2024

De Bernardini N, Zampieri G, Campanaro S, Zimmermann J, Waschina S, Treu L.
pan-Draft: automated reconstruction of species-representative metabolic models from multiple genomes
Genome Biology. 2024. 25(1). doi: 10.1186/s13059-024-03425-1

Welz L, Harris DMM, Kim NM, Alsaadi AI, Wu Q, Oumari M, Taubenheim J, Volk V, Credido G, Koncina E, Mukherjee PK, Tran F, Sievers LK, Pavlidis P, Powell N, Rieder F, Letellier E, Waschina S, Kaleta C, Feuerhake F, Verstockt B, McReynolds MR, Rosenstiel P, Schreiber S, Aden K.
A metabolic constraint in the kynurenine pathway drives mucosal inflammation in IBD
(preprint) medRxiv. 2024. doi: 10.1101/2024.08.08.24311598

Harris DMM, Szymczak S, Schuchardt S, Labrenz J, Tran F, Welz L, Graßhoff H, Zirpel H, Sümbül M, Oumari M, Engelbogen N, Junker R, Conrad C, Thaçi D, Frey N, Franke A, Weidinger S, Hoyer B, Rosenstiel P, Waschina S, Schreiber S, Aden K.
Tryptophan degradation as a systems phenomenon in inflammation – an analysis across 13 chronic inflammatory diseases
eBioMedicine. 2024. 102. doi: 10.1016/j.ebiom.2024.105056

Best L, Dost T, Esser D, Flor S, Haase M, Kadibalban AS, Marinos G, Walker A, Zimmermann J, Simon R, Schmidt S, Taubenheim J, Kunzel S, Hasler R, Groth M, Waschina S, Witte OW, Schmitt-Kopplin P, Baines JF, Frahm C, Kaleta C.
Metabolic modeling reveals the aging-associated decline of host-microbiome metabolic interactions in mice
(preprint) bioRxiv. 2024. doi: 10.1101/2024.03.28.587009

Marinos G, Hamerich IK, Debray R, Obeng N, Petersen C, Taubenheim J, Zimmermann J, Blackburn D, Samuel BS, Dierking K, Franke A, Laudes M, Waschina S, Schulenburg H, Kaleta C.
Metabolic model predictions enable targeted microbiome manipulation through precision prebiotics
Microbiology Spectrum. 2024. . doi: 10.1128/spectrum.01144-23

Rühlemann MC, Bang C, Gogarten JF, Hermes BM, Groussin M, Waschina S, Poyet M, Ulrich M, Akoua-Koffi C, Deschner T, Muyembe-Tamfum JJ, Robbins MM, Surbeck M, Wittig RM, Zuberbühler K, Baines JF, Leendertz FH, Franke A.
Functional host-specific adaptation of the intestinal microbiome in hominids
Nature Communications. 2024. 15(1). doi: 10.1038/s41467-023-44636-7

2023

Rühlemann M, Waschina S, Wacker EM, Rausch P, Schaan A, Zafroon Z, Franzpötter K, Jacobs G, Ellinghaus D, Kruse R, Bergemalm D, Halfvarson J, Ziemann M, Görg S, Lieb W, Schreiber S, Poyet M, Bang C, Franke A, Groussin M.
Disease signatures in the gut metagenome of a prospective family cohort of inflammatory bowel disease
(preprint) medRxiv. 2023. doi: 10.1101/2023.12.10.23299783

Wijewardene L, Schwenker JA, Friedrichsen M, Jensen A, Löbel F, Austen T, Ulrich U, Fohrer N, Bang C, Waschina S, Hölzel CS.
Selection of aquatic microbiota exposed to the herbicides flufenacet and metazachlor
Environmental Microbiology. 2023. 25(12). doi: 10.1111/1462-2920.16535

Saha S, Kalathera J, Sumi TS, Mane V, Zimmermann S, Waschina S, Pande S.
Mass lysis of bacterial predators drives the enrichment of antibiotic resistance in soil microbial communities
(preprint) bioRxiv. 2023. doi: 10.1101/2023.11.20.567171

Starke S, Harris DMM, Zimmermann J, Schuchardt S, Oumari M, Frank D, Bang C, Rosenstiel P, Schreiber S, Frey N, Franke A, Aden K, Waschina S.
Amino acid auxotrophies in human gut bacteria are linked to higher microbiome diversity and long-term stability
The ISME Journal. 2023. 17(12). doi: 10.1038/s41396-023-01537-3

Blesl A, Wurm P, Waschina S, Gröchenig HP, Novacek G, Primas C, Reinisch W, Kutschera M, Illiasch C, Hennlich B, Steiner P, Koch R, Tillinger W, Haas T, Reicht G, Mayer A, Ludwiczek O, Miehsler W, Steidl K, Binder L, Reider S, Watschinger C, Fürst S, Kump P, Moschen A, Aden K, Gorkiewicz G, Högenauer C.
Prediction of Response to Systemic Corticosteroids in Active UC by Microbial Composition—A Prospective Multicenter Study
Inflammatory Bowel Diseases. 2023. 30(1). doi: 10.1093/ibd/izad126

Effenberger M, Waschina S, Bronowski C, Sturm G, Tassiello O, Sommer F, Zollner A, Watschinger C, Grabherr F, Gstir R, Grander C, Enrich B, Bale R, Putzer D, Djanani A, Moschen AR, Zoller H, Rupp J, Schreiber S, Burcelin R, Lass-Flörl C, Trajanoski Z, Oberhuber G, Rosenstiel P, Adolph TE, Aden K, Tilg H.
A gut bacterial signature in blood and liver tissue characterizes cirrhosis and hepatocellular carcinoma
Hepatology Communications. 2023. 7(7). doi: 10.1097/hc9.0000000000000182

2022

Jensen-Kroll J, Demetrowitsch T, Clawin-Rädecker I, Klempt M, Waschina S, Schwarz K.
Microbiota independent effects of oligosaccharides on Caco-2 cells -A semi-targeted metabolomics approach using DI-FT-ICR-MS coupled with pathway enrichment analysis
Frontiers in Molecular Biosciences. 2022. 9. doi: 10.3389/fmolb.2022.968643

Waschina S, Seeger K.
Using in-tube extraction and slice selective NMR experiments allow imaging via statistical analysis of metabolic profiles
Analytica Chimica Acta. 2022. 1231. doi: 10.1016/j.aca.2022.340419

Troci A, Rausch P, Waschina S, Lieb W, Franke A, Bang C.
Long‐Term Dietary Effects on Human Gut Microbiota Composition Employing Shotgun Metagenomics Data Analysis
Molecular Nutrition & Food Research. 2022. 67(24). doi: 10.1002/mnfr.202101098

Schwenker JA, Friedrichsen M, Waschina S, Bang C, Franke A, Mayer R, Hölzel CS.
Bovine milk microbiota: Evaluation of different DNA extraction protocols for challenging samples
MicrobiologyOpen. 2022. 11(2). doi: 10.1002/mbo3.1275

Bossung V, Lupatsii M, Dashdorj L, Tassiello O, Jonassen S, Pagel J, Demmert M, Wolf EA, Rody A, Waschina S, Graspeuntner S, Rupp J, Härtel C.
Timing of antimicrobial prophylaxis for cesarean section is critical for gut microbiome development in term born infants
Gut Microbes. 2022. 14(1). doi: 10.1080/19490976.2022.2038855

2021

Giri S, Oña L, Waschina S, Shitut S, Yousif G, Kaleta C, Kost C.
Metabolic dissimilarity determines the establishment of cross-feeding interactions in bacteria
Current Biology. 2021. 31(24). doi: 10.1016/j.cub.2021.10.019

Schönborn JW, Stewart FA, Enriquez KM, Akhtar I, Droste A, Waschina S, Beller M.
Modeling Drosophila gut microbe interactions reveals metabolic interconnectivity
iScience. 2021. 24(11). doi: 10.1016/j.isci.2021.103216

Josephs-Spaulding J, Krogh TJ, Rettig HC, Lyng M, Chkonia M, Waschina S, Graspeuntner S, Rupp J, Møller-Jensen J, Kaleta C.
Recurrent Urinary Tract Infections: Unraveling the Complicated Environment of Uncomplicated rUTIs
Frontiers in Cellular and Infection Microbiology. 2021. 11. doi: 10.3389/fcimb.2021.562525

Zimmermann J, Kaleta C, Waschina S.
gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models
Genome Biology. 2021. 22(1). doi: 10.1186/s13059-021-02295-1

Schilf P, Künstner A, Olbrich M, Waschina S, Fuchs B, Galuska CE, Braun A, Neuschütz K, Seutter M, Bieber K, Hellberg L, Sina C, Laskay T, Rupp J, Ludwig RJ, Zillikens D, Busch H, Sadik CD, Hirose M, Ibrahim SM.
A Mitochondrial Polymorphism Alters Immune Cell Metabolism and Protects Mice from Skin Inflammation
International Journal of Molecular Sciences. 2021. 22(3). doi: 10.3390/ijms22031006

2020

Effenberger M, Reider S, Waschina S, Bronowski C, Enrich B, Adolph TE, Koch R, Moschen AR, Rosenstiel P, Aden K, Tilg H.
Microbial Butyrate Synthesis Indicates Therapeutic Efficacy of Azathioprine in IBD Patients
Journal of Crohn’s and Colitis. 2020. 15(1). doi: 10.1093/ecco-jcc/jjaa152

Demetrowitsch TJ, Schlicht K, Knappe C, Zimmermann J, Jensen-Kroll J, Pisarevskaja A, Brix F, Brandes J, Geisler C, Marinos G, Sommer F, Schulte DM, Kaleta C, Andersen V, Laudes M, Schwarz K, Waschina S.
Precision Nutrition in Chronic Inflammation
Frontiers in Immunology. 2020. 11. doi: 10.3389/fimmu.2020.587895

Pagel J, Twisselmann N, Rausch TK, Waschina S, Hartz A, Steinbeis M, Olbertz J, Nagel K, Steinmetz A, Faust K, Demmert M, Göpel W, Herting E, Rupp J, Härtel C.
Increased Regulatory T Cells Precede the Development of Bronchopulmonary Dysplasia in Preterm Infants
Frontiers in Immunology. 2020. 11. doi: 10.3389/fimmu.2020.565257

Bhat J, Bergmann AK, Waschina S, Nerl C, Kaleta C, Siebert R, Ammerpohl O, Kabelitz D.
DNA methylation profile of a hepatosplenic gamma/delta T-cell lymphoma patient associated with response to interferon-α therapy
Cellular & Molecular Immunology. 2020. 18(5). doi: 10.1038/s41423-020-0518-4

Marinos G, Kaleta C, Waschina S.
Defining the nutritional input for genome-scale metabolic models: A roadmap
PLOS ONE. 2020. 15(8). doi: 10.1371/journal.pone.0236890

2019

Aden K, Rehman A, Waschina S, Pan WH, Walker A, Lucio M, Nunez AM, Bharti R, Zimmerman J, Bethge J, Schulte B, Schulte D, Franke A, Nikolaus S, Schroeder JO, Vandeputte D, Raes J, Szymczak S, Waetzig GH, Zeuner R, Schmitt-Kopplin P, Kaleta C, Schreiber S, Rosenstiel P.
Metabolic Functions of Gut Microbes Associate With Efficacy of Tumor Necrosis Factor Antagonists in Patients With Inflammatory Bowel Diseases
Gastroenterology. 2019. 157(5). doi: 10.1053/j.gastro.2019.07.025

Giri S, Waschina S, Kaleta C, Kost C.
Defining Division of Labor in Microbial Communities
Journal of Molecular Biology. 2019. 431(23). doi: 10.1016/j.jmb.2019.06.023

Zimmermann J, Obeng N, Yang W, Pees B, Petersen C, Waschina S, Kissoyan KA, Aidley J, Hoeppner MP, Bunk B, Spröer C, Leippe M, Dierking K, Kaleta C, Schulenburg H.
The functional repertoire contained within the native microbiota of the model nematodeCaenorhabditis elegans
The ISME Journal. 2019. 14(1). doi: 10.1038/s41396-019-0504-y

Pryor R, Norvaisas P, Marinos G, Best L, Thingholm LB, Quintaneiro LM, De Haes W, Esser D, Waschina S, Lujan C, Smith RL, Scott TA, Martinez-Martinez D, Woodward O, Bryson K, Laudes M, Lieb W, Houtkooper RH, Franke A, Temmerman L, Bjedov I, Cochemé HM, Kaleta C, Cabreiro F.
Host-Microbe-Drug-Nutrient Screen Identifies Bacterial Effectors of Metformin Therapy
Cell. 2019. 178(6). doi: 10.1016/j.cell.2019.08.003

Yang W, Petersen C, Pees B, Zimmermann J, Waschina S, Dirksen P, Rosenstiel P, Tholey A, Leippe M, Dierking K, Kaleta C, Schulenburg H.
The Inducible Response of the Nematode Caenorhabditis elegans to Members of Its Natural Microbiota Across Development and Adult Life
Frontiers in Microbiology. 2019. 10. doi: 10.3389/fmicb.2019.01793

2018

Graspeuntner S, Waschina S, Künzel S, Twisselmann N, Rausch TK, Cloppenborg-Schmidt K, Zimmermann J, Viemann D, Herting E, Göpel W, Baines JF, Kaleta C, Rupp J, Härtel C, Pagel J.
Gut Dysbiosis With Bacilli Dominance and Accumulation of Fermentation Products Precedes Late-onset Sepsis in Preterm Infants
Clinical Infectious Diseases. 2018. 69(2). doi: 10.1093/cid/ciy882

D’Souza G, Shitut S, Preussger D, Yousif G, Waschina S, Kost C.
Ecology and evolution of metabolic cross-feeding interactions in bacteria
Natural Product Reports. 2018. 35(5). doi: 10.1039/c8np00009c

2016

Waschina S, D’Souza G, Kost C, Kaleta C.
Metabolic network architecture and carbon source determine metabolite production costs
The FEBS Journal. 2016. 283(11). doi: 10.1111/febs.13727

Gebauer J, Gentsch C, Mansfeld J, Schmeißer K, Waschina S, Brandes S, Klimmasch L, Zamboni N, Zarse K, Schuster S, Ristow M, Schäuble S, Kaleta C.
A Genome-Scale Database and Reconstruction of Caenorhabditis elegans Metabolism
Cell Systems. 2016. 2(5). doi: 10.1016/j.cels.2016.04.017

2015

D’Souza G, Waschina S, Kaleta C, Kost C.
Plasticity and epistasis strongly affect bacterial fitness after losing multiple metabolic genes
Evolution. 2015. 69(5). doi: 10.1111/evo.12640

2014

Schmidt R, Waschina S, Boettger-Schmidt D, Kost C, Kaleta C.
Computing autocatalytic sets to unravel inconsistencies in metabolic network reconstructions
Bioinformatics. 2014. 31(3). doi: 10.1093/bioinformatics/btu658

D’Souza G, Waschina S, Pande S, Bohl K, Kaleta C, Kost C.
LESS IS MORE: SELECTIVE ADVANTAGES CAN EXPLAIN THE PREVALENT LOSS OF BIOSYNTHETIC GENES IN BACTERIA
Evolution. 2014. 68(9). doi: 10.1111/evo.12468