{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,30]],"date-time":"2026-03-30T14:24:03Z","timestamp":1774880643529,"version":"3.50.1"},"reference-count":86,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2021,6,11]],"date-time":"2021-06-11T00:00:00Z","timestamp":1623369600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001824","name":"Grantov\u00e1 Agentura \u010cesk\u00e9 Republiky","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001824","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>The bacterial genus <jats:italic>Sodalis<\/jats:italic> is represented by insect endosymbionts as well as free-living species. While the former have been studied frequently, the distribution of the latter is not yet clear. Here, we present a description of a free-living strain, <jats:italic>Sodalis ligni<\/jats:italic> sp. nov., originating from decomposing deadwood. The favored occurrence of <jats:italic>S. ligni<\/jats:italic> in deadwood is confirmed by both 16S rRNA gene distribution and metagenome data. Pangenome analysis of available <jats:italic>Sodalis<\/jats:italic> genomes shows at least three groups within the <jats:italic>Sodalis<\/jats:italic> genus: deadwood-associated strains, tsetse fly endosymbionts and endosymbionts of other insects. This differentiation is consistent in terms of the gene frequency level, genome similarity and carbohydrate-active enzyme composition of the genomes. Deadwood-associated strains contain genes for active decomposition of biopolymers of plant and fungal origin and can utilize more diverse carbon sources than their symbiotic relatives. Deadwood-associated strains, but not other <jats:italic>Sodalis<\/jats:italic> strains, have the genetic potential to fix N<jats:sub>2<\/jats:sub>, and the corresponding genes are expressed in deadwood. Nitrogenase genes are located within the genomes of <jats:italic>Sodalis<\/jats:italic>, including <jats:italic>S. ligni<\/jats:italic>, at multiple loci represented by more gene variants. We show decomposing wood to be a previously undescribed habitat of the genus <jats:italic>Sodalis<\/jats:italic> that appears to show striking ecological divergence.<\/jats:p>","DOI":"10.3389\/fmicb.2021.668644","type":"journal-article","created":{"date-parts":[[2021,6,11]],"date-time":"2021-06-11T10:42:55Z","timestamp":1623408175000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":30,"title":["Ecological Divergence Within the Enterobacterial Genus Sodalis: From Insect Symbionts to Inhabitants of Decomposing Deadwood"],"prefix":"10.3389","volume":"12","author":[{"given":"Vojt\u011bch","family":"Tl\u00e1skal","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Victor Satler","family":"Pylro","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lucia","family":"\u017dif\u010d\u00e1kov\u00e1","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Petr","family":"Baldrian","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2021,6,11]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"402","DOI":"10.1038\/ng986","article-title":"Genome sequence of the endocellular obligate symbiont of tsetse flies, Wigglesworthia glossinidia.","volume":"32","author":"Akman","year":"2002","journal-title":"Nat. Genet."},{"key":"B2","doi-asserted-by":"publisher","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"B3","doi-asserted-by":"publisher","first-page":"143","DOI":"10.1128\/mr.59.1.143-169.1995","article-title":"Phylogenetic identification and in situ detection of individual microbial cells without cultivation.","volume":"59","author":"Amann","year":"1995","journal-title":"Microbiol. Rev."},{"key":"B4","doi-asserted-by":"publisher","first-page":"528","DOI":"10.1111\/gcb.12712","article-title":"CTFS-ForestGEO: a worldwide network monitoring forests in an era of global change.","volume":"21","author":"Anderson-Teixeira","year":"2015","journal-title":"Glob. Chang. Biol."},{"key":"B5","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1016\/j.funeco.2016.07.001","article-title":"Fungi associated with decomposing deadwood in a natural beech-dominated forest.","volume":"23","author":"Baldrian","year":"2016","journal-title":"Fungal Ecol."},{"key":"B6","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.","volume":"19","author":"Bankevich","year":"2012","journal-title":"J. Comput. Biol."},{"key":"B7","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.02475-19","article-title":"A genus definition for Bacteria and Archaea based on a standard genome relatedness index.","volume":"11","author":"Barco","year":"2020","journal-title":"mBio"},{"key":"B8","doi-asserted-by":"publisher","first-page":"2637","DOI":"10.1111\/j.1365-294X.2005.02615.x","article-title":"Enterobacteria-mediated nitrogen fixation in natural populations of the fruit fly Ceratitis capitata.","volume":"14","author":"Behar","year":"2005","journal-title":"Mol. Ecol."},{"key":"B9","doi-asserted-by":"publisher","DOI":"10.1186\/s12862-018-1272-4","article-title":"Factors driving effective population size and pan-genome evolution in bacteria.","volume":"18","author":"Bobay","year":"2018","journal-title":"BMC Evol. Biol."},{"key":"B10","doi-asserted-by":"publisher","first-page":"3185","DOI":"10.1128\/AEM.00282-16","article-title":"Two bacterial genera, Sodalis and Rickettsia, associated with the Seal Louse Proechinophthirus fluctus (Phthiraptera: Anoplura).","volume":"82","author":"Boyd","year":"2016","journal-title":"Appl. Environ. Microbiol."},{"key":"B11","doi-asserted-by":"publisher","first-page":"1400","DOI":"10.1099\/ijs.0.000091","article-title":"Phenotypic characterization of Sodalis praecaptivus sp. nov., a close non-insect-associated member of the Sodalis-allied lineage of insect endosymbionts.","volume":"65","author":"Chari","year":"2015","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"B12","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1007\/PL00006444","article-title":"Concordant evolution of a symbiont with its host insect species: molecular phylogeny of genus Glossina and its bacteriome-associated endosymbiont, Wigglesworthia glossinidia.","volume":"48","author":"Chen","year":"1999","journal-title":"J. Mol. Evol."},{"key":"B13","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0040354","article-title":"Candidatus Sodalis melophagi sp. nov.: phylogenetically independent comparative model to the tsetse fly symbiont Sodalis glossinidius. PLoS One","author":"Chrudimsk\u00fd","year":"2012"},{"key":"B14","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1002990","article-title":"A novel human-infection-derived bacterium provides insights into the evolutionary origins of mutualistic insect-bacterial symbioses.","volume":"8","author":"Clayton","year":"2012","journal-title":"PLoS Genet."},{"key":"B15","author":"de Mendiburu","year":"2017","journal-title":"Agricolae: Statistical Procedures for Agricultural Research. R Package Version 1.2-4."},{"key":"B16","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1002195","article-title":"Accelerated profile HMM searches.","volume":"7","author":"Eddy","year":"2011","journal-title":"PLoS Comput. Biol."},{"key":"B17","doi-asserted-by":"publisher","first-page":"143","DOI":"10.1111\/j.1574-6941.2000.tb00679.x","article-title":"Humus bacteria of Norway spruce stands: plant growth promoting properties and birch, red fescue and alder colonizing capacity.","volume":"31","author":"Elo","year":"2000","journal-title":"FEMS Microbiol. Ecol."},{"key":"B18","doi-asserted-by":"publisher","first-page":"629","DOI":"10.1016\/j.chom.2017.04.003","article-title":"Quorum sensing attenuates virulence in Sodalis praecaptivus.","volume":"21","author":"Enomoto","year":"2017","journal-title":"Cell Host Microb."},{"key":"B19","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.1319","article-title":"Anvi\u2019o: an advanced analysis and visualization platform for \u2018Omics data.","volume":"3","author":"Eren","year":"2015","journal-title":"PeerJ"},{"key":"B20","doi-asserted-by":"publisher","first-page":"6660","DOI":"10.1128\/AEM.01131-07","article-title":"Bacterial endosymbiont of the slender pigeon louse, Columbicola columbae, allied to endosymbionts of grain weevils and tsetse flies.","volume":"73","author":"Fukatsu","year":"2007","journal-title":"Appl. Environ. Microbiol."},{"key":"B21","doi-asserted-by":"publisher","first-page":"1553","DOI":"10.1038\/ismej.2014.60","article-title":"Implications of streamlining theory for microbial ecology.","volume":"8","author":"Giovannoni","year":"2014","journal-title":"ISME J."},{"key":"B22","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000285","article-title":"Large-scale and significant expression from pseudogenes in Sodalis glossinidius - A facultative bacterial endosymbiont.","volume":"6","author":"Goodhead","year":"2020","journal-title":"Microb. Genom."},{"key":"B23","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.02106-18","article-title":"A tale of three species: adaptation of Sodalis glossinidius to tsetse biology, Wigglesworthia metabolism, and host diet.","volume":"10","author":"Hall","year":"2019","journal-title":"mBio"},{"key":"B24","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000378","article-title":"Simulating the evolutionary trajectories of metabolic pathways for insect symbionts in the genus Sodalis.","volume":"6","author":"Hall","year":"2020","journal-title":"Microb. Genomics"},{"key":"B25","doi-asserted-by":"publisher","first-page":"6814","DOI":"10.1073\/pnas.96.12.6814","article-title":"Four intracellular genomes direct weevil biology: nuclear, mitochondrial, principal endosymbiont, and Wolbachia.","volume":"96","author":"Heddi","year":"1999","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"B26","doi-asserted-by":"publisher","first-page":"518","DOI":"10.1093\/molbev\/msx281","article-title":"UFBoot2: improving the ultrafast bootstrap approximation.","volume":"35","author":"Hoang","year":"2017","journal-title":"Mol. Biol. Evol."},{"key":"B27","doi-asserted-by":"publisher","DOI":"10.1038\/srep09456","article-title":"A pyrosequencing insight into sprawling bacterial diversity and community dynamics in decaying deadwood logs of Fagus sylvatica and Picea abies.","volume":"5","author":"Hoppe","year":"2015","journal-title":"Sci. Rep."},{"key":"B28","doi-asserted-by":"publisher","first-page":"3486","DOI":"10.1128\/AEM.00421-10","article-title":"Primary gut symbiont and secondary, Sodalis-allied symbiont of the scutellerid stinkbug Cantao ocellatus.","volume":"76","author":"Kaiwa","year":"2010","journal-title":"Appl. Environ. Microbiol."},{"key":"B29","doi-asserted-by":"publisher","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":"B30","doi-asserted-by":"publisher","first-page":"1160","DOI":"10.1093\/bib\/bbx108","article-title":"MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization.","volume":"20","author":"Katoh","year":"2018","journal-title":"Brief. Bioinform."},{"key":"B31","author":"Kolde","year":"2019","journal-title":"pheatmap: Pretty Heatmaps. R Package Version 1.0.12."},{"key":"B32","doi-asserted-by":"publisher","first-page":"1929","DOI":"10.1098\/rstb.2006.1920","article-title":"The bacterial species definition in the genomic era.","volume":"361","author":"Konstantinidis","year":"2006","journal-title":"Philos. Trans. R. Soc. Lond. B. Biol. Sci."},{"key":"B33","doi-asserted-by":"publisher","first-page":"2196","DOI":"10.1016\/j.foreco.2010.09.020","article-title":"Local variability of stand structural features in beech dominated natural forests of Central Europe: implications for sampling.","volume":"260","author":"Kr\u00e1l","year":"2010","journal-title":"For. Ecol. Manag."},{"key":"B34","doi-asserted-by":"publisher","first-page":"3100","DOI":"10.1093\/nar\/gkm160","article-title":"RNAmmer: consistent and rapid annotation of ribosomal RNA genes.","volume":"35","author":"Lagesen","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"B35","article-title":"16S\/23S rRNA sequencing","author":"Lane","year":"1991","journal-title":"Nucleic Acid Techniques in Bacterial Systematics"},{"key":"B36","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2009-10-3-r25","article-title":"Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.","volume":"10","author":"Langmead","year":"2009","journal-title":"Genome Biol."},{"key":"B37","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0214422","article-title":"Bacteria from the endosphere and rhizosphere of Quercus spp. use mainly cell wall-associated enzymes to decompose organic matter.","volume":"14","author":"Lasa","year":"2019","journal-title":"PLoS One"},{"key":"B38","doi-asserted-by":"publisher","first-page":"W475","DOI":"10.1093\/nar\/gkr201","article-title":"Interactive Tree of Life v2: online annotation and display of phylogenetic trees made easy.","volume":"39","author":"Letunic","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"B39","article-title":"Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM.","author":"Li","year":"2013","journal-title":"arXiv"},{"key":"B40","doi-asserted-by":"publisher","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":"B41","doi-asserted-by":"publisher","first-page":"275","DOI":"10.1016\/j.soilbio.2019.05.010","article-title":"Tracking of the activity of individual bacteria in temperate forest soils shows guild-specific responses to seasonality.","volume":"135","author":"Llad\u00f3","year":"2019","journal-title":"Soil Biol. Biochem."},{"key":"B42","doi-asserted-by":"publisher","first-page":"7200","DOI":"10.1073\/pnas.1015622108","article-title":"Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species.","volume":"108","author":"Luo","year":"2011","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"B43","doi-asserted-by":"publisher","first-page":"19347","DOI":"10.1073\/pnas.2007151117","article-title":"Spatial and morphological reorganization of endosymbiosis during metamorphosis accommodates adult metabolic requirements in a weevil.","volume":"117","author":"Maire","year":"2020","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"B44","doi-asserted-by":"publisher","first-page":"3744","DOI":"10.1111\/1462-2920.14376","article-title":"Bacteria inhabiting deadwood of 13 tree species reveal great heterogeneous distribution between sapwood and heartwood.","volume":"20","author":"Moll","year":"2018","journal-title":"Environ. Microbiol."},{"key":"B45","author":"Moynihan","year":"2020","journal-title":"nifHdada2 GitHub Repository. Zenodo."},{"key":"B46","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1008992","article-title":"Quorum sensing sets the stage for the establishment and vertical transmission of Sodalis praecaptivus in tsetse flies.","volume":"16","author":"Munoz","year":"2020","journal-title":"PLoS Genet."},{"key":"B47","doi-asserted-by":"publisher","first-page":"555","DOI":"10.1111\/j.1574-6976.2011.00264.x","article-title":"Insects as alternative hosts for phytopathogenic bacteria.","volume":"35","author":"Nadarasah","year":"2011","journal-title":"FEMS Microbiol. Rev."},{"key":"B48","doi-asserted-by":"publisher","first-page":"499","DOI":"10.1038\/s41587-020-0718-6","article-title":"A genomic catalog of Earth\u2019s microbiomes.","volume":"39","author":"Nayfach","year":"2020","journal-title":"Nat. Biotechnol."},{"key":"B49","doi-asserted-by":"publisher","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":"2014","journal-title":"Mol. Biol. Evol."},{"key":"B50","doi-asserted-by":"publisher","first-page":"131","DOI":"10.1111\/j.1574-6968.2006.00620.x","article-title":"A new Sodalis lineage from bloodsucking fly Craterina melbae (Diptera, Hippoboscoidea) originated independently of the tsetse flies symbiont Sodalis glossinidius.","volume":"269","author":"Nov\u00e1kov\u00e1","year":"2007","journal-title":"FEMS Microbiol. Lett."},{"key":"B51","doi-asserted-by":"publisher","first-page":"76","DOI":"10.1093\/gbe\/evt210","article-title":"Genome degeneration and adaptation in a nascent stage of symbiosis.","volume":"6","author":"Oakeson","year":"2014","journal-title":"Genome Biol. Evol."},{"key":"B52","doi-asserted-by":"publisher","DOI":"10.1128\/mSystems.01017-20","article-title":"Fungal communities are important determinants of bacterial community composition in deadwood.","volume":"6","author":"Odriozola","year":"2021","journal-title":"mSystems"},{"key":"B53","doi-asserted-by":"publisher","first-page":"1043","DOI":"10.1101\/gr.186072.114","article-title":"CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes.","volume":"25","author":"Parks","year":"2015","journal-title":"Genome Res."},{"key":"B54","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1038\/s41579-019-0309-z","article-title":"Microorganisms in the reproductive tissues of arthropods.","volume":"18","author":"Perlmutter","year":"2020","journal-title":"Nat. Rev. Microbiol."},{"key":"B55","doi-asserted-by":"publisher","first-page":"1120","DOI":"10.1126\/science.1173036","article-title":"Symbiotic nitrogen fixation in the fungus gardens of leaf-cutter ants.","volume":"326","author":"Pinto-Tom\u00e1s","year":"2009","journal-title":"Science"},{"key":"B56","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1039\/C5AY02550H","article-title":"Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens.","volume":"8","author":"Pritchard","year":"2015","journal-title":"Anal. Methods"},{"key":"B57","doi-asserted-by":"publisher","first-page":"177","DOI":"10.1016\/j.foreco.2016.09.033","article-title":"How do environmental conditions affect the deadwood decomposition of European beech (Fagus sylvatica L.)?","volume":"381","author":"P\u0159\u00edv\u011btiv\u00fd","year":"2016","journal-title":"For. Ecol. Manag."},{"key":"B58","doi-asserted-by":"publisher","first-page":"3657","DOI":"10.1111\/1462-2920.14359","article-title":"Bacterial communities of decaying Norway spruce follow distinct slope exposure and time-dependent trajectories.","volume":"20","author":"Probst","year":"2018","journal-title":"Environ. Microbiol."},{"key":"B59","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features.","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"B60","year":"2020","journal-title":"R: A Language and Environment for Statistical Computing."},{"key":"B61","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-08973-w","article-title":"The Wolbachia mobilome in Culex pipiens includes a putative plasmid.","volume":"10","author":"Reveillaud","year":"2019","journal-title":"Nat. Commun."},{"key":"B62","doi-asserted-by":"publisher","first-page":"19126","DOI":"10.1073\/pnas.0906412106","article-title":"Shifting the genomic gold standard for the prokaryotic species definition.","volume":"106","author":"Richter","year":"2009","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"B63","doi-asserted-by":"publisher","first-page":"W282","DOI":"10.1093\/nar\/gky467","article-title":"The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level.","volume":"46","author":"Rodriguez-R","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"B64","doi-asserted-by":"publisher","first-page":"115","DOI":"10.5772\/66442","article-title":"The symbiome of Llaveia cochineals (Hemiptera: Coccoidea: Monophlebidae) includes a gammaproteobacterial cosymbiont Sodalis TME1 and the known Candidatus Walczuchella monophlebidarum","author":"Rosas-P\u00e9rez","year":"2017","journal-title":"Insect Physiology and Ecology"},{"key":"B65","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1078\/0723-2020-00261","article-title":"Klebsiella variicola, a novel species with clinical and plant-associated isolates.","volume":"27","author":"Rosenblueth","year":"2004","journal-title":"Syst. Appl. Microbiol."},{"key":"B66","doi-asserted-by":"publisher","DOI":"10.1098\/rsos.180369","article-title":"Social behaviour in bees influences the abundance of Sodalis (Enterobacteriaceae) symbionts.","volume":"5","author":"Rubin","year":"2018","journal-title":"R. Soc. Open Sci."},{"key":"B67","doi-asserted-by":"publisher","first-page":"19521","DOI":"10.1073\/pnas.0907504106","article-title":"Nitrogen recycling and nutritional provisioning by Blattabacterium, the cockroach endosymbiont.","volume":"106","author":"Sabree","year":"2009","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"B68","doi-asserted-by":"publisher","DOI":"10.1016\/j.geoderma.2020.114499","article-title":"Convergence, divergence or chaos? Consequences of tree trunk decay for pedogenesis and the soil microbiome in a temperate natural forest.","volume":"376","author":"\u0160amonil","year":"2020","journal-title":"Geoderma"},{"key":"B69","doi-asserted-by":"publisher","first-page":"123","DOI":"10.1016\/j.foreco.2013.06.045","article-title":"Crossdating of disturbances by tree uprooting: can treethrow microtopography persist for 6000 years?","volume":"307","author":"\u0160amonil","year":"2013","journal-title":"For. Ecol. Manag."},{"key":"B70","doi-asserted-by":"publisher","first-page":"2893","DOI":"10.1093\/gbe\/evx202","article-title":"The all-rounder Sodalis: a new bacteriome-associated endosymbiont of the lygaeoid bug Henestaris halophilus (Heteroptera: Henestarinae) and a critical examination of its evolution.","volume":"9","author":"Santos-Garcia","year":"2017","journal-title":"Genome Biol. Evol."},{"key":"B71","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome annotation.","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"B72","doi-asserted-by":"publisher","first-page":"D593","DOI":"10.1093\/nar\/gku1201","article-title":"rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development.","volume":"43","author":"Stoddard","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"B73","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1038\/nrmicro2298","article-title":"The population genetics of commensal Escherichia coli.","volume":"8","author":"Tenaillon","year":"2010","journal-title":"Nat. Rev. Microbiol."},{"key":"B74","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2021.685303","article-title":"Deadwood-inhabiting bacteria show adaptations to changing carbon and nitrogen availability during decomposition.","volume":"12","author":"Tl\u00e1skal","year":"2021","journal-title":"Front. Microbiol."},{"key":"B75","doi-asserted-by":"publisher","DOI":"10.1128\/mSystems.01078-20","article-title":"Complementary roles of wood-inhabiting fungi and bacteria facilitate deadwood decomposition.","volume":"6","author":"Tl\u00e1skal","year":"2021","journal-title":"mSystems"},{"key":"B76","doi-asserted-by":"publisher","DOI":"10.1093\/femsec\/fix157","article-title":"Bacteria associated with decomposing dead wood in a natural temperate forest.","volume":"93","author":"Tl\u00e1skal","year":"2017","journal-title":"FEMS Microbiol. Ecol."},{"key":"B77","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1101\/gr.4106106","article-title":"Massive genome erosion and functional adaptations provide insights into the symbiotic lifestyle of Sodalis glossinidius in the tsetse host.","volume":"16","author":"Toh","year":"2006","journal-title":"Genome Res."},{"key":"B78","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0057923","article-title":"The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses.","volume":"8","author":"V\u011btrovsk\u00fd","year":"2013","journal-title":"PLoS One"},{"key":"B79","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0112963","article-title":"Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly omprovement.","volume":"9","author":"Walker","year":"2014","journal-title":"PLoS One"},{"key":"B80","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gky212","article-title":"riboSeed: leveraging prokaryotic genomic architecture to assemble across ribosomal regions.","volume":"46","author":"Waters","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"B81","doi-asserted-by":"publisher","first-page":"7013","DOI":"10.1128\/AEM.01507-06","article-title":"Interspecific transfer of bacterial endosymbionts between tsetse fly species: infection establishment and effect on host fitness.","volume":"72","author":"Weiss","year":"2006","journal-title":"Appl. Environ. Microbiol."},{"key":"B82","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1005595","article-title":"Unicycler: resolving bacterial genome assemblies from short and long sequencing reads.","volume":"13","author":"Wick","year":"2017","journal-title":"PLoS Comput. Biol."},{"key":"B83","doi-asserted-by":"publisher","DOI":"10.21105\/joss.01686","article-title":"Welcome to the Tidyverse.","volume":"4","author":"Wickham","year":"2019","journal-title":"J. Open Source Softw."},{"key":"B84","doi-asserted-by":"publisher","first-page":"96","DOI":"10.1016\/0014-5793(93)81499-P","article-title":"Structure of the 16S ribosomal RNA of the thermophilic cyanobacterium Chlorogloeopsis HTF (\u2018Mastigocladus laminosus HTF\u2019) strain PCC7518, and phylogenetic analysis.","volume":"317","author":"Wilmotte","year":"1993","journal-title":"FEBS Lett."},{"key":"B85","author":"Yong","year":"2016","journal-title":"I Contain Multitudes: The Microbes Within us and a Grander View of Life."},{"key":"B86","doi-asserted-by":"publisher","first-page":"W95","DOI":"10.1093\/nar\/gky418","article-title":"dbCAN2: a meta server for automated carbohydrate-active enzyme annotation.","volume":"46","author":"Zhang","year":"2018","journal-title":"Nucleic Acids Res."}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2021.668644\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,6,11]],"date-time":"2021-06-11T10:43:05Z","timestamp":1623408185000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2021.668644\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,6,11]]},"references-count":86,"alternative-id":["10.3389\/fmicb.2021.668644"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2021.668644","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,6,11]]},"article-number":"668644"}}