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However, the bioprocess remains challenging due to its complex microbial ecology, dynamic biochemical pathways and sensitivity to perturbations. Over the past decade, using meta\u2010omics like metataxonomics, metagenomics, metatranscriptomics, metaproteomics and metabolomics to diagnose its functioning has become necessary and common. However, a single meta\u2010omics method can only provide limited biological understanding of the bioprocess. This led to the use of multi\u2010meta\u2010omics analyses in tandem; however, most studies still examine and interpret each meta\u2010omics separately, limiting their ability to uncover functional interactions across molecular levels. Currently, the frontier is integrated meta\u2010omics, where multi\u2010meta\u2010omics and process data are systematically combined into a single and interpretable system to unlock mechanistic understanding, diagnostic and predictive control of AD. This review critically examines specific application of meta\u2010omics in AD, discussing their strengths, limitations and distinct position in integrated meta\u2010omics approach. Importantly, it explores the computational frameworks, methodologies and challenges of integrated meta\u2010omics. Discovering diagnostic biomarkers with high predictive power and transferability across AD systems through cross\u2010omics validation is highlighted. As workflows standardise and technologies mature, integrated meta\u2010omics would significantly contribute to the advancement of AD bioprocess for bioenergy.<\/jats:p>","DOI":"10.1111\/1758-2229.70417","type":"journal-article","created":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T09:02:57Z","timestamp":1790240577000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Diagnosing Anaerobic Digesters' Function and Performance: From Meta\u2010Omics to Integrated Meta\u2010Omics Analyses"],"prefix":"10.1111","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2195-9646","authenticated-orcid":false,"given":"Kevin Iyere","family":"Ehiosun","sequence":"first","affiliation":[{"name":"Universit\u00e9 Paris\u2010Saclay, INRAE, PRoc\u00e9d\u00e9s Biotechnologiques Au Service de L'environnement  Antony France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9460-921X","authenticated-orcid":false,"given":"Olivier","family":"Chapleur","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Paris\u2010Saclay, INRAE, PRoc\u00e9d\u00e9s Biotechnologiques Au Service de L'environnement  Antony France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9001-3475","authenticated-orcid":false,"given":"Laurent","family":"Maz\u00e9as","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Paris\u2010Saclay, INRAE, PRoc\u00e9d\u00e9s Biotechnologiques Au Service de L'environnement  Antony France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,9,24]]},"reference":[{"key":"e_1_2_10_2_1","doi-asserted-by":"publisher","DOI":"10.4236\/abb.2015.63020"},{"key":"e_1_2_10_3_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.biortech.2017.08.210"},{"key":"e_1_2_10_4_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.premed.2026.100047"},{"key":"e_1_2_10_5_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13059\u2010020\u201002015\u20101"},{"key":"e_1_2_10_6_1","doi-asserted-by":"publisher","DOI":"10.15252\/MSB.20178124"},{"key":"e_1_2_10_7_1","doi-asserted-by":"publisher","DOI":"10.1039\/D3MO00089C"},{"key":"e_1_2_10_8_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.trac.2021.116355"},{"key":"e_1_2_10_9_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.envres.2024.118351"},{"key":"e_1_2_10_10_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.watres.2015.10.029"},{"key":"e_1_2_10_11_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.scitotenv.2020.138479"},{"key":"e_1_2_10_12_1","doi-asserted-by":"publisher","DOI":"10.1016\/J.CHEMOSPHERE.2023.140743"},{"key":"e_1_2_10_13_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btab664"},{"key":"e_1_2_10_14_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13040\u2010024\u201000406\u20109"},{"key":"e_1_2_10_15_1","first-page":"317","volume-title":"Reference Module in Chemistry, Molecular Sciences and Chemical Engineering","author":"Brown S. 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