Parasite microbiome project: Grand challenges
Autoři:
Nolwenn M. Dheilly aff001; Joaquín Martínez Martínez aff002; Karyna Rosario aff003; Paul J. Brindley aff004; Raina N. Fichorova aff006; Jonathan Z. Kaye aff007; Kevin D. Kohl aff008; Laura J. Knoll aff009; Julius Lukeš aff010; Susan L. Perkins aff011; Robert Poulin aff012; Lynn Schriml aff013; Luke R. Thompson aff014
Působiště autorů:
School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, United States of America
aff001; Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, United States of America
aff002; College of Marine Science, University of South Florida, Saint Petersburg, Florida, United States of America
aff003; Department of Microbiology, Immunology and Tropical Medicine, George Washington University, Washington, DC, United States of America
aff004; Research Center for Neglected Diseases of Poverty, School of Medicine & Health Sciences, George Washington University, Washington, DC, United States of America
aff005; 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
aff006; Gordon and Betty Moore Foundation, Palo Alto, California, United States of America
aff007; Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
aff008; Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
aff009; Institute of Parasitology, Biology Centre, Czech Academy of Sciences and Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
aff010; Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
aff011; Department of Zoology, University of Otago, Dunedin, New Zealand
aff012; Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
aff013; Department of Biological Sciences and Northern Gulf Institute, University of Southern Mississippi, Hattiesburg, Mississippi, United States of America
aff014; Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, La Jolla, California, United States of America
aff015
Vyšlo v časopise:
Parasite microbiome project: Grand challenges. PLoS Pathog 15(10): e32767. doi:10.1371/journal.ppat.1008028
Kategorie:
Opinion
doi:
https://doi.org/10.1371/journal.ppat.1008028
Zdroje
1. Weinstein SB, Kuris AM. Independent origins of parasitism in Animalia. Biol Lett. 2016;12: 20160324. doi: 10.1098/rsbl.2016.0324 27436119
2. Westwood JH, Yoder JI, Timko MP, dePamphilis CW. The evolution of parasitism in plants. Trends Plant Sci. 2010;15: 227–235. doi: 10.1016/j.tplants.2010.01.004 20153240
3. Poulin R, Morand S. The diversity of parasites. Q Rev Biol. 2000;75: 277–293. https://www.jstor.org/stable/2665190 11008700
4. Baker JR. The origins of parasitism in the protists. Int J Parasitol. 1994;24: 1131–1137. doi: 10.1016/0020-7519(94)90187-2 7729973
5. 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. doi: 10.1111/jeu.12691 30257078
6. Dybdahl MF, Jenkins CE, Nuismer SL. Identifying the molecular basis of host-parasite coevolution: merging models and mechanisms. Am Nat. 2014;184: 1–13. doi: 10.1086/676591 24921596
7. 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. doi: 10.1002/ece3.3785 29721258
8. 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. doi: 10.1098/rstb.2016.0088 28289256
9. 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. doi: 10.7554/eLife.41463 30644359
10. Yurchenko V, Lukeš J. Parasites and their (endo)symbiotic microbes. Parasitology. 2018;145: 1261–1264. doi: 10.1017/S0031182018001257 30086814
11. 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. doi: 10.1128/mSystems.00028-16 27822520
12. 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. doi: 10.1111/j.1574-6976.2008.00123.x 18549407
13. Bordenstein SR, Theis KR. Host biology in light of the microbiome: ten principles of holobionts and hologenomes. PLoS Biol. 2015;13: e1002226. doi: 10.1371/journal.pbio.1002226 26284777
14. Lukeš J, Stensvold CR, Jirků-Pomajbíková K, Wegener Parfrey L. Are human intestinal eukaryotes beneficial or commensals? PLoS Pathog. 2015;11: e1005039. doi: 10.1371/journal.ppat.1005039 26270819
15. Dheilly NM. Holobiont-holobiont interactions: redefining host-parasite interactions. PLoS Pathog. 2014;10: e1004093. doi: 10.1371/journal.ppat.1004093 24992663
16. Dheilly NM, Poulin R, Thomas F. Biological warfare: microorganisms as drivers of host-parasite interactions. Infect Genet Evol. 2015;34: 251–259. doi: 10.1016/j.meegid.2015.05.027 26026593
17. 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. doi: 10.1128/mSystems.00050-17 28761932
18. 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. doi: 10.1038/nbt.1823 https://www.nature.com/articles/nbt.1823#supplementary-information. 21552244
19. 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. doi: 10.1038/nbt.3893 https://www.nature.com/articles/nbt.3893#supplementary-information. 28787424
20. 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. doi: 10.1038/nbt.4306 https://www.nature.com/articles/nbt.4306#supplementary-information. 30556814
21. 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. doi: 10.1371/journal.pone.0048418 23144878
22. 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. doi: 10.1136/sextrans-2013-051052 23903808
23. 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. doi: 10.1038/ncomms15892 https://www.nature.com/articles/ncomms15892#supplementary-information. 28643787
24. Edwards RA, Rohwer F. Viral metagenomics. Nat Rev Microbiol. 2005;3: 504–510. doi: 10.1038/nrmicro1163 15886693
25. 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. doi: 10.1038/ismej.2017.61 28498373
26. 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. doi: 10.1111/j.0014-3820.2001.tb00633.x 11475049
27. 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. doi: 10.1038/nrmicro2540 https://www.nature.com/articles/nrmicro2540#supplementary-information. 21407244
28. 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. doi: 10.1038/nature20167 27880757
29. 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. doi: 10.1073/pnas.1522149113 26811460
30. 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. doi: 10.1128/mBio.01751-14 25516613
31. Ondov BD, Bergman NH, Phillippy AM. Interactive metagenomic visualization in a Web browser. BMC Bioinformatics. 2011;12: 385. doi: 10.1186/1471-2105-12-385 21961884
32. 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. doi: 10.1128/mSystems.00039-18 29657970
33. 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. doi: 10.1038/nmeth.3589 https://www.nature.com/articles/nmeth.3589#supplementary-information. 26418763
34. 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. doi: 10.1038/s41592-018-0176-y 30377376
35. 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. doi: 10.1038/nature24621 https://www.nature.com/articles/nature24621#supplementary-information. 29088705
36. 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. doi: 10.1038/nmeth.3869 https://www.nature.com/articles/nmeth.3869#supplementary-information. 27214047
37. 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. doi: 10.1128/mSystems.00191-16 28289731
38. 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. doi: 10.1038/nmeth.f.303 20383131
39. 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. doi: 10.1038/s41587-019-0209-9 31341288
40. 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. doi: 10.1038/s41592-018-0141-9 30275573
41. 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. doi: 10.1016/j.ympev.2008.03.024 18424089
42. 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. doi: 10.1016/j.tree.2014.08.001 25175416
43. 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. doi: 10.4056/aigs.1443528 21304728
44. Klein M, Lanka S, Muller D, Knippers R. Single-stranded regions in the genome of the Ectocarpus siliculosus virus. Virology. 1994;202: 1076–1078. doi: 10.1006/viro.1994.1443 8030215
45. Ebert D. The epidemiology and evolution of symbionts with mixed-mode transmission. Annu Rev Ecol Evol Syst. 2013;44: 623–643. doi: 10.1146/annurev-ecolsys-032513-100555
46. 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. doi: 10.1098/rstb.2014.0295 26150661
47. 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. doi: 10.1098/rstb.2010.0331 21444318
48. Thompson J. The Geographic Mosaic of Coevolution. Chicago, IL, USA: University of Chicago Press; 2005.
49. King KC, Bonsall MB. The evolutionary and coevolutionary consequences of defensive microbes for host-parasite interactions. BMC Evol Biol. 2017;17: 190. doi: 10.1186/s12862-017-1030-z 28806933
50. Ford SA, King KC. Harnessing the power of defensive microbes: evolutionary implications in nature and disease control. PLoS Pathog. 2016;12: e1005465. doi: 10.1371/journal.ppat.1005465 27058881
51. Dennis AB, Patel V, Oliver KM, Vorburger C. Parasitoid gene expression changes after adaptation to symbiont-protected hosts. Evolution. 2017;71: 2599–2617. doi: 10.1111/evo.13333 28841224
52. 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. doi: 10.1016/j.chom.2014.08.014 25211071
53. Hahn MA, Dheilly NM. Experimental models to study the role of microbes in host-parasite interactions. Front Microbiol. 2016;7: 1300. doi: 10.3389/fmicb.2016.01300 27602023
54. 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. doi: 10.1128/IAI.00009-17 28138021.
55. 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. doi: 10.7314/apjcp.2015.16.5.1751 25773821.
56. 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. doi: 10.1038/srep42744 28198451
57. 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. doi: 10.1371/journal.pone.0048418 23144878
58. Onderdonk AB, Delaney ML, Fichorova RN. The human microbiome during bacterial vaginosis. Clin microbiol rev. 2016;29(2):223–38. Epub 02/10. doi: 10.1128/CMR.00075-15 26864580.
59. 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. doi: 10.1126/science.1199326 21311023
60. 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. doi: 10.1093/infdis/jiv354 26123565
61. 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. doi: 10.1371/journal.ppat.1002351 22072969
62. Slatko BE, Taylor MJ, Foster JM. The Wolbachia endosymbiont as an anti-filarial nematode target. Symbiosis. 2010;51(1):55–65. Epub 06/05. doi: 10.1007/s13199-010-0067-1 20730111.
63. 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. doi: 10.1017/S0031182017000725 28534452
64. 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). doi: 10.1098/rspb.2014.2773 25673681
65. 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. doi: 10.1073/pnas.1717934115 29712862
66. 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. doi: 10.1093/gbe/evv108 26025560.
67. 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. doi: 10.1093/gbe/evv016 25618142.
68. 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. doi: 10.1128/AEM.67.4.1536–1541.2001
69. 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. doi: 10.1126/science.1187703 20538949
70. 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. doi: 10.1371/journal.pone.0125495 25942314
71. 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. doi: 10.1128/IAI.00141-12 22493085
72. 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. doi: 10.1126/science.aaf3229 27080105
73. 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.
74. 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. doi: 10.1371/journal.pgen.1006537 28060841
75. 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. doi: 10.1186/s40168-019-0622-9 30678738
Štítky
Hygiena a epidemiologie Infekční lékařství LaboratořČlánek vyšel v časopise
PLOS Pathogens
2019 Číslo 10
- Stillova choroba: vzácné a závažné systémové onemocnění
- Perorální antivirotika jako vysoce efektivní nástroj prevence hospitalizací kvůli COVID-19 − otázky a odpovědi pro praxi
- Diagnostický algoritmus při podezření na syndrom periodické horečky
- Jak souvisí postcovidový syndrom s poškozením mozku?
- Diagnostika virových hepatitid v kostce – zorientujte se (nejen) v sérologii
Nejčtenější v tomto čísle
- Alterations in cellular expression in EBV infected epithelial cell lines and tumors
- Correction: A specific sequence in the genome of respiratory syncytial virus regulates the generation of copy-back defective viral genomes
- Influenza virus polymerase subunits co-evolve to ensure proper levels of dimerization of the heterotrimer
- Induction of PGRN by influenza virus inhibits the antiviral immune responses through downregulation of type I interferons signaling