Publikationen

2024

Ramaboli, M. C.; Ocvirk, S.; Khan Mirzaei, M.; Eberhart, B. L.; Valdivia-Garcia, M.; Metwaly, A.; Neuhaus, K.; Barker, G.; Ru, J.; Nesengani, L. T.; Mahdi-Joest, D.; Wilson, A. S.; Joni, S. K.; Layman, D. C.; Zheng, J.; Mandal, R.; Chen, Q.; Perez, M. R.; Fortuin, S.; Gaunt, B.; Wishart, D.; Methé, B.; Haller, D.; Li, J. V.; Deng, L.; Swart, R.; O’Keefe, S. J. D.: Diet changes due to urbanization in South Africa are linked to microbiome and metabolome signatures of Westernization and colorectal cancer. Nature Communications 15 (1), 2024 mehr…

2023

Schult, David; Maurer, H. Carlo; Frolova, Marina; Ringelhan, Marc; Mayr, Ulrich; Ulrich, Jörg; Heilmaier, Markus; Rasch, Sebastian; Lahmer, Tobias; Reitmeier, Sandra; Hennig, Chiara; Gassner, Christina; Thur, Niklas; Will, Theresa; Janssen, Klaus-Peter; Steiger, Katja; Jesinghaus, Moritz; Neuhaus, Klaus; Quante, Michael; Haller, Dirk; Abdelhafez, Mohamed; Schmid, Roland M.; Middelhoff, Moritz: Systematic Evaluation of Clinical, Nutritional and Fecal Microbial Factors for their Association with Colorectal Polyps. Clinical and Translational Gastroenterology, 2023 mehr…

2022

Wahl, Anika; Huptas, Christopher; Neuhaus, Klaus: Comparison of rRNA depletion methods for efficient bacterial mRNA sequencing. Scientific Reports 12 (1), 2022 mehr…

2021

Abellan-Schneyder I, Schusser AJ, Neuhaus K: ddPCR allows 16S rRNA gene amplicon sequencing of very small DNA amounts from low-biomass samples. -, 2021, mehr…
Abellan-Schneyder, Isabel; Siebert, Annemarie; Hofmann, Katharina; Wenning, Mareike; Neuhaus, Klaus: Full-Length SSU rRNA Gene Sequencing Allows Species-Level Detection of Bacteria, Archaea, and Yeasts Present in Milk. Microorganisms 9 (6), 2021, 1251 mehr…
Amar, Yacine; Lagkouvardos, Ilias; Silva, Rafaela L.; Ishola, Oluwaseun Ayodeji; Foesel, Bärbel U.; Kublik, Susanne; Schöler, Anne; Niedermeier, Sebastian; Bleuel, Rachela; Zink, Alexander; Neuhaus, Klaus; Schloter, Michael; Biedermann, Tilo; Köberle, Martin: Pre-digest of unprotected DNA by Benzonase improves the representation of living skin bacteria and efficiently depletes host DNA. Microbiome 9 (1), 2021 mehr…
Heidebrecht, Hans-Jürgen; Lagkouvardos, Ilias; Reitmeier, Sandra; Hengst, Claudia; Kulozik, Ulrich; Pfaffl, Michael W.: Alteration of Intestinal Microbiome of Clostridioides difficile-Infected Hamsters during the Treatment with Specific Cow Antibodies. Antibiotics 10 (6), 2021, 724 mehr…
Isabel Abellan-Schneyder, Monica Steffi Matchado, Sandra Reitmeier, Alina Sommer, Zeno Sewald, Jan Baumbach, Markus List, Klaus Neuhaus: Primer, Pipelines, Parameters: Issues in 16S rRNA Gene Sequencing. mSphere, 2021 mehr…
Kreitmeier M, Ardern Z, Abele M, Ludwig C, Scherer S, Neuhaus K: Spotlight on alternative frame coding: two long overlapping genes in Pseudomonas aeruginosa are translated and under purifying selection. -, 2021, mehr…
Maheshwari, Garima; Gessner, Denise K.; Neuhaus, Klaus; Most, Erika; Zorn, Holger; Eder, Klaus; Ringseis, Robert: Influence of a Biotechnologically Produced Oyster Mushroom (Pleurotus sajor-caju) on the Gut Microbiota and Microbial Metabolites in Obese Zucker Rats. Journal of Agricultural and Food Chemistry 69 (5), 2021, 1524-1535 mehr…
Prax, Nicoletta; Wagner, Stefanie; Schardt, Jakob; Neuhaus, Klaus; Clavel, Thomas; Fuchs, Thilo M.: A diet-specific microbiota drives Salmonella Typhimurium to adapt its in vivo response to plant-derived substrates. Animal Microbiome 3 (1), 2021 mehr…
Reitmeier, Sandra; Hitch, Thomas C. A.; Treichel, Nicole; Fikas, Nikolaos; Hausmann, Bela; Ramer-Tait, Amanda E.; Neuhaus, Klaus; Berry, David; Haller, Dirk; Lagkouvardos, Ilias; Clavel, Thomas: Handling of spurious sequences affects the outcome of high-throughput 16S rRNA gene amplicon profiling. ISME Communications 1 (1), 2021 mehr…
Rühlemann, Malte Christoph; Hermes, Britt Marie; Bang, Corinna; Doms, Shauni; Moitinho-Silva, Lucas; Thingholm, Louise Bruun; Frost, Fabian; Degenhardt, Frauke; Wittig, Michael; Kässens, Jan; Weiss, Frank Ulrich; Peters, Annette; Neuhaus, Klaus; Völker, Uwe; Völzke, Henry; Homuth, Georg; Weiss, Stefan; Grallert, Harald; Laudes, Matthias; Lieb, Wolfgang; Haller, Dirk; Lerch, Markus M.; Baines, John F.; Franke, Andre: Genome-wide association study in 8,956 German individuals identifies influence of ABO histo-blood groups on gut microbiome. Nature Genetics 53 (2), 2021, 147-155 mehr…
Wenderlein, Jasmin; Böswald, Linda F.; Ulrich, Sebastian; Kienzle, Ellen; Neuhaus, Klaus; Lagkouvardos, Ilias; Zenner, Christian; Straubinger, Reinhard K.: Processing Matters in Nutrient-Matched Laboratory Diets for Mice—Microbiome. Animals 11 (3), 2021, 862 mehr…
Zenner, Christian; Hitch, Thomas C. A.; Riedel, Thomas; Wortmann, Esther; Tiede, Stefan; Buhl, Eva M.; Abt, Birte; Neuhaus, Klaus; Velge, Philippe; Overmann, Jörg; Kaspers, Bernd; Clavel, Thomas: Early-Life Immune System Maturation in Chickens Using a Synthetic Community of Cultured Gut Bacteria. mSystems 6 (3), 2021 mehr…

2020

Ardern, Zachary; Neuhaus, Klaus; Scherer, Siegfried: Are Antisense Proteins in Prokaryotes Functional? Frontiers in Molecular Biosciences 7, 2020 mehr…
Glaub, Alina; Huptas, Christopher; Neuhaus, Klaus; Ardern, Zachary: Recommendations for bacterial ribosome profiling experiments based on bioinformatic evaluation of published data. Journal of Biological Chemistry 295 (27), 2020, 8999-9011 mehr…
Reitmeier, Sandra; Kiessling, Silke; Neuhaus, Klaus; Haller, Dirk: Comparing Circadian Rhythmicity in the Human Gut Microbiome. STAR Protocols 1 (3), 2020, 100148 mehr…
Rettenmaier, Regina; Lo, Yat Kei; Schmidt, Larissa; Munk, Bernhard; Lagkouvardos, Ilias; Neuhaus, Klaus; Schwarz, Wolfgang; Liebl, Wolfgang; Zverlov, Vladimir: A Novel Primer Mixture for GH48 Genes: Quantification and Identification of Truly Cellulolytic Bacteria in Biogas Fermenters. Microorganisms 8 (9), 2020, 1297 mehr…
Troll, Martina; Brandmaier, Stefan; Reitmeier, Sandra; Adam, Jonathan; Sharma, Sapna; Sommer, Alice; Bind, Marie-Abèle; Neuhaus, Klaus; Clavel, Thomas; Adamski, Jerzy; Haller, Dirk; Peters, Annette; Grallert, Harald: Investigation of Adiposity Measures and Operational Taxonomic unit (OTU) Data Transformation Procedures in Stool Samples from a German Cohort Study Using Machine Learning Algorithms. Microorganisms 8 (4), 2020, 547 mehr…
Wylensek, David; Hitch, Thomas C. A.; Riedel, Thomas; Afrizal, Afrizal; Kumar, Neeraj; Wortmann, Esther; Liu, Tianzhe; Devendran, Saravanan; Lesker, Till R.; Hernández, Sara B.; Heine, Viktoria; Buhl, Eva M.; M. D’Agostino, Paul; Cumbo, Fabio; Fischöder, Thomas; Wyschkon, Marzena; Looft, Torey; Parreira, Valeria R.; Abt, Birte; Doden, Heidi L.; Ly, Lindsey; Alves, João M. P.; Reichlin, Markus; Flisikowski, Krzysztof; Suarez, Laura Navarro; Neumann, Anthony P.; Suen, Garret; de Wouters, Tomas; Rohn, Sascha; Lagkouvardos, Ilias; Allen-Vercoe, Emma; Spröer, Cathrin; Bunk, Boyke; Taverne-Thiele, Anja J.; Giesbers, Marcel; Wells, Jerry M.; Neuhaus, Klaus; Schnieke, Angelika; Cava, Felipe; Segata, Nicola; Elling, Lothar; Strowig, Till; Ridlon, Jason M.; Gulder, Tobias A. M.; Overmann, Jörg; Clavel, Thomas: A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity. Nature Communications 11 (1), 2020 mehr…

2019

Lagkouvardos, Ilias; Lesker, Till R.; Hitch, Thomas C. A.; Gálvez, Eric J. C.; Smit, Nathiana; Neuhaus, Klaus; Wang, Jun; Baines, John F.; Abt, Birte; Stecher, Bärbel; Overmann, Jörg; Strowig, Till; Clavel, Thomas: Sequence and cultivation study of Muribaculaceae reveals novel species, host preference, and functional potential of this yet undescribed family. Microbiome 7 (1), 2019 mehr…
Lengfelder, Isabella; Sava, Irina G.; Hansen, Jonathan J.; Kleigrewe, Karin; Herzog, Jeremy; Neuhaus, Klaus; Hofmann, Thomas; Sartor, R. Balfour; Haller, Dirk: Complex Bacterial Consortia Reprogram the Colitogenic Activity of Enterococcus faecalis in a Gnotobiotic Mouse Model of Chronic, Immune-Mediated Colitis. Frontiers in Immunology 10, 2019 mehr…
Rettenmaier, Regina; Duerr, Carina; Neuhaus, Klaus; Liebl, Wolfgang; Zverlov, Vladimir V.: Comparison of sampling techniques and different media for the enrichment and isolation of cellulolytic organisms from biogas fermenters. Systematic and Applied Microbiology 42 (4), 2019, 481-487 mehr…

2018

Bossert, Martin; Kracht, David; Scherer, Siegfried; Landstorfer, Richard; Neuhaus, Klaus: Improving the reliability of RNA-seq: Approaching single-cell transciptomics to explore individuality in bacteria. In: M. Bossert (Hrsg.): Information- and Communication Theory in Molecular Biology. Springer International Publishing, 2018, 181 - 198 mehr…
Hücker, Sarah M.; Vanderhaeghen, Sonja; Abellan-Schneyder, Isabel; Scherer, Siegfried; Neuhaus, Klaus: The Novel Anaerobiosis-Responsive Overlapping Gene ano Is Overlapping Antisense to the Annotated Gene ECs2385 of Escherichia coli O157:H7 Sakai. Frontiers in Microbiology 9, 2018 mehr…
Hücker, Sarah M.; Vanderhaeghen, Sonja; Abellan-Schneyder, Isabel; Wecko, Romy; Simon, Svenja; Scherer, Siegfried; Neuhaus, Klaus: A novel short L-arginine responsive protein-coding gene (laoB) antiparallel overlapping to a CadC-like transcriptional regulator in Escherichia coli O157:H7 Sakai originated by overprinting. BMC Evolutionary Biology 18 (1), 2018 mehr…
Scherer, Siedfried; Neuhaus, Klaus; Bossert, Martin; Mir, Katharina; Keim, Daniel; Simon, Svenja,: Finding new overlapping genes and their theory (FOG Theory). In: M. Bossert (Hrsg.): Information- and Communication Theory in Molecular Biology. Springer International Publishing, 2018, 137-159 mehr…
Vanderhaeghen, Sonja; Zehentner, Barbara; Scherer, Siegfried; Neuhaus, Klaus; Ardern, Zachary: The novel EHEC gene asa overlaps the TEGT transporter gene in antisense and is regulated by NaCl and growth phase. Scientific Reports 8 (1), 2018 mehr…

2017

Bazanella, Monika; Maier, Tanja V; Clavel, Thomas; Lagkouvardos, Ilias; Lucio, Marianna; Maldonado-Gòmez, Maria X; Autran, Chloe; Walter, Jens; Bode, Lars; Schmitt-Kopplin, Philippe; Haller, Dirk: Randomized controlled trial on the impact of early-life intervention with bifidobacteria on the healthy infant fecal microbiota and metabolome. The American Journal of Clinical Nutrition, 2017, ajcn157529 mehr…
Bossert, Martin; Kracht, David; Scherer, Siegfried; Landstorfer, Richard; Neuhaus, Klaus: Improving the Reliability of RNA-seq: Approaching Single-Cell Transcriptomics To Explore Individuality in Bacteria. In: Information- and Communication Theory in Molecular Biology. Springer International Publishing, 2017 mehr…
Hücker, Sarah M.; Ardern, Zachary; Goldberg, Tatyana; Schafferhans, Andrea; Bernhofer, Michael; Vestergaard, Gisle; Nelson, Chase W.; Schloter, Michael; Rost, Burkhard; Scherer, Siegfried; Neuhaus, Klaus: Discovery of numerous novel small genes in the intergenic regions of the Escherichia coli O157:H7 Sakai genome. PLOS ONE 12 (9), 2017, e0184119 mehr…
Lagkouvardos, Ilias; Fischer, Sandra; Kumar, Neeraj; Clavel, Thomas: Rhea: a transparent and modular R pipeline for microbial profiling based on 16S rRNA gene amplicons. PeerJ 5, 2017, e2836 mehr…
Neuhaus, Klaus; Landstorfer, Richard; Simon, Svenja; Schober, Steffen; Wright, Patrick R.; Smith, Cameron; Backofen, Rolf; Wecko, Romy; Keim, Daniel A.; Scherer, Siegfried: Differentiation of ncRNAs from small mRNAs in Escherichia coli O157:H7 EDL933 (EHEC) by combined RNAseq and RIBOseq – ryhB encodes the regulatory RNA RyhB and a peptide, RyhP. BMC Genomics 18 (1), 2017 mehr…
Panés, J.; D'Haens, G.R.; Higgins, P.D.R.; Mele, L.; Moscariello, M.; Chan, G.; Wang, W.; Niezychowski, W.; Su, C.; Maller, E.: OP031 Long-term safety and tolerability of oral tofacitinib in patients with Crohn's disease: results from a phase 2 open-label 48-week extension study. Journal of Crohn's and Colitis 11 (suppl_1), 2017, S18-S19 mehr…

2016

Fellner, Lea; Huptas, Christopher; Simon, Svenja; Mühlig, Anna; Scherer, Siegfried; Neuhaus, Klaus: Draft Genome Sequences of Three European Laboratory Derivatives from EnterohemorrhagicEscherichia coliO157:H7 Strain EDL933, Including Two Plasmids: TABLE 1 . Genome Announcements 4 (2), 2016, e01331-15 mehr…
Hücker, Sarah Maria; Simon, Svenja; Scherer, Siegfried; Neuhaus, Klaus: Transcriptional and translational regulation by RNA thermometers, riboswitches and the sRNA DsrA inEscherichia coliO157:H7 Sakai under combined cold and osmotic stress adaptation. FEMS Microbiology Letters 364 (2), 2016, fnw262 mehr…
Lagkouvardos, Ilias; Joseph, Divya; Kapfhammer, Martin; Giritli, Sabahattin; Horn, Matthias; Haller, Dirk; Clavel, Thomas: IMNGS: A comprehensive open resource of processed 16S rRNA microbial profiles for ecology and diversity studies. Scientific Reports 6 (1), 2016 mehr…
Lagkouvardos, Ilias; Pukall, Rüdiger; Abt, Birte; Foesel, Bärbel U.; Meier-Kolthoff, Jan P.; Kumar, Neeraj; Bresciani, Anne; Martínez, Inés; Just, Sarah; Ziegler, Caroline; Brugiroux, Sandrine; Garzetti, Debora; Wenning, Mareike; Bui, Thi P. N.; Wang, Jun; Hugenholtz, Floor; Plugge, Caroline M.; Peterson, Daniel A.; Hornef, Mathias W.; Baines, John F.; Smidt, Hauke; Walter, Jens; Kristiansen, Karsten; Nielsen, Henrik B.; Haller, Dirk; Overmann, Jörg; Stecher, Bärbel; Clavel, Thomas: The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota. Nature Microbiology 1 (10), 2016, 16131 mehr…
Lagkouvardos, Ilias; Pukall, Rüdiger; Abt, Birte; Foesel, Bärbel U.; Meier-Kolthoff, Jan P.; Kumar, Neeraj; Bresciani, Anne; Martínez, Inés; Just, Sarah; Ziegler, Caroline; Brugiroux, Sandrine; Garzetti, Debora; Wenning, Mareike; Bui, Thi P. N.; Wang, Jun; Hugenholtz, Floor; Plugge, Caroline M.; Peterson, Daniel A.; Hornef, Mathias W.; Baines, John F.; Smidt, Hauke; Walter, Jens; Kristiansen, Karsten; Nielsen, Henrik B.; Haller, Dirk; Overmann, Jörg; Stecher, Bärbel; Clavel, Thomas: Corrigendum: The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota. Nature Microbiology 1 (11), 2016, 16219 mehr…
Lee, Thomas; Clavel, Thomas; Smirnov, Kirill; Schmidt, Annemarie; Lagkouvardos, Ilias; Walker, Alesia; Lucio, Marianna; Michalke, Bernhard; Schmitt-Kopplin, Philippe; Fedorak, Richard; Haller, Dirk: Oral versus intravenous iron replacement therapy distinctly alters the gut microbiota and metabolome in patients with IBD. Gut 66 (5), 2016, 863-871 mehr…
Neuhaus, Klaus; Landstorfer, Richard; Fellner, Lea; Simon, Svenja; Schafferhans, Andrea; Goldberg, Tatyana; Marx, Harald; Ozoline, Olga N.; Rost, Burkhard; Kuster, Bernhard; Keim, Daniel A.; Scherer, Siegfried: Translatomics combined with transcriptomics and proteomics reveals novel functional, recently evolved orphan genes in Escherichia coli O157:H7 (EHEC). BMC Genomics 17 (1), 2016 mehr…
Simon, Svenja; Mittelstädt, Sebastian; Kwon, Bum Chul; Stoffel, Andreas; Landstorfer, Richard; Neuhaus, Klaus; Mühlig, Anna; Scherer, Siegfried; Keim, Daniel A: VisExpress: Visual exploration of differential gene expression data. Information Visualization 16 (1), 2016, 48-73 mehr…

2015

Schaubeck, Monika; Clavel, Thomas; Calasan, Jelena; Lagkouvardos, Ilias; Haange, Sven Bastiaan; Jehmlich, Nico; Basic, Marijana; Dupont, Aline; Hornef, Mathias; Bergen, Martin von; Bleich, André; Haller, Dirk: Dysbiotic gut microbiota causes transmissible Crohn's disease-like ileitis independent of failure in antimicrobial defence. Gut 65 (2), 2015, 225-237 mehr…

2014

Landstorfer, Richard; Simon, Svenja; Schober, Steffen; Keim, Daniel; Scherer, Siegfried; Neuhaus, Klaus: Comparison of strand-specific transcriptomes of enterohemorrhagic Escherichia coli O157:H7 EDL933 (EHEC) under eleven different environmental conditions including radish sprouts and cattle feces. BMC Genomics 15 (1), 2014, 353 mehr…

2013

Mir, Katharina; Neuhaus, Klaus; Bossert, Martin; Schober, Steffen: Short Barcodes for Next Generation Sequencing. PLoS ONE 8 (12), 2013, e82933 mehr…

2012

Lang Halter, E.; Neuhaus, K.; Scherer, S.: Listeria weihenstephanensis sp. nov., isolated from the water plant Lemna trisulca taken from a freshwater pond. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 63 (Pt 2), 2012, 641-647 mehr…