{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,28]],"date-time":"2026-04-28T03:58:20Z","timestamp":1777348700609,"version":"3.51.4"},"publisher-location":"Cham","reference-count":37,"publisher":"Springer International Publishing","isbn-type":[{"value":"9783319444840","type":"print"},{"value":"9783319444857","type":"electronic"}],"license":[{"start":{"date-parts":[[2016,1,1]],"date-time":"2016-01-01T00:00:00Z","timestamp":1451606400000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016]]},"DOI":"10.1007\/5584_2016_25","type":"book-chapter","created":{"date-parts":[[2016,6,16]],"date-time":"2016-06-16T13:02:55Z","timestamp":1466082175000},"page":"89-98","source":"Crossref","is-referenced-by-count":31,"title":["Metagenomic Analysis of Cerebrospinal Fluid from Patients with Multiple Sclerosis"],"prefix":"10.1007","author":[{"given":"Karol","family":"Perlejewski","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Iwona","family":"Bukowska-O\u015bko","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shota","family":"Nakamura","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daisuke","family":"Motooka","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tomasz","family":"Stokowy","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rafa\u0142","family":"P\u0142oski","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ma\u0142gorzata","family":"Rydzanicz","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Beata","family":"Zakrzewska-Pniewska","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aleksandra","family":"Podlecka-Pi\u0119towska","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Monika","family":"Nojszewska","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anna","family":"Gogol","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kamila","family":"Caraballo Cort\u00e9s","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Urszula","family":"Demkow","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Adam","family":"St\u0119pie\u0144","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tomasz","family":"Laskus","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marek","family":"Radkowski","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2016,6,17]]},"reference":[{"issue":"6","key":"25_CR1","doi-asserted-by":"crossref","first-page":"504","DOI":"10.1002\/ana.21141","volume":"61","author":"A Ascherio","year":"2007","unstructured":"Ascherio A, Munger KL (2007) Environmental risk factors for multiple sclerosis. Part II: Noninfectious factors. Ann Neurol 61(6):504\u2013513","journal-title":"Ann Neurol"},{"issue":"9","key":"25_CR2","doi-asserted-by":"crossref","first-page":"1139","DOI":"10.1007\/s10096-010-0979-y","volume":"29","author":"J Benito-Leon","year":"2010","unstructured":"Benito-Leon J, Pisa D, Alonso R, Calleja P, Diaz-Sanchez M, Carrasco L (2010) Association between multiple sclerosis and Candida species: evidence from a case-control study. Eur J Clin Microbiol Infect Dis 29(9):1139\u20131145","journal-title":"Eur J Clin Microbiol Infect Dis"},{"issue":"2","key":"25_CR3","doi-asserted-by":"publisher","first-page":"e32160","DOI":"10.1371\/journal.pone.0032160","volume":"7","author":"SS Borkosky","year":"2012","unstructured":"Borkosky SS, Whitley C, Kopp-Schneider A, zur Hausen H, de Villiers EM (2012) Epstein-Barr virus stimulates torque teno virus replication: a possible relationship to multiple sclerosis. PLoS ONE 7(2):e32160. doi: 10.1371\/journal.pone.0032160","journal-title":"PLoS ONE"},{"issue":"1","key":"25_CR4","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1002\/ana.22057","volume":"68","author":"M Brahic","year":"2010","unstructured":"Brahic M (2010) Multiple sclerosis and viruses. Ann Neurol 68(1):6\u20138","journal-title":"Ann Neurol"},{"issue":"5","key":"25_CR5","doi-asserted-by":"crossref","first-page":"729","DOI":"10.1097\/JIM.0000000000000192","volume":"63","author":"BL Cantarel","year":"2015","unstructured":"Cantarel BL, Waubant E, Chehoud C, Kuczynski J, DeSantis TZ, Warrington J, Venkatesan A, Fraser CM, Mowry EM (2015) Gut microbiota in multiple sclerosis: possible influence of immunomodulators. J Investig Med 63(5):729\u2013734","journal-title":"J Investig Med"},{"key":"25_CR6","first-page":"532","volume":"15","author":"P Chomczynski","year":"1993","unstructured":"Chomczynski P (1993) A reagent for the single-step simultaneous isolation of RNA, DNA and proteins from cell and tissue samples. BioTechniques 15:532\u2013537","journal-title":"BioTechniques"},{"key":"25_CR7","unstructured":"FASTX-Toolkit (2016) FASTQ\/A short-reads pre-processing tools. http:\/\/hannonlab.cshl.edu\/fastx_toolkit\/index.html . Accessed on 11 April 2016"},{"issue":"20","key":"25_CR8","doi-asserted-by":"crossref","first-page":"2617","DOI":"10.1093\/bioinformatics\/btq475","volume":"26","author":"N Goto","year":"2010","unstructured":"Goto N, Prins P, Nakao M, Bonnal R, Aerts J, Katayama T (2010) BioRuby: bioinformatics software for the Ruby programming language. Bioinformatics 26(20):2617\u20132619","journal-title":"Bioinformatics"},{"issue":"10","key":"25_CR9","doi-asserted-by":"publisher","first-page":"562","DOI":"10.1007\/s11882-015-0562-9","volume":"15","author":"JJ Hansen","year":"2015","unstructured":"Hansen JJ (2015) Immune responses to intestinal microbes in inflammatory bowel diseases. Curr Allergy Asthma Rep 15(10):562. doi: 10.1007\/s11882-015-0562-9","journal-title":"Curr Allergy Asthma Rep"},{"issue":"6","key":"25_CR10","doi-asserted-by":"crossref","first-page":"1181","DOI":"10.1128\/CDLI.8.6.1181-1188.2001","volume":"8","author":"LE Hughes","year":"2001","unstructured":"Hughes LE, Bonell S, Natt RS, Wilson C, Tiwana H, Ebringer A, Cunningham P, Chamoun V, Thompson EJ, Croker J, Vowles J (2001) Antibody responses to Acinetobacter spp. and Pseudomonas aeruginosa in multiple sclerosis: prospects for diagnosis using the myelin-acinetobacter-neurofilament antibody index. Clin Diagn Lab Immunol 8(6):1181\u20131188","journal-title":"Clin Diagn Lab Immunol"},{"issue":"12","key":"25_CR11","doi-asserted-by":"crossref","first-page":"1553","DOI":"10.1177\/1352458514541579","volume":"20","author":"J Joscelyn","year":"2014","unstructured":"Joscelyn J, Kasper LH (2014) Digesting the emerging role for the gut microbiome in central nervous system demyelination. Mult Scler 20(12):1553\u20131559","journal-title":"Mult Scler"},{"issue":"2","key":"25_CR12","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1016\/j.bbadis.2010.06.012","volume":"1812","author":"K Kakalacheva","year":"2011","unstructured":"Kakalacheva K, Munz C, Lunemann JD (2011) Viral triggers of multiple sclerosis. Biochim Biophys Acta 1812(2):132\u2013140","journal-title":"Biochim Biophys Acta"},{"issue":"1","key":"25_CR13","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1191\/135245801676514804","volume":"7","author":"D Krametter","year":"2001","unstructured":"Krametter D, Niederwieser G, Berghold A, Birnbaum G, Strasser-Fuchs S, Hartung HP, Archelos JJ (2001) Chlamydia pneumoniae in multiple sclerosis: humoral immune responses in serum and cerebrospinal fluid and correlation with disease activity marker. Mult Scler 7(1):13\u201318","journal-title":"Mult Scler"},{"issue":"5","key":"25_CR14","doi-asserted-by":"publisher","first-page":"e97876","DOI":"10.1371\/journal.pone.0097876","volume":"9","author":"M Laurence","year":"2014","unstructured":"Laurence M, Hatzis C, Brash DE (2014) Common contaminants in next-generation sequencing that hinder discovery of low-abundance microbes. PLoS ONE 9(5):e97876. doi: 10.1371\/journal.pone.0097876","journal-title":"PLoS ONE"},{"issue":"6","key":"25_CR15","doi-asserted-by":"crossref","first-page":"936","DOI":"10.1101\/gr.111120.110","volume":"21","author":"G Lunter","year":"2011","unstructured":"Lunter G, Goodson M (2011) Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. Genome Res 21(6):936\u2013939","journal-title":"Genome Res"},{"issue":"2","key":"25_CR16","doi-asserted-by":"crossref","first-page":"192","DOI":"10.1002\/jmv.20777","volume":"79","author":"R Mancuso","year":"2007","unstructured":"Mancuso R, Delbue S, Borghi E, Pagani E, Calvo MG, Caputo D, Granieri E, Ferrante P (2007) Increased prevalence of varicella zoster virus DNA in cerebrospinal fluid from patients with multiple sclerosis. J Med Virol 79(2):192\u2013199","journal-title":"J Med Virol"},{"issue":"12","key":"25_CR17","doi-asserted-by":"crossref","first-page":"709","DOI":"10.1016\/S1474-4422(04)00933-0","volume":"3","author":"RA Marrie","year":"2004","unstructured":"Marrie RA (2004) Environmental risk factors in multiple sclerosis aetiology. Lancet Neurol 3(12):709\u2013718","journal-title":"Lancet Neurol"},{"key":"25_CR18","doi-asserted-by":"crossref","unstructured":"Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. 17(1); doi: 10.14806\/ej.17.1.200","DOI":"10.14806\/ej.17.1.200"},{"issue":"9","key":"25_CR19","doi-asserted-by":"publisher","first-page":"81","DOI":"10.1186\/gm485","volume":"5","author":"RR Miller","year":"2013","unstructured":"Miller RR, Montoya V, Gardy JL, Patrick DM, Tang P (2013) Metagenomics for pathogen detection in public health. Genome Med 5(9):81. doi: 10.1186\/gm485","journal-title":"Genome Med"},{"issue":"9","key":"25_CR20","doi-asserted-by":"publisher","first-page":"e0137429","DOI":"10.1371\/journal.pone.0137429","volume":"10","author":"S Miyake","year":"2015","unstructured":"Miyake S, Kim S, Suda W, Oshima K, Nakamura M, Matsuoka T, Chihara N, Tomita A, Sato W, Kim SW, Morita H, Hattori M, Yamamura T (2015) Dysbiosis in the gut microbiota of patients with multiple sclerosis, with a striking depletion of species belonging to Clostridia XIVa and IV clusters. PLoS ONE 10(9):e0137429. doi: 10.1371\/journal.pone.0137429","journal-title":"PLoS ONE"},{"issue":"4","key":"25_CR21","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1001\/archneur.1974.00490340013002","volume":"30","author":"E Norrby","year":"1974","unstructured":"Norrby E, Link H, Olsson JE (1974) Measles virus antibodies in multiple sclerosis. Comparison of antibody titers in cerebrospinal fluid and serum. Arch Neurol 30(4):285\u2013292","journal-title":"Arch Neurol"},{"issue":"9","key":"25_CR22","doi-asserted-by":"crossref","first-page":"11718","DOI":"10.3390\/ijms130911718","volume":"13","author":"C O\u2019Gorman","year":"2012","unstructured":"O\u2019Gorman C, Lucas R, Taylor B (2012) Environmental risk factors for multiple sclerosis: a review with a focus on molecular mechanisms. Int J Mol Sci 13(9):11718\u201311752","journal-title":"Int J Mol Sci"},{"issue":"4","key":"25_CR23","doi-asserted-by":"crossref","first-page":"529","DOI":"10.1001\/archneur.61.4.529","volume":"61","author":"G Ordonez","year":"2004","unstructured":"Ordonez G, Pineda B, Garcia-Navarrete R, Sotelo J (2004) Brief presence of varicella-zoster vral DNA in mononuclear cells during relapses of multiple sclerosis. Arch Neurol 61(4):529\u2013532","journal-title":"Arch Neurol"},{"issue":"3","key":"25_CR24","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1016\/j.mimet.2013.10.006","volume":"95","author":"R Padmanabhan","year":"2013","unstructured":"Padmanabhan R, Mishra AK, Raoult D, Fournier PE (2013) Genomics and metagenomics in medical microbiology. J Microbiol Methods 95(3):415\u2013424","journal-title":"J Microbiol Methods"},{"issue":"10","key":"25_CR25","doi-asserted-by":"publisher","first-page":"e27","DOI":"10.1038\/cti.2014.25","volume":"3","author":"MP Pender","year":"2014","unstructured":"Pender MP, Burrows SR (2014) Epstein-Barr virus and multiple sclerosis: potential opportunities for immunotherapy. Clin Transl Immunol 3(10):e27. doi: 10.1038\/cti.2014.25","journal-title":"Clin Transl Immunol"},{"key":"25_CR26","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.jviromet.2015.09.010","volume":"226","author":"K Perlejewski","year":"2015","unstructured":"Perlejewski K, Popiel M, Laskus T, Nakamura S, Motooka D, Stokowy T, Lipowski D, Pollak A, Lechowicz U, Caraballo Cort\u00e9s K, St\u0119pie\u0144 A, Radkowski M, Bukowska-Osko I (2015) Next-generation sequencing (NGS) in the identification of encephalitis-causing viruses: unexpected detection of human herpesvirus 1 while searching for RNA pathogens. J Virol Methods 226:1\u20136","journal-title":"J Virol Methods"},{"issue":"2","key":"25_CR27","doi-asserted-by":"crossref","first-page":"292","DOI":"10.1002\/ana.22366","volume":"69","author":"CH Polman","year":"2011","unstructured":"Polman CH, Reingold SC, Banwell B, Clanet M, Cohen JA, Filippi M, Fujihara K, Havrdova E, Hutchinson M, Kappos L, Lublin FD, Montalban X, O\u2019Connor P, Sandberg-Wollheim M, Thompson AJ, Waubant E, Weinshenker B, Wolinsky JS (2011) Diagnostic criteria for multiple sclerosis: 2010 revisions to the McDonald criteria. Ann Neurol 69(2):292\u2013302","journal-title":"Ann Neurol"},{"issue":"5","key":"25_CR28","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1038\/nri2515","volume":"9","author":"JL Round","year":"2009","unstructured":"Round JL, Mazmanian SK (2009) The gut microbiota shapes intestinal immune responses during health and disease. Nat Rev Immunol 9(5):313\u2013323","journal-title":"Nat Rev Immunol"},{"key":"25_CR29","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1186\/s12915-014-0087-z","volume":"12","author":"SJ Salter","year":"2014","unstructured":"Salter SJ, Cox MJ, Turek EM, Calus ST, Cookson WO, Moffatt MF, Turner P, Parkhill J, Loman NJ, Walker AW (2014) Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol 12:87. doi: 10.1186\/s12915-014-0087-z","journal-title":"BMC Biol"},{"issue":"2","key":"25_CR30","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1001\/archneur.1996.00550020029012","volume":"53","author":"VJ Sanders","year":"1996","unstructured":"Sanders VJ, Waddell AE, Felisan SL, Li X, Conrad AJ, Tourtellotte WW (1996) Herpes simplex virus in postmortem multiple sclerosis brain tissue. Arch Neurol 53(2):125\u2013133","journal-title":"Arch Neurol"},{"issue":"5","key":"25_CR31","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1111\/j.1472-765X.2008.02444.x","volume":"47","author":"RD Sleator","year":"2008","unstructured":"Sleator RD, Shortall C, Hill C (2008) Metagenomics. Lett Appl Microbiol 47(5):361\u2013366","journal-title":"Lett Appl Microbiol"},{"issue":"3","key":"25_CR32","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1002\/ana.21316","volume":"63","author":"J Sotelo","year":"2008","unstructured":"Sotelo J, Martinez-Palomo A, Ordonez G, Pineda B (2008) Varicella-zoster virus in cerebrospinal fluid at relapses of multiple sclerosis. Ann Neurol 63(3):303\u2013311","journal-title":"Ann Neurol"},{"key":"25_CR33","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1016\/j.clineuro.2013.12.020","volume":"119","author":"J Sotelo","year":"2014","unstructured":"Sotelo J, Ordonez G, Pineda B, Flores J (2014) The participation of varicella zoster virus in relapses of multiple sclerosis. Clin Neurol Neurosurg 119:44\u201348","journal-title":"Clin Neurol Neurosurg"},{"issue":"1\u20132","key":"25_CR34","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/S0165-5728(02)00465-4","volume":"136","author":"RH Swanborg","year":"2003","unstructured":"Swanborg RH, Whittum-Hudson JA, Hudson AP (2003) Infectious agents and multiple sclerosis\u2013are Chlamydia pneumoniae and human herpes virus 6 involved? J Neuroimmunol 136(1\u20132):1\u20138","journal-title":"J Neuroimmunol"},{"issue":"12","key":"25_CR35","doi-asserted-by":"publisher","first-page":"564","DOI":"10.1186\/s13059-014-0564-2","volume":"15","author":"S Weiss","year":"2014","unstructured":"Weiss S, Amir A, Hyde ER, Metcalf JL, Song SJ, Knight R (2014) Tracking down the sources of experimental contamination in microbiome studies. Genome Biol 15(12):564. doi: 10.1186\/s13059-014-0564-2","journal-title":"Genome Biol"},{"key":"25_CR36","doi-asserted-by":"crossref","first-page":"758","DOI":"10.5604\/17322693.1015041","volume":"66","author":"M Zawada","year":"2012","unstructured":"Zawada M (2012) Potential pathogens in multiple sclerosis (MS). Postepy Hig Med Dosw (Online) 66:758\u2013770","journal-title":"Postepy Hig Med Dosw (Online)"},{"issue":"3","key":"25_CR37","doi-asserted-by":"crossref","first-page":"262","DOI":"10.1179\/016164106X98134","volume":"28","author":"R Zivadinov","year":"2006","unstructured":"Zivadinov R, Nasuelli D, Tommasi MA, Serafin M, Bratina A, Ukmar M, Pirko I, Johnson AJ, Furlan C, Pozzi-Mucelli RS, Monti-Bragadin L, Grop A, Zambon M, Antonello RM, Cazzato G, Zorzon M (2006) Positivity of cytomegalovirus antibodies predicts a better clinical and radiological outcome in multiple sclerosis patients. Neurol Res 28(3):262\u2013269","journal-title":"Neurol Res"}],"container-title":["Advances in Experimental Medicine and Biology","Pulmonary Infection and Inflammation"],"original-title":[],"link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/5584_2016_25","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,9,22]],"date-time":"2020-09-22T10:38:04Z","timestamp":1600771084000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/5584_2016_25"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016]]},"ISBN":["9783319444840","9783319444857"],"references-count":37,"URL":"https:\/\/doi.org\/10.1007\/5584_2016_25","relation":{},"ISSN":["0065-2598","2214-8019"],"issn-type":[{"value":"0065-2598","type":"print"},{"value":"2214-8019","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016]]}}}