinformatics/btu170
[25]

Roehr JT, Dieterich C, Reinert K. 2017. Flexbar 3.0-SIMD and multicore parallelization. Bioinformatics 33:2941−2942

doi: 10.1093/bioinformatics/btx330
[26]

Jiang H, Lei R, Ding SW, Zhu S. 2014. Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads. BMC Bioinformatics 15:182

doi: 10.1186/1471-2105-15-182
[27]

Kopylova E, Noé L, Touzet H. 2012. SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics 28:3211−3217

doi: 10.1093/bioinformatics/bts611
[28]

Li D, Liu CM, Luo R, Sadakane K, Lam TW. 2015. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 31:1674−1676

doi: 10.1093/bioinformatics/btv033
[29]

Nayfach S, Camargo AP, Schulz F, Eloe-Fadrosh E, Roux S, et al. 2021. CheckV assesses the quality and completeness of metagenome-assembled viral genomes. Nature Biotechnology 39:578−585

doi: 10.1038/s41587-020-00774-7
[30]

Ren J, Song K, Deng C, Ahlgren NA, Fuhrman JA, et al. 2020. Identifying viruses from metagenomic data using deep learning. Quantitative Biology 8:64−77

doi: 10.1007/s40484-019-0187-4
[31]

Guo J, Bolduc B, Zayed AA, Varsani A, Dominguez-Huerta G, et al. 2021. VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses. Microbiome 9:37

doi: 10.1186/s40168-020-00990-y
[32]

Kieft K, Zhou Z, Anantharaman K. 2020. VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences. Microbiome 8:90

doi: 10.1186/s40168-020-00867-0
[33]

Shaffer M, Borton MA, McGivern BB, Zayed AA, La Rosa SL, et al. 2020. DRAM for distilling microbial metabolism to automate the curation of microbiome function. Nucleic Acids Research 48:8883−8900

doi: 10.1093/nar/gkaa621
[34]

Feldgarden M, Brover V, Haft DH, Prasad AB, Slotta DJ, et al. 2020. Validating the AMRFinder tool and resistance gene database by using antimicrobial resistance genotype-phenotype correlations in a collection of isolates. Antimicrobial Agents and Chemotherapy 64:10.1128/aac.00483-19

doi: 10.1128/AAC.00483-19
[35]

Roux S, Camargo AP, Coutinho FH, Dabdoub SM, Dutilh BE, et al. 2023. iPHoP: an integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria. PLoS Biology 21:e3002083

doi: 10.1371/journal.pbio.3002083
[36]

Uritskiy GV, DiRuggiero J, Taylor J. 2018. MetaWRAP − a flexible pipeline for genome-resolved metagenomic data analysis. Microbiome 6:158

doi: 10.1186/s40168-018-0541-1
[37]

Chaumeil PA, Mussig AJ, Hugenholtz P, Parks DH. 2020. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics 36:1925−1927

doi: 10.1093/bioinformatics/btz848
[38]

Hong W, Mei H, Shi X, Lin X, Wang S, et al. 2024. Viral community distribution, assembly mechanism, and associated hosts in an industrial park wastewater treatment plant. Environmental Research 247:118156

doi: 10.1016/j.envres.2024.118156
[39]

Fan X, Ji M, Mu D, Zeng X, Tian Z, et al. 2023. Global diversity and biogeography of DNA viral communities in activated sludge systems. Microbiome 11:234

doi: 10.1186/s40168-023-01672-1
[40]

Al-Faliti M, Wang P, Smith AL, Delgado Vela J. 2024. Phage phylogeny, molecular signaling, and auxiliary antimicrobial resistance in aerobic and anaerobic membrane bioreactors. Water Research 256:121620

doi: 10.1016/j.watres.2024.121620
[41]

Jansson JK, Wu R. 2023. Soil viral diversity, ecology and climate change. Nature Reviews Microbiology 21:296−311

doi: 10.1038/s41579-022-00811-z
[42]

Chakraborty S, Rohit A, Prasanthi SJ, Chauhan A. 2024. A new Casjensviridae bacteriophage isolated from hospital sewage for inactivation of biofilms of carbapenem resistant Klebsiella pneumoniae clinical isolates. Pharmaceutics 16:904

doi: 10.3390/pharmaceutics16070904
[43]

Ramos-Barbero MD, Gómez-Gómez C, Sala-Comorera L, Rodríguez-Rubio L, Morales-Cortes S, et al. 2023. Characterization of crAss-like phage isolates highlights Crassvirales genetic heterogeneity and worldwide distribution. Nature Communications 14:4295

doi: 10.1038/s41467-023-40098-z
[44]

Troshin K, Sykilinda N, Shuraleva S, Tokmakova A, Tkachenko N, et al. 2025. Pseudomonas phage Lydia and the evolution of the Mesyanzhinovviridae family. Viruses 17:369

doi: 10.3390/v17030369
[45]

Yan M, Yu Z. 2024. Viruses contribute to microbial diversification in the rumen ecosystem and are associated with certain animal production traits. Microbiome 12:82

doi: 10.1186/s40168-024-01791-3
[46]

World Health Organization (WHO). 2024. Pathogens prioritization: a scientific framework for epidemic and pandemic research preparedness. Meeting report. WHO, Geneva, Switzerland. https://cdn.who.int/media/docs/default-source/consultation-rdb/prioritization-pathogens-v6final.pdf?sfvrsn=c98effa7_9&download=true

[47]

Li J, Zhou L, Zhao J, Zhang W, Pan B, et al. 2025. Enhanced methanogenesis of wastewater anaerobic digestion by nanoscale zero-valent iron: mechanism on intracellular energy conservation and amino acid metabolism. Bioresource Technology 423:132243

doi: 10.1016/j.biortech.2025.132243
[48]

Xu Q, Zhang H, Vandenkoornhuyse P, Guo S, Kuzyakov Y, et al. 2024. Carbon starvation raises capacities in bacterial antibiotic resistance and viral auxiliary carbon metabolism in soils. Proceedings of the National Academy of Sciences of the United States of America 121:e231816012

doi: 10.1073/pnas.2318160121
[49]

Su Y. 2021. Revisiting carbon, nitrogen, and phosphorus metabolisms in microalgae for wastewater treatment. Science of The Total Environment 762:144590

doi: 10.1016/j.scitotenv.2020.144590
[50]

Li X, Li S, Xie P, Chen X, Chu Y, et al. 2024. Advanced wastewater treatment with microalgae-indigenous bacterial interactions. Environmental Science and Ecotechnology 20:100374

doi: 10.1016/j.ese.2023.100374
[51]

Lopatkin AJ, Bening SC, Manson AL, Stokes JM, Kohanski MA, et al. 2021. Clinically relevant mutations in core metabolic genes confer antibiotic resistance. Science 371:eaba0862

doi: 10.1126/science.aba0862
[52]

Kim HS, Lee BY, Won EJ, Han J, Hwang DS, et al. 2015. Identification of xenobiotic biodegradation and metabolism-related genes in the copepod Tigriopus japonicus whole transcriptome analysis. Marine Genomics 24:207−208

doi: 10.1016/j.margen.2015.05.011
[53]

Niu L, Zhao S, Chen Y, Li Y, Zou G, et al. 2023. Diversity and potential functional characteristics of phage communities colonizing microplastic biofilms. Environmental Research 219:115103

doi: 10.1016/j.envres.2022.115103
[54]

Zang B, Zhou H, Zhao Y, Sano D, Chen R. 2024. Investigating potential auxiliary anaerobic digestion activity of phage under polyvinyl chloride microplastic stress. Journal of Hazardous Materials 480:135950

doi: 10.1016/j.jhazmat.2024.135950
[55]

Wang L, Lin D, Xiao KQ, Ma LJ, Fu YM, et al. 2024. Soil viral-host interactions regulate microplastic- dependent carbon storage. Proceedings of the National Academy of Sciences of the United States of America 121:e241324512

doi: 10.1073/pnas.2413245121
[56]

Pang Z, Raudonis R, Glick BR, Lin TJ, Cheng Z. 2019. Antibiotic resistance in Pseudomonas aeruginosa: mechanisms and alternative therapeutic strategies. Biotechnology Advances 37:177−192

doi: 10.1016/j.biotechadv.2018.11.013
[57]

Yu M, Zhang M, Zeng R, Cheng R, Zhang R, et al. 2024. Diversity and potential host-interactions of viruses inhabiting deep-sea seamount sediments. Nature Communications 15:3228

doi: 10.1038/s41467-024-47600-1
[58]

Zou H, Zhou Z, Berglund B, Zheng B, Meng M, et al. 2023. Persistent transmission of carbapenem-resistant, hypervirulent Klebsiella pneumoniae between a hospital and urban aquatic environments. Water Research 242:120263

doi: 10.1016/j.watres.2023.120263
[59]

Wang Y, Wang W, Yu X, Wang Z, Zhou Z, et al. 2024. Global diversity of airborne pathogenic bacteria and fungi from wastewater treatment plants. Water Research 258:121764

doi: 10.1016/j.watres.2024.121764
[60]

Liu P, Huang ML, Guo H, McCallum M, Si JY, et al. 2024. Design of customized coronavirus receptors. Nature 635:978−986

doi: 10.1038/s41586-024-08121-5
[61]

Wang Q, Wang M, Yang Q, Feng L, Zhang H, et al. 2025. The role of bacteriophages in facilitating the horizontal transfer of antibiotic resistance genes in municipal wastewater treatment plants. Water Research 268:122776

doi: 10.1016/j.watres.2024.122776
[62]

Huang L, Pu H, Sun DW. 2024. Spatiotemporally guided single-atom bionanozyme for targeted antibiofilm treatment. Small 20:2407747

doi: 10.1002/smll.202407747