{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,22]],"date-time":"2026-07-22T20:15:18Z","timestamp":1784751318250,"version":"3.55.0"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2026,7,22]],"date-time":"2026-07-22T00:00:00Z","timestamp":1784678400000},"content-version":"vor","delay-in-days":21,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Innovation Yongjiang 2035 Key R&D Program","award":["2025Z154"],"award-info":[{"award-number":["2025Z154"]}]},{"DOI":"10.13039\/501100014761","name":"Qingdao Natural Science Foundation","doi-asserted-by":"publisher","award":["25-3-1-11-zyyd-jch"],"award-info":[{"award-number":["25-3-1-11-zyyd-jch"]}],"id":[{"id":"10.13039\/501100014761","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32572519"],"award-info":[{"award-number":["32572519"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,7,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Microbes exist within complex community contexts, particularly for key functional species whose stable colonization critically depends on specific ecological partners. However, conventional microbial correlation analyses predominantly rely on isolated pairwise metrics (e.g. Spearman, SparCC, and FlashWeave), which ignore community-level dependencies. This limitation leads to spurious associations in large-scale datasets and obscures the true structure of microbial interactions. Here, we introduce CAM-Net, a context-aware framework that identifies a target microbe's optimal consortium, a fully connected network subset that accurately predicts its abundance. By constructing networks via multi-hop information propagation, CAM-Net effectively filters false positives from indirect associations and captures complex, context-dependent patterns that are inaccessible to traditional pairwise approaches. We evaluated CAM-Net on over 25 000 human gut microbiome samples using Akkermansia muciniphila and Lactobacillus acidophilus as representatives of indigenous and transient colonizers. CAM-Net identified a coherent and reproducible consortium for A. muciniphila, but only weak association structures for L. acidophilus, consistent with their ecological behaviors. In contrast, pairwise methods produced spurious associations for both species. Notably, despite substantial geographic heterogeneity, Alistipes shahii consistently emerged as a conserved core member of the A. muciniphila consortium, demonstrating the advantage of context-aware modeling. The source code is available at https:\/\/github.com\/qdu-bioinfo\/CAM-Net.<\/jats:p>","DOI":"10.1093\/bib\/bbag394","type":"journal-article","created":{"date-parts":[[2026,7,22]],"date-time":"2026-07-22T19:31:39Z","timestamp":1784748699000},"source":"Crossref","is-referenced-by-count":0,"title":["CAM-Net: a context-aware network for identifying reliable microbial relations via optimal consortium"],"prefix":"10.1093","volume":"27","author":[{"given":"Junhui","family":"Zhang","sequence":"first","affiliation":[{"name":"College of Computer Science and Technology, Qingdao University , No. 308 Ningxia Road, Qingdao, Shandong Province, 266071,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenfei","family":"Xu","sequence":"additional","affiliation":[{"name":"College of Computer Science and Technology, Qingdao University , No. 308 Ningxia Road, Qingdao, Shandong Province, 266071,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jieqi","family":"Xing","sequence":"additional","affiliation":[{"name":"College of Computer Science and Technology, Qingdao University , No. 308 Ningxia Road, Qingdao, Shandong Province, 266071,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yangyang","family":"Sun","sequence":"additional","affiliation":[{"name":"College of Computer Science and Technology, Qingdao University , No. 308 Ningxia Road, Qingdao, Shandong Province, 266071,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shi","family":"Huang","sequence":"additional","affiliation":[{"name":"Faculty of Dentistry, The University of Hong Kong, 34 Hospital Road, Sai Ying Pun , Hong Kong SAR,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2144-1991","authenticated-orcid":false,"given":"Xiaoquan","family":"Su","sequence":"additional","affiliation":[{"name":"College of Computer Science and Technology, Qingdao University , No. 308 Ningxia Road, Qingdao, Shandong Province, 266071,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,7,22]]},"reference":[{"key":"2026072215313133600_ref1","doi-asserted-by":"publisher","first-page":"725","DOI":"10.3390\/antiox14060725","article-title":"Functional and therapeutic roles of plant-derived antioxidants in type 2 diabetes mellitus: mechanisms, challenges, and considerations for Special populations","volume":"14","author":"Clemente-Su\u00e1rez","year":"2025","journal-title":"Antioxidants (Basel)"},{"key":"2026072215313133600_ref2","doi-asserted-by":"publisher","first-page":"538","DOI":"10.1038\/nrmicro2832","article-title":"Microbial interactions: from networks to models","volume":"10","author":"Faust","year":"2012","journal-title":"Nat Rev Microbiol"},{"key":"2026072215313133600_ref3","first-page":"1713","article-title":"Progress of application of artificial intelligence foundation models in epidemiological research","volume":"46","author":"Wang","year":"2025","journal-title":"Zhonghua Liu Xing Bing Xue Za Zhi"},{"key":"2026072215313133600_ref4","doi-asserted-by":"publisher","first-page":"e1002687","DOI":"10.1371\/journal.pcbi.1002687","article-title":"Inferring correlation networks from genomic survey data","volume":"8","author":"Friedman","year":"2012","journal-title":"PLoS Comput Biol"},{"key":"2026072215313133600_ref5","doi-asserted-by":"publisher","first-page":"286","DOI":"10.1016\/j.cels.2019.08.002","article-title":"Rapid inference of direct interactions in large-scale ecological networks from heterogeneous microbial sequencing data","volume":"9","author":"Tackmann","year":"2019","journal-title":"Cell Syst"},{"key":"2026072215313133600_ref6","doi-asserted-by":"publisher","first-page":"2647","DOI":"10.1038\/s41396-019-0459-z","article-title":"Use and abuse of correlation analyses in microbial ecology","volume":"13","author":"Carr","year":"2019","journal-title":"ISME J"},{"key":"2026072215313133600_ref7","doi-asserted-by":"publisher","first-page":"1669","DOI":"10.1038\/ismej.2015.235","article-title":"Correlation detection strategies in microbial data sets vary widely in sensitivity and precision","volume":"10","author":"Weiss","year":"2016","journal-title":"ISME J"},{"key":"2026072215313133600_ref8","doi-asserted-by":"publisher","first-page":"251","DOI":"10.1016\/j.cels.2017.08.014","article-title":"Gene regulatory network inference from single-cell data using multivariate information measures","volume":"5","author":"Chan","year":"2017","journal-title":"Cell Syst"},{"key":"2026072215313133600_ref9","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1038\/s41540-025-00568-0","article-title":"A computational framework for inferring species dynamics and interactions with applications in microbiota ecology","volume":"11","author":"Xu","year":"2025","journal-title":"NPJ Syst Biol Appl"},{"key":"2026072215313133600_ref10","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1186\/s13059-024-03357-w","article-title":"scPriorGraph: constructing biosemantic cell\u2013cell graphs with prior gene set selection for cell type identification from scRNA-seq data","volume":"25","author":"Cao","year":"2024","journal-title":"Genome Biol"},{"key":"2026072215313133600_ref11","doi-asserted-by":"publisher","first-page":"1508","DOI":"10.1038\/s42003-025-08788-0","article-title":"scGSDR: harnessing gene semantics for single-cell pharmacological profiling","volume":"8","author":"Huang","year":"2025","journal-title":"Commun Biol"},{"key":"2026072215313133600_ref12","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1186\/s12915-025-02128-8","article-title":"Consensus representation of multiple cell\u2013cell graphs from gene signaling pathways for cell type annotation","volume":"23","author":"Huang","year":"2025","journal-title":"BMC Biol"},{"key":"2026072215313133600_ref13","doi-asserted-by":"publisher","first-page":"3184","DOI":"10.1109\/JBHI.2025.3607687","article-title":"scGraphDap: integrating functional state pseudo-labels and graph structure learning for robust cell type annotation in tumor microenvironments","volume":"30","author":"Li","year":"2026","journal-title":"IEEE J Biomed Health Inform"},{"key":"2026072215313133600_ref14","doi-asserted-by":"publisher","first-page":"e0140523","DOI":"10.1128\/msystems.01405-23","article-title":"Decoding host-microbiome interactions through co-expression network analysis within the non-human primate intestine","volume":"9","author":"Uehara","journal-title":"mSystems"},{"key":"2026072215313133600_ref15","doi-asserted-by":"publisher","first-page":"384","DOI":"10.1016\/j.tree.2026.01.003","article-title":"Mapping microbial symbiont impacts using ecological networks","volume":"41","author":"Morente","year":"2026","journal-title":"Trends Ecol Evol"},{"key":"2026072215313133600_ref16","doi-asserted-by":"publisher","first-page":"567","DOI":"10.1038\/s41579-018-0024-1","article-title":"Keystone taxa as drivers of microbiome structure and functioning","volume":"16","author":"Banerjee","year":"2018","journal-title":"Nat Rev Microbiol"},{"key":"2026072215313133600_ref17","doi-asserted-by":"publisher","DOI":"10.3390\/nu15081815","article-title":"Role of Akkermansia in human diseases: from causation to therapeutic properties","volume":"15","author":"Pellegrino","year":"2023","journal-title":"Nutrients"},{"key":"2026072215313133600_ref18","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.00770-17","article-title":"Microbial metabolic networks at the mucus layer lead to diet-independent butyrate and vitamin B(12) production by intestinal symbionts","volume":"8","author":"Belzer","year":"2017","journal-title":"mBio"},{"key":"2026072215313133600_ref19","doi-asserted-by":"publisher","DOI":"10.1128\/mSystems.00943-20","article-title":"Microbiome search engine 2: a platform for taxonomic and functional search of global microbiomes on the whole-microbiome level","volume":"6","author":"Jing","year":"2021","journal-title":"mSystems"},{"key":"2026072215313133600_ref20","doi-asserted-by":"publisher","first-page":"554","DOI":"10.1038\/s41592-025-02923-9","article-title":"MaAsLin 3: refining and extending generalized multivariable linear models for meta-omic association discovery","volume":"23","author":"Nickols","year":"2026","journal-title":"Nat Methods"},{"key":"2026072215313133600_ref21","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1038\/s42003-020-0859-7","article-title":"The gut microbiome but not the resistome is associated with urogenital schistosomiasis in preschool-aged children","volume":"3","author":"Osakunor","year":"2020","journal-title":"Commun Biol"},{"key":"2026072215313133600_ref22","doi-asserted-by":"publisher","first-page":"253","DOI":"10.1023\/A:1023866030544","article-title":"Dealing with zeros and missing values in compositional data sets using nonparametric imputation","volume":"35","author":"Mart\u00edn-Fern\u00e1ndez","year":"2003","journal-title":"Math Geol"},{"key":"2026072215313133600_ref23","doi-asserted-by":"publisher","first-page":"28","DOI":"10.1093\/biomet\/34.1-2.28","article-title":"The generalisation of student's problems when several different population variances are involved","volume":"34","author":"Welch","year":"1947","journal-title":"Biometrika"},{"key":"2026072215313133600_ref24","doi-asserted-by":"publisher","first-page":"1100","DOI":"10.1016\/j.cell.2024.12.017","article-title":"Integration of 168,000 samples reveals global patterns of the human gut microbiome","volume":"188","author":"Abdill","journal-title":"Cell"},{"key":"2026072215313133600_ref25","doi-asserted-by":"publisher","first-page":"115","DOI":"10.1007\/s00240-024-01610-2","article-title":"Species-level characterization of gut microbiota and their metabolic role in kidney stone formation using full-length 16S rRNA sequencing","volume":"52","author":"Hussain","journal-title":"Urolithiasis"},{"key":"2026072215313133600_ref26","doi-asserted-by":"publisher","volume":"19","DOI":"10.1016\/j.mucimm.2026.100377"},{"key":"2026072215313133600_ref27","doi-asserted-by":"publisher","first-page":"14330","DOI":"10.1038\/s41598-020-71113-8","article-title":"Akkermansia muciniphila uses human milk oligosaccharides to thrive in the early life conditions in vitro","volume":"10","author":"Kostopoulos","year":"2020","journal-title":"Sci Rep"},{"key":"2026072215313133600_ref28","doi-asserted-by":"publisher","first-page":"11779322231166229","DOI":"10.1177\/11779322231166229","article-title":"The alteration of Akkermansiaceae\/Lachnospiraceae ratio is a microbial feature of antibiotic-induced microbiota remodeling","volume":"17","author":"Chen","year":"2023","journal-title":"Bioinform Biol Insights"},{"key":"2026072215313133600_ref29","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1007\/s00394-024-03535-3","article-title":"Protective effect of a newly probiotic lactobacillus reuteri LY2-2 on DSS-induced colitis","volume":"64","author":"Yang","year":"2025","journal-title":"Eur J Nutr"},{"key":"2026072215313133600_ref30","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1038\/s41538-024-00339-x","article-title":"Akkermansia muciniphila ONE effectively ameliorates dextran sulfate sodium (DSS)-induced ulcerative colitis in mice","volume":"8","author":"Zhang","year":"2024","journal-title":"NPJ Sci Food"},{"key":"2026072215313133600_ref31","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2023.112464","article-title":"MetaPhlAn 4 profiling of unknown species-level genome bins improves the characterization of diet-associated microbiome changes in mice","volume":"42","author":"Manghi","year":"2023","journal-title":"Cell Rep"},{"key":"2026072215313133600_ref32","doi-asserted-by":"publisher","first-page":"D243","DOI":"10.1093\/nar\/gkae1038","article-title":"NCBI RefSeq: reference sequence standards through 25 years of curation and annotation","volume":"53","author":"Goldfarb","year":"2025","journal-title":"Nucleic Acids Res"},{"key":"2026072215313133600_ref33","doi-asserted-by":"publisher","first-page":"e1","DOI":"10.1002\/imt2.1","article-title":"Parallel-meta suite: interactive and rapid microbiome data analysis on multiple platforms","volume":"1","author":"Chen","year":"2022","journal-title":"iMeta"},{"key":"2026072215313133600_ref34","doi-asserted-by":"publisher","first-page":"5069","DOI":"10.1128\/AEM.03006-05","article-title":"Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB","volume":"72","author":"DeSantis","year":"2006","journal-title":"Appl Environ Microbiol"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/27\/4\/bbag394\/69806075\/bbag394.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/27\/4\/bbag394\/69806075\/bbag394.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,22]],"date-time":"2026-07-22T19:31:40Z","timestamp":1784748700000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbag394\/8740057"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7]]},"references-count":34,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2026,7,3]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbag394","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,7]]},"published":{"date-parts":[[2026,7]]},"article-number":"bbag394"}}