{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,9]],"date-time":"2026-10-09T07:10:03Z","timestamp":1791529803061,"version":"4.3.4"},"reference-count":148,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2026,6,15]],"date-time":"2026-06-15T00:00:00Z","timestamp":1781481600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100007192","name":"National Institute for Public Health and the Environment","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100007192","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002999","name":"Ministerie van Volksgezondheid, Welzijn en Sport","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002999","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Environmental Research"],"published-print":{"date-parts":[[2026,9]]},"DOI":"10.1016\/j.envres.2026.125050","type":"journal-article","created":{"date-parts":[[2026,6,15]],"date-time":"2026-06-15T16:30:31Z","timestamp":1781541031000},"page":"125050","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":2,"special_numbering":"P2","title":["Use of metagenomics for the detection of pathogens in the environment: A scoping review"],"prefix":"10.1016","volume":"305","author":[{"ORCID":"https:\/\/orcid.org\/0009-0006-9288-1563","authenticated-orcid":false,"given":"Milou A.M.","family":"Maas","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7851-3402","authenticated-orcid":false,"given":"Saskia A.","family":"Rutjes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6586-717X","authenticated-orcid":false,"given":"Alex","family":"Bossers","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2020-2702","authenticated-orcid":false,"given":"Paul B.","family":"Stege","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4901-2278","authenticated-orcid":false,"given":"Rozemarijn Q.J.","family":"van der Plaats","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-6320-0060","authenticated-orcid":false,"given":"Irene","family":"Kuiper","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3289-1576","authenticated-orcid":false,"given":"Kees C.H.","family":"van der Ark","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9651-0504","authenticated-orcid":false,"given":"Ana Maria","family":"de Roda Husman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.envres.2026.125050_bib1","doi-asserted-by":"crossref","DOI":"10.1016\/j.watres.2020.116112","article-title":"Metagenomic water quality monitoring with a portable laboratory","volume":"184","author":"Acharya","year":"2020","journal-title":"Water Res."},{"issue":"5","key":"10.1016\/j.envres.2026.125050_bib2","doi-asserted-by":"crossref","DOI":"10.1093\/bib\/bbae424","article-title":"CAIM: coverage-based analysis for identification of microbiome","volume":"25","author":"Acheampong","year":"2024","journal-title":"Briefings Bioinf."},{"key":"10.1016\/j.envres.2026.125050_bib3","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1007\/978-1-0716-4192-7_1","article-title":"The evolution of next-generation sequencing technologies","volume":"2866","author":"Akintunde","year":"2025","journal-title":"Methods Mol. Biol."},{"issue":"1","key":"10.1016\/j.envres.2026.125050_bib4","doi-asserted-by":"crossref","DOI":"10.3390\/ijerph20010600","article-title":"Metagenomic analysis of microbial contamination in the U.S. portion of the Tijuana River watershed","volume":"20","author":"Allsing","year":"2022","journal-title":"Int. J. Environ. Res. Publ. Health"},{"key":"10.1016\/j.envres.2026.125050_bib5","doi-asserted-by":"crossref","DOI":"10.1016\/j.mam.2024.101253","article-title":"Principles of digital sequencing using unique molecular identifiers","volume":"96","author":"Andersson","year":"2024","journal-title":"Mol. Aspect. Med."},{"issue":"14","key":"10.1016\/j.envres.2026.125050_bib6","doi-asserted-by":"crossref","first-page":"4126","DOI":"10.1093\/bioinformatics\/btaa490","article-title":"Metaviral SPAdes: assembly of viruses from metagenomic data","volume":"36","author":"Antipov","year":"2020","journal-title":"Bioinformatics"},{"issue":"1","key":"10.1016\/j.envres.2026.125050_bib7","doi-asserted-by":"crossref","first-page":"3078","DOI":"10.1038\/s41467-021-23296-5","article-title":"Strengthening the united nations secretary-general's mechanism to an alleged use of bioweapons through a quality-assured laboratory response","volume":"12","author":"Appelt","year":"2021","journal-title":"Nat. Commun."},{"issue":"3","key":"10.1016\/j.envres.2026.125050_bib8","doi-asserted-by":"crossref","DOI":"10.1128\/spectrum.00481-23","article-title":"Nonbacterial microflora in wastewater treatment plants: an underappreciated potential source of pathogens microbiology spectrum","volume":"11","author":"Ariyadasa","year":"2023","journal-title":"Microbiol. Spectr."},{"issue":"3","key":"10.1016\/j.envres.2026.125050_bib9","doi-asserted-by":"crossref","DOI":"10.1128\/aem.01845-21","article-title":"Extracellular DNA in environmental samples: occurrence, extraction, quantification, and impact on microbial biodiversity assessment","volume":"88","author":"Bairoliya","year":"2022","journal-title":"Appl. Environ. Microbiol."},{"issue":"1","key":"10.1016\/j.envres.2026.125050_bib10","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-024-80584-y","article-title":"Statistical design approach enables optimised mechanical lysis for enhanced long-read soil metagenomics","volume":"14","author":"Barber","year":"2024","journal-title":"Sci. Rep."},{"key":"10.1016\/j.envres.2026.125050_bib11","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2023.1186424","article-title":"Clinical metagenomics-challenges and future prospects","volume":"14","author":"Batool","year":"2023","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.envres.2026.125050_bib12","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2021.644662","article-title":"Improved microbial community characterization of 16S rRNA via metagenome hybridization capture enrichment","volume":"12","author":"Beaudry","year":"2021","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.envres.2026.125050_bib13","doi-asserted-by":"crossref","DOI":"10.7717\/peerj.9762","article-title":"DATMA: distributed AuTomatic metagenomic assembly and annotation framework","volume":"8","author":"Benavides","year":"2020","journal-title":"PeerJ"},{"issue":"3","key":"10.1016\/j.envres.2026.125050_bib14","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0032942","article-title":"Deep sequencing analyses of low density microbial communities: working at the boundary of accurate microbiota detection","volume":"7","author":"Biesbroek","year":"2012","journal-title":"PLoS One"},{"issue":"1","key":"10.1016\/j.envres.2026.125050_bib15","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s40793-019-0349-z","article-title":"Performance evaluation of a new custom, multi-component DNA isolation method optimized for use in shotgun metagenomic sequencing-based aerosol microbiome research","volume":"15","author":"Boifot","year":"2020","journal-title":"Environ Microbio."},{"issue":"12","key":"10.1016\/j.envres.2026.125050_bib16","doi-asserted-by":"crossref","DOI":"10.1002\/mbo3.1133","article-title":"A low-cost pipeline for soil microbiome profiling","volume":"9","author":"Bollmann-Giolai","year":"2020","journal-title":"Microbiologyopen"},{"issue":"21","key":"10.1016\/j.envres.2026.125050_bib17","first-page":"1","article-title":"Abundance tracking by long-read nanopore sequencing of complex microbial communities in samples from 20 different biogas\/wastewater plants","volume":"10","author":"Brandt","year":"2020","journal-title":"Appl. Sci. Basel"},{"issue":"4","key":"10.1016\/j.envres.2026.125050_bib18","doi-asserted-by":"crossref","first-page":"1125","DOI":"10.1093\/bib\/bbx120","article-title":"A review of methods and databases for metagenomic classification and assembly","volume":"20","author":"Breitwieser","year":"2019","journal-title":"Briefings Bioinf."},{"key":"10.1016\/j.envres.2026.125050_bib19","doi-asserted-by":"crossref","DOI":"10.1093\/femsle\/fnae044","article-title":"Impacts of sample handling and storage conditions on archiving physiologically active soil microbial communities","volume":"371","author":"Brock","year":"2024","journal-title":"FEMS Microbiol. Lett."},{"issue":"10","key":"10.1016\/j.envres.2026.125050_bib20","doi-asserted-by":"crossref","DOI":"10.3390\/v13102006","article-title":"Utilizing the VirIdAl pipeline to search for viruses in the metagenomic data of bat samples","volume":"13","author":"Budkina","year":"2021","journal-title":"Viruses"},{"issue":"6","key":"10.1016\/j.envres.2026.125050_bib21","doi-asserted-by":"crossref","first-page":"633","DOI":"10.1089\/cmb.2022.0208","article-title":"ClassGraph: improving metagenomic read classification with overlap graphs","volume":"30","author":"Cavattoni","year":"2023","journal-title":"J. Comput. Biol."},{"key":"10.1016\/j.envres.2026.125050_bib22","doi-asserted-by":"crossref","DOI":"10.3389\/fvets.2023.1257573","article-title":"Metagenomic analysis fecal microbiota of dysentery-like diarrhoea in a pig farm using next-generation sequencing","volume":"10","author":"Chen","year":"2023","journal-title":"Front. Vet. Sci."},{"issue":"1","key":"10.1016\/j.envres.2026.125050_bib23","doi-asserted-by":"crossref","first-page":"226","DOI":"10.1186\/s13059-024-03363-y","article-title":"Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes","volume":"25","author":"Chen","year":"2024","journal-title":"Genome Biol."},{"issue":"1","key":"10.1016\/j.envres.2026.125050_bib24","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1186\/s13059-015-0697-y","article-title":"The impact of read length on quantification of differentially expressed genes and splice junction detection","volume":"16","author":"Chhangawala","year":"2015","journal-title":"Genome Biol."},{"issue":"9","key":"10.1016\/j.envres.2026.125050_bib25","article-title":"Comparative evaluation of soil DNA extraction kits for long read metagenomic sequencing","volume":"6","author":"Child","year":"2024","journal-title":"Access Microbio."},{"issue":"6","key":"10.1016\/j.envres.2026.125050_bib26","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1038\/s41576-019-0113-7","article-title":"Clinical metagenomics","volume":"20","author":"Chiu","year":"2019","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.envres.2026.125050_bib27","doi-asserted-by":"crossref","DOI":"10.3389\/fbinf.2024.1278228","article-title":"Ten common issues with reference sequence databases and how to mitigate them","volume":"4","author":"Chorlton","year":"2024","journal-title":"Front Bioinform."},{"issue":"3","key":"10.1016\/j.envres.2026.125050_bib28","doi-asserted-by":"crossref","DOI":"10.1128\/mSystems.00804-20","article-title":"DOE JGI metagenome workflow","volume":"6","author":"Clum","year":"2021","journal-title":"mSystems"},{"issue":"2","key":"10.1016\/j.envres.2026.125050_bib29","doi-asserted-by":"crossref","DOI":"10.3390\/soilsystems8020046","article-title":"Uncovering hidden microbial diversity in nitrate\/iodide deposits (NIDs) in the domeyko district, Atacama desert, Chile","volume":"8","author":"Cortes","year":"2024","journal-title":"Soil Syst."},{"key":"10.1016\/j.envres.2026.125050_bib30","doi-asserted-by":"crossref","DOI":"10.1016\/j.mex.2024.103134","article-title":"Ultra pure high molecular weight DNA from soil for nanopore shotgun metagenomics and metabarcoding sequencing","volume":"14","author":"Cousson","year":"2025","journal-title":"MethodsX"},{"issue":"1","key":"10.1016\/j.envres.2026.125050_bib31","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1186\/s12859-024-05859-7","article-title":"AFITbin: a metagenomic contig binning method using aggregate l-mer frequency based on initial and terminal nucleotides","volume":"25","author":"Darabi","year":"2024","journal-title":"BMC Bioinf."},{"key":"10.1016\/j.envres.2026.125050_bib32","doi-asserted-by":"crossref","DOI":"10.1016\/j.copbio.2023.102901","article-title":"Harnessing the omics revolution to address the global biodiversity crisis","volume":"80","author":"De Leon","year":"2023","journal-title":"Curr. Opin. Biotechnol."},{"issue":"2","key":"10.1016\/j.envres.2026.125050_bib33","doi-asserted-by":"crossref","DOI":"10.3390\/w15020271","article-title":"Comparative analysis of metagenomic (Amplicon and shotgun) DNA sequencing to characterize microbial communities in household On-Site wastewater treatment systems","volume":"15","author":"de Vries","year":"2023","journal-title":"Water"},{"issue":"1","key":"10.1016\/j.envres.2026.125050_bib34","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-023-48804-z","article-title":"Benchmarking DNA isolation methods for marine metagenomics","volume":"13","author":"Demkina","year":"2023","journal-title":"Sci. Rep."},{"issue":"9","key":"10.1016\/j.envres.2026.125050_bib35","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1010493","article-title":"HAYSTAC: a Bayesian framework for robust and rapid species identification in high-throughput sequencing data","volume":"18","author":"Dimopoulos","year":"2022","journal-title":"PLoS Comput. Biol."},{"issue":"1","key":"10.1016\/j.envres.2026.125050_bib36","doi-asserted-by":"crossref","first-page":"3030","DOI":"10.1038\/s41598-021-82726-y","article-title":"Comparison between 16S rRNA and shotgun sequencing data for the taxonomic characterization of the gut microbiota","volume":"11","author":"Durazzi","year":"2021","journal-title":"Sci. Rep."},{"issue":"1","key":"10.1016\/j.envres.2026.125050_bib37","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-023-33959-6","article-title":"Comparison of DNA extraction methods for 16S rRNA gene sequencing in the analysis of the human gut microbiome","volume":"13","author":"Elie","year":"2023","journal-title":"Sci. Rep."},{"issue":"1","key":"10.1016\/j.envres.2026.125050_bib38","doi-asserted-by":"crossref","first-page":"471","DOI":"10.1186\/s12859-020-03815-9","article-title":"MetaLAFFA: a flexible, end-to-end, distributed computing-compatible metagenomic functional annotation pipeline","volume":"21","author":"Eng","year":"2020","journal-title":"BMC Bioinf."},{"key":"10.1016\/j.envres.2026.125050_bib39","doi-asserted-by":"crossref","first-page":"348","DOI":"10.3389\/fgene.2015.00348","article-title":"The road to metagenomics: from microbiology to DNA sequencing technologies and bioinformatics","volume":"6","author":"Escobar-Zepeda","year":"2015","journal-title":"Front. Genet."},{"issue":"1","key":"10.1016\/j.envres.2026.125050_bib40","doi-asserted-by":"crossref","first-page":"9785","DOI":"10.1038\/s41598-024-57981-4","article-title":"Variability and bias in microbiome metagenomic sequencing: an interlaboratory study comparing experimental protocols","volume":"14","author":"Forry","year":"2024","journal-title":"Sci. Rep."},{"key":"10.1016\/j.envres.2026.125050_bib41","doi-asserted-by":"crossref","DOI":"10.7717\/peerj.14292","article-title":"MTSv: rapid alignment-based taxonomic classification and high-confidence metagenomic analysis","volume":"10","author":"Furstenau","year":"2022","journal-title":"PeerJ"},{"issue":"1","key":"10.1016\/j.envres.2026.125050_bib42","doi-asserted-by":"crossref","first-page":"438","DOI":"10.1186\/s12864-023-09537-5","article-title":"Comparison of 6 DNA extraction methods for isolation of high yield of high molecular weight DNA suitable for shotgun metagenomics nanopore sequencing to detect bacteria","volume":"24","author":"Gand","year":"2023","journal-title":"BMC Genom."},{"key":"10.1016\/j.envres.2026.125050_bib43","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2024.1336532","article-title":"Towards facilitated interpretation of shotgun metagenomics long-read sequencing data analyzed with KMA for the detection of bacterial pathogens and their antimicrobial resistance genes","volume":"15","author":"Gand","year":"2024","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.envres.2026.125050_bib44","doi-asserted-by":"crossref","DOI":"10.1016\/j.marpolbul.2021.112593","article-title":"Assessing the in situ bacterial diversity and composition at anthropogenically active sites using the environmental DNA (eDNA)","volume":"170","author":"Garlapati","year":"2021","journal-title":"Mar. Pollut. Bull."},{"issue":"5","key":"10.1016\/j.envres.2026.125050_bib45","doi-asserted-by":"crossref","DOI":"10.1128\/msystems.00440-21","article-title":"Evaluation of the effects of library preparation procedure and sample characteristics on the accuracy of metagenomic profiles","volume":"6","author":"Gaulke","year":"2021","journal-title":"mSystems"},{"issue":"16","key":"10.1016\/j.envres.2026.125050_bib46","doi-asserted-by":"crossref","first-page":"3778","DOI":"10.1016\/j.cub.2024.07.030","article-title":"Measuring air metagenomic diversity in an agricultural ecosystem","volume":"34","author":"Giolai","year":"2024","journal-title":"Curr. Biol."},{"issue":"6","key":"10.1016\/j.envres.2026.125050_bib47","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1038\/nrg.2016.49","article-title":"Coming of age: ten years of next-generation sequencing technologies","volume":"17","author":"Goodwin","year":"2016","journal-title":"Nat. Rev. Genet."},{"issue":"9","key":"10.1016\/j.envres.2026.125050_bib48","doi-asserted-by":"crossref","DOI":"10.1128\/JCM.02916-20","article-title":"Metagenomic sequencing as a pathogen-agnostic clinical diagnostic tool for infectious diseases: a systematic review and meta-analysis of diagnostic test accuracy studies","volume":"59","author":"Govender","year":"2021","journal-title":"J. Clin. Microbiol."},{"issue":"1","key":"10.1016\/j.envres.2026.125050_bib49","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1111\/2041-210X.13802","article-title":"Harmonizing taxon names in biodiversity data: a review of tools, databases and best practices","volume":"14","author":"Greni\u00e9","year":"2023","journal-title":"Methods Ecol. Evol."},{"issue":"1","key":"10.1016\/j.envres.2026.125050_bib50","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1016\/j.tree.2016.09.012","article-title":"Urbanization and disease emergence: dynamics at the wildlife-livestock-human interface","volume":"32","author":"Hassell","year":"2017","journal-title":"Trends Ecol. Evol."},{"key":"10.1016\/j.envres.2026.125050_bib51","doi-asserted-by":"crossref","DOI":"10.1016\/j.onehlt.2023.100617","article-title":"Developing one health surveillance systems","volume":"17","author":"Hayman","year":"2023","journal-title":"One Health"},{"issue":"1","key":"10.1016\/j.envres.2026.125050_bib52","article-title":"Metagenomic analysis of fungal assemblages at a regional scale in high-altitude temperate forest soils: alternative methods to determine diversity, composition and environmental drivers","volume":"13","author":"Hereira-Pacheco","year":"2025","journal-title":"PeerJ"},{"issue":"2","key":"10.1016\/j.envres.2026.125050_bib53","doi-asserted-by":"crossref","DOI":"10.1128\/mbio.02444-21","article-title":"Inferring species compositions of complex fungal communities from Long- and short-read sequence data","volume":"13","author":"Hu","year":"2022","journal-title":"mBio"},{"issue":"5","key":"10.1016\/j.envres.2026.125050_bib54","doi-asserted-by":"crossref","DOI":"10.1093\/bib\/bbab064","article-title":"Snipe: highly sensitive pathogen detection from metagenomic sequencing data","volume":"22","author":"Huang","year":"2021","journal-title":"Briefings Bioinf."},{"issue":"2","key":"10.1016\/j.envres.2026.125050_bib55","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1038\/nmeth.2772","article-title":"Quantitative single-cell RNA-seq with unique molecular identifiers","volume":"11","author":"Islam","year":"2014","journal-title":"Nat. Methods"},{"issue":"1","key":"10.1016\/j.envres.2026.125050_bib56","doi-asserted-by":"crossref","DOI":"10.3390\/toxins13010025","article-title":"Can cyanobacterial diversity in the source predict the diversity in sludge and the risk of toxin release in a drinking water treatment plant?","volume":"13","author":"Jalili","year":"2021","journal-title":"Toxins"},{"issue":"10","key":"10.1016\/j.envres.2026.125050_bib57","doi-asserted-by":"crossref","DOI":"10.3390\/biom13101466","article-title":"Metagenomic analysis of the composition of microbial consortia involved in spruce degradation over time in Bialowieza natural forest","volume":"13","author":"Janusz","year":"2023","journal-title":"Biomolecules"},{"issue":"4","key":"10.1016\/j.envres.2026.125050_bib58","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0301446","article-title":"High-throughput DNA extraction and cost-effective miniaturized metagenome and amplicon library preparation of soil samples for DNA sequencing","volume":"19","author":"Jensen","year":"2024","journal-title":"PLoS One"},{"issue":"3","key":"10.1016\/j.envres.2026.125050_bib59","doi-asserted-by":"crossref","DOI":"10.3390\/soilsystems7030070","article-title":"Comparison of the structure of soil microbial communities of different ecosystems using the microbiome sequencing approach","volume":"7","author":"Kacergius","year":"2023","journal-title":"Soil Syst."},{"issue":"9","key":"10.1016\/j.envres.2026.125050_bib60","article-title":"High-resolution microbiome analysis enabled by linking of 16S rRNA gene sequences with adjacent genomic contexts","volume":"7","author":"Kapustina","year":"2021","journal-title":"Microb. Genom."},{"issue":"2","key":"10.1016\/j.envres.2026.125050_bib61","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1038\/s41592-020-01041-y","article-title":"High-accuracy long-read amplicon sequences using unique molecular identifiers with nanopore or PacBio sequencing","volume":"18","author":"Karst","year":"2021","journal-title":"Nat. Methods"},{"key":"10.1016\/j.envres.2026.125050_bib62","doi-asserted-by":"crossref","DOI":"10.7717\/peerj.16695","article-title":"Metagenomic assembly is the main bottleneck in the identification of mobile genetic elements","volume":"12","author":"Kerkvliet","year":"2024","journal-title":"PeerJ"},{"key":"10.1016\/j.envres.2026.125050_bib63","doi-asserted-by":"crossref","DOI":"10.1155\/2020\/2348560","article-title":"A comparison of two DNA metagenomic bioinformatic pipelines while evaluating the microbial diversity in feces of Tanzanian small holder dairy cattle","volume":"2020","author":"Kibegwa","year":"2020","journal-title":"Biomed Res. Int."},{"issue":"1","key":"10.1016\/j.envres.2026.125050_bib64","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1186\/s12967-024-04917-1","article-title":"Unraveling metagenomics through long-read sequencing: a comprehensive review","volume":"22","author":"Kim","year":"2024","journal-title":"J. Transl. Med."},{"issue":"1","key":"10.1016\/j.envres.2026.125050_bib65","doi-asserted-by":"crossref","first-page":"72","DOI":"10.1038\/nmeth.1778","article-title":"Counting absolute numbers of molecules using unique molecular identifiers","volume":"9","author":"Kivioja","year":"2011","journal-title":"Nat. Methods"},{"key":"10.1016\/j.envres.2026.125050_bib66","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2023.1039292","article-title":"Exploring taxonomic and functional microbiome of Hawaiian stream and spring irrigation water systems using Illumina and Oxford Nanopore sequencing platforms","volume":"14","author":"Klair","year":"2023","journal-title":"Front. Microbiol."},{"issue":"9","key":"10.1016\/j.envres.2026.125050_bib67","article-title":"RAPiD: a rapid and accurate plant pathogen identification pipeline for on-site nanopore sequencing","volume":"12","author":"Knobloch","year":"2024","journal-title":"PeerJ"},{"issue":"5","key":"10.1016\/j.envres.2026.125050_bib68","doi-asserted-by":"crossref","DOI":"10.1128\/mSystems.00095-16","article-title":"Impact of sample type and DNA isolation procedure on genomic inference of microbiome composition","volume":"1","author":"Knudsen","year":"2016","journal-title":"mSystems"},{"issue":"4","key":"10.1016\/j.envres.2026.125050_bib69","doi-asserted-by":"crossref","first-page":"486","DOI":"10.1038\/s41564-022-01089-w","article-title":"Metagenomics-enabled microbial surveillance","volume":"7","author":"Ko","year":"2022","journal-title":"Nat. Microbiol."},{"issue":"1","key":"10.1016\/j.envres.2026.125050_bib70","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-022-20701-x","article-title":"Establishing farm dust as a useful viral metagenomic surveillance matrix","volume":"12","author":"Kwok","year":"2022","journal-title":"Sci. Rep."},{"issue":"4","key":"10.1016\/j.envres.2026.125050_bib71","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1038\/s41579-022-00835-5","article-title":"Sewage surveillance of antibiotic resistance holds both opportunities and challenges","volume":"21","author":"Larsson","year":"2023","journal-title":"Nat. Rev. Microbiol."},{"issue":"1","key":"10.1016\/j.envres.2026.125050_bib72","doi-asserted-by":"crossref","DOI":"10.1038\/srep19233","article-title":"An evaluation of the accuracy and speed of metagenome analysis tools","volume":"6","author":"Lindgreen","year":"2016","journal-title":"Sci. Rep."},{"issue":"10","key":"10.1016\/j.envres.2026.125050_bib73","doi-asserted-by":"crossref","DOI":"10.1128\/spectrum.04208-23","article-title":"An interlaboratory proficiency test using metagenomic sequencing as a diagnostic tool for the detection of RNA viruses in swine fecal material","volume":"12","author":"Liu","year":"2024","journal-title":"Microbiol. Spectr."},{"issue":"9","key":"10.1016\/j.envres.2026.125050_bib74","doi-asserted-by":"crossref","DOI":"10.1128\/msystems.00242-24","article-title":"Decomposing a San Francisco estuary microbiome using long-read metagenomics reveals species- and strain-level dominance from picoeukaryotes to viruses","volume":"9","author":"Lui","year":"2024","journal-title":"mSystems"},{"key":"10.1016\/j.envres.2026.125050_bib75","doi-asserted-by":"crossref","DOI":"10.3389\/fenvs.2022.830300","article-title":"Metagenomic survey of agricultural water using long read sequencing: considerations for a successful analysis","volume":"10","author":"Maguire","year":"2022","journal-title":"Front. Environ. Sci."},{"issue":"1","key":"10.1016\/j.envres.2026.125050_bib76","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1186\/s13059-020-02014-2","article-title":"CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data","volume":"21","author":"Marcelino","year":"2020","journal-title":"Genome Biol."},{"key":"10.1016\/j.envres.2026.125050_bib77","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1186\/s40168-015-0094-5","article-title":"The vocabulary of microbiome research: a proposal","volume":"3","author":"Marchesi","year":"2015","journal-title":"Microbiome"},{"issue":"1","key":"10.1016\/j.envres.2026.125050_bib78","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1186\/s12859-024-05634-8","article-title":"Comparative analysis of metagenomic classifiers for long-read sequencing datasets","volume":"25","author":"Maric","year":"2024","journal-title":"BMC Bioinf."},{"issue":"11\u201312","key":"10.1016\/j.envres.2026.125050_bib79","doi-asserted-by":"crossref","first-page":"1201","DOI":"10.1007\/s00439-019-02064-y","article-title":"Long-read sequencing in deciphering human genetics to a greater depth","volume":"138","author":"Midha","year":"2019","journal-title":"Hum. Genet."},{"issue":"1","key":"10.1016\/j.envres.2026.125050_bib80","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1093\/clinchem\/hvab173","article-title":"The role of metagenomics and next-generation sequencing in infectious disease diagnosis","volume":"68","author":"Miller","year":"2021","journal-title":"Clin. Chem."},{"issue":"6","key":"10.1016\/j.envres.2026.125050_bib81","doi-asserted-by":"crossref","first-page":"3635","DOI":"10.1016\/j.ygeno.2021.08.016","article-title":"MicFunPred: a conserved approach to predict functional profiles from 16S rRNA gene sequence data","volume":"113","author":"Mongad","year":"2021","journal-title":"Genomics"},{"key":"10.1016\/j.envres.2026.125050_bib82","doi-asserted-by":"crossref","DOI":"10.3389\/fgene.2022.814437","article-title":"MEDUSA: a pipeline for sensitive taxonomic classification and flexible functional annotation of metagenomic shotgun sequences","volume":"13","author":"Morais","year":"2022","journal-title":"Front. Genet."},{"issue":"1","key":"10.1016\/j.envres.2026.125050_bib83","doi-asserted-by":"crossref","first-page":"112","DOI":"10.3390\/ruminants2010007","article-title":"Bovine rumen microbiome: impact of DNA extraction methods and comparison of non-invasive sampling sites","volume":"2","author":"Mott","year":"2022","journal-title":"Ruminants"},{"key":"10.1016\/j.envres.2026.125050_bib84","doi-asserted-by":"crossref","DOI":"10.1016\/j.scitotenv.2023.169602","article-title":"Profiling pathogenic protozoan and their functional pathways in wastewater using 18S rRNA and shotgun metagenomics","volume":"912","author":"Mthethwa-Hlongwa","year":"2024","journal-title":"Sci. Total Environ."},{"key":"10.1016\/j.envres.2026.125050_bib85","series-title":"The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet","isbn-type":"print","article-title":"What is metagenomics?","year":"2007","ISBN":"https:\/\/id.crossref.org\/isbn\/9780309106764"},{"issue":"1","key":"10.1016\/j.envres.2026.125050_bib86","article-title":"An inter-laboratory study to investigate the impact of the bioinformatics component on microbiome analysis using mock communities","volume":"11","author":"O'Sullivan","year":"2021","journal-title":"Sci. Rep."},{"issue":"1","key":"10.1016\/j.envres.2026.125050_bib87","doi-asserted-by":"crossref","first-page":"ycae024","DOI":"10.1093\/ismeco\/ycae024","article-title":"Evaluation of multiple displacement amplification for metagenomic analysis of low biomass samples","volume":"4","author":"Ospino","year":"2024","journal-title":"ISME Commun."},{"key":"10.1016\/j.envres.2026.125050_bib88","doi-asserted-by":"crossref","first-page":"n71","DOI":"10.1136\/bmj.n71","article-title":"The PRISMA 2020 statement: an updated guideline for reporting systematic reviews","volume":"372","author":"Page","year":"2021","journal-title":"BMJ"},{"issue":"2","key":"10.1016\/j.envres.2026.125050_bib89","doi-asserted-by":"crossref","DOI":"10.3390\/tropicalmed8020121","article-title":"Development and optimization of an unbiased, metagenomics-based pathogen detection workflow for infectious disease and biosurveillance applications","volume":"8","author":"Parker","year":"2023","journal-title":"Trop. Med. Infect. Dis."},{"issue":"1","key":"10.1016\/j.envres.2026.125050_bib90","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1186\/s12859-015-0788-5","article-title":"Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities","volume":"16","author":"Peabody","year":"2015","journal-title":"BMC Bioinf."},{"key":"10.1016\/j.envres.2026.125050_bib91","doi-asserted-by":"crossref","DOI":"10.1177\/1177932220915459","article-title":"Comparative analysis of sample extraction and library construction for shotgun metagenomics","volume":"14","author":"Peng","year":"2020","journal-title":"Bioinf. Biol. Insights"},{"key":"10.1016\/j.envres.2026.125050_bib92","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2022.854423","article-title":"Comparative analysis of metagenomics and metataxonomics for the characterization of vermicompost microbiomes","volume":"13","author":"Perez-Losada","year":"2022","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.envres.2026.125050_bib93","doi-asserted-by":"crossref","DOI":"10.1016\/j.jhazmat.2024.135567","article-title":"The integration of omics and cultivation-dependent methods could effectively determine the biological risks associated with the utilization of soil conditioners in agriculture","volume":"478","author":"Peruzzo","year":"2024","journal-title":"J. Hazard Mater."},{"issue":"3\u20134","key":"10.1016\/j.envres.2026.125050_bib94","doi-asserted-by":"crossref","first-page":"188","DOI":"10.1080\/03014223.2020.1831556","article-title":"Microbial diversity in water and animal faeces: a metagenomic analysis to assess public health risk","volume":"48","author":"Phiri","year":"2021","journal-title":"N. Z. J. Zool"},{"issue":"18","key":"10.1016\/j.envres.2026.125050_bib95","doi-asserted-by":"crossref","DOI":"10.3390\/ijms26189206","article-title":"Computational metagenomics: state of the art","volume":"26","author":"Pita-Galeana","year":"2025","journal-title":"Int. J. Mol. Sci."},{"issue":"2","key":"10.1016\/j.envres.2026.125050_bib96","doi-asserted-by":"crossref","DOI":"10.1093\/ve\/veaa091","article-title":"Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types","volume":"6","author":"Plyusnin","year":"2020","journal-title":"Virus Evol."},{"issue":"2","key":"10.1016\/j.envres.2026.125050_bib97","doi-asserted-by":"crossref","DOI":"10.3390\/v15020431","article-title":"Enhanced viral metagenomics with Lazypipe 2","volume":"15","author":"Plyusnin","year":"2023","journal-title":"Viruses"},{"issue":"1","key":"10.1016\/j.envres.2026.125050_bib98","doi-asserted-by":"crossref","first-page":"541","DOI":"10.1186\/s12859-022-05103-0","article-title":"Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets","volume":"23","author":"Portik","year":"2022","journal-title":"BMC Bioinf."},{"issue":"2","key":"10.1016\/j.envres.2026.125050_bib99","doi-asserted-by":"crossref","DOI":"10.1128\/spectrum.00090-22","article-title":"Library preparation and sequencing platform introduce bias in metagenomic-based characterizations of microbiomes","volume":"10","author":"Poulsen","year":"2022","journal-title":"Microbiol. Spectr."},{"issue":"9","key":"10.1016\/j.envres.2026.125050_bib100","doi-asserted-by":"crossref","first-page":"833","DOI":"10.1038\/nbt.3935","article-title":"Shotgun metagenomics, from sampling to analysis","volume":"35","author":"Quince","year":"2017","journal-title":"Nat. Biotechnol."},{"issue":"2","key":"10.1016\/j.envres.2026.125050_bib101","doi-asserted-by":"crossref","first-page":"72","DOI":"10.1007\/s10661-021-09668-w","article-title":"eDNA profiling of mammals, birds, and fish of surface waters by mitochondrial metagenomics: application for source tracking of fecal contamination in surface waters","volume":"194","author":"Ragot","year":"2022","journal-title":"Environ. Monit. Assess."},{"issue":"7","key":"10.1016\/j.envres.2026.125050_bib102","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0070460","article-title":"Investigating the impact of storage conditions on microbial community composition in soil samples","volume":"8","author":"Rubin","year":"2013","journal-title":"PLoS One"},{"issue":"6808","key":"10.1016\/j.envres.2026.125050_bib103","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1038\/35040695","article-title":"Global spread of microorganisms by ships","volume":"408","author":"Ruiz","year":"2000","journal-title":"Nature"},{"issue":"9","key":"10.1016\/j.envres.2026.125050_bib104","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1007\/s00203-023-03664-z","article-title":"Unveiling the microbial diversity and functional dynamics of Shiv Kund, Sohna hot spring, India through a shotgun metagenomics approach","volume":"205","author":"Saini","year":"2023","journal-title":"Arch. Microbiol."},{"issue":"3","key":"10.1016\/j.envres.2026.125050_bib105","doi-asserted-by":"crossref","DOI":"10.3390\/biom12030364","article-title":"Sequencing depth has a stronger effect than DNA extraction on soil bacterial richness discovery","volume":"12","author":"Sanchez-Cid","year":"2022","journal-title":"Biomolecules"},{"issue":"1","key":"10.1016\/j.envres.2026.125050_bib106","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1186\/s13073-024-01334-3","article-title":"INSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic detection and routine genomic surveillance","volume":"16","author":"Santos","year":"2024","journal-title":"Genome Med."},{"key":"10.1016\/j.envres.2026.125050_bib107","series-title":"Asreview: Active Learning for Systematic Reviews","author":"Schoot","year":"2020"},{"issue":"7","key":"10.1016\/j.envres.2026.125050_bib108","doi-asserted-by":"crossref","first-page":"314","DOI":"10.1007\/s00203-024-04047-8","article-title":"Comparative analysis of commercially available kits for optimal DNA extraction from bovine fecal samples","volume":"206","author":"Seethalakshmi","year":"2024","journal-title":"Arch. Microbiol."},{"key":"10.1016\/j.envres.2026.125050_bib109","doi-asserted-by":"crossref","first-page":"2029","DOI":"10.3389\/fmicb.2017.02029","article-title":"High throughput sequencing for detection of foodborne pathogens","volume":"8","author":"Sekse","year":"2017","journal-title":"Front. Microbiol."},{"issue":"1","key":"10.1016\/j.envres.2026.125050_bib110","doi-asserted-by":"crossref","first-page":"154","DOI":"10.1111\/1755-0998.13095","article-title":"Sampling strategy optimization to increase statistical power in landscape genomics: a simulation-based approach","volume":"20","author":"Selmoni","year":"2020","journal-title":"Mol. Ecol. Resour."},{"issue":"20","key":"10.1016\/j.envres.2026.125050_bib111","doi-asserted-by":"crossref","first-page":"4659","DOI":"10.1093\/bioinformatics\/btab790","article-title":"Theory of local k-mer selection with applications to long-read alignment","volume":"38","author":"Shaw","year":"2022","journal-title":"Bioinformatics"},{"key":"10.1016\/j.envres.2026.125050_bib112","doi-asserted-by":"crossref","DOI":"10.3389\/fgene.2021.600111","article-title":"Toward accurate and robust environmental surveillance using metagenomics","volume":"12","author":"Shen","year":"2021","journal-title":"Front. Genet."},{"issue":"5","key":"10.1016\/j.envres.2026.125050_bib113","doi-asserted-by":"crossref","first-page":"252","DOI":"10.1007\/s13205-021-02809-5","article-title":"Prokaryotic diversity of tropical coastal sand dunes ecosystem using metagenomics","volume":"11","author":"Shet","year":"2021","journal-title":"3 Biotech"},{"issue":"3","key":"10.1016\/j.envres.2026.125050_bib114","doi-asserted-by":"crossref","first-page":"808","DOI":"10.1021\/acsinfecdis.3c00625","article-title":"Holistic one health surveillance framework: synergizing environmental, animal, and human determinants for enhanced infectious disease management","volume":"10","author":"Singh","year":"2024","journal-title":"ACS Infect. Dis."},{"issue":"1","key":"10.1016\/j.envres.2026.125050_bib115","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-020-70141-8","article-title":"Influence of 16S rRNA target region on the outcome of microbiome studies in soil and saliva samples","volume":"10","author":"Soriano-Lerma","year":"2020","journal-title":"Sci. Rep."},{"key":"10.1016\/j.envres.2026.125050_bib116","doi-asserted-by":"crossref","first-page":"953","DOI":"10.3389\/fmicb.2020.00953","article-title":"Impact of DNA extraction method on variation in human and built environment microbial community and functional profiles assessed by shotgun metagenomics sequencing","volume":"11","author":"Sui","year":"2020","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.envres.2026.125050_bib117","doi-asserted-by":"crossref","first-page":"2028","DOI":"10.3389\/fmicb.2020.02028","article-title":"Assessment of inter-laboratory variation in the characterization and analysis of the mucosal microbiota in Crohn's disease and ulcerative colitis","volume":"11","author":"Szamosi","year":"2020","journal-title":"Front. Microbiol."},{"issue":"2","key":"10.1016\/j.envres.2026.125050_bib118","doi-asserted-by":"crossref","DOI":"10.1111\/1755-0998.13909","article-title":"In situ metagenomics: a platform for rapid sequencing and analysis of metagenomes in less than one day","volume":"24","author":"Tamames","year":"2024","journal-title":"Mol. Ecol. Resour."},{"issue":"2","key":"10.1016\/j.envres.2026.125050_bib119","doi-asserted-by":"crossref","DOI":"10.1093\/bib\/bbac011","article-title":"RdRp-based sensitive taxonomic classification of RNA viruses for metagenomic data","volume":"23","author":"Tang","year":"2022","journal-title":"Briefings Bioinf."},{"issue":"5","key":"10.1016\/j.envres.2026.125050_bib120","doi-asserted-by":"crossref","DOI":"10.1093\/gbe\/evae102","article-title":"Application and comparison of machine learning and database-based methods in taxonomic classification of high-throughput sequencing data","volume":"16","author":"Tian","year":"2024","journal-title":"Genome Biol. Evol."},{"issue":"1","key":"10.1016\/j.envres.2026.125050_bib121","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1186\/s40168-021-01048-3","article-title":"Validation and standardization of DNA extraction and library construction methods for metagenomics-based human fecal microbiome measurements","volume":"9","author":"Tourlousse","year":"2021","journal-title":"Microbiome"},{"issue":"1","key":"10.1016\/j.envres.2026.125050_bib122","doi-asserted-by":"crossref","DOI":"10.1186\/s12859-020-3416-y","article-title":"Pre- and post-sequencing recommendations for functional annotation of human fecal metagenomes","volume":"21","author":"Treiber","year":"2020","journal-title":"BMC Bioinform."},{"issue":"7","key":"10.1016\/j.envres.2026.125050_bib123","doi-asserted-by":"crossref","first-page":"467","DOI":"10.7326\/M18-0850","article-title":"PRISMA extension for scoping reviews (PRISMA-ScR): checklist and explanation","volume":"169","author":"Tricco","year":"2018","journal-title":"Ann. Intern. Med."},{"issue":"1","key":"10.1016\/j.envres.2026.125050_bib124","doi-asserted-by":"crossref","first-page":"1","DOI":"10.4103\/jvbd.jvbd_13_25","article-title":"Anthropogenic influence, microbes and zoonotic diseases: ecological imbalance, diverse impact and the one health approach","volume":"63","author":"Ullah","year":"2026","journal-title":"J. Vector Borne Dis."},{"key":"10.1016\/j.envres.2026.125050_bib125","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.61504","article-title":"Freshwater monitoring by nanopore sequencing","volume":"10","author":"Urban","year":"2021","journal-title":"eLife"},{"issue":"20","key":"10.1016\/j.envres.2026.125050_bib126","doi-asserted-by":"crossref","DOI":"10.3390\/ijms242015243","article-title":"Physical pretreatments applied in three commercial kits for the extraction of high-quality DNA from activated sewage sludge","volume":"24","author":"Vasquez","year":"2023","journal-title":"Int. J. Mol. Sci."},{"issue":"2","key":"10.1016\/j.envres.2026.125050_bib127","doi-asserted-by":"crossref","DOI":"10.1093\/bib\/bbac013","article-title":"Computational analyses of bacterial strains from shotgun reads","volume":"23","author":"Ventolero","year":"2022","journal-title":"Briefings Bioinf."},{"key":"10.1016\/j.envres.2026.125050_bib128","article-title":"Predicting biosecurity threats: deployment and detection of biological","author":"Volk","year":"2021","journal-title":"NATO Sci. Peace Secur. Ser. C: Environ. Secur."},{"issue":"6","key":"10.1016\/j.envres.2026.125050_bib129","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0234128","article-title":"Comparative metagenomics reveals the microbial diversity and metabolic potentials in the sediments and surrounding seawaters of Qinhuangdao mariculture area","volume":"15","author":"Wang","year":"2020","journal-title":"PLoS One"},{"issue":"2","key":"10.1016\/j.envres.2026.125050_bib130","doi-asserted-by":"crossref","DOI":"10.1093\/bib\/bbad092","article-title":"GPMeta: a GPU-accelerated method for ultrarapid pathogen identification from metagenomic sequences","volume":"24","author":"Wang","year":"2023","journal-title":"Briefings Bioinf."},{"key":"10.1016\/j.envres.2026.125050_bib131","article-title":"Metagenomics reveals novel microbial signatures of farm exposures in house dust","volume":"14","author":"Wang","year":"2023","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.envres.2026.125050_bib132","doi-asserted-by":"crossref","DOI":"10.7717\/peerj.9378","article-title":"The effects of humic substances on DNA isolation from soils","volume":"8","author":"Wnuk","year":"2020","journal-title":"PeerJ"},{"issue":"1","key":"10.1016\/j.envres.2026.125050_bib133","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1186\/s13059-019-1891-0","article-title":"Improved metagenomic analysis with Kraken 2","volume":"20","author":"Wood","year":"2019","journal-title":"Genome Biol."},{"issue":"21\u201322","key":"10.1016\/j.envres.2026.125050_bib134","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1002\/pmic.13983","article-title":"Sample preparation for multi-omics analysis: considerations and guidance for identifying the ideal workflow","volume":"25","author":"Woodland","year":"2025","journal-title":"Proteomics"},{"issue":"3","key":"10.1016\/j.envres.2026.125050_bib136","article-title":"From defaults to databases: parameter and database choice dramatically impact the performance of metagenomic taxonomic classification tools","volume":"9","author":"Wright","year":"2023","journal-title":"Microb. Genom."},{"issue":"2","key":"10.1016\/j.envres.2026.125050_bib137","doi-asserted-by":"crossref","first-page":"163","DOI":"10.21037\/tp.2020.03.06","article-title":"The third generation sequencing: the advanced approach to genetic diseases","volume":"9","author":"Xiao","year":"2020","journal-title":"Transl. Pediatr."},{"issue":"4","key":"10.1016\/j.envres.2026.125050_bib138","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0284031","article-title":"The selection of software and database for metagenomics sequence analysis impacts the outcome of microbial profiling and pathogen detection","volume":"18","author":"Xu","year":"2023","journal-title":"PLoS One"},{"key":"10.1016\/j.envres.2026.125050_bib139","doi-asserted-by":"crossref","DOI":"10.1016\/j.scitotenv.2023.163666","article-title":"The hidden diversity of microbes in ballast water and sediments revealed by metagenomic sequencing","volume":"882","author":"Xue","year":"2023","journal-title":"Sci. Total Environ."},{"key":"10.1016\/j.envres.2026.125050_bib140","doi-asserted-by":"crossref","DOI":"10.1016\/j.scitotenv.2021.146960","article-title":"Metagenomic analysis of a mega-city river network reveals microbial compositional heterogeneity among urban and peri-urban river stretch","volume":"783","author":"Yadav","year":"2021","journal-title":"Sci. Total Environ."},{"issue":"7","key":"10.1016\/j.envres.2026.125050_bib141","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/giaa071","article-title":"Assessment of fecal DNA extraction protocols for metagenomic studies","volume":"9","author":"Yang","year":"2020","journal-title":"GigaScience"},{"issue":"3","key":"10.1016\/j.envres.2026.125050_bib142","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/giaa022","article-title":"PEMA: a flexible pipeline for environmental DNA metabarcoding analysis of the 16S\/18S ribosomal RNA, ITS, and COI marker genes","volume":"9","author":"Zafeiropoulos","year":"2020","journal-title":"GigaScience"},{"issue":"22","key":"10.1016\/j.envres.2026.125050_bib143","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkaf1304","article-title":"ConSeqUMI, an error-free nanopore sequencing pipeline to identify and extract individual nucleic acid molecules from heterogeneous samples","volume":"53","author":"Zahm","year":"2025","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.envres.2026.125050_bib144","article-title":"16S-FASAS: an integrated pipeline for synthetic full-length 16S rRNA gene sequencing data analysis","volume":"10","author":"Zhang","year":"2022","journal-title":"PeerJ"},{"issue":"6","key":"10.1016\/j.envres.2026.125050_bib145","doi-asserted-by":"crossref","DOI":"10.1002\/mbo3.70007","article-title":"Evaluation of DNA extraction methods for microbial community profiling in deadwood decomposition","volume":"13","author":"Zhang","year":"2024","journal-title":"Microbiologyopen"},{"issue":"4","key":"10.1016\/j.envres.2026.125050_bib146","doi-asserted-by":"crossref","DOI":"10.3390\/v16040535","article-title":"A metagenomic investigation of potential health risks and element cycling functions of bacteria and viruses in wastewater treatment plants","volume":"16","author":"Zhao","year":"2024","journal-title":"Viruses"},{"issue":"3","key":"10.1016\/j.envres.2026.125050_bib147","doi-asserted-by":"crossref","first-page":"204","DOI":"10.1016\/S0958-1669(02)00319-1","article-title":"Challenges in applying microarrays to environmental studies","volume":"13","author":"Zhou","year":"2002","journal-title":"Curr. Opin. Biotechnol."},{"issue":"1","key":"10.1016\/j.envres.2026.125050_bib148","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1186\/s12859-023-05512-9","article-title":"cgMSI: pathogen detection within species from nanopore metagenomic sequencing data","volume":"24","author":"Zhu","year":"2023","journal-title":"BMC Bioinf."},{"issue":"1","key":"10.1016\/j.envres.2026.125050_bib149","doi-asserted-by":"crossref","first-page":"6023","DOI":"10.1038\/s41467-020-19687-9","article-title":"UMI-linked consensus sequencing enables phylogenetic analysis of directed evolution","volume":"11","author":"Zurek","year":"2020","journal-title":"Nat. Commun."}],"container-title":["Environmental Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0013935126013812?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0013935126013812?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T04:05:55Z","timestamp":1789013155000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0013935126013812"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9]]},"references-count":148,"alternative-id":["S0013935126013812"],"URL":"https:\/\/doi.org\/10.1016\/j.envres.2026.125050","relation":{},"ISSN":["0013-9351"],"issn-type":[{"value":"0013-9351","type":"print"}],"subject":[],"published":{"date-parts":[[2026,9]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Use of metagenomics for the detection of pathogens in the environment: A scoping review","name":"articletitle","label":"Article Title"},{"value":"Environmental Research","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.envres.2026.125050","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2026 The Authors. Published by Elsevier Inc.","name":"copyright","label":"Copyright"}],"article-number":"125050"}}