{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T23:48:46Z","timestamp":1790207326616,"version":"4.1.0"},"reference-count":102,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2018,4,25]],"date-time":"2018-04-25T00:00:00Z","timestamp":1524614400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"name":"Portuguese Foundation for Science and Technology","award":["PTDC\/BIA-MIC\/3865\/2012"],"award-info":[{"award-number":["PTDC\/BIA-MIC\/3865\/2012"]}]},{"name":"Portuguese Foundation for Science and Technology","award":["PTDC\/MAR-BIO\/1547\/2014"],"award-info":[{"award-number":["PTDC\/MAR-BIO\/1547\/2014"]}]},{"DOI":"10.13039\/501100000614","name":"Federation of European Microbiological Societies","doi-asserted-by":"crossref","award":["FEMS-RG-2015\u20130115"],"award-info":[{"award-number":["FEMS-RG-2015\u20130115"]}],"id":[{"id":"10.13039\/501100000614","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,6,1]]},"DOI":"10.1093\/femsec\/fiy074","type":"journal-article","created":{"date-parts":[[2018,4,24]],"date-time":"2018-04-24T02:50:18Z","timestamp":1524538218000},"source":"Crossref","is-referenced-by-count":63,"title":["Metagenomic binning reveals versatile nutrient cycling and distinct adaptive features in alphaproteobacterial symbionts of marine sponges"],"prefix":"10.1093","volume":"94","author":[{"given":"Elham","family":"Karimi","sequence":"first","affiliation":[{"name":"Centre of Marine Sciences (CCMAR), Faculty of Science and Technology (FCT), Algarve University, 8005-139 Faro, Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Beate M","family":"Slaby","sequence":"additional","affiliation":[{"name":"RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research Kiel, 24105 Kiel, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andr\u00e9 R","family":"Soares","sequence":"additional","affiliation":[{"name":"Institute of Geography and Earth Sciences, Aberystwyth University, SY23 3DB Aberystwyth, Wales, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jochen","family":"Blom","sequence":"additional","affiliation":[{"name":"Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, 35392 Giessen, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ute","family":"Hentschel","sequence":"additional","affiliation":[{"name":"RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research Kiel, 24105 Kiel, Germany"},{"name":"Christian-Albrechts-Universit\u00e4t zu Kiel, 24118 Kiel, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rodrigo","family":"Costa","sequence":"additional","affiliation":[{"name":"Centre of Marine Sciences (CCMAR), Faculty of Science and Technology (FCT), Algarve University, 8005-139 Faro, Portugal"},{"name":"Institute for Bioengineering and Biosciences (IBB), Instituto Superior T\u00e9cnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2018,4,25]]},"reference":[{"key":"key\n\t\t\t\t20180613122821_bib1","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1038\/nbt.2579","article-title":"Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes","volume":"31","author":"Albertsen","year":"2013","journal-title":"Nat Biotechnol"},{"key":"key\n\t\t\t\t20180613122821_bib2","first-page":"205","article-title":"Taurine in marine invertebrates","volume-title":"Adv Mar Biol","volume":"9","author":"Allen","year":"1971"},{"key":"key\n\t\t\t\t20180613122821_bib3","first-page":"58","article-title":"Glutathione transferases in bacteria","volume":"9","author":"Allocati","year":"2009"},{"key":"key\n\t\t\t\t20180613122821_bib4","doi-asserted-by":"crossref","first-page":"1144","DOI":"10.1038\/nmeth.3103","article-title":"Binning metagenomic contigs by coverage and composition","volume":"11","author":"Alneberg","year":"2014","journal-title":"Nat Methods"},{"key":"key\n\t\t\t\t20180613122821_bib5","article-title":"CONCOCT: clustering contigs on coverage and composition","author":"Alneberg","year":"2013"},{"key":"key\n\t\t\t\t20180613122821_bib6","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1038\/nature14488","article-title":"Interaction and signalling between a cosmopolitan phytoplankton and associated bacteria","volume":"522","author":"Amin","year":"2015","journal-title":"Nature"},{"key":"key\n\t\t\t\t20180613122821_bib7","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2164-9-75","article-title":"The RAST server: rapid annotations using subsystems technology","volume":"9","author":"Aziz","year":"2008","journal-title":"BMC Genomics"},{"key":"key\n\t\t\t\t20180613122821_bib8","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1007\/978-3-642-30197-1_300","article-title":"The family Rhodospirillaceae","volume-title":"The Prokaryotes: Alphaproteobacteria and Betaproteobacteria","author":"Baldani","year":"2014"},{"key":"key\n\t\t\t\t20180613122821_bib9","doi-asserted-by":"crossref","first-page":"154","DOI":"10.1186\/1471-2105-10-154","article-title":"EDGAR: a software framework for the comparative analysis of prokaryotic genomes","volume":"10","author":"Blom","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20180613122821_bib10","doi-asserted-by":"crossref","first-page":"W22","DOI":"10.1093\/nar\/gkw255","article-title":"EDGAR 2.0: an enhanced software platform for comparative gene content analyses","volume":"44","author":"Blom","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20180613122821_bib11","doi-asserted-by":"crossref","first-page":"1274","DOI":"10.1128\/AEM.03111-15","article-title":"A new N-Acyl homoserine lactone synthase in an uncultured symbiont of the Red Sea sponge theonella swinhoei","volume":"82","author":"Britstein","year":"2016","journal-title":"Appl Environ Microbiol"},{"key":"key\n\t\t\t\t20180613122821_bib12","doi-asserted-by":"crossref","first-page":"5665","DOI":"10.1128\/AEM.71.10.5665-5677.2005","article-title":"Overview of the marine Roseobacter lineage","volume":"71","author":"Buchan","year":"2005","journal-title":"Appl Environ Microbiol"},{"key":"key\n\t\t\t\t20180613122821_bib13","doi-asserted-by":"crossref","first-page":"e00391","DOI":"10.1128\/mBio.00391-15","article-title":"Lifestyle evolution in cyanobacterial symbionts of sponges","volume":"6","author":"Burgsdorf","year":"2015","journal-title":"mBio"},{"key":"key\n\t\t\t\t20180613122821_bib14","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1186\/s13062-015-0085-2","article-title":"Pan-genomic analysis to redefine species and subspecies based on quantum discontinuous variation: the Klebsiella paradigm","volume":"10","author":"Caputo","year":"2015","journal-title":"Biol Direct"},{"key":"key\n\t\t\t\t20180613122821_bib15","doi-asserted-by":"crossref","first-page":"2136","DOI":"10.1111\/j.1462-2920.2006.01096.x","article-title":"Cultivation-independent analysis of Pseudomonas species in soil and in the rhizosphere of field-grown Verticillium dahliae host plants","volume":"8","author":"Costa","year":"2006","journal-title":"Environ Microbiol"},{"key":"key\n\t\t\t\t20180613122821_bib16","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1042\/bse0500085","article-title":"ABC solute importers in bacteria","volume":"50","author":"Cui","year":"2011","journal-title":"Essays Biochem"},{"key":"key\n\t\t\t\t20180613122821_bib17","doi-asserted-by":"crossref","first-page":"5682","DOI":"10.1016\/j.tet.2006.03.087","article-title":"Irciniasulfonic acid B, a novel taurine conjugated fatty acid derivative from a Japanese marine sponge, Ircinia sp","volume":"62","author":"Emura","year":"2006","journal-title":"Tetrahedron"},{"key":"key\n\t\t\t\t20180613122821_bib18","doi-asserted-by":"crossref","first-page":"3724","DOI":"10.1128\/AEM.72.5.3724-3732.2006","article-title":"Characterization of a culturable alphaproteobacterial symbiont common to many marine sponges and evidence for vertical transmission via sponge larvae","volume":"72","author":"Enticknap","year":"2006","journal-title":"Appl Environ Microbiol"},{"key":"key\n\t\t\t\t20180613122821_bib19","doi-asserted-by":"crossref","first-page":"575","DOI":"10.1038\/ismej.2013.188","article-title":"Down under the tunic: bacterial biodiversity hotspots and widespread ammonia-oxidizing archaea in coral reef ascidians","volume":"8","author":"Erwin","year":"2014","journal-title":"ISME J"},{"key":"key\n\t\t\t\t20180613122821_bib20","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1111\/1574-6941.12140","article-title":"Molecular richness and biotechnological potential of bacteria cultured from Irciniidae sponges in the north-east Atlantic","volume":"85","author":"Esteves","year":"2013","journal-title":"FEMS Microbiol Ecol"},{"key":"key\n\t\t\t\t20180613122821_bib21","doi-asserted-by":"crossref","first-page":"E1878","DOI":"10.1073\/pnas.1203287109","article-title":"Functional equivalence and evolutionary convergence in complex communities of microbial sponge symbionts","volume":"109","author":"Fan","year":"2012","journal-title":"Proc Natl Acad Sci"},{"key":"key\n\t\t\t\t20180613122821_bib22","doi-asserted-by":"crossref","first-page":"W29","DOI":"10.1093\/nar\/gkr367","article-title":"HMMER web server: interactive sequence similarity searching","volume":"39","author":"Finn","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20180613122821_bib23","doi-asserted-by":"crossref","first-page":"e00079","DOI":"10.1128\/mBio.00079-14","article-title":"Symbiotic Adaptation drives genome streamlining of the cyanobacterial sponge symbiont \"Candidatus Synechococcus spongiarum\"","volume":"5","author":"Gao","year":"2014","journal-title":"mBio"},{"key":"key\n\t\t\t\t20180613122821_bib24","first-page":"1","article-title":"Class I. Alphaproteobacteria class","volume-title":"novBergey's Manual\u00ae of Systematic Bacteriology","author":"Garrity","year":"2005"},{"key":"key\n\t\t\t\t20180613122821_bib25","doi-asserted-by":"crossref","first-page":"196","DOI":"10.3389\/fmars.2016.00196","article-title":"Draft genomes shed Light on the dual bacterial symbiosis that dominates the microbiome of the coral reef sponge Amphimedon queenslandica","volume":"3","author":"Gauthier","year":"2016","journal-title":"Front Mar Sci"},{"key":"key\n\t\t\t\t20180613122821_bib26","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1038\/ismej.2010.87","article-title":"Distribution of roseobacter RCA and SAR11 lineages in the North Sea and characteristics of an abundant RCA isolate","volume":"5","author":"Giebel","year":"2011","journal-title":"ISME J"},{"key":"key\n\t\t\t\t20180613122821_bib27","first-page":"47","article-title":"Evolution, diversity, and molecular ecology of marine prokaryotes","volume-title":"DOI citeulike-article-id:7826625","author":"Giovannoni","year":"2000"},{"key":"key\n\t\t\t\t20180613122821_bib28","doi-asserted-by":"crossref","first-page":"12078","DOI":"10.1073\/pnas.1105347108","article-title":"Paracatenula, an ancient symbiosis between thiotrophic Alphaproteobacteria and catenulid flatworms","volume":"108","author":"Gruber-Vodicka","year":"2011","journal-title":"Proc Natl Acad Sci"},{"key":"key\n\t\t\t\t20180613122821_bib29","doi-asserted-by":"crossref","first-page":"e0146307","DOI":"10.1371\/journal.pone.0146307","article-title":"Macroalgal morphogenesis induced by waterborne compounds and bacteria in coastal seawater","volume":"11","author":"Grueneberg","year":"2016","journal-title":"PLoS ONE"},{"key":"key\n\t\t\t\t20180613122821_bib30","doi-asserted-by":"crossref","first-page":"551","DOI":"10.3109\/10408449609037477","article-title":"New applications of bacterial systems to problems in toxicology","volume":"26","author":"Guengerich","year":"1996","journal-title":"Crit Rev Toxicol"},{"key":"key\n\t\t\t\t20180613122821_bib31","doi-asserted-by":"crossref","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","article-title":"QUAST: quality assessment tool for genome assemblies","volume":"29","author":"Gurevich","year":"2013","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180613122821_bib32","doi-asserted-by":"crossref","first-page":"611","DOI":"10.3389\/fmicb.2014.00611","article-title":"Effects of sample handling and cultivation bias on the specificity of bacterial communities in keratose marine sponges","volume":"5","author":"Hardoim","year":"2014","journal-title":"Front Microbiol"},{"key":"key\n\t\t\t\t20180613122821_bib33","doi-asserted-by":"crossref","first-page":"3331","DOI":"10.1128\/AEM.02101-08","article-title":"Diversity of bacteria in the marine sponge Aplysina fulva in Brazilian coastal waters","volume":"75","author":"Hardoim","year":"2009","journal-title":"Appl Environ Microbiol"},{"key":"key\n\t\t\t\t20180613122821_bib34","doi-asserted-by":"crossref","first-page":"e53029","DOI":"10.1371\/journal.pone.0053029","article-title":"Phylogenetically and spatially close marine sponges harbour divergent bacterial communities","volume":"7","author":"Hardoim","year":"2012","journal-title":"PLoS ONE"},{"key":"key\n\t\t\t\t20180613122821_bib35","doi-asserted-by":"crossref","first-page":"4431","DOI":"10.1128\/AEM.68.9.4431-4440.2002","article-title":"Molecular evidence for a uniform microbial community in sponges from different oceans","volume":"68","author":"Hentschel","year":"2002","journal-title":"Appl Environ Microbiol"},{"key":"key\n\t\t\t\t20180613122821_bib36","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1111\/j.1574-6941.2005.00046.x","article-title":"Marine sponges as microbial fermenters","volume":"55","author":"Hentschel","year":"2006","journal-title":"FEMS Microbiol Ecol"},{"key":"key\n\t\t\t\t20180613122821_bib37","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1016\/S0923-2508(01)01193-7","article-title":"ABC transporters: physiology, structure and mechanism\u2014an overview","volume":"152","author":"Higgins","year":"2001","journal-title":"Res Microbiol"},{"key":"key\n\t\t\t\t20180613122821_bib39","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1007\/s10600-015-1335-3","article-title":"A new N-Acyl Taurine from the South China Sea Marine Sponge Callyspongia sp","volume":"51","author":"Huang","year":"2015","journal-title":"Chem Nat Compd"},{"key":"key\n\t\t\t\t20180613122821_bib40","doi-asserted-by":"crossref","first-page":"1537","DOI":"10.1080\/14786419.2012.733389","article-title":"A new taurine derivative from South China Sea marine sponge Axinella sp","volume":"27","author":"Huang","year":"2013","journal-title":"Natural Product Research"},{"key":"key\n\t\t\t\t20180613122821_bib41","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1186\/1471-2105-11-119","article-title":"Prodigal: prokaryotic gene recognition and translation initiation site identification","volume":"11","author":"Hyatt","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20180613122821_bib42","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1126\/science.1212665","article-title":"Untangling genomes from metagenomes: revealing an uncultured class of marine Euryarchaeota","volume":"335","author":"Iverson","year":"2012","journal-title":"Science"},{"key":"key\n\t\t\t\t20180613122821_bib43","doi-asserted-by":"crossref","first-page":"e87353","DOI":"10.1371\/journal.pone.0087353","article-title":"The candidate phylum poribacteria by single-cell genomics: new insights into phylogeny, cell-compartmentation, eukaryote-Like repeat proteins, and other genomic features","volume":"9","author":"Kamke","year":"2014","journal-title":"PLoS One"},{"key":"key\n\t\t\t\t20180613122821_bib44","doi-asserted-by":"crossref","first-page":"2499","DOI":"10.3389\/fmicb.2017.02499","article-title":"Comparative metagenomics reveals the distinctive adaptive features of the Spongia officinalis endosymbiotic consortium","volume":"8","author":"Karimi","year":"2017","journal-title":"Front Microbiol"},{"key":"key\n\t\t\t\t20180613122821_bib45","doi-asserted-by":"crossref","first-page":"346","DOI":"10.1099\/ijs.0.059774-0","article-title":"Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes","volume":"64","author":"Kim","year":"2014","journal-title":"Int J Sys Evol Microbiol"},{"key":"key\n\t\t\t\t20180613122821_bib46","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1016\/S0378-1097(03)00684-0","article-title":"Aerobic tryptophan degradation pathway in bacteria: novel kynurenine formamidase","volume":"227","author":"Kurnasov","year":"2003","journal-title":"FEMS Microbiol Lett"},{"key":"key\n\t\t\t\t20180613122821_bib47","doi-asserted-by":"crossref","first-page":"E347","DOI":"10.1073\/pnas.1616234114","article-title":"Insights into the lifestyle of uncultured bacterial natural product factories associated with marine sponges","volume":"114","author":"Lackner","year":"2017","journal-title":"Proc Natl Acad Sci USA"},{"key":"key\n\t\t\t\t20180613122821_bib48","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat Methods"},{"key":"key\n\t\t\t\t20180613122821_bib49","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180613122821_bib50","doi-asserted-by":"crossref","first-page":"e88339","DOI":"10.1371\/journal.pone.0088339","article-title":"Variation, evolution, and correlation analysis of C+G content and genome or chromosome size in different kingdoms and phyla","volume":"9","author":"Li","year":"2014","journal-title":"PLoS One"},{"key":"key\n\t\t\t\t20180613122821_bib51","doi-asserted-by":"crossref","first-page":"898","DOI":"10.1038\/ismej.2011.147","article-title":"Individual genome assembly from complex community short-read metagenomic datasets","volume":"6","author":"Luo","year":"2012","journal-title":"ISME J"},{"key":"key\n\t\t\t\t20180613122821_bib52","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1111\/j.1462-2920.2011.02528.x","article-title":"Genome content of uncultivated marine Roseobacters in the surface ocean","volume":"14","author":"Luo","year":"2012","journal-title":"Environ Microbiol"},{"key":"key\n\t\t\t\t20180613122821_bib53","doi-asserted-by":"crossref","first-page":"563","DOI":"10.1046\/j.1365-2958.1998.00701.x","article-title":"The role of glyoxalase I in the detoxification of methylglyoxal and in the activation of the KefB K+ efflux system in Escherichia coli","volume":"27","author":"MacLean","year":"1998","journal-title":"Mol Microbiol"},{"key":"key\n\t\t\t\t20180613122821_bib54","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1016\/B978-0-12-394283-8.00003-5","article-title":"Nutrient fluxes through sponges: biology, budgets, and ecological implications","volume":"62","author":"Maldonado","year":"2012","journal-title":"Adv Mar Biol"},{"key":"key\n\t\t\t\t20180613122821_bib55","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1111\/1462-2920.12309","article-title":"The metabolic cost of flagellar motion in Pseudomonas putida KT2440","volume":"16","author":"Mart\u00ednez-Garc\u00eda","year":"2014","journal-title":"Environ Microbiol"},{"key":"key\n\t\t\t\t20180613122821_bib56","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1038\/nrmicro2670","article-title":"Extreme genome reduction in symbiotic bacteria","volume":"10","author":"McCutcheon","year":"2012","journal-title":"Nat Rev Micro"},{"key":"key\n\t\t\t\t20180613122821_bib57","doi-asserted-by":"crossref","first-page":"1651","DOI":"10.1038\/ismej.2017.25","article-title":"Integrated metabolism in sponge-microbe symbiosis revealed by genome-centered metatranscriptomics","volume":"11","author":"Moitinho-Silva","year":"2017","journal-title":"ISME J"},{"key":"key\n\t\t\t\t20180613122821_bib58","doi-asserted-by":"crossref","first-page":"806","DOI":"10.1038\/nature01240","article-title":"SAR11 clade dominates ocean surface bacterioplankton communities","volume":"420","author":"Morris","year":"2002","journal-title":"Nature"},{"key":"key\n\t\t\t\t20180613122821_bib59","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1038\/nrg2319","article-title":"Learning how to live together: genomic insights into prokaryote-animal symbioses","volume":"9","author":"Moya","year":"2008","journal-title":"Nat Rev Genet"},{"key":"key\n\t\t\t\t20180613122821_bib60","doi-asserted-by":"crossref","first-page":"236","DOI":"10.1126\/science.1128794","article-title":"Selective silencing of foreign DNA with low GC Content by the H-NS protein in Salmonella","volume":"313","author":"Navarre","year":"2006","journal-title":"Science"},{"key":"key\n\t\t\t\t20180613122821_bib61","doi-asserted-by":"crossref","first-page":"822","DOI":"10.1038\/nbt.2939","article-title":"Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes","volume":"32","author":"Nielsen","year":"2014","journal-title":"Nat Biotechnol"},{"key":"key\n\t\t\t\t20180613122821_bib62","first-page":"824","volume-title":"Genome Res","author":"Nurk","year":"2016"},{"key":"key\n\t\t\t\t20180613122821_bib63","doi-asserted-by":"crossref","first-page":"1495","DOI":"10.1111\/j.1365-2672.2011.05008.x","article-title":"Diversity and antimicrobial activity of Pseudovibrio spp. from Irish marine sponges","volume":"110","author":"O'Halloran","year":"2011","journal-title":"J Appl Microbiol"},{"key":"key\n\t\t\t\t20180613122821_bib64","doi-asserted-by":"crossref","first-page":"1285","DOI":"10.1021\/acs.jnatprod.5b00966","article-title":"Metabolomic profiling reveals the N-Acyl-taurine geodiataurine in extracts from the marine sponge Geodia macandrewii (Bowerbank)","volume":"79","author":"Olsen","year":"2016","journal-title":"J Nat Prod"},{"key":"key\n\t\t\t\t20180613122821_bib65","doi-asserted-by":"crossref","first-page":"D206","DOI":"10.1093\/nar\/gkt1226","article-title":"The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST)","volume":"42","author":"Overbeek","year":"2014","journal-title":"Nucl Acids Res"},{"key":"key\n\t\t\t\t20180613122821_bib66","doi-asserted-by":"crossref","first-page":"1916","DOI":"10.1038\/ismej.2015.3","article-title":"Habitat-specific environmental conditions primarily control the microbiomes of the coral Seriatopora hystrix","volume":"9","author":"Pantos","year":"2015","journal-title":"ISME J"},{"key":"key\n\t\t\t\t20180613122821_bib67","doi-asserted-by":"crossref","first-page":"3123","DOI":"10.1093\/bioinformatics\/btu494","article-title":"STAMP: statistical analysis of taxonomic and functional profiles","volume":"30","author":"Parks","year":"2014","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180613122821_bib68","first-page":"426","article-title":"IDBA\u2014a practical iterative de Bruijn graph de novo assembler","volume-title":"Research in Computational Molecular Biology: 14th Annual International Conference, RECOMB 2010, Lisbon, Portugal, April 25\u201328, 2010 Proceedings","author":"Peng"},{"key":"key\n\t\t\t\t20180613122821_bib69","doi-asserted-by":"crossref","first-page":"1420","DOI":"10.1093\/bioinformatics\/bts174","article-title":"IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth","volume":"28","author":"Peng","year":"2012","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180613122821_bib70","doi-asserted-by":"crossref","first-page":"16222","DOI":"10.1073\/pnas.0405976101","article-title":"Antitumor polyketide biosynthesis by an uncultivated bacterial symbiont of the marine sponge Theonella swinhoei","volume":"101","author":"Piel","year":"2004","journal-title":"Proc Natl Acad Sci"},{"key":"key\n\t\t\t\t20180613122821_bib71","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1159\/000099639","article-title":"Large-scale comparative genomic analyses of cytoplasmic membrane transport systems in prokaryotes","volume":"12","author":"Ren","year":"2007","journal-title":"J Mol Microbiol Biotechnol"},{"key":"key\n\t\t\t\t20180613122821_bib72","doi-asserted-by":"crossref","first-page":"929","DOI":"10.1093\/bioinformatics\/btv681","article-title":"JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison","volume":"32","author":"Richter","year":"2016","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180613122821_bib73","doi-asserted-by":"crossref","first-page":"e1004483","DOI":"10.1371\/journal.ppat.1004483","article-title":"Bacterial flagella: twist and stick, or dodge across the kingdoms","volume":"11","author":"Rossez","year":"2015","journal-title":"PLoS Pathog"},{"key":"key\n\t\t\t\t20180613122821_bib74","doi-asserted-by":"crossref","first-page":"564","DOI":"10.1038\/ismej.2011.116","article-title":"Assessing the complex sponge microbiota: core, variable and species-specific bacterial communities in marine sponges","volume":"6","author":"Schmitt","year":"2012","journal-title":"ISME J"},{"key":"key\n\t\t\t\t20180613122821_bib75","doi-asserted-by":"crossref","first-page":"2067","DOI":"10.1128\/AEM.01944-06","article-title":"Vertical transmission of a phylogenetically complex microbial consortium in the viviparous sponge Ircinia felix","volume":"73","author":"Schmitt","year":"2007","journal-title":"Appl Environ Microbiol"},{"key":"key\n\t\t\t\t20180613122821_bib76","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1016\/S0378-1097(03)00611-6","article-title":"Taurine: new implications for an old amino acid","volume":"226","author":"Schuller-Levis","year":"2003","journal-title":"FEMS Microbiol Lett"},{"key":"key\n\t\t\t\t20180613122821_bib77","doi-asserted-by":"crossref","first-page":"1057","DOI":"10.1126\/science.1247023","article-title":"Genomes from metagenomics","volume":"342","author":"Sharon","year":"2013","journal-title":"Science"},{"key":"key\n\t\t\t\t20180613122821_bib78","doi-asserted-by":"crossref","first-page":"517","DOI":"10.1111\/j.1462-2920.2011.02664.x","article-title":"Sponge-specific clusters revisited: a comprehensive phylogeny of sponge-associated microorganisms","volume":"14","author":"Simister","year":"2012","journal-title":"Environ Microbiol"},{"key":"key\n\t\t\t\t20180613122821_bib79","doi-asserted-by":"crossref","first-page":"1483","DOI":"10.1038\/ismej.2016.198","article-title":"Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats","volume":"11","author":"Simon","year":"2017","journal-title":"ISME J"},{"key":"key\n\t\t\t\t20180613122821_bib80","doi-asserted-by":"crossref","first-page":"1626","DOI":"10.1126\/science.1099930","article-title":"Iron-source preference of Staphylococcus aureus infections","volume":"305","author":"Skaar","year":"2004","journal-title":"Science"},{"key":"key\n\t\t\t\t20180613122821_bib81","doi-asserted-by":"crossref","first-page":"2465","DOI":"10.1038\/ismej.2017.101","article-title":"Metagenomic binning of a marine sponge microbiome reveals unity in defense but metabolic specialization","volume":"11","author":"Slaby","year":"2017","journal-title":"ISME J"},{"key":"key\n\t\t\t\t20180613122821_bib82","doi-asserted-by":"crossref","first-page":"1433","DOI":"10.1111\/j.1529-8817.2012.01231.x","article-title":"Growth and thallus morphogenesis of Ulva mutabilis (Chlorophyta) depends on a combination of two bacterial species excreting regulatory factors","volume":"48","author":"Spoerner","year":"2012","journal-title":"J Phycol"},{"key":"key\n\t\t\t\t20180613122821_bib83","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1186\/1471-2105-4-41","article-title":"The COG database: an updated version includes eukaryotes","volume":"4","author":"Tatusov","year":"2003","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20180613122821_bib84","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1128\/MMBR.00040-06","article-title":"Sponge-associated microorganisms: evolution, ecology, and biotechnological potential","volume":"71","author":"Taylor","year":"2007","journal-title":"Microbiol Mol Biol Rev"},{"key":"key\n\t\t\t\t20180613122821_bib85","doi-asserted-by":"crossref","first-page":"1854","DOI":"10.1126\/science.1144387","article-title":"GENETICS: evolutionary insights from sponges","volume":"316","author":"Taylor","year":"2007","journal-title":"Science"},{"key":"key\n\t\t\t\t20180613122821_bib86","doi-asserted-by":"crossref","first-page":"438","DOI":"10.1038\/ismej.2012.111","article-title":"\u2018Sponge-specific' bacteria are widespread (but rare) in diverse marine environments","volume":"7","author":"Taylor","year":"2013","journal-title":"ISME J"},{"key":"key\n\t\t\t\t20180613122821_bib87","doi-asserted-by":"crossref","first-page":"11870","DOI":"10.1038\/ncomms11870","article-title":"Diversity, structure and convergent evolution of the global sponge microbiome","volume":"7","author":"Thomas","year":"2016","journal-title":"Nat Comms"},{"key":"key\n\t\t\t\t20180613122821_bib88","doi-asserted-by":"crossref","first-page":"1557","DOI":"10.1038\/ismej.2010.74","article-title":"Functional genomic signatures of sponge bacteria reveal unique and shared features of symbiosis","volume":"4","author":"Thomas","year":"2010","journal-title":"ISME J"},{"key":"key\n\t\t\t\t20180613122821_bib89","doi-asserted-by":"crossref","first-page":"913","DOI":"10.1186\/1471-2164-14-913","article-title":"Microbial genomic taxonomy","volume":"14","author":"Thompson","year":"2013","journal-title":"BMC Genomics"},{"key":"key\n\t\t\t\t20180613122821_bib90","doi-asserted-by":"crossref","first-page":"3548","DOI":"10.1111\/1462-2920.12586","article-title":"Genomic analysis reveals versatile heterotrophic capacity of a potentially symbiotic sulfur-oxidizing bacterium in sponge","volume":"16","author":"Tian","year":"2014","journal-title":"Environ Microbiol"},{"key":"key\n\t\t\t\t20180613122821_bib91","doi-asserted-by":"crossref","first-page":"e1000344","DOI":"10.1371\/journal.pgen.1000344","article-title":"Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths","volume":"5","author":"Touchon","year":"2009","journal-title":"PLoS Genet"},{"key":"key\n\t\t\t\t20180613122821_bib92","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1038\/ismej.2009.107","article-title":"Variability and abundance of the epiphytic bacterial community associated with a green marine Ulvacean alga","volume":"4","author":"Tujula","year":"2010","journal-title":"ISME J"},{"key":"key\n\t\t\t\t20180613122821_bib93","doi-asserted-by":"crossref","first-page":"4913","DOI":"10.1038\/ncomms5913","article-title":"Vibrio cholerae use pili and flagella synergistically to effect motility switching and conditional surface attachment","volume":"5","author":"Utada","year":"2014","journal-title":"Nat Comms"},{"key":"key\n\t\t\t\t20180613122821_bib94","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1016\/0022-0981(77)90038-7","article-title":"Electron microscope study of the association between some sponges and bacteria","volume":"30","author":"Vacelet","year":"1977","journal-title":"J Exp Marine Biol Ecol"},{"key":"key\n\t\t\t\t20180613122821_bib95","doi-asserted-by":"crossref","first-page":"860","DOI":"10.1093\/glycob\/cwp059","article-title":"Sulfated polysaccharides from marine sponges (Porifera): an ancestor cell-cell adhesion event based on the carbohydrate-carbohydrate interaction","volume":"19","author":"Vilanova","year":"2009","journal-title":"Glycobiology"},{"key":"key\n\t\t\t\t20180613122821_bib96","doi-asserted-by":"crossref","first-page":"1431","DOI":"10.1128\/jb.179.5.1431-1441.1997","article-title":"Bacterial glutathione S-transferases: what are they good for?","volume":"179","author":"Vuilleumier","year":"1997","journal-title":"J Bacteriol"},{"key":"key\n\t\t\t\t20180613122821_bib97","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1146\/annurev.micro.60.080805.142115","article-title":"Environmental biology of the marine Roseobacter lineage","volume":"60","author":"Wagner-D\u00f6bler","year":"2006","journal-title":"Annu Rev Microbiol"},{"key":"key\n\t\t\t\t20180613122821_bib98","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1111\/j.1462-2920.2011.02460.x","article-title":"Marine sponges and their microbial symbionts: love and other relationships","volume":"14","author":"Webster","year":"2012","journal-title":"Environ Microbiol"},{"key":"key\n\t\t\t\t20180613122821_bib99","doi-asserted-by":"crossref","first-page":"e00135","DOI":"10.1128\/mBio.00135-16","article-title":"The sponge hologenome","volume":"7","author":"Webster","year":"2016","journal-title":"mBio"},{"key":"key\n\t\t\t\t20180613122821_bib100","doi-asserted-by":"crossref","first-page":"e1000352","DOI":"10.1371\/journal.pcbi.1000352","article-title":"Statistical methods for detecting differentially abundant features in clinical metagenomic samples","volume":"5","author":"White","year":"2009","journal-title":"PLoS Comput Biol"},{"key":"key\n\t\t\t\t20180613122821_bib101","doi-asserted-by":"crossref","first-page":"14","DOI":"10.12703\/P7-14","article-title":"Structure and mechanism of ABC transporters","volume":"7","author":"Wilkens","year":"2015","journal-title":"F1000Prime Rep"},{"key":"key\n\t\t\t\t20180613122821_bib102","doi-asserted-by":"crossref","first-page":"58","DOI":"10.1038\/nature12959","article-title":"An environmental bacterial taxon with a large and distinct metabolic repertoire","volume":"506","author":"Wilson","year":"2014","journal-title":"Nature"},{"key":"key\n\t\t\t\t20180613122821_bib103","doi-asserted-by":"crossref","first-page":"4381","DOI":"10.1073\/pnas.1423768112","article-title":"Phosphorus sequestration in the form of polyphosphate by microbial symbionts in marine sponges","volume":"112","author":"Zhang","year":"2015","journal-title":"Proc Natl Acad Sci USA"}],"container-title":["FEMS Microbiology Ecology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/femsec\/article\/doi\/10.1093\/femsec\/fiy074\/4985835","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,10,16]],"date-time":"2019-10-16T19:00:14Z","timestamp":1571252414000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/femsec\/article\/doi\/10.1093\/femsec\/fiy074\/4985835"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,4,25]]},"references-count":102,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2018,4,25]]},"published-print":{"date-parts":[[2018,6,1]]}},"URL":"https:\/\/doi.org\/10.1093\/femsec\/fiy074","relation":{},"ISSN":["1574-6941"],"issn-type":[{"value":"1574-6941","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,6]]},"published":{"date-parts":[[2018,4,25]]}}}