{"created":"2023-05-15T11:59:34.468666+00:00","id":6058,"links":{},"metadata":{"_buckets":{"deposit":"6ad634cb-b886-44a9-b46a-3c5bf36db920"},"_deposit":{"created_by":3,"id":"6058","owners":[3],"pid":{"revision_id":0,"type":"depid","value":"6058"},"status":"published"},"_oai":{"id":"oai:kyutech.repo.nii.ac.jp:00006058","sets":["8:9"]},"author_link":["24857","24859","24877"],"item_21_biblio_info_6":{"attribute_name":"書誌情報","attribute_value_mlt":[{"bibliographicIssueDates":{"bibliographicIssueDate":"2019-06-13","bibliographicIssueDateType":"Issued"},"bibliographicPageEnd":"329-14","bibliographicPageStart":"329-1","bibliographicVolumeNumber":"20","bibliographic_titles":[{"bibliographic_title":"BMC Bioinformatics"}]}]},"item_21_description_4":{"attribute_name":"抄録","attribute_value_mlt":[{"subitem_description":"Background Co-occurrence networks—ecological associations between sampled populations of microbial communities inferred from taxonomic composition data obtained from high-throughput sequencing techniques—are widely used in microbial ecology. Several co-occurrence network methods have been proposed. Co-occurrence network methods only infer ecological associations and are often used to discuss species interactions. However, validity of this application of co-occurrence network methods is currently debated. In particular, they simply evaluate using parametric statistical models, even though microbial compositions are determined through population dynamics. Results We comprehensively evaluated the validity of common methods for inferring microbial ecological networks through realistic simulations. We evaluated how correctly nine widely used methods describe interaction patterns in ecological communities. Contrary to previous studies, the performance of the co-occurrence network methods on compositional data was almost equal to or less than that of classical methods (e.g., Pearson’s correlation). The methods described the interaction patterns in dense and/or heterogeneous networks rather inadequately. Co-occurrence network performance also depended upon interaction types; specifically, the interaction patterns in competitive communities were relatively accurately predicted while those in predator–prey (parasitic) communities were relatively inadequately predicted. Conclusions Our findings indicated that co-occurrence network approaches may be insufficient in interpreting species interactions in microbiome studies. However, the results do not diminish the importance of these approaches. Rather, they highlight the need for further careful evaluation of the validity of these much-used methods and the development of more suitable methods for inferring microbial ecological networks.","subitem_description_type":"Abstract"}]},"item_21_description_60":{"attribute_name":"資源タイプ","attribute_value_mlt":[{"subitem_description":"Journal Article","subitem_description_type":"Other"}]},"item_21_full_name_3":{"attribute_name":"著者別名","attribute_value_mlt":[{"nameIdentifiers":[{"nameIdentifier":"24859","nameIdentifierScheme":"WEKO"}],"names":[{"name":"Hirano,  H"}]},{"affiliations":[{"affiliationNames":[{"affiliationName":"","lang":"ja"}],"nameIdentifiers":[]}],"familyNames":[{"familyName":"Takemoto","familyNameLang":"en"},{"familyName":"竹本","familyNameLang":"ja"},{"familyName":"タケモト","familyNameLang":"ja-Kana"}],"givenNames":[{"givenName":"Kazuhiro","givenNameLang":"en"},{"givenName":"和広","givenNameLang":"ja"},{"givenName":"カズヒロ","givenNameLang":"ja-Kana"}],"nameIdentifiers":[{"nameIdentifier":"24877","nameIdentifierScheme":"WEKO"},{"nameIdentifier":"40512356","nameIdentifierScheme":"e-Rad","nameIdentifierURI":"https://nrid.nii.ac.jp/ja/nrid/1000040512356"},{"nameIdentifier":"35270356700 ","nameIdentifierScheme":"Scopus著者ID","nameIdentifierURI":"https://www.scopus.com/authid/detail.uri?authorId=35270356700 "},{"nameIdentifier":"0000-0002-6355-1366","nameIdentifierScheme":"ORCiD","nameIdentifierURI":"https://orcid.org/0000-0002-6355-1366"},{"nameIdentifier":"100000509","nameIdentifierScheme":"九工大研究者情報","nameIdentifierURI":"https://hyokadb02.jimu.kyutech.ac.jp/html/100000509_ja.html"}],"names":[{"name":"Takemoto, Kazuhiro","nameLang":"en"},{"name":"竹本, 和広","nameLang":"ja"},{"name":"タケモト, カズヒロ","nameLang":"ja-Kana"}]}]},"item_21_link_62":{"attribute_name":"研究者情報","attribute_value_mlt":[{"subitem_link_url":"https://hyokadb02.jimu.kyutech.ac.jp/html/100000509_ja.html"}]},"item_21_publisher_7":{"attribute_name":"出版者","attribute_value_mlt":[{"subitem_publisher":"Biomed Central"}]},"item_21_relation_12":{"attribute_name":"DOI","attribute_value_mlt":[{"subitem_relation_type":"isIdenticalTo","subitem_relation_type_id":{"subitem_relation_type_id_text":"info:doi/10.1186/s12859-019-2915-1","subitem_relation_type_select":"DOI"}}]},"item_21_relation_14":{"attribute_name":"情報源","attribute_value_mlt":[{"subitem_relation_name":[{"subitem_relation_name_text":"https://doi.org/10.1186/s12859-019-2915-1"}],"subitem_relation_type_id":{"subitem_relation_type_id_text":"https://doi.org/10.1186/s12859-019-2915-1","subitem_relation_type_select":"DOI"}}]},"item_21_rights_13":{"attribute_name":"権利","attribute_value_mlt":[{"subitem_rights":"Copyright (c) The Author(s). 2019"},{"subitem_rights":"Creative Commons Attribution 4.0 International License"},{"subitem_rights":"http://creativecommons.org/licenses/by/4.0/"}]},"item_21_select_59":{"attribute_name":"査読の有無","attribute_value_mlt":[{"subitem_select_item":"yes"}]},"item_21_source_id_8":{"attribute_name":"ISSN","attribute_value_mlt":[{"subitem_source_identifier":"1471-2105","subitem_source_identifier_type":"ISSN"}]},"item_21_subject_16":{"attribute_name":"日本十進分類法","attribute_value_mlt":[{"subitem_subject":"465","subitem_subject_scheme":"NDC"}]},"item_21_text_28":{"attribute_name":"論文ID（連携）","attribute_value_mlt":[{"subitem_text_value":"10342784"}]},"item_21_text_36":{"attribute_name":"著者所属","attribute_value_mlt":[{"subitem_text_value":"Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan"},{"subitem_text_value":"Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan"}]},"item_21_text_63":{"attribute_name":"連携ID","attribute_value_mlt":[{"subitem_text_value":"7787"}]},"item_21_version_type_58":{"attribute_name":"著者版フラグ","attribute_value_mlt":[{"subitem_version_resource":"http://purl.org/coar/version/c_970fb48d4fbd8a85","subitem_version_type":"VoR"}]},"item_creator":{"attribute_name":"著者","attribute_type":"creator","attribute_value_mlt":[{"creatorNames":[{"creatorName":"Hirano,  Hokuto"}],"nameIdentifiers":[{}]},{"creatorAffiliations":[{"affiliationNameIdentifiers":[],"affiliationNames":[{"affiliationName":""}]}],"creatorNames":[{"creatorName":"Takemoto, Kazuhiro","creatorNameLang":"en"},{"creatorName":"竹本, 和広","creatorNameLang":"ja"},{"creatorName":"タケモト, カズヒロ","creatorNameLang":"ja-Kana"}],"familyNames":[{},{},{}],"givenNames":[{},{},{}],"nameIdentifiers":[{},{},{},{},{}]}]},"item_files":{"attribute_name":"ファイル情報","attribute_type":"file","attribute_value_mlt":[{"accessrole":"open_date","date":[{"dateType":"Available","dateValue":"2019-07-02"}],"displaytype":"detail","filename":"s12859-019-2915-1.pdf","filesize":[{"value":"1.4 MB"}],"format":"application/pdf","licensetype":"license_note","mimetype":"application/pdf","url":{"label":"s12859-019-2915-1.pdf","url":"https://kyutech.repo.nii.ac.jp/record/6058/files/s12859-019-2915-1.pdf"},"version_id":"5f7be924-f8f6-4f5b-b526-a9de05bd4611"}]},"item_keyword":{"attribute_name":"キーワード","attribute_value_mlt":[{"subitem_subject":"Microbiome","subitem_subject_scheme":"Other"},{"subitem_subject":"Correlation network analysis","subitem_subject_scheme":"Other"},{"subitem_subject":"Microbial ecology","subitem_subject_scheme":"Other"},{"subitem_subject":"Complex networks","subitem_subject_scheme":"Other"}]},"item_language":{"attribute_name":"言語","attribute_value_mlt":[{"subitem_language":"eng"}]},"item_resource_type":{"attribute_name":"資源タイプ","attribute_value_mlt":[{"resourcetype":"journal article","resourceuri":"http://purl.org/coar/resource_type/c_6501"}]},"item_title":"Difficulty in inferring microbial community structure based on co-occurrence network approaches","item_titles":{"attribute_name":"タイトル","attribute_value_mlt":[{"subitem_title":"Difficulty in inferring microbial community structure based on co-occurrence network approaches"}]},"item_type_id":"21","owner":"3","path":["9"],"pubdate":{"attribute_name":"公開日","attribute_value":"2019-07-02"},"publish_date":"2019-07-02","publish_status":"0","recid":"6058","relation_version_is_last":true,"title":["Difficulty in inferring microbial community structure based on co-occurrence network approaches"],"weko_creator_id":"3","weko_shared_id":3},"updated":"2024-04-02T08:36:43.690816+00:00"}