{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T13:55:24Z","timestamp":1790776524190,"version":"4.1.0"},"reference-count":167,"publisher":"Elsevier BV","issue":"6","license":[{"start":{"date-parts":[[2020,3,1]],"date-time":"2020-03-01T00:00:00Z","timestamp":1583020800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2020,3,1]],"date-time":"2020-03-01T00:00:00Z","timestamp":1583020800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2021,3,23]],"date-time":"2021-03-23T00:00:00Z","timestamp":1616457600000},"content-version":"vor","delay-in-days":387,"URL":"http:\/\/www.elsevier.com\/open-access\/userlicense\/1.0\/"}],"funder":[{"DOI":"10.13039\/501100007051","name":"Uppsala Universitet","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100007051","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Current Biology"],"published-print":{"date-parts":[[2020,3]]},"DOI":"10.1016\/j.cub.2020.02.016","type":"journal-article","created":{"date-parts":[[2020,3,9]],"date-time":"2020-03-09T02:39:33Z","timestamp":1583721573000},"page":"1032-1048.e7","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":75,"title":["Marine Sediments Illuminate Chlamydiae Diversity and Evolution"],"prefix":"10.1016","volume":"30","author":[{"given":"Jennah E.","family":"Dharamshi","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel","family":"Tamarit","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laura","family":"Eme","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Courtney W.","family":"Stairs","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joran","family":"Martijn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Felix","family":"Homa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steffen L.","family":"J\u00f8rgensen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anja","family":"Spang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thijs J.G.","family":"Ettema","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.cub.2020.02.016_bib1","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1016\/j.copbio.2006.05.005","article-title":"The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance","volume":"17","author":"Wagner","year":"2006","journal-title":"Curr. Opin. Biotechnol."},{"key":"10.1016\/j.cub.2020.02.016_bib2","doi-asserted-by":"crossref","first-page":"1217","DOI":"10.1111\/1462-2920.12349","article-title":"Mind the PVCs","volume":"16","author":"Devos","year":"2014","journal-title":"Environ. Microbiol."},{"key":"10.1016\/j.cub.2020.02.016_bib3","doi-asserted-by":"crossref","first-page":"779","DOI":"10.1111\/1574-6976.12059","article-title":"Chlamydial metabolism revisited: interspecies metabolic variability and developmental stage-specific physiologic activities","volume":"38","author":"Omsland","year":"2014","journal-title":"FEMS Microbiol. Rev."},{"key":"10.1016\/j.cub.2020.02.016_bib4","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/femspd\/ftu009","article-title":"Twenty years of research into Chlamydia-like organisms: a revolution in our understanding of the biology and pathogenicity of members of the phylum Chlamydiae","volume":"73","author":"Taylor-Brown","year":"2015","journal-title":"Pathog. Dis."},{"key":"10.1016\/j.cub.2020.02.016_bib5","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1038\/nrmicro.2016.30","article-title":"Chlamydia cell biology and pathogenesis","volume":"14","author":"Elwell","year":"2016","journal-title":"Nat. Rev. Microbiol."},{"key":"10.1016\/j.cub.2020.02.016_bib6","doi-asserted-by":"crossref","first-page":"687","DOI":"10.1111\/j.1365-2958.2010.07241.x","article-title":"Raman microspectroscopy reveals long-term extracellular activity of Chlamydiae","volume":"77","author":"Haider","year":"2010","journal-title":"Mol. Microbiol."},{"key":"10.1016\/j.cub.2020.02.016_bib7","doi-asserted-by":"crossref","first-page":"e1003553","DOI":"10.1371\/journal.ppat.1003553","article-title":"Metabolic features of Protochlamydia amoebophila elementary bodies--a link between activity and infectivity in Chlamydiae","volume":"9","author":"Sixt","year":"2013","journal-title":"PLoS Pathog."},{"key":"10.1016\/j.cub.2020.02.016_bib8","doi-asserted-by":"crossref","first-page":"464","DOI":"10.1016\/j.tim.2014.04.013","article-title":"Chlamydia genomics: providing novel insights into chlamydial biology","volume":"22","author":"Bachmann","year":"2014","journal-title":"Trends Microbiol."},{"key":"10.1016\/j.cub.2020.02.016_bib9","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1016\/j.meegid.2014.01.029","article-title":"Evolution, phylogeny, and molecular epidemiology of Chlamydia","volume":"23","author":"Nunes","year":"2014","journal-title":"Infect. Genet. Evol."},{"key":"10.1016\/j.cub.2020.02.016_bib10","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1128\/aem.63.1.115-121.1997","article-title":"Obligate intracellular bacterial parasites of acanthamoebae related to Chlamydia spp","volume":"63","author":"Amann","year":"1997","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.cub.2020.02.016_bib11","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1111\/j.1574-6968.2001.tb10865.x","article-title":"Evidence for additional genus-level diversity of Chlamydiales in the environment","volume":"204","author":"Horn","year":"2001","journal-title":"FEMS Microbiol. Lett."},{"key":"10.1016\/j.cub.2020.02.016_bib12","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1038\/ismej.2013.142","article-title":"Integrating metagenomic and amplicon databases to resolve the phylogenetic and ecological diversity of the Chlamydiae","volume":"8","author":"Lagkouvardos","year":"2014","journal-title":"ISME J."},{"key":"10.1016\/j.cub.2020.02.016_bib13","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1146\/annurev.micro.62.081307.162818","article-title":"Chlamydiae as symbionts in eukaryotes","volume":"62","author":"Horn","year":"2008","journal-title":"Annu. Rev. Microbiol."},{"key":"10.1016\/j.cub.2020.02.016_bib14","doi-asserted-by":"crossref","first-page":"728","DOI":"10.1126\/science.1096330","article-title":"Illuminating the evolutionary history of chlamydiae","volume":"304","author":"Horn","year":"2004","journal-title":"Science"},{"key":"10.1016\/j.cub.2020.02.016_bib15","doi-asserted-by":"crossref","first-page":"3253","DOI":"10.1093\/molbev\/msr161","article-title":"Unity in variety--the pan-genome of the Chlamydiae","volume":"28","author":"Collingro","year":"2011","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.cub.2020.02.016_bib16","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1186\/s40168-017-0360-9","article-title":"Towards a balanced view of the bacterial tree of life","volume":"5","author":"Schulz","year":"2017","journal-title":"Microbiome"},{"key":"10.1016\/j.cub.2020.02.016_bib17","doi-asserted-by":"crossref","first-page":"2334","DOI":"10.1038\/ismej.2017.95","article-title":"Unexpected genomic features in widespread intracellular bacteria: evidence for motility of marine chlamydiae","volume":"11","author":"Collingro","year":"2017","journal-title":"ISME J."},{"key":"10.1016\/j.cub.2020.02.016_bib18","doi-asserted-by":"crossref","first-page":"1899","DOI":"10.1111\/1462-2920.13694","article-title":"Culture-independent genomics of a novel chlamydial pathogen of fish provides new insight into host-specific adaptations utilized by these intracellular bacteria","volume":"19","author":"Taylor-Brown","year":"2017","journal-title":"Environ. Microbiol."},{"key":"10.1016\/j.cub.2020.02.016_bib19","doi-asserted-by":"crossref","first-page":"2587","DOI":"10.1093\/gbe\/evy195","article-title":"Metagenomic analysis of fish-associated Ca. Parilichlamydiaceae reveals striking metabolic similarities to the terrestrial Chlamydiaceae","volume":"10","author":"Taylor-Brown","year":"2018","journal-title":"Genome Biol. Evol."},{"key":"10.1016\/j.cub.2020.02.016_bib20","doi-asserted-by":"crossref","first-page":"1334","DOI":"10.1093\/gbe\/evz072","article-title":"Sequencing the obligate intracellular Rhabdochlamydia helvetica within its tick host Ixodes ricinus to investigate their symbiotic relationship","volume":"11","author":"Pillonel","year":"2019","journal-title":"Genome Biol. Evol."},{"key":"10.1016\/j.cub.2020.02.016_bib21","article-title":"Metagenomic evidence for the presence of comammox nitrospira-like bacteria in a drinking water system","volume":"1","author":"Pinto","year":"2015","journal-title":"MSphere"},{"key":"10.1016\/j.cub.2020.02.016_bib22","doi-asserted-by":"crossref","first-page":"2036","DOI":"10.3389\/fmicb.2017.02036","article-title":"Benefits of genomic insights and CRISPR-Cas signatures to monitor potential pathogens across drinking water production and distribution systems","volume":"8","author":"Zhang","year":"2017","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.cub.2020.02.016_bib23","doi-asserted-by":"crossref","first-page":"4929","DOI":"10.1111\/1462-2920.12936","article-title":"Bioreactor microbial ecosystems for thiocyanate and cyanide degradation unravelled with genome-resolved metagenomics","volume":"17","author":"Kantor","year":"2015","journal-title":"Environ. Microbiol."},{"key":"10.1016\/j.cub.2020.02.016_bib24","doi-asserted-by":"crossref","first-page":"13219","DOI":"10.1038\/ncomms13219","article-title":"Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system","volume":"7","author":"Anantharaman","year":"2016","journal-title":"Nat. Commun."},{"key":"10.1016\/j.cub.2020.02.016_bib25","doi-asserted-by":"crossref","first-page":"328","DOI":"10.1038\/s41564-017-0098-y","article-title":"Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface","volume":"3","author":"Probst","year":"2018","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.cub.2020.02.016_bib26","doi-asserted-by":"crossref","first-page":"170203","DOI":"10.1038\/sdata.2017.203","article-title":"The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans","volume":"5","author":"Tully","year":"2018","journal-title":"Sci. Data"},{"key":"10.1016\/j.cub.2020.02.016_bib27","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1186\/s40168-015-0077-6","article-title":"Genomic resolution of linkages in carbon, nitrogen, and sulfur cycling among widespread estuary sediment bacteria","volume":"3","author":"Baker","year":"2015","journal-title":"Microbiome"},{"key":"10.1016\/j.cub.2020.02.016_bib28","doi-asserted-by":"crossref","first-page":"126","DOI":"10.1038\/ncomms1124","article-title":"Discovery of a black smoker vent field and vent fauna at the Arctic Mid-Ocean Ridge","volume":"1","author":"Pedersen","year":"2010","journal-title":"Nat. Commun."},{"key":"10.1016\/j.cub.2020.02.016_bib29","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1038\/nature14447","article-title":"Complex archaea that bridge the gap between prokaryotes and eukaryotes","volume":"521","author":"Spang","year":"2015","journal-title":"Nature"},{"key":"10.1016\/j.cub.2020.02.016_bib30","first-page":"1","article-title":"Pitfalls in supermatrix phylogenomics","volume":"283","author":"Philippe","year":"2017","journal-title":"Eur. J. Taxon."},{"key":"10.1016\/j.cub.2020.02.016_bib31","doi-asserted-by":"crossref","first-page":"79","DOI":"10.3389\/fmicb.2018.00079","article-title":"Environmental metagenomic assemblies reveal seven new highly divergent chlamydial lineages and hallmarks of a conserved intracellular lifestyle","volume":"9","author":"Pillonel","year":"2018","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.cub.2020.02.016_bib32","doi-asserted-by":"crossref","first-page":"1375","DOI":"10.1093\/gbe\/evs113","article-title":"Analysis of genome content evolution in pvc bacterial super-phylum: assessment of candidate genes associated with cellular organization and lifestyle","volume":"4","author":"Kamneva","year":"2012","journal-title":"Genome Biol. Evol."},{"key":"10.1016\/j.cub.2020.02.016_bib33","doi-asserted-by":"crossref","first-page":"1381","DOI":"10.1099\/ijs.0.000090","article-title":"Taxogenomics of the order Chlamydiales","volume":"65","author":"Pillonel","year":"2015","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"10.1016\/j.cub.2020.02.016_bib34","doi-asserted-by":"crossref","first-page":"465","DOI":"10.1038\/nrg2798","article-title":"Evolutionary microbial genomics: insights into bacterial host adaptation","volume":"11","author":"Toft","year":"2010","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.cub.2020.02.016_bib35","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1016\/j.tplants.2013.10.005","article-title":"Tracing the primordial Chlamydiae: extinct parasites of plants?","volume":"19","author":"Subtil","year":"2014","journal-title":"Trends Plant Sci."},{"key":"10.1016\/j.cub.2020.02.016_bib36","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1111\/j.1574-695X.2009.00522.x","article-title":"Analysis of proteins in Chlamydia trachomatis L2 outer membrane complex, COMC","volume":"55","author":"Birkelund","year":"2009","journal-title":"FEMS Immunol. Med. Microbiol."},{"key":"10.1016\/j.cub.2020.02.016_bib37","doi-asserted-by":"crossref","first-page":"R911","DOI":"10.1016\/S0960-9822(00)80102-5","article-title":"Chlamydial homologues of the MACPF (MAC\/perforin) domain","volume":"9","author":"Ponting","year":"1999","journal-title":"Curr. Biol."},{"key":"10.1016\/j.cub.2020.02.016_bib38","doi-asserted-by":"crossref","first-page":"571","DOI":"10.1128\/IAI.00825-10","article-title":"Identification of a family of effectors secreted by the type III secretion system that are conserved in pathogenic Chlamydiae","volume":"79","author":"Muschiol","year":"2011","journal-title":"Infect. Immun."},{"key":"10.1016\/j.cub.2020.02.016_bib39","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1111\/j.1574-695X.2009.00581.x","article-title":"Identification of Chlamydia trachomatis CT621, a protein delivered through the type III secretion system to the host cell cytoplasm and nucleus","volume":"57","author":"Hobolt-Pedersen","year":"2009","journal-title":"FEMS Immunol. Med. Microbiol."},{"key":"10.1016\/j.cub.2020.02.016_bib40","doi-asserted-by":"crossref","first-page":"2417","DOI":"10.1111\/j.1462-5822.2007.00970.x","article-title":"Human GCIP interacts with CT847, a novel Chlamydia trachomatis type III secretion substrate, and is degraded in a tissue-culture infection model","volume":"9","author":"Chellas-G\u00e9ry","year":"2007","journal-title":"Cell. Microbiol."},{"key":"10.1016\/j.cub.2020.02.016_bib41","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1186\/1471-2180-14-40","article-title":"Identification of type III secretion substrates of Chlamydia trachomatis using Yersinia enterocolitica as a heterologous system","volume":"14","author":"da Cunha","year":"2014","journal-title":"BMC Microbiol."},{"key":"10.1016\/j.cub.2020.02.016_bib42","doi-asserted-by":"crossref","first-page":"888","DOI":"10.1111\/mmi.12804","article-title":"The transcriptional repressor EUO regulates both subsets of Chlamydia late genes","volume":"94","author":"Rosario","year":"2014","journal-title":"Mol. Microbiol."},{"key":"10.1016\/j.cub.2020.02.016_bib43","doi-asserted-by":"crossref","first-page":"2129","DOI":"10.1038\/ismej.2016.23","article-title":"Regulatory (pan-)genome of an obligate intracellular pathogen in the PVC superphylum","volume":"10","author":"de Barsy","year":"2016","journal-title":"ISME J."},{"key":"10.1016\/j.cub.2020.02.016_bib44","doi-asserted-by":"crossref","first-page":"3937","DOI":"10.1073\/pnas.88.9.3937","article-title":"Chlamydia trachomatis developmentally regulated protein is homologous to eukaryotic histone H1","volume":"88","author":"Hackstadt","year":"1991","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.cub.2020.02.016_bib45","doi-asserted-by":"crossref","first-page":"2125","DOI":"10.1073\/pnas.89.6.2125","article-title":"A developmentally regulated chlamydial gene with apparent homology to eukaryotic histone H1","volume":"89","author":"Perara","year":"1992","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.cub.2020.02.016_bib46","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1126\/science.256.5055.377","article-title":"Nucleoid condensation in Escherichia coli that express a chlamydial histone homolog","volume":"256","author":"Barry","year":"1992","journal-title":"Science"},{"key":"10.1016\/j.cub.2020.02.016_bib47","doi-asserted-by":"crossref","first-page":"1785","DOI":"10.1128\/jb.175.6.1785-1795.1993","article-title":"Interaction between the Chlamydia trachomatis histone H1-like protein (Hc1) and DNA","volume":"175","author":"Christiansen","year":"1993","journal-title":"J.\u00a0Bacteriol."},{"key":"10.1016\/j.cub.2020.02.016_bib48","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1111\/1462-2920.12299","article-title":"Architecture and host interface of environmental chlamydiae revealed by electron cryotomography","volume":"16","author":"Pilhofer","year":"2014","journal-title":"Environ. Microbiol."},{"key":"10.1016\/j.cub.2020.02.016_bib49","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1128\/jb.161.1.25-31.1985","article-title":"Disulfide-mediated interactions of the chlamydial major outer membrane protein: role in the differentiation of chlamydiae?","volume":"161","author":"Hackstadt","year":"1985","journal-title":"J.\u00a0Bacteriol."},{"key":"10.1016\/j.cub.2020.02.016_bib50","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1016\/S0092-8674(02)00665-7","article-title":"Microbial minimalism: genome reduction in bacterial pathogens","volume":"108","author":"Moran","year":"2002","journal-title":"Cell"},{"key":"10.1016\/j.cub.2020.02.016_bib51","doi-asserted-by":"crossref","first-page":"e10890","DOI":"10.1371\/journal.pone.0010890","article-title":"The Waddlia genome: a window into chlamydial biology","volume":"5","author":"Bertelli","year":"2010","journal-title":"PLoS ONE"},{"key":"10.1016\/j.cub.2020.02.016_bib52","doi-asserted-by":"crossref","first-page":"101","DOI":"10.3389\/fmicb.2015.00101","article-title":"Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: training students and biological insights","volume":"6","author":"Bertelli","year":"2015","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.cub.2020.02.016_bib53","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.00036-12","article-title":"The Black Queen Hypothesis: evolution of dependencies through adaptive gene loss","volume":"3","author":"Morris","year":"2012","journal-title":"MBio"},{"key":"10.1016\/j.cub.2020.02.016_bib54","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1038\/s41579-018-0046-8","article-title":"Ecology and evolution of seafloor and subseafloor microbial communities","volume":"16","author":"Orsi","year":"2018","journal-title":"Nat. Rev. Microbiol."},{"key":"10.1016\/j.cub.2020.02.016_bib55","doi-asserted-by":"crossref","first-page":"858","DOI":"10.1038\/ngeo983","article-title":"Sedimentary membrane lipids recycled by deep-sea benthic archaea","volume":"3","author":"Takano","year":"2010","journal-title":"Nat. Geosci."},{"key":"10.1016\/j.cub.2020.02.016_bib56","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1038\/ismej.2007.40","article-title":"Distribution and diversity of phytate-mineralizing bacteria","volume":"1","author":"Lim","year":"2007","journal-title":"ISME J."},{"key":"10.1016\/j.cub.2020.02.016_bib57","doi-asserted-by":"crossref","first-page":"E2846","DOI":"10.1073\/pnas.1207574109","article-title":"Correlating microbial community profiles with geochemical data in highly stratified sediments from the Arctic Mid-Ocean Ridge","volume":"109","author":"Jorgensen","year":"2012","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.cub.2020.02.016_bib58","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1038\/nrmicro2836","article-title":"Nutritional immunity: transition metals at the pathogen-host interface","volume":"10","author":"Hood","year":"2012","journal-title":"Nat. Rev. Microbiol."},{"key":"10.1016\/j.cub.2020.02.016_bib59","doi-asserted-by":"crossref","first-page":"1257","DOI":"10.2217\/fmb.13.100","article-title":"Bacterial killing in macrophages and amoeba: do they all use a brass dagger?","volume":"8","author":"German","year":"2013","journal-title":"Future Microbiol."},{"key":"10.1016\/j.cub.2020.02.016_bib60","doi-asserted-by":"crossref","first-page":"609","DOI":"10.1099\/mic.0.037143-0","article-title":"Metals, minerals and microbes: geomicrobiology and bioremediation","volume":"156","author":"Gadd","year":"2010","journal-title":"Microbiology"},{"key":"10.1016\/j.cub.2020.02.016_bib61","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1038\/s41586-019-1804-0","article-title":"Light-driven anaerobic microbial oxidation of manganese","volume":"576","author":"Daye","year":"2019","journal-title":"Nature"},{"key":"10.1016\/j.cub.2020.02.016_bib63","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1186\/1471-2180-10-18","article-title":"Interactions between flagellar and type III secretion proteins in Chlamydia pneumoniae","volume":"10","author":"Stone","year":"2010","journal-title":"BMC Microbiol."},{"key":"10.1016\/j.cub.2020.02.016_bib62","doi-asserted-by":"crossref","first-page":"23080","DOI":"10.1038\/srep23080","article-title":"Identification of protein secretion systems in bacterial genomes","volume":"6","author":"Abby","year":"2016","journal-title":"Sci. Rep."},{"key":"10.1016\/j.cub.2020.02.016_bib64","doi-asserted-by":"crossref","first-page":"e1002983","DOI":"10.1371\/journal.pgen.1002983","article-title":"The non-flagellar type III secretion system evolved from the bacterial flagellum and diversified into host-cell adapted systems","volume":"8","author":"Abby","year":"2012","journal-title":"PLoS Genet."},{"key":"10.1016\/j.cub.2020.02.016_bib65","doi-asserted-by":"crossref","first-page":"211","DOI":"10.3389\/fmicb.2011.00211","article-title":"Genomic and experimental evidence suggests that Verrucomicrobium spinosum interacts with eukaryotes","volume":"2","author":"Sait","year":"2011","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.cub.2020.02.016_bib66","doi-asserted-by":"crossref","first-page":"e0119317","DOI":"10.1371\/journal.pone.0119317","article-title":"T346Hunter: a novel web-based tool for the prediction of type III, type IV and type VI secretion systems in bacterial genomes","volume":"10","author":"Mart\u00ednez-Garc\u00eda","year":"2015","journal-title":"PLoS ONE"},{"key":"10.1016\/j.cub.2020.02.016_bib67","doi-asserted-by":"crossref","first-page":"1454","DOI":"10.3389\/fmicb.2017.01454","article-title":"The type VI secretion system: A dynamic system for bacterial communication?","volume":"8","author":"Gallique","year":"2017","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.cub.2020.02.016_bib68","doi-asserted-by":"crossref","first-page":"16183","DOI":"10.1038\/nmicrobiol.2016.183","article-title":"The type VII secretion system of Staphylococcus aureus secretes a nuclease toxin that targets competitor bacteria","volume":"2","author":"Cao","year":"2017","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.cub.2020.02.016_bib69","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1038\/nature09490","article-title":"A widespread family of polymorphic contact-dependent toxin delivery systems in bacteria","volume":"468","author":"Aoki","year":"2010","journal-title":"Nature"},{"key":"10.1016\/j.cub.2020.02.016_bib70","doi-asserted-by":"crossref","first-page":"6453","DOI":"10.1038\/ncomms7453","article-title":"Bacterial killing via a type IV secretion system","volume":"6","author":"Souza","year":"2015","journal-title":"Nat. Commun."},{"key":"10.1016\/j.cub.2020.02.016_bib71","doi-asserted-by":"crossref","first-page":"e24869","DOI":"10.7554\/eLife.24869","article-title":"Contact-dependent killing by Caulobacter crescentus via cell surface-associated, glycine zipper proteins","volume":"6","author":"Garc\u00eda-Bayona","year":"2017","journal-title":"eLife"},{"key":"10.1016\/j.cub.2020.02.016_bib72","doi-asserted-by":"crossref","first-page":"3569","DOI":"10.1099\/mic.0.2006\/000497-0","article-title":"Type IV pili and type II secretion play a limited role in Legionella pneumophila biofilm colonization and retention","volume":"152","author":"Lucas","year":"2006","journal-title":"Microbiology"},{"key":"10.1016\/j.cub.2020.02.016_bib73","doi-asserted-by":"crossref","first-page":"3793","DOI":"10.1128\/IAI.00620-13","article-title":"Dissection of the role of pili and type 2 and 3 secretion systems in adherence and biofilm formation of an atypical enteropathogenic Escherichia coli strain","volume":"81","author":"Hernandes","year":"2013","journal-title":"Infect. Immun."},{"key":"10.1016\/j.cub.2020.02.016_bib74","doi-asserted-by":"crossref","first-page":"1537","DOI":"10.1128\/JB.01531-08","article-title":"Surface translocation by Legionella pneumophila: a form of sliding motility that is dependent upon type II protein secretion","volume":"191","author":"Stewart","year":"2009","journal-title":"J.\u00a0Bacteriol."},{"key":"10.1016\/j.cub.2020.02.016_bib75","doi-asserted-by":"crossref","first-page":"683","DOI":"10.1016\/j.cell.2019.02.022","article-title":"Pathogenic E. coli extracts nutrients from infected host cells utilizing injectisome components","volume":"177","author":"Pal","year":"2019","journal-title":"Cell"},{"key":"10.1016\/j.cub.2020.02.016_bib76","doi-asserted-by":"crossref","first-page":"639","DOI":"10.1128\/JB.187.2.639-648.2005","article-title":"The Erwinia chrysanthemi type III secretion system is required for multicellular behavior","volume":"187","author":"Yap","year":"2005","journal-title":"J.\u00a0Bacteriol."},{"key":"10.1016\/j.cub.2020.02.016_bib77","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1016\/j.femsre.2005.01.001","article-title":"Bioinformatics, genomics and evolution of non-flagellar type-III secretion systems: a Darwinian perspective","volume":"29","author":"Pallen","year":"2005","journal-title":"FEMS Microbiol. Rev."},{"key":"10.1016\/j.cub.2020.02.016_bib78","doi-asserted-by":"crossref","DOI":"10.1093\/femspd\/ftx059","article-title":"Comparative genomics of free-living Gammaproteobacteria: pathogenesis-related genes or interaction-related genes?","volume":"75","author":"V\u00e1zquez-Rosas-Landa","year":"2017","journal-title":"Pathog. Dis."},{"key":"10.1016\/j.cub.2020.02.016_bib79","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1046\/j.1365-313X.1997.11010073.x","article-title":"Characterization of a novel eukaryotic ATP\/ADP translocator located in the plastid envelope of Arabidopsis thaliana L","volume":"11","author":"Neuhaus","year":"1997","journal-title":"Plant J."},{"key":"10.1016\/j.cub.2020.02.016_bib80","doi-asserted-by":"crossref","first-page":"9630","DOI":"10.1074\/jbc.273.16.9630","article-title":"Expression of a plastidic ATP\/ADP transporter gene in Escherichia coli leads to a functional adenine nucleotide transport system in the bacterial cytoplasmic membrane","volume":"273","author":"Tjaden","year":"1998","journal-title":"J.\u00a0Biol. Chem."},{"key":"10.1016\/j.cub.2020.02.016_bib81","doi-asserted-by":"crossref","first-page":"1196","DOI":"10.1128\/JB.181.4.1196-1202.1999","article-title":"Two nucleotide transport proteins in Chlamydia trachomatis, one for net nucleoside triphosphate uptake and the other for transport of energy","volume":"181","author":"Tjaden","year":"1999","journal-title":"J.\u00a0Bacteriol."},{"key":"10.1016\/j.cub.2020.02.016_bib82","doi-asserted-by":"crossref","first-page":"683","DOI":"10.1128\/JB.186.3.683-691.2004","article-title":"ATP\/ADP translocases: a common feature of obligate intracellular amoebal symbionts related to Chlamydiae and Rickettsiae","volume":"186","author":"Schmitz-Esser","year":"2004","journal-title":"J.\u00a0Bacteriol."},{"key":"10.1016\/j.cub.2020.02.016_bib83","doi-asserted-by":"crossref","first-page":"480","DOI":"10.1093\/gbe\/evx015","article-title":"Phylogenetic diversity of NTT nucleotide transport proteins in free-living and parasitic bacteria and eukaryotes","volume":"9","author":"Major","year":"2017","journal-title":"Genome Biol. Evol."},{"key":"10.1016\/j.cub.2020.02.016_bib84","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1128\/JB.00919-10","article-title":"Nucleotide parasitism by Simkania negevensis (Chlamydiae)","volume":"193","author":"Knab","year":"2011","journal-title":"J.\u00a0Bacteriol."},{"key":"10.1016\/j.cub.2020.02.016_bib85","doi-asserted-by":"crossref","first-page":"754","DOI":"10.1126\/science.282.5389.754","article-title":"Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis","volume":"282","author":"Stephens","year":"1998","journal-title":"Science"},{"key":"10.1016\/j.cub.2020.02.016_bib86","doi-asserted-by":"crossref","first-page":"3381","DOI":"10.1128\/JB.00433-13","article-title":"Chlamydia trachomatis transports NAD via the Npt1 ATP\/ADP translocase","volume":"195","author":"Fisher","year":"2013","journal-title":"J.\u00a0Bacteriol."},{"key":"10.1016\/j.cub.2020.02.016_bib87","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1007\/s00239-002-2387-0","article-title":"Deep origin of plastid\/parasite ATP\/ADP translocases","volume":"56","author":"Amiri","year":"2003","journal-title":"J.\u00a0Mol. Evol."},{"key":"10.1016\/j.cub.2020.02.016_bib88","doi-asserted-by":"crossref","first-page":"5530","DOI":"10.1128\/AEM.69.9.5530-5535.2003","article-title":"History of the ADP\/ATP-translocase-encoding gene, a parasitism gene transferred from a Chlamydiales ancestor to plants 1 billion years ago","volume":"69","author":"Greub","year":"2003","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.cub.2020.02.016_bib89","doi-asserted-by":"crossref","first-page":"1534","DOI":"10.1111\/j.1365-2958.2006.05193.x","article-title":"Tapping the nucleotide pool of the host: novel nucleotide carrier proteins of Protochlamydia amoebophila","volume":"60","author":"Haferkamp","year":"2006","journal-title":"Mol. Microbiol."},{"key":"10.1016\/j.cub.2020.02.016_bib90","doi-asserted-by":"crossref","first-page":"915","DOI":"10.1093\/molbev\/msv281","article-title":"Comparative genomics of candidate phylum TM6 suggests that parasitism is widespread and ancestral in this lineage","volume":"33","author":"Yeoh","year":"2016","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.cub.2020.02.016_bib91","doi-asserted-by":"crossref","first-page":"766","DOI":"10.1111\/1462-2920.13171","article-title":"Bacterial predation: 75 years and counting!","volume":"18","author":"P\u00e9rez","year":"2016","journal-title":"Environ. Microbiol."},{"key":"10.1016\/j.cub.2020.02.016_bib92","doi-asserted-by":"crossref","first-page":"622","DOI":"10.1038\/nature03131","article-title":"A candidate NAD+ transporter in an intracellular bacterial symbiont related to Chlamydiae","volume":"432","author":"Haferkamp","year":"2004","journal-title":"Nature"},{"key":"10.1016\/j.cub.2020.02.016_bib93","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1111\/j.1462-2920.2010.02318.x","article-title":"Marine subsurface eukaryotes: the fungal majority","volume":"13","author":"Edgcomb","year":"2011","journal-title":"Environ. Microbiol."},{"key":"10.1016\/j.cub.2020.02.016_bib94","doi-asserted-by":"crossref","first-page":"e56335","DOI":"10.1371\/journal.pone.0056335","article-title":"Deep sequencing of subseafloor eukaryotic rRNA reveals active Fungi across marine subsurface provinces","volume":"8","author":"Orsi","year":"2013","journal-title":"PLoS ONE"},{"key":"10.1016\/j.cub.2020.02.016_bib95","doi-asserted-by":"crossref","first-page":"642","DOI":"10.1111\/j.1365-294X.2010.04958.x","article-title":"Preservation, origin and genetic imprint of extracellular DNA in permanently anoxic deep-sea sediments","volume":"20","author":"Corinaldesi","year":"2011","journal-title":"Mol. Ecol."},{"key":"10.1016\/j.cub.2020.02.016_bib96","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1128\/EC.00158-13","article-title":"Evolution of the cytosolic iron-sulfur cluster assembly machinery in Blastocystis species and other microbial eukaryotes","volume":"13","author":"Tsaousis","year":"2014","journal-title":"Eukaryot. Cell"},{"key":"10.1016\/j.cub.2020.02.016_bib97","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1016\/j.jip.2007.05.002","article-title":"Chlamydial symbionts in the enigmatic Xenoturbella (Deuterostomia)","volume":"96","author":"Israelsson","year":"2007","journal-title":"J.\u00a0Invertebr. Pathol."},{"key":"10.1016\/j.cub.2020.02.016_bib98","doi-asserted-by":"crossref","first-page":"2657","DOI":"10.1128\/AEM.01092-09","article-title":"Two types of endosymbiotic bacteria in the enigmatic marine worm Xenoturbella bocki","volume":"76","author":"Kjeldsen","year":"2010","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.cub.2020.02.016_bib99","doi-asserted-by":"crossref","first-page":"1256","DOI":"10.1038\/nbt.3704","article-title":"Measurement of bacterial replication rates in microbial communities","volume":"34","author":"Brown","year":"2016","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.cub.2020.02.016_bib100","doi-asserted-by":"crossref","first-page":"457","DOI":"10.1038\/nature24621","article-title":"A communal catalogue reveals Earth\u2019s multiscale microbial diversity","volume":"551","author":"Thompson","year":"2017","journal-title":"Nature"},{"key":"10.1016\/j.cub.2020.02.016_bib101","doi-asserted-by":"crossref","first-page":"e1","DOI":"10.1093\/nar\/gks808","article-title":"Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies","volume":"41","author":"Klindworth","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.cub.2020.02.016_bib102","doi-asserted-by":"crossref","first-page":"3481","DOI":"10.1093\/nar\/gkf450","article-title":"PRIMROSE: a computer program for generating and estimating the phylogenetic range of 16S rRNA oligonucleotide probes and primers in conjunction with the RDP-II database","volume":"30","author":"Ashelford","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.cub.2020.02.016_bib103","doi-asserted-by":"crossref","first-page":"10","DOI":"10.14806\/ej.17.1.200","article-title":"Cutadapt removes adapter sequences from high-throughput sequencing reads","volume":"17","author":"Martin","year":"2011","journal-title":"EMBnet. Journal"},{"key":"10.1016\/j.cub.2020.02.016_bib104","doi-asserted-by":"crossref","first-page":"e2584","DOI":"10.7717\/peerj.2584","article-title":"VSEARCH: a versatile open source tool for metagenomics","volume":"4","author":"Rognes","year":"2016","journal-title":"PeerJ"},{"key":"10.1016\/j.cub.2020.02.016_bib105","doi-asserted-by":"crossref","first-page":"2194","DOI":"10.1093\/bioinformatics\/btr381","article-title":"UCHIME improves sensitivity and speed of chimera detection","volume":"27","author":"Edgar","year":"2011","journal-title":"Bioinformatics"},{"key":"10.1016\/j.cub.2020.02.016_bib106","doi-asserted-by":"crossref","first-page":"e49334","DOI":"10.1371\/journal.pone.0049334","article-title":"CREST--classification resources for environmental sequence tags","volume":"7","author":"Lanz\u00e9n","year":"2012","journal-title":"PLoS ONE"},{"key":"10.1016\/j.cub.2020.02.016_bib107","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"10.1016\/j.cub.2020.02.016_bib108","series-title":"FastQC: a quality control tool for high throughput sequence data","author":"Andrews","year":"2010"},{"key":"10.1016\/j.cub.2020.02.016_bib109","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":"10.1016\/j.cub.2020.02.016_bib110","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":"10.1016\/j.cub.2020.02.016_bib111","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":"10.1016\/j.cub.2020.02.016_bib112","series-title":"barrnap 0.8: rapid ribosomal RNA prediction.","author":"Seemann","year":"2013"},{"key":"10.1016\/j.cub.2020.02.016_bib113","doi-asserted-by":"crossref","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome annotation","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"issue":"D1","key":"10.1016\/j.cub.2020.02.016_bib114","doi-asserted-by":"crossref","first-page":"D286","DOI":"10.1093\/nar\/gkv1248","article-title":"eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences","volume":"44","author":"Huerta-Cepas","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.cub.2020.02.016_bib115","doi-asserted-by":"crossref","first-page":"2115","DOI":"10.1093\/molbev\/msx148","article-title":"Fast genome-wide functional annotation through orthology assignment by eggNOG-Mapper","volume":"34","author":"Huerta-Cepas","year":"2017","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.cub.2020.02.016_bib116","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"10.1016\/j.cub.2020.02.016_bib117","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1038\/nbt.3519","article-title":"Near-optimal probabilistic RNA-seq quantification","volume":"34","author":"Bray","year":"2016","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.cub.2020.02.016_bib118","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":"10.1016\/j.cub.2020.02.016_bib119","doi-asserted-by":"crossref","first-page":"936","DOI":"10.1093\/bioinformatics\/btz664","article-title":"miComplete: weighted quality evaluation of assembled microbial genomes","volume":"36","author":"Hugoson","year":"2020","journal-title":"Bioinformatics"},{"key":"10.1016\/j.cub.2020.02.016_bib120","article-title":"mmgenome: a toolbox for reproducible genome extraction from metagenomes","author":"Karst","year":"2016","journal-title":"bioRxiv"},{"key":"10.1016\/j.cub.2020.02.016_bib121","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":"10.1016\/j.cub.2020.02.016_bib122","doi-asserted-by":"crossref","first-page":"1312","DOI":"10.1093\/bioinformatics\/btu033","article-title":"RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies","volume":"30","author":"Stamatakis","year":"2014","journal-title":"Bioinformatics"},{"key":"10.1016\/j.cub.2020.02.016_bib123","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nmeth.3176","article-title":"Fast and sensitive protein alignment using DIAMOND","volume":"12","author":"Buchfink","year":"2015","journal-title":"Nat. Methods"},{"key":"10.1016\/j.cub.2020.02.016_bib124","doi-asserted-by":"crossref","first-page":"1236","DOI":"10.1093\/bioinformatics\/btu031","article-title":"InterProScan 5: genome-scale protein function classification","volume":"30","author":"Jones","year":"2014","journal-title":"Bioinformatics"},{"key":"10.1016\/j.cub.2020.02.016_bib125","doi-asserted-by":"crossref","first-page":"726","DOI":"10.1016\/j.jmb.2015.11.006","article-title":"BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences","volume":"428","author":"Kanehisa","year":"2016","journal-title":"J.\u00a0Mol. Biol."},{"key":"10.1016\/j.cub.2020.02.016_bib126","doi-asserted-by":"crossref","first-page":"e110726","DOI":"10.1371\/journal.pone.0110726","article-title":"MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems","volume":"9","author":"Abby","year":"2014","journal-title":"PLoS ONE"},{"issue":"D1","key":"10.1016\/j.cub.2020.02.016_bib127","doi-asserted-by":"crossref","first-page":"D669","DOI":"10.1093\/nar\/gkv1269","article-title":"EffectiveDB--updates and novel features for a better annotation of bacterial secreted proteins and Type III, IV, VI secretion systems","volume":"44","author":"Eichinger","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.cub.2020.02.016_bib128","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT multiple sequence alignment software version 7: improvements in performance and usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.cub.2020.02.016_bib129","doi-asserted-by":"crossref","first-page":"1972","DOI":"10.1093\/bioinformatics\/btp348","article-title":"trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses","volume":"25","author":"Capella-Guti\u00e9rrez","year":"2009","journal-title":"Bioinformatics"},{"key":"10.1016\/j.cub.2020.02.016_bib130","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1093\/molbev\/msu300","article-title":"IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies","volume":"32","author":"Nguyen","year":"2015","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.cub.2020.02.016_bib131","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1093\/sysbio\/syt022","article-title":"PhyloBayes MPI: phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment","volume":"62","author":"Lartillot","year":"2013","journal-title":"Syst. Biol."},{"key":"10.1016\/j.cub.2020.02.016_bib132","doi-asserted-by":"crossref","first-page":"210","DOI":"10.1186\/1471-2148-10-210","article-title":"BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments","volume":"10","author":"Criscuolo","year":"2010","journal-title":"BMC Evol. Biol."},{"key":"10.1016\/j.cub.2020.02.016_bib133","doi-asserted-by":"crossref","first-page":"e9490","DOI":"10.1371\/journal.pone.0009490","article-title":"FastTree 2--approximately maximum-likelihood trees for large alignments","volume":"5","author":"Price","year":"2010","journal-title":"PLoS ONE"},{"key":"10.1016\/j.cub.2020.02.016_bib134","doi-asserted-by":"crossref","first-page":"33721","DOI":"10.1038\/srep33721","article-title":"IMNGS: A comprehensive open resource of processed 16S rRNA microbial profiles for ecology and diversity studies","volume":"6","author":"Lagkouvardos","year":"2016","journal-title":"Sci. Rep."},{"key":"10.1016\/j.cub.2020.02.016_bib135","series-title":"FigTree v1.3.1","author":"Rambaut","year":"2010"},{"issue":"W1","key":"10.1016\/j.cub.2020.02.016_bib136","doi-asserted-by":"crossref","first-page":"W242","DOI":"10.1093\/nar\/gkw290","article-title":"Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees","volume":"44","author":"Letunic","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.cub.2020.02.016_bib137","doi-asserted-by":"crossref","first-page":"299","DOI":"10.3389\/fmicb.2013.00299","article-title":"Quantitative and phylogenetic study of the Deep Sea Archaeal Group in sediments of the Arctic mid-ocean spreading ridge","volume":"4","author":"J\u00f8rgensen","year":"2013","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.cub.2020.02.016_bib138","doi-asserted-by":"crossref","first-page":"366","DOI":"10.1128\/JB.180.2.366-376.1998","article-title":"Novel division level bacterial diversity in a Yellowstone hot spring","volume":"180","author":"Hugenholtz","year":"1998","journal-title":"J.\u00a0Bacteriol."},{"key":"10.1016\/j.cub.2020.02.016_bib139","doi-asserted-by":"crossref","first-page":"8966","DOI":"10.1128\/AEM.71.12.8966-8969.2005","article-title":"PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample","volume":"71","author":"Acinas","year":"2005","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.cub.2020.02.016_bib140","doi-asserted-by":"crossref","first-page":"D590","DOI":"10.1093\/nar\/gks1219","article-title":"The SILVA ribosomal RNA gene database project: improved data processing and web-based tools","volume":"41","author":"Quast","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.cub.2020.02.016_bib141","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1146\/annurev.ge.11.120177.001501","article-title":"Genetics of bacterial ribosomes","volume":"11","author":"Nomura","year":"1977","journal-title":"Annu. Rev. Genet."},{"key":"10.1016\/j.cub.2020.02.016_bib142","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1038\/s41586-018-0059-5","article-title":"Deep mitochondrial origin outside the sampled alphaproteobacteria","volume":"557","author":"Martijn","year":"2018","journal-title":"Nature"},{"key":"10.1016\/j.cub.2020.02.016_bib143","doi-asserted-by":"crossref","first-page":"6670","DOI":"10.1073\/pnas.1420858112","article-title":"The two-domain tree of life is linked to a new root for the Archaea","volume":"112","author":"Raymann","year":"2015","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.cub.2020.02.016_bib144","doi-asserted-by":"crossref","first-page":"e95567","DOI":"10.1371\/journal.pone.0095567","article-title":"Systematic design of 18S rRNA gene primers for determining eukaryotic diversity in microbial consortia","volume":"9","author":"Hugerth","year":"2014","journal-title":"PLoS ONE"},{"key":"10.1016\/j.cub.2020.02.016_bib145","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1186\/s13059-015-0834-7","article-title":"Metagenome-assembled genomes uncover a global brackish microbiome","volume":"16","author":"Hugerth","year":"2015","journal-title":"Genome Biol."},{"key":"10.1016\/j.cub.2020.02.016_bib146","doi-asserted-by":"crossref","first-page":"725","DOI":"10.1038\/nbt.3893","article-title":"Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea","volume":"35","author":"Bowers","year":"2017","journal-title":"Nat. Biotechnol."},{"issue":"D1","key":"10.1016\/j.cub.2020.02.016_bib147","doi-asserted-by":"crossref","first-page":"D279","DOI":"10.1093\/nar\/gkv1344","article-title":"The Pfam protein families database: towards a more sustainable future","volume":"44","author":"Finn","year":"2016","journal-title":"Nucleic Acids Res."},{"issue":"D1","key":"10.1016\/j.cub.2020.02.016_bib148","doi-asserted-by":"crossref","first-page":"D190","DOI":"10.1093\/nar\/gkw1107","article-title":"InterPro in 2017-beyond protein family and domain annotations","volume":"45","author":"Finn","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.cub.2020.02.016_bib149","doi-asserted-by":"crossref","first-page":"D459","DOI":"10.1093\/nar\/gkt1103","article-title":"The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway\/Genome Databases","volume":"42","author":"Caspi","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.cub.2020.02.016_bib150","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1093\/nar\/28.1.27","article-title":"KEGG: kyoto encyclopedia of genes and genomes","volume":"28","author":"Kanehisa","year":"2000","journal-title":"Nucleic Acids Res."},{"issue":"D1","key":"10.1016\/j.cub.2020.02.016_bib151","doi-asserted-by":"crossref","first-page":"D457","DOI":"10.1093\/nar\/gkv1070","article-title":"KEGG as a reference resource for gene and protein annotation","volume":"44","author":"Kanehisa","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.cub.2020.02.016_bib152","doi-asserted-by":"crossref","first-page":"905","DOI":"10.1128\/IAI.73.2.905-911.2005","article-title":"The Salmonella enterica serovar typhimurium-encoded type III secretion systems can translocate Chlamydia trachomatis proteins into the cytosol of host cells","volume":"73","author":"Ho","year":"2005","journal-title":"Infect. Immun."},{"key":"10.1016\/j.cub.2020.02.016_bib153","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1038\/nmeth.4285","article-title":"ModelFinder: fast model selection for accurate phylogenetic estimates","volume":"14","author":"Kalyaanamoorthy","year":"2017","journal-title":"Nat. Methods"},{"key":"10.1016\/j.cub.2020.02.016_bib154","doi-asserted-by":"crossref","first-page":"1307","DOI":"10.1093\/molbev\/msn067","article-title":"An improved general amino acid replacement matrix","volume":"25","author":"Le","year":"2008","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.cub.2020.02.016_bib155","doi-asserted-by":"crossref","first-page":"2317","DOI":"10.1093\/bioinformatics\/btn445","article-title":"Empirical profile mixture models for phylogenetic reconstruction","volume":"24","author":"Quang","year":"2008","journal-title":"Bioinformatics"},{"key":"10.1016\/j.cub.2020.02.016_bib156","doi-asserted-by":"crossref","first-page":"2921","DOI":"10.1093\/molbev\/mss112","article-title":"Modeling protein evolution with several amino acid replacement matrices depending on site rates","volume":"29","author":"Le","year":"2012","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.cub.2020.02.016_bib157","first-page":"57","article-title":"Some probabilistic and statistical problems in the analysis of DNA sequences","volume":"17","author":"Tavar\u00e9","year":"1986","journal-title":"Lect. Math Life Sci."},{"key":"10.1016\/j.cub.2020.02.016_bib158","doi-asserted-by":"crossref","first-page":"2305","DOI":"10.1128\/JB.01480-09","article-title":"Phylogeny of gammaproteobacteria","volume":"192","author":"Williams","year":"2010","journal-title":"J.\u00a0Bacteriol."},{"key":"10.1016\/j.cub.2020.02.016_bib159","doi-asserted-by":"crossref","first-page":"216","DOI":"10.1093\/sysbio\/syx068","article-title":"Modeling site heterogeneity with posterior mean site frequency profiles accelerates accurate phylogenomic estimation","volume":"67","author":"Wang","year":"2018","journal-title":"Syst. Biol."},{"key":"10.1016\/j.cub.2020.02.016_bib160","doi-asserted-by":"crossref","first-page":"599","DOI":"10.1093\/molbev\/msr203","article-title":"Independent genome reduction and phylogenetic reclassification of the oceanic SAR11 clade","volume":"29","author":"Viklund","year":"2012","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.cub.2020.02.016_bib161","doi-asserted-by":"crossref","first-page":"2373","DOI":"10.1038\/ismej.2015.46","article-title":"Single-cell genomics of a rare environmental alphaproteobacterium provides unique insights into Rickettsiaceae evolution","volume":"9","author":"Martijn","year":"2015","journal-title":"ISME J."},{"key":"10.1016\/j.cub.2020.02.016_bib162","doi-asserted-by":"crossref","first-page":"1095","DOI":"10.1093\/molbev\/msh112","article-title":"A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process","volume":"21","author":"Lartillot","year":"2004","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.cub.2020.02.016_bib163","doi-asserted-by":"crossref","first-page":"208","DOI":"10.1111\/j.1462-2920.2007.01445.x","article-title":"Characterization of \u2018Candidatus Clavochlamydia salmonicola\u2019: an intracellular bacterium infecting salmonid fish","volume":"10","author":"Karlsen","year":"2008","journal-title":"Environ. Microbiol."},{"key":"10.1016\/j.cub.2020.02.016_bib164","series-title":"ggplot2: Elegant Graphics for Data Analysis","author":"Wickham","year":"2016"},{"key":"10.1016\/j.cub.2020.02.016_bib165","series-title":"gplots: Various R programming tools for plotting data. R package version","author":"Warnes","year":"2016"},{"key":"10.1016\/j.cub.2020.02.016_bib166","doi-asserted-by":"crossref","first-page":"1983","DOI":"10.1109\/TVCG.2014.2346248","article-title":"UpSet: visualization of intersecting sets","volume":"20","author":"Lex","year":"2014","journal-title":"IEEE Trans. Vis. Comput. Graph."},{"key":"10.1016\/j.cub.2020.02.016_bib167","doi-asserted-by":"crossref","first-page":"2334","DOI":"10.1093\/bioinformatics\/btq413","article-title":"genoPlotR: comparative gene and genome visualization in R","volume":"26","author":"Guy","year":"2010","journal-title":"Bioinformatics"}],"container-title":["Current Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0960982220301895?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0960982220301895?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,10,18]],"date-time":"2025-10-18T09:41:24Z","timestamp":1760780484000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0960982220301895"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,3]]},"references-count":167,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2020,3]]}},"alternative-id":["S0960982220301895"],"URL":"https:\/\/doi.org\/10.1016\/j.cub.2020.02.016","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/577767","asserted-by":"object"}]},"ISSN":["0960-9822"],"issn-type":[{"value":"0960-9822","type":"print"}],"subject":[],"published":{"date-parts":[[2020,3]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Marine Sediments Illuminate Chlamydiae Diversity and Evolution","name":"articletitle","label":"Article Title"},{"value":"Current Biology","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.cub.2020.02.016","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2020 Elsevier Inc.","name":"copyright","label":"Copyright"}]}}