Publications

Treichel NS, Pauvert C, Séneca J, Pjevac P, Berry D, Penders J et al. Benchmarking of shotgun sequencing depth reveals the potential and limitations of shallow metagenomics and strain-level analysis. Nature Microbiology. 2026 Apr 21. Epub 2026 Apr 21. doi: 10.1038/s41564-026-02334-2

Vogel MA, Machairas F, Ferchiou S, Osvatic J, Alzubaidy H, Séneca J et al. Symbiont diversity within Loripes orbiculatus and the case for multiple hosts. The ISME Journal. 2026 Apr 15. doi: 10.1093/ismejo/wrag094

Schmelz P, Eckensperger S, Osvatic J, Séneca Cardoso Da Silva J, Alzubaidy H, Petersen J. Host depletion kits improve microbiome analyses in environmental samples: Seagrass as a test case. ISME Communications. 2026 Mar 28. Epub 2026 Mar 28. doi: 10.1093/ismeco/ycag082

Rigou S, Aldaroub J, Horn M, Aylward FO. Rise of the viral giants: common themes underlying genome gigantism in eukaryotic viruses and bacteriophages. Current Opinion in Microbiology. 2026 Mar 28;91:1-9. 102741. Epub 2026 Mar 28. doi: 10.1016/j.mib.2026.102741

Krasenbrink J, Chen SC, Tanabe TS, Sarikeçe H, Meurs P, Borusak S et al. Sulfoquinovose degradation by cow rumen microbiota. The ISME Journal. 2026 Mar 27. doi: 10.1093/ismejo/wrag069

Barrajon-Santos V, Nepel M, Sudhaus W, Hausmann B, Woebken D, Mayer VE. Vertically transmitted bacterivorous nematodes are consistent nest inhabitants in the Azteca-Cecropia ant-plant mutualism. Scientific Reports. 2026 Feb 25;16(1):1-12. 9624. doi: 10.1038/s41598-025-34231-9

Mohammadzadeh R, Mahnert A, Zurabishvili T, Wink L, Kumpitsch C, Habisch H et al. Cross-domain metabolic interactions link Methanobrevibacter smithii to colorectal cancer microbial ecosystems. Nature Communications. 2026 Feb 20. Epub 2026 Feb 20. doi: 10.1038/s41467-026-69711-7

Zöhrer PA, Unterberger S, Aschauer R, Draxler A, Somloi S, Kapeller M et al. The impact of a high-protein diet with strength training on the gastrointestinal microbiota in community-dwelling older adults: subanalysis of a randomized controlled trial. Frontiers in Nutrition. 2026 Jan 20;12:1-12. 1712451. doi: 10.3389/fnut.2025.1712451

Zhang R, Mayer L, Hikida H, Shichino Y, Mito M, Willemsen A et al. A giant virus forms a specialized subcellular environment within its amoeba host for efficient translation. Nature Microbiology. 2026 Jan 9;584-596. doi: 10.1101/2024.10.07.616867, 10.1038/s41564-025-02234-x

Ye H, Šlipogor V, Hanson BT, Séneca J, Hausmann B, Herbold CW et al. Associations between gut microbiota and personality traits: insights from a captive common marmoset (Callithrix jacchus) colony. Microbiology Spectrum. 2026 Jan 6;14(1):e00443-25. Epub 2025 Nov 18. doi: 10.1128/spectrum.00443-25

Plöchl K, Böttcher T. A novel class of small-molecule inhibitors targeting bacteriophage infection. RSC Chemical Biology. 2026 Jan 1;7(1):31-37. doi: 10.1039/d5cb00120j

Jancheva M, Nguyen THN, Anderl F, Joge S, Neubauer J, Rominger-Baumann C et al. A phage-selective trigger hints at an SOS-independent mechanism of prophage induction by oxidative stress. Chemical Science. 2026;17(2):1151-1157 . doi: 10.1039/d5sc04923g

Iriarte-Mesa C, Juère E, Bileck A, Kremsmayr T, Goodson ML, Ehrlich A et al. Mesoporous Silica Nanoparticles-Based Formulations for Enhanced Oral Delivery of Peptide Drugs: A Case Study on Insulin. Small. 2026. doi: 10.1002/smll.202513347

Bachtsevani E, Hink L, Meng Y, Sedlacek CJ, Lee S, Daims H et al. Acidotolerant soil nitrite oxidizer "Candidatus Nitrobacter laanbroekii" NHB1 alleviates constraints on growth of acidophilic soil ammonia oxidizers. ISME Communications. 2025 Dec 23;6(1):1-10. ycaf244. doi: 10.1093/ismeco/ycaf244

Stuehrenberg J, Kitzinger K, von Arx JN, Graf JS, Lavik G, Littmann S et al. Urea use drives niche separation between dominant marine ammonia oxidizing archaea. Nature Communications. 2025 Dec 6;16(1):1-12. 10946. doi: 10.1038/s41467-025-67048-1

Bauchinger F, Berry D. Metatranscriptomic-driven insights into mucosal glycan degradation by the human gut microbiota. FEMS microbiology ecology. 2025 Dec 4;102(1):fiaf118. doi: 10.1093/femsec/fiaf118

The Microflora Danica Consortium, Singleton CM, Jensen TBN, Delogu F, Knudsen KS, Sørensen EA et al. The Microflora Danica atlas of Danish environmental microbiomes. Nature. 2025 Dec 3;649(8098):971-981. doi: 10.1038/s41586-025-09794-2

Hu H, Karwautz C, Duszka K, Karner T, Anderson-Wagner I, Grander C et al. Revised 16S rRNA V4 hypervariable region targeting primers enhance detection of Patescibacteria and other lineages across diverse environments. bioRxiv : the preprint server for biology. 2025 Dec 2.

Krasenbrink J, Hanson BT, Weiss AS, Borusak S, Tanabe TS, Lang M et al. Sulfoquinovose is exclusively metabolized by the gut microbiota and degraded differently in mice and humans. Microbiome. 2025 Dec;13(1):184. doi: 10.1186/s40168-025-02175-x

Plöchl K, Böttcher T. The solute-binding proteins DppA1–5 of Pseudomonas aeruginosa have distinct substrate profiles. Scientific Reports. 2025 Dec;15(1):44346. doi: 10.1038/s41598-025-27865-2