References
- Asnicar F, Weingart G, Tickle TL, Huttenhower C, Segata N. Compact graphical representation of phylogenetic data and metadata with GraPhlAn. PeerJ. 2015 Jun 18;3:e1029. https://doi.org/10.7717/peerj.1029
- Bosch TCG. Cnidarian-microbe interactions and the origin of innate immunity in metazoans. Annu Rev Microbiol. 2013 Sep 08;67(1):499–518. https://doi.org/10.1146/annurev-micro-092412-155626
- Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010 May;7(5):335–336. https://doi.org/10.1038/nmeth.f.303
- Cleary DFR, Becking LE, Polónia ARM, Freitas RM, Gomes NCM. Jellyfish-associated bacterial communities and bacterioplankton in Indonesian Marine lakes. FEMS Microbiol Ecol. 2016 May 01;92(5):fiw064. https://doi.org/10.1093/femsec/fiw064
- Cortés-Lara S, Urdiain M, Mora-Ruiz M, Prieto L, Rosselló-Móra R. Prokaryotic microbiota in the digestive cavity of the jellyfish Cotylorhiza tuberculata. Syst Appl Microbiol. 2015 Oct;38(7): 494–500. https://doi.org/10.1016/j.syapm.2015.07.001
- Daley MC, Urban-Rich J, Moisander PH. Bacterial associations with the hydromedusa Nemopsis bachei and scyphomedusa Aurelia aurita from the North Atlantic Ocean. Mar Biol Res. 2016 Nov 25; 12 (10):1088–1100. https://doi.org/10.1080/17451000.2016.1228974
- DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol. 2006 Jul 01;72(7):5069–5072. https://doi.org/10.1128/AEM.03006-05
- Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010 Oct 1;26(19):2460–2461. https://doi.org/10.1093/bioinformatics/btq461
- Gans J, Wolinsky M, Dunbar J. Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science. 2005 Aug 26;309(5739):1387–1390. https://doi.org/10.1126/science.1112665
- Langille MGI, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Vega Thurber RL, Knight R, et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol. 2013 Sep;31(9):814–821. https://doi.org/10.1038/nbt.2676
- Lee MD, Kling JD, Araya R, Ceh J. Jellyfish life stages shape associated microbial communities, while a core microbiome is maintained across all. Front Microbiol. 2018 Jul 12;9:1534. https://doi.org/10.3389/fmicb.2018.01534
- Magoč T, Salzberg SL. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics. 2011 Nov 01; 27(21):2957–2963. https://doi.org/10.1093/bioinformatics/btr507
- Mulkidjanian AY, Koonin EV, Makarova KS, Mekhedov SL, Sorokin A, Wolf YI, Dufresne A, Partensky F, Burd H, Kaznadzey D, et al. The cyanobacterial genome core and the origin of photosynthesis. Proc Natl Acad Sci USA. 2006 Aug 29;103(35):13126–13131. https://doi.org/10.1073/pnas.0605709103
- Paharik AE, Horswill AR. The staphylococcal biofilm: Adhesins, regulation, and host response. Microbiol Spectr. 2016 Apr; 4(2): 126–135. https://doi.org/10.1128/microbiolspec.VMBF-0022-2015
- Ramette A. Multivariate analyses in microbial ecology. FEMS Microbiol Ecol. 2007 Nov;62(2):142–160. https://doi.org/10.1111/j.1574-6941.2007.00375.x
- Rosenberg E, Koren O, Reshef L, Efrony R, Zilber-Rosenberg I. The role of microorganisms in coral health, disease and evolution. Nat Rev Microbiol. 2007 May;5(5):355–362. https://doi.org/10.1038/nrmicro1635
- Schuergers N, Mullineaux CW, Wilde A. Cyanobacteria in motion. Curr Opin Plant Biol. 2017 Jun;37:109–115. https://doi.org/10.1016/j.pbi.2017.03.018
- Schuett C, Doepke H. Endobiotic bacteria and their pathogenic potential in cnidarian tentacles. Helgol Mar Res. 2010 Sep;64(3): 205–212. https://doi.org/10.1007/s10152-009-0179-2
- Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, Huttenhower C. Metagenomic biomarker discovery and explanation. Genome Biol. 2011;12(6):R60. https://doi.org/10.1186/gb-2011-12-6-r60
- Sevellec M, Derome N, Bernatchez L. Holobionts and ecological speciation: the intestinal microbiota of lake whitefish species pairs. Microbiome. 2018 Dec;6(1):47. https://doi.org/10.1186/s40168-018-0427-2
- Shanmugam SG, Magbanua ZV, Williams MA, Jangid K, Whitman WB, Peterson DG, Kingery WL. Bacterial diversity patterns differ in soils developing in sub-tropical and cool-temperate ecosystems. Microb Ecol. 2017 Apr;73(3):556–569. https://doi.org/10.1007/s00248-016-0884-8
- Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003 Nov 01;13(11):2498–2504. https://doi.org/10.1101/gr.1239303
- Stephens WZ, Burns AR, Stagaman K, Wong S, Rawls JF, Guillemin K, Bohannan BJM. The composition of the zebrafish intestinal microbial community varies across development. ISME J. 2016 Mar;10(3):644–654. https://doi.org/10.1038/ismej.2015.140
- Tinta T, Kogovšek T, Klun K, Malej A, Herndl GJ, Turk V. Jelly-fish-associated microbiome in the marine environment: exploring its biotechnological potential. Mar Drugs. 2019 Feb 01; 17(2):94. https://doi.org/10.3390/md17020094
- van de Water JAJM, Allemand D, Ferrier-Pagès C. Host-microbe interactions in octocoral holobionts – recent advances and perspectives. Microbiome. 2018 Dec;6(1):64. https://doi.org/10.1186/s40168-018-0431-6
- Viver T, Orellana LH, Hatt JK, Urdiain M, Díaz S, Richter M, Antón J, Avian M, Amann R, Konstantinidis KT, et al. The low diverse gastric microbiome of the jellyfish Cotylorhiza tuberculata is dominated by four novel taxa. Environ Microbiol. 2017 Aug; 19(8):3039–3058. https://doi.org/10.1111/1462-2920.13763
- Weiland-Bräuer N, Neulinger SC, Pinnow N, Künzel S, Baines JF, Schmitz RA. Composition of bacterial communities associated with Aurelia aurita changes with compartment, life stage, and population. Appl Environ Microbiol. 2015 Sep 01;81(17):6038–6052. https://doi.org/10.1128/AEM.01601-15
- White JR, Nagarajan N, Pop M. Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLOS Comput Biol. 2009 Apr 10;5(4):e1000352. https://doi.org/10.1371/journal.pcbi.1000352
- Yin M, Liu D, Xu F, Xiao L, Wang Q, Wang B, Chang Y, Zheng J, Tao X, Liu G, et al. A specific antimicrobial protein CAP-1 from Pseudomonas sp. isolated from the jellyfish Cyanea capillata. Int J Biol Macromol. 2016 Jan;82:488–496. https://doi.org/10.1016/j.ijbiomac.2015.10.056