{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,6]],"date-time":"2025-11-06T12:15:26Z","timestamp":1762431326784,"version":"3.37.3"},"reference-count":44,"publisher":"Public Library of Science (PLoS)","issue":"4","license":[{"start":{"date-parts":[[2017,4,27]],"date-time":"2017-04-27T00:00:00Z","timestamp":1493251200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Institut Philippe Meyer"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1005435","type":"journal-article","created":{"date-parts":[[2017,4,27]],"date-time":"2017-04-27T13:27:21Z","timestamp":1493299641000},"page":"e1005435","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":12,"title":["Variable habitat conditions drive species covariation in the human microbiota"],"prefix":"10.1371","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8835-1096","authenticated-orcid":true,"given":"Charles K.","family":"Fisher","sequence":"first","affiliation":[]},{"given":"Thierry","family":"Mora","sequence":"additional","affiliation":[]},{"given":"Aleksandra M.","family":"Walczak","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2017,4,27]]},"reference":[{"issue":"921","key":"ref1","doi-asserted-by":"publisher","first-page":"377","DOI":"10.1086\/282505","article-title":"The Limiting Similarity, Convergence, and Divergence of Coexisting Species","volume":"101","author":"R Macarthur","year":"1967","journal-title":"The American Naturalist"},{"key":"ref2","doi-asserted-by":"publisher","first-page":"343","DOI":"10.1146\/annurev.ecolsys.31.1.343","article-title":"Mechanisms of maintenance of species diversity","author":"P Chesson","year":"2000","journal-title":"Annual review of Ecology and Systematics"},{"issue":"7164","key":"ref3","doi-asserted-by":"publisher","first-page":"804","DOI":"10.1038\/nature06244","article-title":"The human microbiome project","volume":"449","author":"PJ Turnbaugh","year":"2007","journal-title":"Nature"},{"issue":"7402","key":"ref4","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1038\/nature11209","article-title":"A framework for human microbiome research","volume":"486","year":"2012","journal-title":"Nature"},{"issue":"7402","key":"ref5","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1038\/nature11234","article-title":"Structure, function and diversity of the healthy human microbiome","volume":"486","year":"2012","journal-title":"Nature"},{"issue":"19","key":"ref6","doi-asserted-by":"publisher","first-page":"5002","DOI":"10.1128\/JB.00542-10","article-title":"The human oral microbiome","volume":"192","author":"FE Dewhirst","year":"2010","journal-title":"Journal of bacteriology"},{"issue":"2","key":"ref7","doi-asserted-by":"publisher","first-page":"e1000667","DOI":"10.1371\/journal.pcbi.1000667","article-title":"A primer on metagenomics","volume":"6","author":"JC Wooley","year":"2010","journal-title":"PLoS Comput Biol"},{"issue":"5","key":"ref8","doi-asserted-by":"publisher","first-page":"R50","DOI":"10.1186\/gb-2011-12-5-r50","article-title":"Moving pictures of the human microbiome","volume":"12","author":"JG Caporaso","year":"2011","journal-title":"Genome Biol"},{"issue":"7402","key":"ref9","doi-asserted-by":"crossref","first-page":"222","DOI":"10.1038\/nature11053","article-title":"Human gut microbiome viewed across age and geography","volume":"486","author":"T Yatsunenko","year":"2012","journal-title":"Nature"},{"issue":"5960","key":"ref10","doi-asserted-by":"publisher","first-page":"1694","DOI":"10.1126\/science.1177486","article-title":"Bacterial community variation in human body habitats across space and time","volume":"326","author":"EK Costello","year":"2009","journal-title":"Science"},{"issue":"Supplement 1","key":"ref11","doi-asserted-by":"publisher","first-page":"4586","DOI":"10.1073\/pnas.1000097107","article-title":"Composition, variability, and temporal stability of the intestinal microbiota of the elderly","volume":"108","author":"MJ Claesson","year":"2011","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"8","key":"ref12","doi-asserted-by":"publisher","first-page":"e1001377","DOI":"10.1371\/journal.pbio.1001377","article-title":"The human microbiome project: a community resource for the healthy human microbiome","volume":"10","author":"D Gevers","year":"2012","journal-title":"PLoS biology"},{"issue":"4","key":"ref13","doi-asserted-by":"publisher","first-page":"1369","DOI":"10.1073\/pnas.64.4.1369","article-title":"Species packing, and what competition minimizes","volume":"64","author":"R Mac Arthur","year":"1969","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"1","key":"ref14","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/0040-5809(70)90039-0","article-title":"Species packing and competitive equilibrium for many species","volume":"1","author":"R MacArthur","year":"1970","journal-title":"Theoretical population biology"},{"issue":"1","key":"ref15","doi-asserted-by":"publisher","first-page":"26","DOI":"10.1016\/0040-5809(90)90025-Q","article-title":"MacArthur\u2019s consumer-resource model","volume":"37","author":"P Chesson","year":"1990","journal-title":"Theoretical Population Biology"},{"issue":"1","key":"ref16","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/s004420100809","article-title":"Plant diversity in tropical forests: a review of mechanisms of species coexistence","volume":"130","author":"JS Wright","year":"2002","journal-title":"Oecologia"},{"issue":"1","key":"ref17","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1145\/584091.584093","article-title":"A mathematical theory of communication","volume":"5","author":"CE Shannon","year":"2001","journal-title":"ACM SIGMOBILE Mobile Computing and Communications Review"},{"issue":"3","key":"ref18","doi-asserted-by":"publisher","first-page":"533","DOI":"10.2307\/1929601","article-title":"Fluctuations of animal populations and a measure of community stability","volume":"36","author":"R MacArthur","year":"1955","journal-title":"ecology"},{"issue":"1","key":"ref19","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1093\/biomet\/74.1.59","article-title":"Two generalizations of the common principal component model","volume":"74","author":"BK Flury","year":"1987","journal-title":"Biometrika"},{"issue":"9","key":"ref20","doi-asserted-by":"publisher","first-page":"3270","DOI":"10.1109\/TSP.2006.877673","article-title":"Quadratic optimization for simultaneous matrix diagonalization","volume":"54","author":"R Vollgraf","year":"2006","journal-title":"Signal Processing, IEEE Transactions on"},{"issue":"12","key":"ref21","doi-asserted-by":"publisher","first-page":"3446","DOI":"10.1016\/j.csda.2010.03.010","article-title":"Stepwise estimation of common principal components","volume":"54","author":"NT Trendafilov","year":"2010","journal-title":"Computational Statistics & Data Analysis"},{"article-title":"Generalized low rank models","year":"2014","author":"M Udell","key":"ref22"},{"issue":"4","key":"ref23","doi-asserted-by":"publisher","first-page":"338","DOI":"10.1080\/00401706.1994.10485840","article-title":"Archetypal analysis","volume":"36","author":"A Cutler","year":"1994","journal-title":"Technometrics"},{"article-title":"k-Means Clustering Is Matrix Factorization","year":"2015","author":"C Bauckhage","key":"ref24"},{"issue":"4","key":"ref25","doi-asserted-by":"publisher","first-page":"325","DOI":"10.2307\/1942268","article-title":"An ordination of the upland forest communities of southern Wisconsin","volume":"27","author":"JR Bray","year":"1957","journal-title":"Ecological monographs"},{"issue":"12","key":"ref26","doi-asserted-by":"publisher","first-page":"8228","DOI":"10.1128\/AEM.71.12.8228-8235.2005","article-title":"UniFrac: a new phylogenetic method for comparing microbial communities","volume":"71","author":"C Lozupone","year":"2005","journal-title":"Applied and environmental microbiology"},{"key":"ref27","article-title":"Multidimensional scaling","volume":"vol. 11","author":"JB Kruskal","year":"1978"},{"key":"ref28","doi-asserted-by":"publisher","unstructured":"Wang H, Banerjee A, Boley D. Common component analysis for multiple covariance matrices. In: Proceedings of the 17th ACM SIGKDD international conference on Knowledge discovery and data mining. ACM; 2011. p. 956\u2013964.","DOI":"10.1145\/2020408.2020565"},{"issue":"D1","key":"ref29","doi-asserted-by":"publisher","first-page":"D136","DOI":"10.1093\/nar\/gkr1178","article-title":"The NCBI taxonomy database","volume":"40","author":"S Federhen","year":"2012","journal-title":"Nucleic acids research"},{"issue":"1","key":"ref30","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1093\/nar\/28.1.27","article-title":"KEGG: kyoto encyclopedia of genes and genomes","volume":"28","author":"M Kanehisa","year":"2000","journal-title":"Nucleic acids research"},{"issue":"10","key":"ref31","doi-asserted-by":"publisher","first-page":"e77617","DOI":"10.1371\/journal.pone.0077617","article-title":"Metabolic proximity in the order of colonization of a microbial community","volume":"8","author":"V Mazumdar","year":"2013","journal-title":"PloS one"},{"issue":"9","key":"ref32","doi-asserted-by":"publisher","first-page":"814","DOI":"10.1038\/nbt.2676","article-title":"Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences","volume":"31","author":"MG Langille","year":"2013","journal-title":"Nature biotechnology"},{"issue":"17","key":"ref33","doi-asserted-by":"publisher","first-page":"2882","DOI":"10.1093\/bioinformatics\/btv287","article-title":"Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data","volume":"31","author":"KP A\u00dfhauer","year":"2015","journal-title":"Bioinformatics"},{"key":"ref34","first-page":"btv037","article-title":"Bayesian feature selection for high-dimensional linear regression via the Ising approximation with applications to genomics","author":"CK Fisher","year":"2015","journal-title":"Bioinformatics"},{"article-title":"Bayesian feature selection with strongly-regularizing priors maps to the Ising Model","year":"2014","author":"CK Fisher","key":"ref35"},{"issue":"7376","key":"ref36","doi-asserted-by":"publisher","first-page":"241","DOI":"10.1038\/nature10571","article-title":"Ecology drives a global network of gene exchange connecting the human microbiome","volume":"480","author":"CS Smillie","year":"2011","journal-title":"Nature"},{"issue":"1","key":"ref37","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1038\/ismej.2014.117","article-title":"Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution","volume":"9","author":"M Tikhonov","year":"2015","journal-title":"The ISME journal"},{"key":"ref38","first-page":"gkt241","article-title":"Surprisingly extensive mixed phylogenetic and ecological signals among bacterial Operational Taxonomic Units","author":"AF Koeppel","year":"2013","journal-title":"Nucleic acids research"},{"issue":"7","key":"ref39","doi-asserted-by":"publisher","first-page":"523","DOI":"10.1038\/nrmicro2367","article-title":"The ecological coherence of high bacterial taxonomic ranks","volume":"8","author":"L Philippot","year":"2010","journal-title":"Nature Reviews Microbiology"},{"issue":"5423","key":"ref40","doi-asserted-by":"publisher","first-page":"2124","DOI":"10.1126\/science.284.5423.2124","article-title":"Phylogenetic classification and the universal tree","volume":"284","author":"WF Doolittle","year":"1999","journal-title":"Science"},{"issue":"7606","key":"ref41","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1038\/nature18301","article-title":"Universality of human microbial dynamics","volume":"534","author":"A Bashan","year":"2016","journal-title":"Nature"},{"issue":"1","key":"ref42","doi-asserted-by":"publisher","first-page":"e1004008","DOI":"10.1371\/journal.pcbi.1004008","article-title":"A RESTful API for accessing microbial community data for MG-RAST","volume":"11","author":"A Wilke","year":"2015","journal-title":"PLoS Comput Biol"},{"key":"ref43","doi-asserted-by":"publisher","DOI":"10.1101\/pdb.prot5368","article-title":"Using the metagenomics RAST server (MG-RAST) for analyzing shotgun metagenomes","volume":"2010","author":"EM Glass","year":"2010","journal-title":"Cold Spring Harbor Protocols"},{"key":"ref44","unstructured":"Wilke A, Glass E, Bischof J, Braithwaite D, Souza M, Gerlach W. MG-RAST technical report and manual for version 3.3. 6\u2013Rev 1; 2013."}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1005435","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,8]],"date-time":"2020-05-08T18:54:22Z","timestamp":1588964062000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1005435"}},"subtitle":[],"editor":[{"given":"Justin","family":"Lessler","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2017,4,27]]},"references-count":44,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2017,4,27]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1005435","relation":{},"ISSN":["1553-7358"],"issn-type":[{"type":"electronic","value":"1553-7358"}],"subject":[],"published":{"date-parts":[[2017,4,27]]}}}