Microbiology

2017

Transcription factor-mediated gene regulation in Archaea

Karr, E. A., Isom, C. E., Trinh, V. & Peeters, E., 1 Dec 2017, RNA metabolism and gene expression in Archaea. Clouet-d'Orval, B. (ed.). Springer, Vol. 32. p. 27-69 (Nucleic Acids and Molecular Biology).

Research output: Chapter in Book/Report/Conference proceeding › Chapter

Wing phosphorylation is a major functional determinant of the Lrs14-type biofilm and motility regulator AbfR1 in Sulfolobus acidocaldarius

Li, L., Banerjee, A., Bischof, L. F., Maklad, H. R., Hoffmann, L., Henche, A-L., Veliz, F., Bildl, W., Schulte, U., Orell, A., Essen, L-O., Peeters, E. & Albers, S-V., Sep 2017, In : Molecular Microbiology. 105, 5, p. 777-793 17 p.

Research output: Contribution to journal › Article

14 Citations (Scopus)

2016

Acetaldehyde as an Intermediate in the Electroreduction of Carbon Monoxide to Ethanol on Oxide-Derived Copper

Bertheussen, E., Verdaguer-Casadevall, A., Ravasio, D., Montoya, J. H., Trimarco, D. B., Roy, C., Meier, S., Wendland, J., Nørskov, J. K., Stephens, I. E. L. & Chorkendorff, I., 22 Jan 2016, In : Angewandte Chemie International Edition. 55, 4, p. 1450-1454 5 p.

Research output: Contribution to journal › Article

116 Citations (Scopus)

Characterization of the role of phosphorylation of the TetR-like transcription factor SaFadR in Sulfolobus acidocaldarius

Maklad, H. R. M. A., Valegard, K., Lindås, A-C. & Peeters, E., 1 Aug 2016.

Research output: Unpublished contribution to conference › Poster

Comparative fluxome and metabolome analysis for overproduction of succinate in Escherichia coli

Taymaz-Nikerel, H., De Mey, M., Baart, G. J. E., Maertens, J., Foulquie Moreno Maria, R., Charlier, D., Heijnen, J. J. & Van Gulik, W. M., Apr 2016, In : Biotechnol Bioeng. 113, 4, p. 817-829 13 p., doi: 10.1002/bit25850.

Research output: Contribution to journal › Article

7 Citations (Scopus)

Correlation detection strategies in microbial data sets vary widely in sensitivity and precision

Weiss, S., Van Treuren, W., Lozupone, C., Faust, K., Friedman, J., Deng, Y., Xia, L. C., Xu, Z. Z., Ursell, L., Alm, E. J., Birmingham, A., Cram, J. A., Fuhrman, J. A., Raes, J., Sun, F., Zhou, J. & Knight, R., Jul 2016, In : The ISME Journal. 10, 7, p. 1669-1681 13 p.

Research output: Contribution to journal › Article

287 Citations (Scopus)

Cyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton

Cornejo-Castillo, F. M., Cabello, A. M., Salazar, G., Sánchez-Baracaldo, P., Lima-Mendez, G., Hingamp, P., Alberti, A., Sunagawa, S., Bork, P., de Vargas, C., Raes, J., Bowler, C., Wincker, P., Zehr, J. P., Gasol, J. M., Massana, R. & Acinas, S. G., 2016, In : Nature Communications. 7, 9 p., 11071.

Research output: Contribution to journal › Article

40 Citations (Scopus)

Dissection of novel resistance mechanisms in Cupriavidus metallidurans

Ali, M. M., Mijnendonckx, K., Leys, N., Monsieurs, P., Charlier, D. & Van Houdt, R., 28 Oct 2016.

Research output: Unpublished contribution to conference › Poster

Donor Species Richness Determines Faecal Microbiota Transplantation Success in Inflammatory Bowel Disease

Vermeire, S., Joossens, M., Verbeke, K., Wang, J., Machiels, K., Sabino, J., Ferrante, M., Van Assche, G., Rutgeerts, P. & Raes, J., 2016, In : J Crohns Colitis. 10, 4, p. 387-394

Research output: Contribution to journal › Article

167 Citations (Scopus)

Effect of Shear Stress on Pseudomonas aeruginosa Isolated from the Cystic Fibrosis Lung

Dingemans, J., Monsieurs, P., Yu, S-H., Crabbé, A., Förstner, K. U., Malfroot, A., Cornelis, P. & Van Houdt, R., 2 Aug 2016, In : mBio. 7, 4, p. 813-816 4 p.

Research output: Contribution to journal › Article

16 Citations (Scopus)

Homeostasis of trace elements in mycorrhizal fungi

Ruytinx, J., Martino, E., Rozpądek, P., Daghino, S., Turnau, K., Colpaert, J. V. & Perotto, S., Oct 2016

Research output: Other contribution

6 Citations (Scopus)

Meta-omics in Inflammatory Bowel Disease Research: Applications, Challenges, and Guidelines

Valles-Colomer, M., El Darzi, Y., Araujo Vieira Da Silva, S. M., Falony, G., Raes, J. & Joossens, M., 2016, In : J Crohns Colitis. 10, 6, p. 735-746 12 p.

Research output: Contribution to journal › Scientific review

22 Citations (Scopus)

Molecular characterization of a GntR-like transcription factor involved in heat stress response in Sulfolobus acidocaldarius

Lemmens, L., De Koning, E. & Peeters, E., 28 Oct 2016.

Research output: Unpublished contribution to conference › Poster

Orthogonal Gene Expression: Creating 3 Promoter Libraries Linked to Different Sigma Factors Which Are Orthogonal Between Each Other and Towards the Host

Bervoets, I., De Mey, M. & Charlier, D., 19 Jul 2016, (Unpublished).

Research output: Unpublished contribution to conference › Poster

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264 Downloads (Pure)

Orthogonal Gene Expression: Creating 3 Promoter Libraries Linked to Different Sigma Factors Which Are Orthogonal Between Each Other and Towards the Host

Bervoets, I., De Mey, M. & Charlier, D., 2016, (Unpublished).

Research output: Unpublished contribution to conference › Unpublished abstract

File

18 Downloads (Pure)

The genome-scale DNA-binding profile of BarR, a β-alanine responsive transcription factor in the archaeon Sulfolobus acidocaldarius

Liu, H., Wang, K., Lindås, A-C. & Peeters, E., 8 Aug 2016, In : BMC Genomics. 17, 11 p., 569.

Research output: Contribution to journal › Article

11 Citations (Scopus)

The role of phosphorylation for the TetR-like transcription factor FadR in Sulfolobus acidocaldarius

Maklad, H. R. M. A., Valegard, K., Lindås, A-C. & Peeters, E., 18 Nov 2016.

Research output: Unpublished contribution to conference › Poster

The trigger enzyme PepA (aminopeptidase A) of Escherichia coli, a transcriptional repressor that generates positive supercoiling. PepA, repressor and chromatin remodeler

Nguyen Le Minh, P., Nadal, M. & Charlier, D., 7 Jun 2016, In : FEBS Letters. 590, 12, p. 1816-1825 10 p., doi: 10.1002/1873-3468:12224.

Research output: Contribution to journal › Article

6 Citations (Scopus)

Transcriptional regulation of fatty acid metabolism in Sulfolobus acidocaldarius

Sybers, D., Lemmens, L., Zhou, X., Shen, L., Brasen, C., Siebers, B. & Peeters, E., 1 Aug 2016.

Research output: Unpublished contribution to conference › Poster

2015

Antibacterial activity and mutagenesis of sponge-associated Pseudomonas fluorescens H41

Ye, L., Santos-Gandelman, J. F., Hardoim, C. C. P., George, I., Cornelis, P. & Laport, M. S., Jul 2015, In : Antonie Van Leeuwenhoek. 108, 1, p. 117-26 10 p.

Research output: Contribution to journal › Article

4 Citations (Scopus)

Belowground fungal communities in pioneer Scots pine stands growing on heavy metal polluted and non-polluted soils

Beeck, M. O. D., Ruytinx, J., Smits, M. M., Vangronsveld, J., Colpaert, J. V. & Rineau, F., Jul 2015, In : Soil Biology and Biochemistry. 86, p. 58-66 9 p.

Research output: Contribution to journal › Article

23 Citations (Scopus)

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

Mysara, M., Saeys, Y., Leys, N., Raes, J. & Monsieurs, P., 2015, In : Applied and Environmental Microbiology. 81, 5, p. 1573-1584 12 p.

Research output: Contribution to journal › Article

Open Access

27 Citations (Scopus)

Characterization of Pseudomonas chlororaphis from Theobroma cacao L. rhizosphere with antagonistic activity against Phytophthora palmivora (Butler)

Acebo-Guerrero, Y., Hernandez-Rodriguez, A., Vandeputte, O., Miguelez-Sierra, Y., Heydrich-Perez, M., Ye, L., Cornelis, P., Bertin, P. & El-Jaziri, M., 2015, In : Journal of Applied Microbiology. 119, 4, p. 1112-1126

Research output: Contribution to journal › Article

10 Citations (Scopus)

Commensal microbiota influence systemic autoimmune responses

Van Praet, J. T., Donovan, E., Vanassche, I., Drennan, M. B., Windels, F., Dendooven, A., Allais, L., Cuvelier, C. A., van de Loo, F., Norris, P. S., Kruglov, A. A., Nedospasov, S. A., Rabot, S., Tito, R., Raes, J., Gaboriau-Routhiau, V., Cerf-Bensussan, N., Van de Wiele, T., Eberl, G., Ware, C. F. & 1 others, Elewaut, D., 19 Jan 2015, In : EMBO Journal. 34, 4, p. 466-474

Research output: Contribution to journal › Article

70 Citations (Scopus)

Computational approaches to predict bacteriophage-host relationships

Edwards, R. A., McNair, K., Faust, K., Raes, J. & Dutilh, B. E., 9 Dec 2015, In : FEMS Microbiology Reviews. 38, 6, p. 258-272 15 p.

Research output: Contribution to journal › Article

Open Access

172 Citations (Scopus)

Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists

Mycorrhizal Genomics Initiative Consortium, Apr 2015, In : Nature Genetics. 47, 4, p. 410-415 6 p.

Research output: Contribution to journal › Article

522 Citations (Scopus)

Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota

Forslund, K., Hildebrand, F., Nielsen, T., Falony, G., Le Chatelier, E., Sunagawa, S., Prifti, E., Araujo Vieira Da Silva, S. M., et al, E. A., Raes, J., Hansen, T., Wang, J., Ehrlich, S. D., Bork, P. & Pederson, O., 2 Dec 2015, In : Nature. 528, 7581, p. 262-266

Research output: Contribution to journal › Article

932 Citations (Scopus)

Expression of the translocator protein (TSPO) from Pseudomonas fluorescens Pf0-1 requires the stress regulatory sigma factors AlgU and RpoH

Leneveu-Jenvrin, C., Bouffartigues, E., Maillot, O., Cornelis, P., Feuilloley, M., Connil, N. & Chevalier, S., 2015, In : Frontiers in Microbiology. 6, 13 p., 1023.

Research output: Contribution to journal › Article

4 Citations (Scopus)

Heterogeneity of the gut microbiome in mice: guidelines for optimizing experimental design

Laukens, D., Brinkman, B. M., Raes, J., De Vos, M. & Vandenabeele, P., 30 Aug 2015, In : FEMS Microbiology Reviews. 38, 6, p. 117-132 15 p.

Research output: Contribution to journal › Article

Open Access

188 Citations (Scopus)

How informative is the mouse for human gut microbiota research?

Nguyen, T. L. A., Araujo Vieira Da Silva, S. M., Liston, A. & Raes, J., Jan 2015, In : Disease Models and Mecanisms. 8, p. 1-16 16 p.

Research output: Contribution to journal › Article

Open Access

585 Citations (Scopus)

Interindividual differences in response to treatment with butyrate-producing Butyricicoccus pullicaecorum 25-3T studied in an in vitro gut model

Geirnaert, A., Wang, J., Tinck, M., Steyaert, A., Van den Abbeele, P., Eeckhaut, V., Vilchez-Vargas, R., Falony, G., Laukens, D., De Vos, M., Van Immerseel, F., Raes, J., Boon, N. & Van de Wiele, T., 20 May 2015, In : FEMS Microbiology Ecology. 91, 6, 12 p., fiv054.

Research output: Contribution to journal › Article

33 Citations (Scopus)

Intestinal microbiota and diet in IBS: causes, consequences, or epiphenomena?

Rajilić-Stojanović, M., Jonkers, D. M., Salonen, A., Havenik, K., Raes, J. & Penders, J., 27 Jan 2015, In : Am J Gastroenterol. 110, 2, p. 278-287

Research output: Contribution to journal › Article

Open Access

201 Citations (Scopus)

Ion current rectification, limiting and overlimiting conductances in nanopores

Van Oeffelen, L., Van Roy, W., Idrissi, H., Charlier, D., Lagae, L. & Borghs, G., 15 May 2015, In : PLoS ONE. 10, 5, 16 p., e0124171.

Research output: Contribution to journal › Article

Open Access

13 Citations (Scopus)

Ligand binding specificity of RutR, a member of the TetR family of transcription regulators in Escherichia coli

Nguyen Le Minh, P., de Cima, S., Bervoets, I., Maes, D., Rubio, V. & Charlier, D., 2015, In : FEBS Open Bio. 5, p. 76-84 9 p.

Research output: Contribution to journal › Article

10 Citations (Scopus)

Ligand binding specificity of RutR, a member of the TetR family of transcription regulators in Escherichia coli

Nguyen Le Minh, P., De Cima, S., Bervoets, I., Maes, D., Rubio, V. & Charlier, D., 2015, FEBS Open Bio, 5, p. 76-84 9 p.

Research output: Contribution to specialist/vulgarizing publication › Article › Specialist

Open Access

File

10 Citations (Scopus)

67 Downloads (Pure)

Low Structural Variation in the Host-Defense Peptide Repertoire of the Dwarf Clawed Frog Hymenochirus boettgeri (Pipidae)

Matthijs, S., Lumeng, Y., Stijlemans, B., Cornelis, P., Bossuyt, F. & Roelants, K., 8 Oct 2015, 22nd Benelux Congress of Zoology. p. 47-47

Research output: Chapter in Book/Report/Conference proceeding › Meeting abstract (Book)

Metagenomics meets time series analysis: unraveling microbial community dynamics

Faust, K., Lahti, L., Gonze, D., de Vos, W. M. & Raes, J., Jun 2015, In : Current Opinion in Microbiology. 25, p. 56-66 11 p.

Research output: Contribution to journal › Article

Open Access

191 Citations (Scopus)

Microbiology Meets Big Data: The Case of Gut Microbiota-Derived Trimethylamine

Falony, G., Araujo Vieira Da Silva, S. M. & Raes, J., 15 Oct 2015, In : Annu Rev Microbiol. 69, p. 305-321

Research output: Contribution to journal › Article

79 Citations (Scopus)

Molecular mechanisms of action by a TetR-family transcription factor in S. acidocaldarius

Lemmens, L., Sybers, D., Wang, K., Lindås, A-C. & Peeters, E., Jan 2015.

Research output: Unpublished contribution to conference › Poster

Molecular mechanisms of action by a TetR-family transcription factor in Sulfolobus acidocaldarius

Lemmens, L., Sybers, D., Wang, K., Lindås, A-C. & Peeters, E., Jun 2015, FEMS 2015 meeting abstract book. FEMS-1447

Research output: Chapter in Book/Report/Conference proceeding › Meeting abstract (Book)

Open Access

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

Mysara, M., Leys, N., Raes, J. & Monsieurs, P., 2015, In : BMC Bioinformatics. 16, 1, p. 88 10 p.

Research output: Contribution to journal › Article

Open Access

10 Citations (Scopus)

Ocean plankton. Determinants of community structure in the global plankton interactome

Lima-Mendez, G., Faust, K., Henry, N., Decelle, J., Colin, S., Carcillo, F., Chaffron, S., Ignacio-Espinosa, J. C., Roux, S., Vincent, F., Bittner, L., Darzi, Y., Wang, J., Audic, S., Berline, L., Bontempi, G., Cabello, A. M., Coppola, L., Cornejo-Castillo, F. M., d'Ovidio, F. & 31 others, De Meester, L., Ferrera, I., Garet-Delmas, M-J., Guidi, L., Lara, E., Pesant, S., Royo-Llonch, M., Salazar, G., Sánchez, P., Sebastian, M., Souffreau, C., Dimier, C., Picheral, M., Searson, S., Kandels-Lewis, S., Gorsky, G., Not, F., Ogata, H., Speich, S., Stemmann, L., Weissenbach, J., Wincker, P., Acinas, S. G., Sunagawa, S., Bork, P., Sullivan, M. B., Karsenti, E., Bowler, C., de Vargas, C., Raes, J. & Tara Oceans Coordinators, 2015, In : Science. 348, 6237, p. 1262073

Research output: Contribution to journal › Article

395 Citations (Scopus)

Ocean plankton. Eukaryotic plankton diversity in the sunlit ocean

de Vargas, C., Audic, S., Henry, N., Decelle, J., Mahé, F., Logares, R., Lara, E., Berney, C., Le Bescot, N., Probert, I., Carmichael, M., Poulain, J., Romac, S., Colin, S., Aury, J-M., Bittner, L., Chaffron, S., Dunthorn, M., Engelen, S., Flegontova, O. & 31 others, Guidi, L., Horák, A., Jaillon, O., Lima-Mendez, G., Lukeš, J., Malviya, S., Morard, R., Mulot, M., Scalco, E., Siano, R., Vincent, F., Zingone, A., Dimier, C., Picheral, M., Searson, S., Kandels-Lewis, S., Acinas, S. G., Bork, P., Bowler, C., Gorsky, G., Grimsley, N., Hingamp, P., Iudicone, D., Not, F., Ogata, H., Pesant, S., Raes, J., Sieracki, M. E., Speich, S., Stemmann, L. & Tara Oceans Coordinators, 2015, In : Science. 348, 6237, p. 1261605

Research output: Contribution to journal › Article

814 Citations (Scopus)

Ocean plankton. Structure and function of the global ocean microbiome

Sunagawa, S., Coelho, L. P., Chaffron, S., Lima Mendez, G., Araujo Vieira Da Silva, S. M., Raes, J., Acinas, S. G. & Bork, P., 22 May 2015, In : Science. 348, 6237, 9 p., 1261359.

Research output: Contribution to journal › Article

964 Citations (Scopus)

Ovarian hyperstimulation syndrome after gonadotropin-releasing hormone agonist triggering and 'freeze-all': in depth analysis of genetic predisposition

Dos Santos Ribeiro, S., Polyzos, N., Stouffs, K., De Vos, M., Seneca, S., Tournaye, H. & Blockeel, C., Jul 2015, In : Journal of Assisted Reproduction and Genetics. 32, 7, p. 1063-1068

Research output: Contribution to journal › Article

23 Citations (Scopus)

Pseudomonas moraviensis subsp. stanleyae, a bacterial endophyte of hyperaccumulator Stanleya pinnata, is capable of efficient selenite reduction to elemental selenium under aerobic conditions

Staicu, L., Ackerson, C. J., Cornelis, P., Ye, L., Berendsen, R., Hunter, W. J., Noblitt, S. D., Henry, C. S., Cappa, J. J., Montenieri, R. L., Wong, A. O., Musilova, L., Sura-de-Jong, M., Van Hullebusch, E. D., Lens, P. N. L., Reynolds, R. J. B. & Pilon-Smits, E. A. H., 2015, In : Journal of Applied Microbiology. 119, 2, p. 400-410

Research output: Contribution to journal › Article

36 Citations (Scopus)

Soil microbiome responses to the short-term effects of Amazonian deforestation

Navarrete, A. A., Tsai, S. M., Mendes, L. W., Faust, K., de Hollander, M., Cassman, N. A., Raes, J., van Veen, J. A. & Kuramae, E. E., May 2015, In : Molecular Ecology. 24, 10, p. 2433-2448

Research output: Contribution to journal › Article

87 Citations (Scopus)

Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates

Vandeputte, D., Falony, G., Araujo Vieira Da Silva, S. M., Tito, R. Y., Joossens, M. & Raes, J., 11 Jun 2015, In : Gut. 65, 1, p. 57-62

Research output: Contribution to journal › Article

Open Access

393 Citations (Scopus)

The interplay between nucleoid organization and transcription in archaeal genomes

Peeters, E., Driessen, R., Werner, F. & Dame, R., 2015, In : Nature Reviews Microbiology. 13, 6, p. 333-341

Research output: Contribution to journal › Article

57 Citations (Scopus)

Towards biome-specific analysis of meta-omics data

Darzi, Y., Falony, G., Araujo Vieira Da Silva, S. M. & Raes, J., 1 Dec 2015, In : The ISME Journal. 2015, p. 1-4

Research output: Contribution to journal › Article

Open Access

29 Citations (Scopus)

Microbiology

Research output

Search results