Bigelow Laboratory for Ocean Sciences East Boothbay Maine United States of America

College of Marine Science University of South Florida Saint Petersburg Florida United States of America

Department of Biological Sciences and Northern Gulf Institute University of Southern Mississippi Hattiesburg Mississippi United States of America

Department of Biological Sciences University of Pittsburgh Pittsburgh Pennsylvania United States of America

Department of Epidemiology and Public Health University of Maryland School of Medicine Baltimore Maryland United States of America

Department of Medical Microbiology and Immunology University of Wisconsin Madison Madison Wisconsin United States of America

Department of Microbiology Immunology and Tropical Medicine George Washington University Washington DC United States of America

Department of Zoology University of Otago Dunedin New Zealand

Genital Tract Biology Division Department of Obstetrics Gynecology and Reproductive Biology Brigham and Women's Hospital Harvard Medical School Boston Massachusetts United States of America

Gordon and Betty Moore Foundation Palo Alto California United States of America

Institute of Parasitology Biology Centre Czech Academy of Sciences and Faculty of Sciences University of South Bohemia České Budějovice Czech Republic

Ocean Chemistry and Ecosystems Division Atlantic Oceanographic and Meteorological Laboratory National Oceanic and Atmospheric Administration La Jolla California United States of America

Research Center for Neglected Diseases of Poverty School of Medicine and Health Sciences George Washington University Washington DC United States of America

Sackler Institute for Comparative Genomics American Museum of Natural History New York New York United States of America

School of Marine and Atmospheric Sciences Stony Brook University Stony Brook New York United States of America

Zobrazit více v PubMed

Weinstein SB, Kuris AM. Independent origins of parasitism in Animalia. Biol Lett. 2016;12: 20160324 10.1098/rsbl.2016.0324 PubMed DOI PMC

Westwood JH, Yoder JI, Timko MP, dePamphilis CW. The evolution of parasitism in plants. Trends Plant Sci. 2010;15: 227–235. 10.1016/j.tplants.2010.01.004 PubMed DOI

Poulin R, Morand S. The diversity of parasites. Q Rev Biol. 2000;75: 277–293. https://www.jstor.org/stable/2665190 PubMed

Baker JR. The origins of parasitism in the protists. Int J Parasitol. 1994;24: 1131–1137. 10.1016/0020-7519(94)90187-2 PubMed DOI

Adl SM, Bass D, Lane CE, Lukeš J, Schoch CL, Smirnov A, et al. Revisions to the classification, nomenclature, and diversity of eukaryotes. J Eukaryot Microbiol. 2019;66: 4–119. 10.1111/jeu.12691 PubMed DOI PMC

Dybdahl MF, Jenkins CE, Nuismer SL. Identifying the molecular basis of host-parasite coevolution: merging models and mechanisms. Am Nat. 2014;184: 1–13. 10.1086/676591 PubMed DOI

Pulgarín-R PC, Gómez JP, Robinson S, Ricklefs RE, Cadena CD. Host species, and not environment, predicts variation in blood parasite prevalence, distribution, and diversity along a humidity gradient in northern South America. Ecol Evol. 2018;8: 3800–3814. 10.1002/ece3.3785 PubMed DOI PMC

Cable J, Barber I, Boag B, Ellison AR, Morgan ER, Murray K, et al. Global change, parasite transmission and disease control: lessons from ecology. Philos Trans R Soc Lond B Biol Sci. 2017;372: 20160088 10.1098/rstb.2016.0088 PubMed DOI PMC

Arunsan P, Ittiprasert W, Smout MJ, Cochran CJ, Mann VH, Chaiyadet S, et al. Programmed knockout mutation of liver fluke granulin attenuates virulence of infection-induced hepatobiliary morbidity. Elife. 2019;8: e41463 10.7554/eLife.41463 PubMed DOI PMC

Yurchenko V, Lukeš J. Parasites and their (endo)symbiotic microbes. Parasitology. 2018;145: 1261–1264. 10.1017/S0031182018001257 PubMed DOI

Theis KR, Dheilly NM, Klassen JL, Brucker RM, Baines JF, Bosch TCG, et al. Getting the hologenome concept right: an eco-evolutionary framework for hosts and their microbiomes. mSystems. 2016; 1:e00028–16. 10.1128/mSystems.00028-16 PubMed DOI PMC

Zilber-Rosenberg I, Rosenberg E. Role of microorganisms in the evolution of animals and plants: the hologenome theory of evolution. FEMS Microb Rev. 2008;32:723–735. 10.1111/j.1574-6976.2008.00123.x PubMed DOI

Bordenstein SR, Theis KR. Host biology in light of the microbiome: ten principles of holobionts and hologenomes. PLoS Biol. 2015;13: e1002226 10.1371/journal.pbio.1002226 PubMed DOI PMC

Lukeš J, Stensvold CR, Jirků-Pomajbíková K, Wegener Parfrey L. Are human intestinal eukaryotes beneficial or commensals? PLoS Pathog. 2015;11: e1005039 10.1371/journal.ppat.1005039 PubMed DOI PMC

Dheilly NM. Holobiont-holobiont interactions: redefining host-parasite interactions. PLoS Pathog. 2014;10: e1004093 10.1371/journal.ppat.1004093 PubMed DOI PMC

Dheilly NM, Poulin R, Thomas F. Biological warfare: microorganisms as drivers of host-parasite interactions. Infect Genet Evol. 2015;34: 251–259. 10.1016/j.meegid.2015.05.027 PubMed DOI

Dheilly NM, Bolnick D, Bordenstein SR, Brindley PJ, Figueres C, Holmes EC, et al. Parasite Microbiome Project: systematic investigation of microbiome dynamics within and across parasite-host interactions. mSystems. 2017;2: e00050–17. 10.1128/mSystems.00050-17 PubMed DOI PMC

Yilmaz P, Kottmann R, Field D, Knight R, Cole JR, Amaral-Zettler L, et al. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat Biotechnol. 2011;29: 415–420. 10.1038/nbt.1823 https://www.nature.com/articles/nbt.1823#supplementary-information. PubMed DOI PMC

Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, et al. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat Biotechnol. 2017;35: 725–731. 10.1038/nbt.3893 https://www.nature.com/articles/nbt.3893#supplementary-information. PubMed DOI PMC

Roux S, Adriaenssens EM, Dutilh BE, Koonin EV, Kropinski AM, Krupovic M, et al. Minimum Information about an Uncultivated Virus Genome (MIUViG). Nat Biotechnol. 2018;37: 29–37. 10.1038/nbt.4306 https://www.nature.com/articles/nbt.4306#supplementary-information. PubMed DOI PMC

Fichorova RN, Lee Y, Yamamoto HS, Takagi Y, Hayes GR, Goodman RP, et al. Endobiont viruses sensed by the human host—beyond conventional antiparasitic therapy. PLoS ONE. 2012;7: e48418 10.1371/journal.pone.0048418 PubMed DOI PMC

Fichorova RN, Buck OR, Yamamoto HS, Fashemi T, Dawood HY, Fashemi B, et al. The villain team-up or how Trichomonas vaginalis and bacterial vaginosis alter innate immunity in concert. Sex Transm Infect. 2013;89: 460–466. 10.1136/sextrans-2013-051052 PubMed DOI PMC

Martinez-Hernandez F, Fornas O, Lluesma Gomez M, Bolduc B, de la Cruz Peña MJ, Martínez Martínez J, et al. Single-virus genomics reveals hidden cosmopolitan and abundant viruses. Nat Commun. 2017;8: 15892 10.1038/ncomms15892 https://www.nature.com/articles/ncomms15892#supplementary-information. PubMed DOI PMC

Edwards RA, Rohwer F. Viral metagenomics. Nat Rev Microbiol. 2005;3: 504–510. 10.1038/nrmicro1163 PubMed DOI

Wilson WH, Gilg IC, Moniruzzaman M, Field EK, Koren S, LeCleir GR, et al. Genomic exploration of individual giant ocean viruses. ISME J. 2017;11: 1736–1745. 10.1038/ismej.2017.61 PubMed DOI PMC

Carius HJ, Little TJ, Ebert D. Genetic variation in a host-parasite association: potential for coevolution and frequency-dependent selection. Evolution. 2001;55: 1136–1145. 10.1111/j.0014-3820.2001.tb00633.x PubMed DOI

Spor A, Koren O, Ley R. Unravelling the effects of the environment and host genotype on the gut microbiome. Nat Rev Microbiol. 2011;9: 279–290. 10.1038/nrmicro2540 https://www.nature.com/articles/nrmicro2540#supplementary-information. PubMed DOI

Shi M, Lin X-D, Tian J-H, Chen L-J, Chen X, Li C-X, et al. Redefining the invertebrate RNA virosphere. Nature. 2016;540: 539–543. 10.1038/nature20167 PubMed DOI

Welch MJL, Rossetti BJ, Rieken CW, Dewhirst FE, Borisy GG. Biogeography of a human oral microbiome at the micron scale. Proc Natl Acad Sci. 2016;113: E791–E800. 10.1073/pnas.1522149113 PubMed DOI PMC

Jemielita M, Taormina MJ, Burns AR, Hampton JS, Rolig AS, Guillemin K, et al. Spatial and temporal features of the growth of a bacterial species colonizing the zebrafish gut. MBio. 2014;5: e01751–14. 10.1128/mBio.01751-14 PubMed DOI PMC

Ondov BD, Bergman NH, Phillippy AM. Interactive metagenomic visualization in a Web browser. BMC Bioinformatics. 2011;12: 385 10.1186/1471-2105-12-385 PubMed DOI PMC

Rodriguez-R LM, Gunturu S, Tiedje JM, Cole JR, Konstantinidis KT. Nonpareil 3: fast estimation of metagenomic coverage and sequence diversity. mSystems. 2018;3: e00039–18. 10.1128/mSystems.00039-18 PubMed DOI PMC

Truong DT, Franzosa EA, Tickle TL, Scholz M, Weingart G, Pasolli E, et al. MetaPhlAn2 for enhanced metagenomic taxonomic profiling. Nat Methods. 2015;12: 902–903. 10.1038/nmeth.3589 https://www.nature.com/articles/nmeth.3589#supplementary-information. PubMed DOI

Franzosa EA, McIver LJ, Rahnavard G, Thompson LR, Schirmer M, Weingart G, et al. Species-level functional profiling of metagenomes and metatranscriptomes. Nat Methods. 2018;15: 962–968. 10.1038/s41592-018-0176-y PubMed DOI PMC

Thompson LR, Sanders JG, McDonald D, Amir A, Ladau J, Locey KJ, et al. A communal catalogue reveals Earth’s multiscale microbial diversity. Nature. 2017;551: 457–463. 10.1038/nature24621 https://www.nature.com/articles/nature24621#supplementary-information. PubMed DOI PMC

Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13: 581–583. 10.1038/nmeth.3869 https://www.nature.com/articles/nmeth.3869#supplementary-information. PubMed DOI PMC

Amir A, McDonald D, Navas-Molina JA, Kopylova E, Morton JT, Zech Xu Z, et al. Deblur rapidly resolves single-nucleotide community sequence patterns. mSystems. 2017;2: e00191–16. 10.1128/mSystems.00191-16 PubMed DOI PMC

Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7: 335–336. 10.1038/nmeth.f.303 PubMed DOI PMC

Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnol. 2019. 10.1038/s41587-019-0209-9 PubMed DOI PMC

Gonzalez A, Navas-Molina JA, Kosciolek T, McDonald D, Vázquez-Baeza Y, Ackermann G, et al. Qiita: rapid, web-enabled microbiome meta-analysis. Nat Methods. 2018;15: 7968 10.1038/s41592-018-0141-9 PubMed DOI PMC

Pleijel F, Jondelius U, Norlinder E, Nygren A, Oxelman B, Schander C, et al. Phylogenies without roots? A plea for the use of vouchers in molecular phylogenetic studies. Mol Phylogenet Evol. 2008;48: 369–371. 10.1016/j.ympev.2008.03.024 PubMed DOI

Cristescu ME. From barcoding single individuals to metabarcoding biological communities: towards an integrative approach to the study of global biodiversity. Trends Ecol Evol. 2014;29: 566–571. 10.1016/j.tree.2014.08.001 PubMed DOI

Gilbert JA, Meyer F, Jansson J, Gordon J, Pace N, Tiedje J, et al. The Earth Microbiome Project: meeting report of the “1 EMP meeting on sample selection and acquisition” at Argonne National Laboratory October 6 2010. Stand Genomic Sci. 2010;3: 249–253. 10.4056/aigs.1443528 PubMed DOI PMC

Klein M, Lanka S, Muller D, Knippers R. Single-stranded regions in the genome of the Ectocarpus siliculosus virus. Virology. 1994;202: 1076–1078. 10.1006/viro.1994.1443 PubMed DOI

Ebert D. The epidemiology and evolution of symbionts with mixed-mode transmission. Annu Rev Ecol Evol Syst. 2013;44: 623–643. 10.1146/annurev-ecolsys-032513-100555 DOI

Kreisinger J, Bastien Gr, Hauffe HC, Marchesi J, Perkins SE. Interactions between multiple helminths and the gut microbiota in wild rodents. Philos Trans R Soc Lond B Biol Sci. 2015;370: 20140295 10.1098/rstb.2014.0295 PubMed DOI PMC

Hersch-Green EI, Turley NE, Johnson MTJ. Community genetics: what have we accomplished and where should we be going? Philos Trans R Soc Lond B Biol Sci. 2011;366: 1453–1460. 10.1098/rstb.2010.0331 PubMed DOI PMC

Thompson J. The Geographic Mosaic of Coevolution. Chicago, IL, USA: University of Chicago Press; 2005.

King KC, Bonsall MB. The evolutionary and coevolutionary consequences of defensive microbes for host-parasite interactions. BMC Evol Biol. 2017;17: 190 10.1186/s12862-017-1030-z PubMed DOI PMC

Ford SA, King KC. Harnessing the power of defensive microbes: evolutionary implications in nature and disease control. PLoS Pathog. 2016;12: e1005465 10.1371/journal.ppat.1005465 PubMed DOI PMC

Dennis AB, Patel V, Oliver KM, Vorburger C. Parasitoid gene expression changes after adaptation to symbiont-protected hosts. Evolution. 2017;71: 2599–2617. 10.1111/evo.13333 PubMed DOI

The Integrative Human Microbiome Project. Dynamic analysis of microbiome-host omics profiles during periods of human health and disease. Cell Host Microbe. 2014;16: 276–289. 10.1016/j.chom.2014.08.014 PubMed DOI PMC

Hahn MA, Dheilly NM. Experimental models to study the role of microbes in host-parasite interactions. Front Microbiol. 2016;7: 1300 10.3389/fmicb.2016.01300 PubMed DOI PMC

Dangtakot R, Pinlaor S, Itthitaetrakool U, Chaidee A, Chomvarin C, Sangka A, et al. Coinfection with Helicobacter pylori and Opisthorchis viverrini enhances the severity of hepatobiliary abnormalities in hamsters. Infect Immun. 2017;85(4):e00009–17. 10.1128/IAI.00009-17 . PubMed DOI PMC

Deenonpoe R, Chomvarin C, Pairojkul C, Chamgramol Y, Loukas A, Brindley PJ, et al. The carcinogenic liver fluke Opisthorchis viverrini is a reservoir for species of Helicobacter. APJCP. 2015;16(5):1751–8. 10.7314/apjcp.2015.16.5.1751 . PubMed DOI PMC

Deenonpoe R, Mairiang E, Mairiang P, Pairojkul C, Chamgramol Y, Rinaldi G, et al. Elevated prevalence of Helicobacter species and virulence factors in opisthorchiasis and associated hepatobiliary disease. Sci Rep. 2017;7:42744 10.1038/srep42744 PubMed DOI PMC

Fichorova RN, Lee Y, Yamamoto HS, Takagi Y, Hayes GR, Goodman RP, et al. Endobiont viruses sensed by the human host‚ beyond conventional antiparasitic therapy. PLoS ONE. 2012;7(11):e48418 10.1371/journal.pone.0048418 PubMed DOI PMC

Onderdonk AB, Delaney ML, Fichorova RN. The human microbiome during bacterial vaginosis. Clin microbiol rev. 2016;29(2):223–38. Epub 02/10. 10.1128/CMR.00075-15 . PubMed DOI PMC

Ives A, Ronet C, Prevel F, Ruzzante G, Fuertes-Marraco S, Schutz F, et al. Leishmania RNA virus controls the severity of mucocutaneous Leishmaniasis. Science. 2011;331(6018):775–8. 10.1126/science.1199326 PubMed DOI PMC

Adaui V, Lye L-F, Akopyants NS, Zimic M, Llanos-Cuentas A, Garcia L, et al. Association of the endobiont double-stranded RNA virus LRV1 with treatment failure for human Leishmaniasis caused by Leishmania braziliensis in Peru and Bolivia. J Infect Dis. 2015;213(1):112–21. 10.1093/infdis/jiv354 PubMed DOI PMC

Landmann F, Voronin D, Sullivan W, Taylor MJ. Anti-filarial activity of antibiotic therapy is due to extensive apoptosis after Wolbachia depletion from filarial nematodes. PLoS Pathog. 2011;7(11):e1002351 10.1371/journal.ppat.1002351 PubMed DOI PMC

Slatko BE, Taylor MJ, Foster JM. The Wolbachia endosymbiont as an anti-filarial nematode target. Symbiosis. 2010;51(1):55–65. Epub 06/05. 10.1007/s13199-010-0067-1 . PubMed DOI PMC

Gauthier J, Drezen J-M, Herniou EA. The recurrent domestication of viruses: major evolutionary transitions in parasitic wasps. Parasitol. 2017;145(6):713–23. Epub 05/23. 10.1017/S0031182017000725 PubMed DOI

Dheilly NM, Maure F, Ravallec M, Galinier R, Doyon J, Duval D, et al. Who is the puppet master? Replication of a parasitic wasp-associated virus correlates with host behaviour manipulation. Proc Roy Soc B Biol Sci. 2015;282(1803). 10.1098/rspb.2014.2773 PubMed DOI PMC

Tan C-W, Peiffer M, Hoover K, Rosa C, Acevedo FE, Felton GW. Symbiotic polydnavirus of a parasite manipulates caterpillar and plant immunity. Proc Nat Acad Sci. 2018;115(20):5199 10.1073/pnas.1717934115 PubMed DOI PMC

Gottlieb Y, Lalzar I, Klasson L. Distinctive Genome Reduction Rates Revealed by Genomic analyses of two Coxiella-like endosymbionts in ticks. Genome Biol Evol. 2015;7(6):1779–96. 10.1093/gbe/evv108 . PubMed DOI PMC

Smith TA, Driscoll T, Gillespie JJ, Raghavan R. A Coxiella-like endosymbiont is a potential vitamin source for the Lone Star tick. Genome Biol Evol. 2015;7(3):831–8. 10.1093/gbe/evv016 . PubMed DOI PMC

Banin E, Khare SK, Naider F, Rosenberg E. Proline-rich peptide from the coral pathogen Vibrio shiloi that inhibits photosynthesis of zooxanthellae. App Env Microbiol. 2001;67(4):1536 10.1128/AEM.67.4.1536-1541.2001 PubMed DOI PMC

Hayes KS, Bancroft AJ, Goldrick M, Portsmouth C, Roberts IS, Grencis RK. Exploitation of the intestinal microflora by the parasitic nematode Trichuris muris. Science. 2010;328(5984):1391 10.1126/science.1187703 PubMed DOI PMC

Holm JB, Sorobetea D, Kiilerich P, Ramayo-Caldas Y, Estellé J, Ma T, et al. Chronic Trichuris muris infection decreases diversity of the intestinal microbiota and concomitantly increases the abundance of Lactobacilli. PLoS ONE. 2015;10(5):e0125495 10.1371/journal.pone.0125495 PubMed DOI PMC

Li RW, Wu S, Li W, Navarro K, Couch RD, Hill D, et al. Alterations in the porcine colon microbiota induced by the gastrointestinal nematode Trichuris suis. Infection and Immunity. 2012;80(6):2150 10.1128/IAI.00141-12 PubMed DOI PMC

Ramanan D, Bowcutt R, Lee SC, Tang MS, Kurtz ZD, Ding Y, et al. Helminth infection promotes colonization resistance via type 2 immunity. Science. 2016;352(6285):608 10.1126/science.aaf3229 PubMed DOI PMC

Vaughan JA, Tkach VV, Greiman SE. Chapter 3—Neorickettsial endosymbionts of the digenea: diversity, transmission and distribution In: Rollinson D, Hay SI, editors. Adv Parasitol. 79: Academic Press; 2012. p. 253–97. PubMed

McNulty SN, Tort JF, Rinaldi G, Fischer K, Rosa BA, Smircich P, et al. Genomes of Fasciola hepatica from the Americas reveal colonization with Neorickettsia endobacteria related to the agents of potomac horse and human sennetsu fevers. PLoS Genet. 2017;13(1):e1006537 10.1371/journal.pgen.1006537 PubMed DOI PMC

Gaulke CA, Martins ML, Watral VG, Humphreys IR, Spagnoli ST, Kent ML, et al. A longitudinal assessment of host-microbe-parasite interactions resolves the zebrafish gut microbiome’s link to Pseudocapillaria tomentosa infection and pathology. Microbiome. 2019;7(1):10 10.1186/s40168-019-0622-9 PubMed DOI PMC

Molecular Cellular Parasitology: The Decades and Challenges Ahead

MIxS-SA: a MIxS extension defining the minimum information standard for sequence data from symbiont-associated micro-organisms