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Sample Preservation and Storage Significantly Impact Taxonomic and Functional Profiles in Metaproteomics Studies of the Human Gut Microbiome.

Hickl O, Heintz-Buschart A, Trautwein-Schult A, Hercog R, Bork P, Wilmes P, Becher D.

Microorganisms. 2019 Sep 19;7(9). pii: E367. doi: 10.3390/microorganisms7090367.


Connecting environmental exposure and neurodegeneration using cheminformatics and high resolution mass spectrometry: potential and challenges.

Schymanski EL, Baker NC, Williams AJ, Singh RR, Trezzi JP, Wilmes P, Kolber PL, Kruger R, Paczia N, Linster CL, Balling R.

Environ Sci Process Impacts. 2019 Sep 18;21(9):1426-1445. doi: 10.1039/c9em00068b.


Integrated In Vitro and In Silico Modeling Delineates the Molecular Effects of a Synbiotic Regimen on Colorectal-Cancer-Derived Cells.

Greenhalgh K, Ramiro-Garcia J, Heinken A, Ullmann P, Bintener T, Pacheco MP, Baginska J, Shah P, Frachet A, Halder R, Fritz JV, Sauter T, Thiele I, Haan S, Letellier E, Wilmes P.

Cell Rep. 2019 Apr 30;27(5):1621-1632.e9. doi: 10.1016/j.celrep.2019.04.001.


Deep neural networks outperform human expert's capacity in characterizing bioleaching bacterial biofilm composition.

Buetti-Dinh A, Galli V, Bellenberg S, Ilie O, Herold M, Christel S, Boretska M, Pivkin IV, Wilmes P, Sand W, Vera M, Dopson M.

Biotechnol Rep (Amst). 2019 Mar 7;22:e00321. doi: 10.1016/j.btre.2019.e00321. eCollection 2019 Jun.


Extensive transmission of microbes along the gastrointestinal tract.

Schmidt TS, Hayward MR, Coelho LP, Li SS, Costea PI, Voigt AY, Wirbel J, Maistrenko OM, Alves RJ, Bergsten E, de Beaufort C, Sobhani I, Heintz-Buschart A, Sunagawa S, Zeller G, Wilmes P, Bork P.

Elife. 2019 Feb 12;8. pii: e42693. doi: 10.7554/eLife.42693.


Weak Iron Oxidation by Sulfobacillus thermosulfidooxidans Maintains a Favorable Redox Potential for Chalcopyrite Bioleaching.

Christel S, Herold M, Bellenberg S, Buetti-Dinh A, El Hajjami M, Pivkin IV, Sand W, Wilmes P, Poetsch A, Vera M, Dopson M.

Front Microbiol. 2018 Dec 12;9:3059. doi: 10.3389/fmicb.2018.03059. eCollection 2018.


Birth mode is associated with earliest strain-conferred gut microbiome functions and immunostimulatory potential.

Wampach L, Heintz-Buschart A, Fritz JV, Ramiro-Garcia J, Habier J, Herold M, Narayanasamy S, Kaysen A, Hogan AH, Bindl L, Bottu J, Halder R, Sjöqvist C, May P, Andersson AF, de Beaufort C, Wilmes P.

Nat Commun. 2018 Nov 30;9(1):5091. doi: 10.1038/s41467-018-07631-x.


Dark matter in host-microbiome metabolomics: Tackling the unknowns-A review.

Peisl BYL, Schymanski EL, Wilmes P.

Anal Chim Acta. 2018 Dec 11;1037:13-27. doi: 10.1016/j.aca.2017.12.034. Epub 2017 Dec 30. Review.


The Gut Microbiota and Hematopoietic Stem Cell Transplantation: Challenges and Potentials.

Noor F, Kaysen A, Wilmes P, Schneider JG.

J Innate Immun. 2019;11(5):405-415. doi: 10.1159/000492943. Epub 2018 Oct 4. Review.


Expanding the Use of Spectral Libraries in Proteomics.

Deutsch EW, Perez-Riverol Y, Chalkley RJ, Wilhelm M, Tate S, Sachsenberg T, Walzer M, Käll L, Delanghe B, Böcker S, Schymanski EL, Wilmes P, Dorfer V, Kuster B, Volders PJ, Jehmlich N, Vissers JPC, Wolan DW, Wang AY, Mendoza L, Shofstahl J, Dowsey AW, Griss J, Salek RM, Neumann S, Binz PA, Lam H, Vizcaíno JA, Bandeira N, Röst H.

J Proteome Res. 2018 Dec 7;17(12):4051-4060. doi: 10.1021/acs.jproteome.8b00485. Epub 2018 Oct 11. Review.


Sequential Isolation of DNA, RNA, Protein, and Metabolite Fractions from Murine Organs and Intestinal Contents for Integrated Omics of Host-Microbiota Interactions.

Shah P, Muller EEL, Lebrun LA, Wampach L, Wilmes P.

Methods Mol Biol. 2018;1841:279-291. doi: 10.1007/978-1-4939-8695-8_19.


The RNA Complement of Outer Membrane Vesicles From Salmonella enterica Serovar Typhimurium Under Distinct Culture Conditions.

Malabirade A, Habier J, Heintz-Buschart A, May P, Godet J, Halder R, Etheridge A, Galas D, Wilmes P, Fritz JV.

Front Microbiol. 2018 Aug 30;9:2015. doi: 10.3389/fmicb.2018.02015. eCollection 2018.


Expressed protein profile of a Tectomicrobium and other microbial symbionts in the marine sponge Aplysina aerophoba as evidenced by metaproteomics.

Chaib De Mares M, Jiménez DJ, Palladino G, Gutleben J, Lebrun LA, Muller EEL, Wilmes P, Sipkema D, van Elsas JD.

Sci Rep. 2018 Aug 7;8(1):11795. doi: 10.1038/s41598-018-30134-0.


Automated Microscopic Analysis of Metal Sulfide Colonization by Acidophilic Microorganisms.

Bellenberg S, Buetti-Dinh A, Galli V, Ilie O, Herold M, Christel S, Boretska M, Pivkin IV, Wilmes P, Sand W, Vera M, Dopson M.

Appl Environ Microbiol. 2018 Oct 1;84(20). pii: e01835-18. doi: 10.1128/AEM.01835-18. Print 2018 Oct 15.


A year of monitoring 20 mesophilic full-scale bioreactors reveals the existence of stable but different core microbiomes in bio-waste and wastewater anaerobic digestion systems.

Calusinska M, Goux X, Fossépré M, Muller EEL, Wilmes P, Delfosse P.

Biotechnol Biofuels. 2018 Jul 19;11:196. doi: 10.1186/s13068-018-1195-8. eCollection 2018.


Small RNA profiling of low biomass samples: identification and removal of contaminants.

Heintz-Buschart A, Yusuf D, Kaysen A, Etheridge A, Fritz JV, May P, de Beaufort C, Upadhyaya BB, Ghosal A, Galas DJ, Wilmes P.

BMC Biol. 2018 May 14;16(1):52. doi: 10.1186/s12915-018-0522-7.


Mechanisms of Persistence of the Ammonia-Oxidizing Bacteria Nitrosomonas to the Biocide Free Nitrous Acid.

Laloo AE, Wei J, Wang D, Narayanasamy S, Vanwonterghem I, Waite D, Steen J, Kaysen A, Heintz-Buschart A, Wang Q, Schulz B, Nouwens A, Wilmes P, Hugenholtz P, Yuan Z, Bond PL.

Environ Sci Technol. 2018 May 1;52(9):5386-5397. doi: 10.1021/acs.est.7b04273. Epub 2018 Apr 16.


Extraction and Analysis of RNA Isolated from Pure Bacteria-Derived Outer Membrane Vesicles.

Habier J, May P, Heintz-Buschart A, Ghosal A, Wienecke-Baldacchino AK, Nolte-'t Hoen ENM, Wilmes P, Fritz JV.

Methods Mol Biol. 2018;1737:213-230. doi: 10.1007/978-1-4939-7634-8_13.


Human Gut Microbiome: Function Matters.

Heintz-Buschart A, Wilmes P.

Trends Microbiol. 2018 Jul;26(7):563-574. doi: 10.1016/j.tim.2017.11.002. Epub 2017 Nov 22. Review.


Multi-omics Reveals the Lifestyle of the Acidophilic, Mineral-Oxidizing Model Species Leptospirillum ferriphilumT.

Christel S, Herold M, Bellenberg S, El Hajjami M, Buetti-Dinh A, Pivkin IV, Sand W, Wilmes P, Poetsch A, Dopson M.

Appl Environ Microbiol. 2018 Jan 17;84(3). pii: e02091-17. doi: 10.1128/AEM.02091-17. Print 2018 Feb 1.


First draft genome sequence of a strain belonging to the Zoogloea genus and its gene expression in situ.

Muller EEL, Narayanasamy S, Zeimes M, Laczny CC, Lebrun LA, Herold M, Hicks ND, Gillece JD, Schupp JM, Keim P, Wilmes P.

Stand Genomic Sci. 2017 Oct 18;12:64. doi: 10.1186/s40793-017-0274-y. eCollection 2017.


Measuring soil sustainability via soil resilience.

Ludwig M, Wilmes P, Schrader S.

Sci Total Environ. 2018 Jun 1;626:1484-1493. doi: 10.1016/j.scitotenv.2017.10.043. Epub 2017 Oct 18.


The nasal and gut microbiome in Parkinson's disease and idiopathic rapid eye movement sleep behavior disorder.

Heintz-Buschart A, Pandey U, Wicke T, Sixel-Döring F, Janzen A, Sittig-Wiegand E, Trenkwalder C, Oertel WH, Mollenhauer B, Wilmes P.

Mov Disord. 2018 Jan;33(1):88-98. doi: 10.1002/mds.27105. Epub 2017 Aug 26.


Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation.

Svartström O, Alneberg J, Terrapon N, Lombard V, de Bruijn I, Malmsten J, Dalin AM, El Muller E, Shah P, Wilmes P, Henrissat B, Aspeborg H, Andersson AF.

ISME J. 2017 Nov;11(11):2538-2551. doi: 10.1038/ismej.2017.108. Epub 2017 Jul 21.


Integrated meta-omic analyses of the gastrointestinal tract microbiome in patients undergoing allogeneic hematopoietic stem cell transplantation.

Kaysen A, Heintz-Buschart A, Muller EEL, Narayanasamy S, Wampach L, Laczny CC, Graf N, Simon A, Franke K, Bittenbring J, Wilmes P, Schneider JG.

Transl Res. 2017 Aug;186:79-94.e1. doi: 10.1016/j.trsl.2017.06.008. Epub 2017 Jun 20.


Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life.

Wampach L, Heintz-Buschart A, Hogan A, Muller EEL, Narayanasamy S, Laczny CC, Hugerth LW, Bindl L, Bottu J, Andersson AF, de Beaufort C, Wilmes P.

Front Microbiol. 2017 May 2;8:738. doi: 10.3389/fmicb.2017.00738. eCollection 2017.


ICoVeR - an interactive visualization tool for verification and refinement of metagenomic bins.

Broeksema B, Calusinska M, McGee F, Winter K, Bongiovanni F, Goux X, Wilmes P, Delfosse P, Ghoniem M.

BMC Bioinformatics. 2017 May 2;18(1):233. doi: 10.1186/s12859-017-1653-5.


IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses.

Narayanasamy S, Jarosz Y, Muller EE, Heintz-Buschart A, Herold M, Kaysen A, Laczny CC, Pinel N, May P, Wilmes P.

Genome Biol. 2016 Dec 16;17(1):260.


Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota.

Magnúsdóttir S, Heinken A, Kutt L, Ravcheev DA, Bauer E, Noronha A, Greenhalgh K, Jäger C, Baginska J, Wilmes P, Fleming RM, Thiele I.

Nat Biotechnol. 2017 Jan;35(1):81-89. doi: 10.1038/nbt.3703. Epub 2016 Nov 28.


A Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen Susceptibility.

Desai MS, Seekatz AM, Koropatkin NM, Kamada N, Hickey CA, Wolter M, Pudlo NA, Kitamoto S, Terrapon N, Muller A, Young VB, Henrissat B, Wilmes P, Stappenbeck TS, Núñez G, Martens EC.

Cell. 2016 Nov 17;167(5):1339-1353.e21. doi: 10.1016/j.cell.2016.10.043.


Erratum: Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes.

Heintz-Buschart A, May P, Laczny CC, Lebrun LA, Bellora C, Krishna A, Wampach L, Schneider JG, Hogan A, Beaufort C, Wilmes P.

Nat Microbiol. 2016 Oct 24;2:16227. doi: 10.1038/nmicrobiol.2016.227. No abstract available.


Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes.

Heintz-Buschart A, May P, Laczny CC, Lebrun LA, Bellora C, Krishna A, Wampach L, Schneider JG, Hogan A, de Beaufort C, Wilmes P.

Nat Microbiol. 2016 Oct 10;2:16180. doi: 10.1038/nmicrobiol.2016.180. Erratum in: Nat Microbiol. 2016 Oct 24;2:16227.


Identification, Recovery, and Refinement of Hitherto Undescribed Population-Level Genomes from the Human Gastrointestinal Tract.

Laczny CC, Muller EE, Heintz-Buschart A, Herold M, Lebrun LA, Hogan A, May P, de Beaufort C, Wilmes P.

Front Microbiol. 2016 Jun 21;7:884. doi: 10.3389/fmicb.2016.00884. eCollection 2016.


Erratum to: Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires.

Bauer E, Laczny CC, Magnusdottir S, Wilmes P, Thiele I.

Microbiome. 2016 Jul 4;4(1):35. No abstract available.


Sources and Functions of Extracellular Small RNAs in Human Circulation.

Fritz JV, Heintz-Buschart A, Ghosal A, Wampach L, Etheridge A, Galas D, Wilmes P.

Annu Rev Nutr. 2016 Jul 17;36:301-36. doi: 10.1146/annurev-nutr-071715-050711. Epub 2016 May 13. Review.


A microfluidics-based in vitro model of the gastrointestinal human-microbe interface.

Shah P, Fritz JV, Glaab E, Desai MS, Greenhalgh K, Frachet A, Niegowska M, Estes M, Jäger C, Seguin-Devaux C, Zenhausern F, Wilmes P.

Nat Commun. 2016 May 11;7:11535. doi: 10.1038/ncomms11535.


The human gut microbiome in health: establishment and resilience of microbiota over a lifetime.

Greenhalgh K, Meyer KM, Aagaard KM, Wilmes P.

Environ Microbiol. 2016 Jul;18(7):2103-16. doi: 10.1111/1462-2920.13318. Review.


A new quantitative measure for radiologic osteoarthritis of the lateral knee compartment distinguishes patients with longstanding lateral meniscectomy from non-pathological knees.

Weber E, Theisen D, Wilmes P, Menetrey J, Hulet C, Seil R.

Knee Surg Sports Traumatol Arthrosc. 2016 May;24(5):1569-74. doi: 10.1007/s00167-016-4084-3. Epub 2016 Mar 29.


Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires.

Bauer E, Laczny CC, Magnusdottir S, Wilmes P, Thiele I.

Microbiome. 2015 Nov 30;3:55. doi: 10.1186/s40168-015-0121-6. Erratum in: Microbiome. 2016;4(1):35.


In situ phenotypic heterogeneity among single cells of the filamentous bacterium Candidatus Microthrix parvicella.

Sheik AR, Muller EE, Audinot JN, Lebrun LA, Grysan P, Guignard C, Wilmes P.

ISME J. 2016 May;10(5):1274-9. doi: 10.1038/ismej.2015.181. Epub 2015 Oct 27.


A decade of metaproteomics: where we stand and what the future holds.

Wilmes P, Heintz-Buschart A, Bond PL.

Proteomics. 2015 Oct;15(20):3409-17. doi: 10.1002/pmic.201500183. Epub 2015 Sep 10.


Comparative integrated omics: identification of key functionalities in microbial community-wide metabolic networks.

Roume H, Heintz-Buschart A, Muller EEL, May P, Satagopam VP, Laczny CC, Narayanasamy S, Lebrun LA, Hoopmann MR, Schupp JM, Gillece JD, Hicks ND, Engelthaler DM, Sauter T, Keim PS, Moritz RL, Wilmes P.

NPJ Biofilms Microbiomes. 2015 Jun 17;1:15007. doi: 10.1038/npjbiofilms.2015.7. eCollection 2015.


Method optimization for fecal sample collection and fecal DNA extraction.

Mathay C, Hamot G, Henry E, Georges L, Bellora C, Lebrun L, de Witt B, Ammerlaan W, Buschart A, Wilmes P, Betsou F.

Biopreserv Biobank. 2015 Apr;13(2):79-93. doi: 10.1089/bio.2014.0031.


Integrated omics for the identification of key functionalities in biological wastewater treatment microbial communities.

Narayanasamy S, Muller EE, Sheik AR, Wilmes P.

Microb Biotechnol. 2015 May;8(3):363-8. doi: 10.1111/1751-7915.12255. Epub 2015 Feb 12.


VizBin - an application for reference-independent visualization and human-augmented binning of metagenomic data.

Laczny CC, Sternal T, Plugaru V, Gawron P, Atashpendar A, Margossian HH, Coronado S, der Maaten Lv, Vlassis N, Wilmes P.

Microbiome. 2015 Jan 20;3(1):1. doi: 10.1186/s40168-014-0066-1. eCollection 2015.


The extracellular RNA complement of Escherichia coli.

Ghosal A, Upadhyaya BB, Fritz JV, Heintz-Buschart A, Desai MS, Yusuf D, Huang D, Baumuratov A, Wang K, Galas D, Wilmes P.

Microbiologyopen. 2015 Apr;4(2):252-266. doi: 10.1002/mbo3.235. Epub 2015 Jan 21.


Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage.

Muller EE, Pinel N, Laczny CC, Hoopmann MR, Narayanasamy S, Lebrun LA, Roume H, Lin J, May P, Hicks ND, Heintz-Buschart A, Wampach L, Liu CM, Price LB, Gillece JD, Guignard C, Schupp JM, Vlassis N, Baliga NS, Moritz RL, Keim PS, Wilmes P.

Nat Commun. 2014 Nov 26;5:5603. doi: 10.1038/ncomms6603.


Lipid-based biofuel production from wastewater.

Muller EE, Sheik AR, Wilmes P.

Curr Opin Biotechnol. 2014 Dec;30:9-16. doi: 10.1016/j.copbio.2014.03.007. Epub 2014 Apr 23. Review.


Systematic design of 18S rRNA gene primers for determining eukaryotic diversity in microbial consortia.

Hugerth LW, Muller EE, Hu YO, Lebrun LA, Roume H, Lundin D, Wilmes P, Andersson AF.

PLoS One. 2014 Apr 22;9(4):e95567. doi: 10.1371/journal.pone.0095567. eCollection 2014. Erratum in: PLoS One. 2015;10(1):e0117636.


Alignment-free visualization of metagenomic data by nonlinear dimension reduction.

Laczny CC, Pinel N, Vlassis N, Wilmes P.

Sci Rep. 2014 Mar 31;4:4516. doi: 10.1038/srep04516.

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