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Items: 41

1.

Impact of commonly used drugs on the composition and metabolic function of the gut microbiota.

Vich Vila A, Collij V, Sanna S, Sinha T, Imhann F, Bourgonje AR, Mujagic Z, Jonkers DMAE, Masclee AAM, Fu J, Kurilshikov A, Wijmenga C, Zhernakova A, Weersma RK.

Nat Commun. 2020 Jan 17;11(1):362. doi: 10.1038/s41467-019-14177-z.

PMID:
31953381
2.

Relationship between gut microbiota and circulating metabolites in population-based cohorts.

Vojinovic D, Radjabzadeh D, Kurilshikov A, Amin N, Wijmenga C, Franke L, Ikram MA, Uitterlinden AG, Zhernakova A, Fu J, Kraaij R, van Duijn CM.

Nat Commun. 2019 Dec 20;10(1):5813. doi: 10.1038/s41467-019-13721-1.

3.

Studying the gut virome in the metagenomic era: challenges and perspectives.

Garmaeva S, Sinha T, Kurilshikov A, Fu J, Wijmenga C, Zhernakova A.

BMC Biol. 2019 Oct 28;17(1):84. doi: 10.1186/s12915-019-0704-y. Review.

4.

Intestinal microbiome composition and its relation to joint pain and inflammation.

Boer CG, Radjabzadeh D, Medina-Gomez C, Garmaeva S, Schiphof D, Arp P, Koet T, Kurilshikov A, Fu J, Ikram MA, Bierma-Zeinstra S, Uitterlinden AG, Kraaij R, Zhernakova A, van Meurs JBJ.

Nat Commun. 2019 Oct 25;10(1):4881. doi: 10.1038/s41467-019-12873-4.

5.

Immunochip meta-analysis in European and Argentinian populations identifies two novel genetic loci associated with celiac disease.

Ricaño-Ponce I, Gutierrez-Achury J, Costa AF, Deelen P, Kurilshikov A, Zorro MM, Platteel M, van der Graaf A; Consortium for the study of genetic associations of celiac disease in Latin-America, Sanna S, Daffra O, Zhernakova A, Fu J, Trynka G, Smecuol E, Niveloni SI, Bai JC, Kumar V, Wijmenga C.

Eur J Hum Genet. 2019 Oct 7. doi: 10.1038/s41431-019-0520-4. [Epub ahead of print]

PMID:
31591516
6.

A novel thermophilic Aeribacillus bacteriophage AP45 isolated from the Valley of Geysers, Kamchatka: genome analysis suggests the existence of a new genus within the Siphoviridae family.

Morozova V, Bokovaya O, Kozlova Y, Kurilshikov A, Babkin I, Tupikin A, Bondar A, Ryabchikova E, Brayanskaya A, Peltek S, Tikunova N.

Extremophiles. 2019 Sep;23(5):599-612. doi: 10.1007/s00792-019-01119-2. Epub 2019 Aug 2.

PMID:
31376001
7.

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage.

Edwards RA, Vega AA, Norman HM, Ohaeri M, Levi K, Dinsdale EA, Cinek O, Aziz RK, McNair K, Barr JJ, Bibby K, Brouns SJJ, Cazares A, de Jonge PA, Desnues C, Díaz Muñoz SL, Fineran PC, Kurilshikov A, Lavigne R, Mazankova K, McCarthy DT, Nobrega FL, Reyes Muñoz A, Tapia G, Trefault N, Tyakht AV, Vinuesa P, Wagemans J, Zhernakova A, Aarestrup FM, Ahmadov G, Alassaf A, Anton J, Asangba A, Billings EK, Cantu VA, Carlton JM, Cazares D, Cho GS, Condeff T, Cortés P, Cranfield M, Cuevas DA, De la Iglesia R, Decewicz P, Doane MP, Dominy NJ, Dziewit L, Elwasila BM, Eren AM, Franz C, Fu J, Garcia-Aljaro C, Ghedin E, Gulino KM, Haggerty JM, Head SR, Hendriksen RS, Hill C, Hyöty H, Ilina EN, Irwin MT, Jeffries TC, Jofre J, Junge RE, Kelley ST, Khan Mirzaei M, Kowalewski M, Kumaresan D, Leigh SR, Lipson D, Lisitsyna ES, Llagostera M, Maritz JM, Marr LC, McCann A, Molshanski-Mor S, Monteiro S, Moreira-Grez B, Morris M, Mugisha L, Muniesa M, Neve H, Nguyen NP, Nigro OD, Nilsson AS, O'Connell T, Odeh R, Oliver A, Piuri M, Prussin Ii AJ, Qimron U, Quan ZX, Rainetova P, Ramírez-Rojas A, Raya R, Reasor K, Rice GAO, Rossi A, Santos R, Shimashita J, Stachler EN, Stene LC, Strain R, Stumpf R, Torres PJ, Twaddle A, Ugochi Ibekwe M, Villagra N, Wandro S, White B, Whiteley A, Whiteson KL, Wijmenga C, Zambrano MM, Zschach H, Dutilh BE.

Nat Microbiol. 2019 Oct;4(10):1727-1736. doi: 10.1038/s41564-019-0494-6. Epub 2019 Jul 8.

PMID:
31285584
8.

Gut Microbial Associations to Plasma Metabolites Linked to Cardiovascular Phenotypes and Risk.

Kurilshikov A, van den Munckhof ICL, Chen L, Bonder MJ, Schraa K, Rutten JHW, Riksen NP, de Graaf J, Oosting M, Sanna S, Joosten LAB, van der Graaf M, Brand T, Koonen DPY, van Faassen M; LifeLines DEEP Cohort Study, BBMRI Metabolomics Consortium, Slagboom PE, Xavier RJ, Kuipers F, Hofker MH, Wijmenga C, Netea MG, Zhernakova A, Fu J.

Circ Res. 2019 Jun 7;124(12):1808-1820. doi: 10.1161/CIRCRESAHA.118.314642. Epub 2019 Apr 11.

PMID:
30971183
9.

Structural variation in the gut microbiome associates with host health.

Zeevi D, Korem T, Godneva A, Bar N, Kurilshikov A, Lotan-Pompan M, Weinberger A, Fu J, Wijmenga C, Zhernakova A, Segal E.

Nature. 2019 Apr;568(7750):43-48. doi: 10.1038/s41586-019-1065-y. Epub 2019 Mar 27.

PMID:
30918406
10.

Causal relationships among the gut microbiome, short-chain fatty acids and metabolic diseases.

Sanna S, van Zuydam NR, Mahajan A, Kurilshikov A, Vich Vila A, Võsa U, Mujagic Z, Masclee AAM, Jonkers DMAE, Oosting M, Joosten LAB, Netea MG, Franke L, Zhernakova A, Fu J, Wijmenga C, McCarthy MI.

Nat Genet. 2019 Apr;51(4):600-605. doi: 10.1038/s41588-019-0350-x. Epub 2019 Feb 18.

11.

The neuroactive potential of the human gut microbiota in quality of life and depression.

Valles-Colomer M, Falony G, Darzi Y, Tigchelaar EF, Wang J, Tito RY, Schiweck C, Kurilshikov A, Joossens M, Wijmenga C, Claes S, Van Oudenhove L, Zhernakova A, Vieira-Silva S, Raes J.

Nat Microbiol. 2019 Apr;4(4):623-632. doi: 10.1038/s41564-018-0337-x. Epub 2019 Feb 4.

PMID:
30718848
12.

Gut microbiota composition and functional changes in inflammatory bowel disease and irritable bowel syndrome.

Vich Vila A, Imhann F, Collij V, Jankipersadsing SA, Gurry T, Mujagic Z, Kurilshikov A, Bonder MJ, Jiang X, Tigchelaar EF, Dekens J, Peters V, Voskuil MD, Visschedijk MC, van Dullemen HM, Keszthelyi D, Swertz MA, Franke L, Alberts R, Festen EAM, Dijkstra G, Masclee AAM, Hofker MH, Xavier RJ, Alm EJ, Fu J, Wijmenga C, Jonkers DMAE, Zhernakova A, Weersma RK.

Sci Transl Med. 2018 Dec 19;10(472). pii: eaap8914. doi: 10.1126/scitranslmed.aap8914.

PMID:
30567928
13.

Shared gut, but distinct oral microbiota composition in primary Sjögren's syndrome and systemic lupus erythematosus.

van der Meulen TA, Harmsen HJM, Vila AV, Kurilshikov A, Liefers SC, Zhernakova A, Fu J, Wijmenga C, Weersma RK, de Leeuw K, Bootsma H, Spijkervet FKL, Vissink A, Kroese FGM.

J Autoimmun. 2019 Feb;97:77-87. doi: 10.1016/j.jaut.2018.10.009. Epub 2018 Nov 9.

14.

Analysis of 1135 gut metagenomes identifies sex-specific resistome profiles.

Sinha T, Vich Vila A, Garmaeva S, Jankipersadsing SA, Imhann F, Collij V, Bonder MJ, Jiang X, Gurry T, Alm EJ, D'Amato M, Weersma RK, Scherjon S, Wijmenga C, Fu J, Kurilshikov A, Zhernakova A.

Gut Microbes. 2019;10(3):358-366. doi: 10.1080/19490976.2018.1528822. Epub 2018 Oct 29.

15.

Author Correction: Individual variations in cardiovascular-disease-related protein levels are driven by genetics and gut microbiome.

Zhernakova DV, Le TH, Kurilshikov A, Atanasovska B, Bonder MJ, Sanna S, Claringbould A, Võsa U, Deelen P, Franke L, de Boer RA, Kuipers F, Netea MG, Hofker MH, Wijmenga C, Zhernakova A, Fu J; LifeLines cohort study; BIOS consortium.

Nat Genet. 2018 Dec;50(12):1752. doi: 10.1038/s41588-018-0275-9.

PMID:
30341443
16.

Individual variations in cardiovascular-disease-related protein levels are driven by genetics and gut microbiome.

Zhernakova DV, Le TH, Kurilshikov A, Atanasovska B, Bonder MJ, Sanna S, Claringbould A, Võsa U, Deelen P, Franke L, de Boer RA, Kuipers F, Netea MG, Hofker MH, Wijmenga C, Zhernakova A, Fu J; LifeLines cohort study; BIOS consortium.

Nat Genet. 2018 Nov;50(11):1524-1532. doi: 10.1038/s41588-018-0224-7. Epub 2018 Sep 24. Erratum in: Nat Genet. 2018 Oct 19;:.

17.

Role of gut microbiota in chronic low-grade inflammation as potential driver for atherosclerotic cardiovascular disease: a systematic review of human studies.

van den Munckhof ICL, Kurilshikov A, Ter Horst R, Riksen NP, Joosten LAB, Zhernakova A, Fu J, Keating ST, Netea MG, de Graaf J, Rutten JHW.

Obes Rev. 2018 Dec;19(12):1719-1734. doi: 10.1111/obr.12750. Epub 2018 Aug 24.

PMID:
30144260
18.

Meta-analysis of human genome-microbiome association studies: the MiBioGen consortium initiative.

Wang J, Kurilshikov A, Radjabzadeh D, Turpin W, Croitoru K, Bonder MJ, Jackson MA, Medina-Gomez C, Frost F, Homuth G, Rühlemann M, Hughes D, Kim HN; MiBioGen Consortium Initiative, Spector TD, Bell JT, Steves CJ, Timpson N, Franke A, Wijmenga C, Meyer K, Kacprowski T, Franke L, Paterson AD, Raes J, Kraaij R, Zhernakova A.

Microbiome. 2018 Jun 8;6(1):101. doi: 10.1186/s40168-018-0479-3.

19.

Microbiome Responses to an Uncontrolled Short-Term Diet Intervention in the Frame of the Citizen Science Project.

Klimenko NS, Tyakht AV, Popenko AS, Vasiliev AS, Altukhov IA, Ischenko DS, Shashkova TI, Efimova DA, Nikogosov DA, Osipenko DA, Musienko SV, Selezneva KS, Baranova A, Kurilshikov AM, Toshchakov SM, Korzhenkov AA, Samarov NI, Shevchenko MA, Tepliuk AV, Alexeev DG.

Nutrients. 2018 May 8;10(5). pii: E576. doi: 10.3390/nu10050576.

20.

Isolation and characterization of a group of new Proteus bacteriophages.

Morozova V, Kozlova Y, Shedko E, Babkin I, Kurilshikov A, Bokovaya O, Bardashova A, Yunusova A, Tikunov A, Tupikin A, Ushakova T, Ryabchikova E, Tikunova N.

Arch Virol. 2018 Aug;163(8):2189-2197. doi: 10.1007/s00705-018-3853-3. Epub 2018 May 2.

PMID:
29721709
21.

Environment dominates over host genetics in shaping human gut microbiota.

Rothschild D, Weissbrod O, Barkan E, Kurilshikov A, Korem T, Zeevi D, Costea PI, Godneva A, Kalka IN, Bar N, Shilo S, Lador D, Vila AV, Zmora N, Pevsner-Fischer M, Israeli D, Kosower N, Malka G, Wolf BC, Avnit-Sagi T, Lotan-Pompan M, Weinberger A, Halpern Z, Carmi S, Fu J, Wijmenga C, Zhernakova A, Elinav E, Segal E.

Nature. 2018 Mar 8;555(7695):210-215. doi: 10.1038/nature25973. Epub 2018 Feb 28.

PMID:
29489753
22.

Detection of stable community structures within gut microbiota co-occurrence networks from different human populations.

Jackson MA, Bonder MJ, Kuncheva Z, Zierer J, Fu J, Kurilshikov A, Wijmenga C, Zhernakova A, Bell JT, Spector TD, Steves CJ.

PeerJ. 2018 Feb 7;6:e4303. doi: 10.7717/peerj.4303. eCollection 2018.

23.

The systemic tumor response to RNase A treatment affects the expression of genes involved in maintaining cell malignancy.

Mironova N, Patutina O, Brenner E, Kurilshikov A, Vlassov V, Zenkova M.

Oncotarget. 2017 Aug 12;8(45):78796-78810. doi: 10.18632/oncotarget.20228. eCollection 2017 Oct 3.

24.

Host Genetics and Gut Microbiome: Challenges and Perspectives.

Kurilshikov A, Wijmenga C, Fu J, Zhernakova A.

Trends Immunol. 2017 Sep;38(9):633-647. doi: 10.1016/j.it.2017.06.003. Epub 2017 Jun 29. Review.

PMID:
28669638
25.

Alteration of the exDNA profile in blood serum of LLC-bearing mice under the decrease of tumour invasion potential by bovine pancreatic DNase I treatment.

Alekseeva LA, Mironova NL, Brenner EV, Kurilshikov AM, Patutina OA, Zenkova MA.

PLoS One. 2017 Feb 21;12(2):e0171988. doi: 10.1371/journal.pone.0171988. eCollection 2017.

26.

Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity.

Schirmer M, Smeekens SP, Vlamakis H, Jaeger M, Oosting M, Franzosa EA, Horst RT, Jansen T, Jacobs L, Bonder MJ, Kurilshikov A, Fu J, Joosten LAB, Zhernakova A, Huttenhower C, Wijmenga C, Netea MG, Xavier RJ.

Cell. 2016 Dec 15;167(7):1897. doi: 10.1016/j.cell.2016.11.046. No abstract available.

27.

Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity.

Schirmer M, Smeekens SP, Vlamakis H, Jaeger M, Oosting M, Franzosa EA, Ter Horst R, Jansen T, Jacobs L, Bonder MJ, Kurilshikov A, Fu J, Joosten LAB, Zhernakova A, Huttenhower C, Wijmenga C, Netea MG, Xavier RJ.

Cell. 2016 Nov 3;167(4):1125-1136.e8. doi: 10.1016/j.cell.2016.10.020. Erratum in: Cell. 2016 Dec 15;167(7):1897. Cell. 2016 Dec 15;167(7):1897.

28.

The effect of host genetics on the gut microbiome.

Bonder MJ, Kurilshikov A, Tigchelaar EF, Mujagic Z, Imhann F, Vila AV, Deelen P, Vatanen T, Schirmer M, Smeekens SP, Zhernakova DV, Jankipersadsing SA, Jaeger M, Oosting M, Cenit MC, Masclee AA, Swertz MA, Li Y, Kumar V, Joosten L, Harmsen H, Weersma RK, Franke L, Hofker MH, Xavier RJ, Jonkers D, Netea MG, Wijmenga C, Fu J, Zhernakova A.

Nat Genet. 2016 Nov;48(11):1407-1412. doi: 10.1038/ng.3663. Epub 2016 Oct 3.

PMID:
27694959
29.

Lytic bacteriophage PM16 specific for Proteus mirabilis: a novel member of the genus Phikmvvirus.

Morozova V, Kozlova Y, Shedko E, Kurilshikov A, Babkin I, Tupikin A, Yunusova A, Chernonosov A, Baykov I, Кondratov I, Kabilov M, Ryabchikova E, Vlassov V, Tikunova N.

Arch Virol. 2016 Sep;161(9):2457-72. doi: 10.1007/s00705-016-2944-2. Epub 2016 Jun 28.

PMID:
27350061
30.

Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity.

Zhernakova A, Kurilshikov A, Bonder MJ, Tigchelaar EF, Schirmer M, Vatanen T, Mujagic Z, Vila AV, Falony G, Vieira-Silva S, Wang J, Imhann F, Brandsma E, Jankipersadsing SA, Joossens M, Cenit MC, Deelen P, Swertz MA; LifeLines cohort study, Weersma RK, Feskens EJ, Netea MG, Gevers D, Jonkers D, Franke L, Aulchenko YS, Huttenhower C, Raes J, Hofker MH, Xavier RJ, Wijmenga C, Fu J.

Science. 2016 Apr 29;352(6285):565-9. doi: 10.1126/science.aad3369. Epub 2016 Apr 28.

31.

Population-level analysis of gut microbiome variation.

Falony G, Joossens M, Vieira-Silva S, Wang J, Darzi Y, Faust K, Kurilshikov A, Bonder MJ, Valles-Colomer M, Vandeputte D, Tito RY, Chaffron S, Rymenans L, Verspecht C, De Sutter L, Lima-Mendez G, D'hoe K, Jonckheere K, Homola D, Garcia R, Tigchelaar EF, Eeckhaudt L, Fu J, Henckaerts L, Zhernakova A, Wijmenga C, Raes J.

Science. 2016 Apr 29;352(6285):560-4. doi: 10.1126/science.aad3503. Epub 2016 Apr 28.

32.

Erratum to: Genetic diversity of Ixodes pavlovskyi and I. persulcatus (Acari: Ixodidae) from the sympatric zone in the south of Western Siberia and Kazakhstan.

Livanova NN, Tikunov AY, Kurilshikov AM, Livanov SG, Fomenko NV, Taranenko DE, Kvashnina AE, Tikunova NV.

Exp Appl Acarol. 2016 Jan;68(1):139-43. doi: 10.1007/s10493-015-9986-0. No abstract available.

PMID:
26597590
33.

Genetic diversity of Ixodes pavlovskyi and I. persulcatus (Acari: Ixodidae) from the sympatric zone in the south of Western Siberia and Kazakhstan.

Livanova NN, Tikunov AY, Kurilshikov AM, Livanov SG, Fomenko NV, Taranenko DE, Kvashnina AE, Tikunova NV.

Exp Appl Acarol. 2015 Nov;67(3):441-56. doi: 10.1007/s10493-015-9947-7. Epub 2015 Jul 23. Erratum in: Exp Appl Acarol. 2016 Jan;68(1):139-43.

PMID:
26201397
34.

Comparative Metagenomic Profiling of Symbiotic Bacterial Communities Associated with Ixodes persulcatus, Ixodes pavlovskyi and Dermacentor reticulatus Ticks.

Kurilshikov A, Livanova NN, Fomenko NV, Tupikin AE, Rar VA, Kabilov MR, Livanov SG, Tikunova NV.

PLoS One. 2015 Jul 8;10(7):e0131413. doi: 10.1371/journal.pone.0131413. eCollection 2015.

35.

Complete Genome Sequencing of Borrelia valaisiana and Borrelia afzelii Isolated from Ixodes persulcatus Ticks in Western Siberia.

Kurilshikov AM, Fomenko NV, Stronin OV, Tikunov AY, Kabilov MR, Tupikin AE, Tikunova NV.

Genome Announc. 2014 Dec 24;2(6). pii: e01315-14. doi: 10.1128/genomeA.01315-14.

36.

MicroRNA drop in the bloodstream and microRNA boost in the tumour caused by treatment with ribonuclease A leads to an attenuation of tumour malignancy.

Mironova N, Patutina O, Brenner E, Kurilshikov A, Vlassov V, Zenkova M.

PLoS One. 2013 Dec 30;8(12):e83482. doi: 10.1371/journal.pone.0083482. eCollection 2013.

37.

Draft Genome Sequence of Bacillus cereus Strain F, Isolated from Ancient Permafrost.

Brenner EV, Brouchkov AV, Kurilshikov AM, Griva GI, Kashuba E, Kashuba VI, Melefors O, Repin VE, Melnikov VP, Vlassov VV.

Genome Announc. 2013 Aug 1;1(4). pii: e00561-13. doi: 10.1128/genomeA.00561-13.

38.

Evolutionary time-scale of primate bocaviruses.

Babkin IV, Tyumentsev AI, Tikunov AY, Kurilshikov AM, Ryabchikova EI, Zhirakovskaya EV, Netesov SV, Tikunova NV.

Infect Genet Evol. 2013 Mar;14:265-74. doi: 10.1016/j.meegid.2012.12.023. Epub 2013 Jan 8.

PMID:
23313830
39.

Whole-genome sequencing of Borrelia garinii BgVir, isolated from Taiga ticks (Ixodes persulcatus).

Brenner EV, Kurilshikov AM, Stronin OV, Fomenko NV.

J Bacteriol. 2012 Oct;194(20):5713.

40.

Unbiased approach to profile the variety of small non-coding RNA of human blood plasma with massively parallel sequencing technology.

Semenov DV, Baryakin DN, Brenner EV, Kurilshikov AM, Vasiliev GV, Bryzgalov LA, Chikova ED, Filippova JA, Kuligina EV, Richter VA.

Expert Opin Biol Ther. 2012 Jun;12 Suppl 1:S43-51. doi: 10.1517/14712598.2012.679653. Epub 2012 Apr 18.

PMID:
22509727
41.

A comparative study of cell-free apoptotic and genomic DNA using FISH and massive parallel sequencing.

Morozkin ES, Loseva EM, Morozov IV, Kurilshikov AM, Bondar AA, Rykova EY, Rubtsov NB, Vlassov VV, Laktionov PP.

Expert Opin Biol Ther. 2012 Jun;12 Suppl 1:S11-7. doi: 10.1517/14712598.2012.670631. Epub 2012 Apr 16.

PMID:
22506740

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