{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,16]],"date-time":"2025-10-16T07:03:45Z","timestamp":1760598225857,"version":"3.41.2"},"reference-count":43,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2023,3,22]],"date-time":"2023-03-22T00:00:00Z","timestamp":1679443200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key R&D Program of China","doi-asserted-by":"publisher","award":["2021YFF0704500"],"award-info":[{"award-number":["2021YFF0704500"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,4,3]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Beta-diversity quantitatively measures the difference among microbial communities thus enlightening the association between microbiome composition and environment properties or host phenotypes. The beta-diversity analysis mainly relies on distances among microbiomes that are calculated by all microbial features. However, in some cases, only a small fraction of members in a community plays crucial roles. Such a tiny proportion is insufficient to alter the overall distance, which is always missed by end-to-end comparison. On the other hand, beta-diversity pattern can also be interfered due to the data sparsity when only focusing on nonabundant microbes.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Here, we develop Flex Meta-Storms (FMS) distance algorithm that implements the \u201clocal alignment\u201d of microbiomes for the first time. Using a flexible extraction that considers the weighted phylogenetic and functional relations of microbes, FMS produces a normalized phylogenetic distance among members of interest for microbiome pairs. We demonstrated the advantage of FMS in detecting the subtle variations of microbiomes among different states using artificial and real datasets, which were neglected by regular distance metrics. Therefore, FMS effectively discriminates microbiomes with higher sensitivity and flexibility, thus contributing to in-depth comprehension of microbe\u2013host interactions, as well as promoting the utilization of microbiome data such as disease screening and prediction.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>FMS is implemented in C++, and the source code is released at https:\/\/github.com\/qdu-bioinfo\/flex-meta-storms.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad148","type":"journal-article","created":{"date-parts":[[2023,3,22]],"date-time":"2023-03-22T02:35:45Z","timestamp":1679452545000},"source":"Crossref","is-referenced-by-count":4,"title":["Flex Meta-Storms elucidates the microbiome local beta-diversity under specific phenotypes"],"prefix":"10.1093","volume":"39","author":[{"given":"Mingqian","family":"Zhang","sequence":"first","affiliation":[{"name":"College of Computer Science and Technology, Qingdao University , Qingdao, China"}]},{"given":"Wenke","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Computer Science and Technology, Qingdao University , Qingdao, China"}]},{"given":"Yuzhu","family":"Chen","sequence":"additional","affiliation":[{"name":"College of Computer Science and Technology, Qingdao University , Qingdao, China"}]},{"given":"Jin","family":"Zhao","sequence":"additional","affiliation":[{"name":"College of Computer Science and Technology, Qingdao University , Qingdao, China"}]},{"given":"Shunyao","family":"Wu","sequence":"additional","affiliation":[{"name":"College of Computer Science and Technology, Qingdao University , Qingdao, China"}]},{"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 , Qingdao, 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