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PaSiT: A novel approach based on short oligo-nucleotide frequencies for efficient bacterial identification and typing.

Goussarov G, Cleenwerck I, Mysara M, Leys N, Monsieurs P, Tahon G, Carlier A, Vandamme P, Van Houdt R.

Bioinformatics. 2020 Jan 3. pii: btz964. doi: 10.1093/bioinformatics/btz964. [Epub ahead of print]


Spontaneous mutation in the AgrRS two-component regulatory system of Cupriavidus metallidurans results in enhanced silver resistance.

Mijnendonckx K, Ali MM, Provoost A, Janssen P, Mergeay M, Leys N, Charlier D, Monsieurs P, Van Houdt R.

Metallomics. 2019 Nov 1;11(11):1912-1924. doi: 10.1039/c9mt00123a. Epub 2019 Oct 14.


Reactivation of Microbial Strains and Synthetic Communities After a Spaceflight to the International Space Station: Corroborating the Feasibility of Essential Conversions in the MELiSSA Loop.

Ilgrande C, Mastroleo F, Christiaens MER, Lindeboom REF, Prat D, Van Hoey O, Ambrozova I, Coninx I, Heylen W, Pommerening-Roser A, Spieck E, Boon N, Vlaeminck SE, Leys N, Clauwaert P.

Astrobiology. 2019 Sep;19(9):1167-1176. doi: 10.1089/ast.2018.1973. Epub 2019 Jun 4.


Food Supplements to Mitigate Detrimental Effects of Pelvic Radiotherapy.

Segers C, Verslegers M, Baatout S, Leys N, Lebeer S, Mastroleo F.

Microorganisms. 2019 Apr 3;7(4). pii: E97. doi: 10.3390/microorganisms7040097. Review.


Fungi and Mycotoxins in Space-A Review.

De Middeleer G, Leys N, Sas B, De Saeger S.

Astrobiology. 2019 Jul;19(7):915-926. doi: 10.1089/ast.2018.1854. Epub 2019 Apr 11.


Gene Expansion and Positive Selection as Bacterial Adaptations to Oligotrophic Conditions.

Props R, Monsieurs P, Vandamme P, Leys N, Denef VJ, Boon N.

mSphere. 2019 Feb 6;4(1). pii: e00011-19. doi: 10.1128/mSphereDirect.00011-19.


Genomic and Transcriptomic Changes that Mediate Increased Platinum Resistance in Cupriavidus metallidurans.

Ali MM, Provoost A, Maertens L, Leys N, Monsieurs P, Charlier D, Van Houdt R.

Genes (Basel). 2019 Jan 18;10(1). pii: E63. doi: 10.3390/genes10010063.


Cupriavidus metallidurans Strains with Different Mobilomes and from Distinct Environments Have Comparable Phenomes.

Van Houdt R, Provoost A, Van Assche A, Leys N, Lievens B, Mijnendonckx K, Monsieurs P.

Genes (Basel). 2018 Oct 18;9(10). pii: E507. doi: 10.3390/genes9100507.


Characterization of the bacterial communities on recent Icelandic volcanic deposits of different ages.

Byloos B, Monsieurs P, Mysara M, Leys N, Boon N, Van Houdt R.

BMC Microbiol. 2018 Sep 24;18(1):122. doi: 10.1186/s12866-018-1262-0.


Nitrogen cycle microorganisms can be reactivated after Space exposure.

Lindeboom REF, Ilgrande C, Carvajal-Arroyo JM, Coninx I, Van Hoey O, Roume H, Morozova J, Udert KM, Sas B, Paille C, Lasseur C, Ilyin V, Clauwaert P, Leys N, Vlaeminck SE.

Sci Rep. 2018 Sep 13;8(1):13783. doi: 10.1038/s41598-018-32055-4.


Production and characterization of bioaerosols for model validation in spacecraft environment.

Salmela A, Kokkonen E, Kulmala I, Veijalainen AM, van Houdt R, Leys N, Berthier A, Viacheslav I, Kharin S, Morozova J, Tikhomirov A, Pasanen P.

J Environ Sci (China). 2018 Jul;69:227-238. doi: 10.1016/j.jes.2017.10.016. Epub 2017 Nov 7.


Potential of higher plants, algae, and cyanobacteria for remediation of radioactively contaminated waters.

Vanhoudt N, Vandenhove H, Leys N, Janssen P.

Chemosphere. 2018 Sep;207:239-254. doi: 10.1016/j.chemosphere.2018.05.034. Epub 2018 May 7. Review.


Effect of microgravity & space radiation on microbes.

Senatore G, Mastroleo F, Leys N, Mauriello G.

Future Microbiol. 2018 Jun 1;13:831-847. doi: 10.2217/fmb-2017-0251. Epub 2018 May 10. Review.


The Impact of Space Flight on Survival and Interaction of Cupriavidus metallidurans CH34 with Basalt, a Volcanic Moon Analog Rock.

Byloos B, Coninx I, Van Hoey O, Cockell C, Nicholson N, Ilyin V, Van Houdt R, Boon N, Leys N.

Front Microbiol. 2017 Apr 28;8:671. doi: 10.3389/fmicb.2017.00671. eCollection 2017.


From reads to operational taxonomic units: an ensemble processing pipeline for MiSeq amplicon sequencing data.

Mysara M, Njima M, Leys N, Raes J, Monsieurs P.

Gigascience. 2017 Feb 1;6(2):1-10. doi: 10.1093/gigascience/giw017.


Reconciliation between operational taxonomic units and species boundaries.

Mysara M, Vandamme P, Props R, Kerckhof FM, Leys N, Boon N, Raes J, Monsieurs P.

FEMS Microbiol Ecol. 2017 Apr 1;93(4). doi: 10.1093/femsec/fix029.


Impact of the electron donor on in situ microbial nitrate reduction in Opalinus Clay: results from the Mont Terri rock laboratory (Switzerland).

Bleyen N, Smets S, Small J, Moors H, Leys N, Albrecht A, De Cannière P, Schwyn B, Wittebroodt C, Valcke E.

Swiss J Geosci. 2017;110(1):355-374. doi: 10.1007/s00015-016-0256-x. Epub 2017 Feb 24.


Reevaluating multicolor flow cytometry to assess microbial viability.

Buysschaert B, Byloos B, Leys N, Van Houdt R, Boon N.

Appl Microbiol Biotechnol. 2016 Nov;100(21):9037-9051. Epub 2016 Sep 29. Review.


IPED: a highly efficient denoising tool for Illumina MiSeq Paired-end 16S rRNA gene amplicon sequencing data.

Mysara M, Leys N, Raes J, Monsieurs P.

BMC Bioinformatics. 2016 Apr 29;17(1):192. doi: 10.1186/s12859-016-1061-2.


Zinc-Induced Transposition of Insertion Sequence Elements Contributes to Increased Adaptability of Cupriavidus metallidurans.

Vandecraen J, Monsieurs P, Mergeay M, Leys N, Aertsen A, Van Houdt R.

Front Microbiol. 2016 Mar 23;7:359. doi: 10.3389/fmicb.2016.00359. eCollection 2016.


Construction and phenotypic characterization of M68, an RruI quorum sensing knockout mutant of the photosynthetic alphaproteobacterium Rhodospirillum rubrum.

Condori S, Atkinson S, Leys N, Wattiez R, Mastroleo F.

Res Microbiol. 2016 Jun;167(5):380-92. doi: 10.1016/j.resmic.2016.02.006. Epub 2016 Mar 16.


Rock geochemistry induces stress and starvation responses in the bacterial proteome.

Bryce CC, Le Bihan T, Martin SF, Harrison JP, Bush T, Spears B, Moore A, Leys N, Byloos B, Cockell CS.

Environ Microbiol. 2016 Apr;18(4):1110-21. doi: 10.1111/1462-2920.13093. Epub 2015 Dec 22.


Temporal Gene Expression of the Cyanobacterium Arthrospira in Response to Gamma Rays.

Badri H, Monsieurs P, Coninx I, Nauts R, Wattiez R, Leys N.

PLoS One. 2015 Aug 26;10(8):e0135565. doi: 10.1371/journal.pone.0135565. eCollection 2015.


Trade-Off between Growth and Carbohydrate Accumulation in Nutrient-Limited Arthrospira sp. PCC 8005 Studied by Integrating Transcriptomic and Proteomic Approaches.

Depraetere O, Deschoenmaeker F, Badri H, Monsieurs P, Foubert I, Leys N, Wattiez R, Muylaert K.

PLoS One. 2015 Jul 21;10(7):e0132461. doi: 10.1371/journal.pone.0132461. eCollection 2015.


NoDe: a fast error-correction algorithm for pyrosequencing amplicon reads.

Mysara M, Leys N, Raes J, Monsieurs P.

BMC Bioinformatics. 2015 Mar 15;16:88. doi: 10.1186/s12859-015-0520-5.


Genome-wide transcriptional analysis suggests hydrogenase- and nitrogenase-mediated hydrogen production in Clostridium butyricum CWBI 1009.

Calusinska M, Hamilton C, Monsieurs P, Mathy G, Leys N, Franck F, Joris B, Thonart P, Hiligsmann S, Wilmotte A.

Biotechnol Biofuels. 2015 Feb 22;8:27. doi: 10.1186/s13068-015-0203-5. eCollection 2015.


Molecular investigation of the radiation resistance of edible cyanobacterium Arthrospira sp. PCC 8005.

Badri H, Monsieurs P, Coninx I, Wattiez R, Leys N.

Microbiologyopen. 2015 Apr;4(2):187-207. doi: 10.1002/mbo3.229. Epub 2015 Feb 12.


Harvesting carbohydrate-rich Arthrospira platensis by spontaneous settling.

Depraetere O, Pierre G, Deschoenmaeker F, Badri H, Foubert I, Leys N, Markou G, Wattiez R, Michaud P, Muylaert K.

Bioresour Technol. 2015 Mar;180:16-21. doi: 10.1016/j.biortech.2014.12.084. Epub 2014 Dec 31.


CATCh, an ensemble classifier for chimera detection in 16S rRNA sequencing studies.

Mysara M, Saeys Y, Leys N, Raes J, Monsieurs P.

Appl Environ Microbiol. 2015 Mar;81(5):1573-84. doi: 10.1128/AEM.02896-14. Epub 2014 Dec 19.


Draft Genome Sequences of Ralstonia pickettii Strains SSH4 and CW2, Isolated from Space Equipment.

Monsieurs P, Mijnendonckx K, Provoost A, Venkateswaran K, Ott CM, Leys N, Van Houdt R.

Genome Announc. 2014 Sep 4;2(5). pii: e00887-14. doi: 10.1128/genomeA.00887-14.


Microbial monitoring of crewed habitats in space-current status and future perspectives.

Yamaguchi N, Roberts M, Castro S, Oubre C, Makimura K, Leys N, Grohmann E, Sugita T, Ichijo T, Nasu M.

Microbes Environ. 2014 Sep 17;29(3):250-60. Epub 2014 Aug 12. Review.


Snow surface microbiome on the High Antarctic Plateau (DOME C).

Michaud L, Lo Giudice A, Mysara M, Monsieurs P, Raffa C, Leys N, Amalfitano S, Van Houdt R.

PLoS One. 2014 Aug 7;9(8):e104505. doi: 10.1371/journal.pone.0104505. eCollection 2014.


Genome Sequences of Cupriavidus metallidurans Strains NA1, NA4, and NE12, Isolated from Space Equipment.

Monsieurs P, Mijnendonckx K, Provoost A, Venkateswaran K, Ott CM, Leys N, Van Houdt R.

Genome Announc. 2014 Jul 24;2(4). pii: e00719-14. doi: 10.1128/genomeA.00719-14.


Quantitative and functional dynamics of Dehalococcoides spp. and its tceA and vcrA genes under TCE exposure.

Doğan-Subaşi E, Bastiaens L, Leys N, Boon N, Dejonghe W.

Biodegradation. 2014 Jul;25(4):493-504.


Genome Sequence of Cupriavidus metallidurans Strain H1130, Isolated from an Invasive Human Infection.

Monsieurs P, Provoost A, Mijnendonckx K, Leys N, Gaudreau C, Van Houdt R.

Genome Announc. 2013 Dec 12;1(6). pii: e01051-13. doi: 10.1128/genomeA.01051-13.


Modelled microgravity cultivation modulates N-acylhomoserine lactone production in Rhodospirillum rubrum S1H independently of cell density.

Mastroleo F, Van Houdt R, Atkinson S, Mergeay M, Hendrickx L, Wattiez R, Leys N.

Microbiology. 2013 Dec;159(Pt 12):2456-2466. doi: 10.1099/mic.0.066415-0. Epub 2013 Sep 11.


Evidence and characteristics of a diverse and metabolically active microbial community in deep subsurface clay borehole water.

Wouters K, Moors H, Boven P, Leys N.

FEMS Microbiol Ecol. 2013 Dec;86(3):458-73. doi: 10.1111/1574-6941.12171. Epub 2013 Jul 29.


Antimicrobial silver: uses, toxicity and potential for resistance.

Mijnendonckx K, Leys N, Mahillon J, Silver S, Van Houdt R.

Biometals. 2013 Aug;26(4):609-21. doi: 10.1007/s10534-013-9645-z. Epub 2013 Jun 15. Review.


Characterization of culturable Paenibacillus spp. from the snow surface on the high Antarctic Plateau (DOME C) and their dissemination in the Concordia research station.

Van Houdt R, Deghorain M, Vermeersch M, Provoost A, Lo Giudice A, Leys N, Perez-Morga D, Van Melderen L, Michaud L.

Extremophiles. 2013 Jul;17(4):565-73. doi: 10.1007/s00792-013-0539-3. Epub 2013 Apr 16.


Characterization of the survival ability of Cupriavidus metallidurans and Ralstonia pickettii from space-related environments.

Mijnendonckx K, Provoost A, Ott CM, Venkateswaran K, Mahillon J, Leys N, Van Houdt R.

Microb Ecol. 2013 Feb;65(2):347-60. doi: 10.1007/s00248-012-0139-2. Epub 2012 Dec 5.


Differential proteomics and physiology of Pseudomonas putida KT2440 under filament-inducing conditions.

Crabbé A, Leroy B, Wattiez R, Aertsen A, Leys N, Cornelis P, Van Houdt R.

BMC Microbiol. 2012 Nov 27;12:282. doi: 10.1186/1471-2180-12-282.


Purification and characterization of the acetone carboxylase of Cupriavidus metallidurans strain CH34.

Rosier C, Leys N, Henoumont C, Mergeay M, Wattiez R.

Appl Environ Microbiol. 2012 Jun;78(12):4516-8. doi: 10.1128/AEM.07974-11. Epub 2012 Apr 6.


Variation in genomic islands contribute to genome plasticity in Cupriavidus metallidurans.

Van Houdt R, Monsieurs P, Mijnendonckx K, Provoost A, Janssen A, Mergeay M, Leys N.

BMC Genomics. 2012 Mar 23;13:111. doi: 10.1186/1471-2164-13-111.


Heavy metal resistance in Cupriavidus metallidurans CH34 is governed by an intricate transcriptional network.

Monsieurs P, Moors H, Van Houdt R, Janssen PJ, Janssen A, Coninx I, Mergeay M, Leys N.

Biometals. 2011 Dec;24(6):1133-51. doi: 10.1007/s10534-011-9473-y. Epub 2011 Jun 25.


Insertion sequence elements in Cupriavidus metallidurans CH34: distribution and role in adaptation.

Mijnendonckx K, Provoost A, Monsieurs P, Leys N, Mergeay M, Mahillon J, Van Houdt R.

Plasmid. 2011 May;65(3):193-203. doi: 10.1016/j.plasmid.2010.12.006. Epub 2010 Dec 24.


Alveolar epithelium protects macrophages from quorum sensing-induced cytotoxicity in a three-dimensional co-culture model.

Crabbé A, Sarker SF, Van Houdt R, Ott CM, Leys N, Cornelis P, Nickerson CA.

Cell Microbiol. 2011 Mar;13(3):469-81. doi: 10.1111/j.1462-5822.2010.01548.x. Epub 2010 Nov 25.


Microarray analysis of a microbe-mineral interaction.

Olsson-Francis K, VAN Houdt R, Mergeay M, Leys N, Cockell CS.

Geobiology. 2010 Dec;8(5):446-56. doi: 10.1111/j.1472-4669.2010.00253.x. Epub 2010 Aug 15.


The complete genome sequence of Cupriavidus metallidurans strain CH34, a master survivalist in harsh and anthropogenic environments.

Janssen PJ, Van Houdt R, Moors H, Monsieurs P, Morin N, Michaux A, Benotmane MA, Leys N, Vallaeys T, Lapidus A, Monchy S, Médigue C, Taghavi S, McCorkle S, Dunn J, van der Lelie D, Mergeay M.

PLoS One. 2010 May 5;5(5):e10433. doi: 10.1371/journal.pone.0010433.


Differential proteomic analysis using isotope-coded protein-labeling strategies: comparison, improvements and application to simulated microgravity effect on Cupriavidus metallidurans CH34.

Leroy B, Rosier C, Erculisse V, Leys N, Mergeay M, Wattiez R.

Proteomics. 2010 Jun;10(12):2281-91. doi: 10.1002/pmic.200900286.


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