Microbiome

In this project, we address methodological issues in the context of high-dimensional data from microbiome studies. A particular focus is on the analysis of complex data structures such as clustered data from longitudinal studies or meta-analyses in combination with pooled analyses of individual patient-level data.

 

For the microbiome subprojects, see the pages for Microbiome of the anterior nares and for Organ Crosstalk.

Publications

Hagenfeld D, Kleine Bardenhorst S, Matern J, et al. Long-term changes in the subgingival microbiota in patients with stage III–IV periodontitis treated by mechanical therapy and adjunctive systemic antibiotics: A secondary analysis of a randomized controlled trial. Journal of Clinical Periodontology. n/a(n/a). doi:10.1111/jcpe.13824

 

Kleine Bardenhorst S, Cereda E, Severgnini M, et al. Gut microbiota dysbiosis in Parkinson disease: A systematic review and pooled analysis. European Journal of Neurology. 2023;n/a(n/a). doi:10.1111/ene.15671

 

Kleine Bardenhorst S, Vital M, Karch A, Rübsamen N. Richness estimation in microbiome data obtained from denoising pipelines. Computational and Structural Biotechnology Journal. 2022;20: 508–520. doi: 10.1016/j.csbj.2021.12.036

 

Kleine Bardenhorst S, Berger T, Klawonn F, Vital M, Karch A, Rübsamen N. Data analysis strategies for microbiome studies in human populations - a systematic review of current practice. mSystems. 2021;6: e01154-20. doi: 10.1128/mSystems.01154-20

 

Rath S, Rox K, Kleine Bardenhorst S, Schminke U, Dörr M, Mayerle J, Frost F, Lerch MM, Karch A, Brönstrup M, Pieper DH, Vital M. Higher Trimethylamine-N-Oxide Plasma Levels with Increasing Age Are Mediated by Diet and Trimethylamine-Forming Bacteria. mSystems. 2021;6:e00945-21. doi: 10.1128/mSystems.00945-21

 

Vital M, Karch A, Pieper DH. Colonic butyrate-producing communities in humans: an overview using Omics data. mSystems. 2017;2(6). pii: e00130-17. doi: 10.1128/mSystems.00130-17.

 

Rath S, Rud T, Karch A, Pieper DH, Vital M. Pathogenic functions of host microbiota. Microbiome. 2018;6(1):174. doi: 10.1186/s40168-018-0542-0.

Caputo M, Zoch-Lesniak B, Karch A, Vital M, Meyer F, Klawonn F, Baillot A, Pieper DH, Mikolajczyk RT. Bacterial community structure and effects of picornavirus infection on the anterior nares microbiome in early childhood. BMC Microbiol. 2019;19(1):1. doi: 10.1186/s12866-018-1372-8.

Kleine Bardenhorst, S., Hagenfeld, D., Matern, J. et al. The role of the oral microbiota in the causal effect of adjunctive antibiotics on clinical outcomes in stage III–IV periodontitis patients. Microbiome 12, 220 (2024). https://doi.org/10.1186/s40168-024-01945-3

Koehlen, S.; Harks, I.; Matern, J.; Prior, K.; Eickholz, P.; Lorenz, K.; Kim, T.-S.; Kocher, T.; Meyle, J.; Kaner, D.; Jockel-Schneider, Y.; Harmsen, D.; Ehmke, B.; Kleine Bardenhorst, S.; Hagenfeld, D. Exhaled Carbon Monoxide Indicates Persistent Subgingival Dysbiosis After Periodontal Therapy. Journal of Clinical Periodontology 2026, 53 (2), 170–178. https://doi.org/10.1111/jcpe.70053.

Pappe, C. L.; Kleine Bardenhorst, S.; Prior, K.; Steckhan, N.; Michalsen, A.; Ehmke, B.; Dommisch, H.; Hagenfeld, D. Impact of Prolonged Fasting on the Oral Microbiome in Patients With Metabolic Syndrome: An Exploratory Secondary Analysis. Journal of Clinical Periodontology 2025, n/a (n/a). https://doi.org/10.1111/jcpe.14171.

Saberi Kakhki, K. C. L.; Harks ,Inga; Matern ,Johannes; Prior ,Karola; Eickholz ,Peter; Lorenz ,Katrin; Kim ,Ti-Sun; Kocher ,Thomas; Meyle ,Jörg; Kaner ,Doğan; Jockel-Schneider ,Yvonne; Harmsen ,Dag; Ehmke ,Benjamin; Kleine Bardenhorst ,Sven; and Hagenfeld, D. Association of Supragingival Plaque Management with Subgingival Microbiota Is Moderated by Adjunctive Antibiotics in Stage III-IV Periodontitis Patients during Periodontal Therapy. Journal of Oral Microbiology 2025, 17 (1), 2517043. https://doi.org/10.1080/20002297.2025.2517043.

Project details

Responsible persons

Sven Kleine Bardenhorst

Angelika Waßmuth

Nicole Rübsamen

André Karch

Project period

July 2021 - July 2023

Cooperation partners

Medizinische Hochschule Hannover

Helmholtz-Zentrum für Infektionsforschung Braunschweig

Funding

Innovative Medical Research (IMF) of the University of Münster (I-RÜ122010)

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