All Stories

  1. microntology: a lightweight, data-driven controlled vocabulary to describe Earth’s microbial habitats

    Article • January 2026, openRxiv

    Dr Thomas Sebastian Benedikt Schmidt

  2. VIRE: a metagenome-derived, planetary-scale virome resource with environmental context

    Article • Nucleic Acids Research, November 2025, Oxford University Press (OUP)

    Dr Thomas Sebastian Benedikt Schmidt

  3. proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes

    Article • Nucleic Acids Research, November 2025, Oxford University Press (OUP)

    Dr Thomas Sebastian Benedikt Schmidt

  4. Effects of lyophilised faecal filtrate compared with lyophilised donor stool on Clostridioides difficile recurrence: a multicentre, randomised, double-blinded, non-inferiority trial

    Article • The Lancet Gastroenterology & Hepatology, November 2025, Elsevier

    Dr Thomas Sebastian Benedikt Schmidt

  5. Metalog: curated and harmonised contextual data for global metagenomics samples

    Article • Nucleic Acids Research, October 2025, Oxford University Press (OUP)

    Dr Thomas Sebastian Benedikt Schmidt

  6. Metalog: curated and harmonised contextual data for global metagenomics samples

    Article • August 2025, Cold Spring Harbor Laboratory Press

    Dr Thomas Sebastian Benedikt Schmidt

  7. A novel approach to Caudoviricetes taxonomy utilising whole proteome structure-structure comparison

    Article • August 2025, Cold Spring Harbor Laboratory Press

    Dr Thomas Sebastian Benedikt Schmidt

  8. The MicrobeAtlas database: Global trends and insights into Earth’s microbial ecosystems

    Article • July 2025, Cold Spring Harbor Laboratory Press

    Dr Thomas Sebastian Benedikt Schmidt

  9. A census of hidden and discoverable microbial diversity beyond genome-centric approaches

    Article • June 2025, Cold Spring Harbor Laboratory Press

    Dr Thomas Sebastian Benedikt Schmidt

  10. Fecal microbial load is a major determinant of gut microbiome variation and a confounder for disease associations

    Article • Cell, January 2025, Elsevier

    Dr Thomas Sebastian Benedikt Schmidt

  11. A catalog of small proteins from the global microbiome

    Article • Nature Communications, August 2024, Springer Science + Business Media

    Dr Thomas Sebastian Benedikt Schmidt

  12. Discovery of antimicrobial peptides in the global microbiome with machine learning

    Article • Cell, July 2024, Elsevier

    Dr Thomas Sebastian Benedikt Schmidt

  13. Paternal microbiome perturbations impact offspring fitness

    Article • Nature, May 2024, Springer Science + Business Media

    Dr Thomas Sebastian Benedikt Schmidt

  14. Fecal microbial load is a major determinant of gut microbiome variation and a confounder for disease associations

    Article • March 2024, Cold Spring Harbor Laboratory Press

    Dr Thomas Sebastian Benedikt Schmidt

  15. Development of non-alcoholic steatohepatitis is associated with gut microbiota but not with oxysterol enzymes CH25H, EBI2, or CYP7B1 in mice

    Article • BMC Microbiology, February 2024, Springer Science + Business Media

    Dr Thomas Sebastian Benedikt Schmidt

  16. A catalogue of small proteins from the global microbiome

    Article • December 2023, Cold Spring Harbor Laboratory Press

    Dr Thomas Sebastian Benedikt Schmidt

  17. Functional and evolutionary significance of unknown genes from uncultivated taxa

    Article • Nature, December 2023, Springer Science + Business Media

    Dr Thomas Sebastian Benedikt Schmidt

  18. SPIRE: a Searchable, Planetary-scale mIcrobiome REsource

    Article • Nucleic Acids Research, October 2023, Oxford University Press (OUP)

    Dr Thomas Sebastian Benedikt Schmidt

  19. C. difficile may be overdiagnosed in adults and is a prevalent commensal in infants

    Article • September 2023, eLife

    Dr Thomas Sebastian Benedikt Schmidt

  20. Computational exploration of the global microbiome for antibiotic discovery

    Article • August 2023, Cold Spring Harbor Laboratory Press

    Dr Thomas Sebastian Benedikt Schmidt

  21. Consistency across multi‐omics layers in a drug‐perturbed gut microbial community

    Article • Molecular Systems Biology, July 2023, Springer Science + Business Media

    Dr Thomas Sebastian Benedikt Schmidt

  22. Alterations of oral microbiota and impact on the gut microbiome in type 1 diabetes mellitus revealed by integrated multi-omic analyses

    Article • Microbiome, December 2022, Springer Science + Business Media

    Dr Thomas Sebastian Benedikt Schmidt

  23. Development of non-alcoholic steatohepatitis is associated with gut microbiota but not oxysterol synthesis

    Article • December 2022, Cold Spring Harbor Laboratory Press

    Dr Thomas Sebastian Benedikt Schmidt

  24. proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes

    Article • Nucleic Acids Research, November 2022, Oxford University Press (OUP)

    Dr Thomas Sebastian Benedikt Schmidt

  25. Dissecting the intracellular pancreatic tumor microbiome at single-cell level

    Article • Cancer Cell, October 2022, Elsevier

    Dr Thomas Sebastian Benedikt Schmidt

  26. Drivers and determinants of strain dynamics following fecal microbiota transplantation

    Article • Nature Reports Stem Cells, September 2022, Springer Science + Business Media

    Dr Thomas Sebastian Benedikt Schmidt

  27. Metagenomic Identification of Microbial Signatures Predicting Pancreatic Cancer From a Multinational Study

    Article • Gastroenterology, July 2022, Elsevier

    Dr Thomas Sebastian Benedikt Schmidt

  28. Landscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes

    Article • Nucleic Acids Research, March 2022, Oxford University Press (OUP)

    Dr Thomas Sebastian Benedikt Schmidt

  29. A faecal microbiota signature with high specificity for pancreatic cancer

    Article • Gut, March 2022, BMJ

    Dr Thomas Sebastian Benedikt Schmidt

  30. C. difficilemay be overdiagnosed in adults and is a prevalent commensal in infants

    Article • February 2022, Cold Spring Harbor Laboratory Press

    Dr Thomas Sebastian Benedikt Schmidt

  31. Alterations of oral microbiota and impact on the gut microbiome in type 1 diabetes mellitus revealed by multi-omic analysis

    Article • February 2022, Cold Spring Harbor Laboratory Press

    Dr Thomas Sebastian Benedikt Schmidt

  32. Microbiome and metabolome features of the cardiometabolic disease spectrum

    Article • Nature Reports Stem Cells, February 2022, Springer Science + Business Media

    Michael Olanipekun, Dr Thomas Sebastian Benedikt Schmidt

  33. Functional and evolutionary significance of unknown genes from uncultivated taxa

    Article • January 2022, Cold Spring Harbor Laboratory Press

    Dr Thomas Sebastian Benedikt Schmidt

  34. Towards the biogeography of prokaryotic genes

    Article • Nature, December 2021, Springer Science + Business Media

    Dr Thomas Sebastian Benedikt Schmidt

  35. Combinatorial, additive and dose-dependent drug–microbiome associations

    Article • Nature, December 2021, Springer Science + Business Media

    Michael Olanipekun, Dr Thomas Sebastian Benedikt Schmidt

  36. Drivers and Determinants of Strain Dynamics Following Faecal Microbiota Transplantation

    Article • September 2021, Cold Spring Harbor Laboratory Press

    Dr Thomas Sebastian Benedikt Schmidt

  37. GUNC: detection of chimerism and contamination in prokaryotic genomes

    Article • Genome Biology, June 2021, Springer Science + Business Media

    Dr Thomas Sebastian Benedikt Schmidt

  38. treeclimbR pinpoints the data-dependent resolution of hierarchical hypotheses

    Article • Genome Biology, May 2021, Springer Science + Business Media

    Dr Thomas Sebastian Benedikt Schmidt

  39. GUNC: Detection of Chimerism and Contamination in Prokaryotic Genomes

    Article • December 2020, Cold Spring Harbor Laboratory Press

    Dr Thomas Sebastian Benedikt Schmidt

  40. treeclimbR pinpoints the data-dependent resolution of hierarchical hypotheses

    Article • June 2020, Cold Spring Harbor Laboratory Press

    Dr Thomas Sebastian Benedikt Schmidt

  41. Disentangling the mechanisms shaping the surface ocean microbiota

    Article • Microbiome, April 2020, Springer Science + Business Media

    Dr Thomas Sebastian Benedikt Schmidt

  42. Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity

    Article • The ISME Journal, February 2020, Oxford University Press (OUP)

    Dr Thomas Sebastian Benedikt Schmidt

  43. proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes

    Article • Nucleic Acids Research, October 2019, Oxford University Press (OUP)

    Dr Thomas Sebastian Benedikt Schmidt

  44. Disentangling the impact of environmental and phylogenetic constraints on prokaryotic strain diversity

    Article • August 2019, Cold Spring Harbor Laboratory Press

    Dr Thomas Sebastian Benedikt Schmidt

  45. Protein tyrosine phosphatase non-receptor type 22 modulates colitis in a microbiota-dependent manner

    Article • Journal of Clinical Investigation, May 2019, American Society for Clinical Investigation

    Dr Thomas Sebastian Benedikt Schmidt

  46. Microbial abundance, activity and population genomic profiling with mOTUs2

    Article • Nature Communications, March 2019, Springer Science + Business Media

    Dr Thomas Sebastian Benedikt Schmidt

  47. Extensive transmission of microbes along the gastrointestinal tract

    Article • eLife, February 2019, eLife

    Dr Thomas Sebastian Benedikt Schmidt

  48. Extensive Transmission of Microbes along the Gastrointestinal Tract

    Article • December 2018, Cold Spring Harbor Laboratory Press

    Dr Thomas Sebastian Benedikt Schmidt

  49. Ecologically informed microbial biomarkers and accurate classification of mixed and unmixed samples in an extensive cross-study of human body sites

    Article • Microbiome, October 2018, Springer Science + Business Media

    Dr Thomas Sebastian Benedikt Schmidt

  50. Different processes shape prokaryotic and picoeukaryotic assemblages in the sunlit ocean microbiome

    Article • July 2018, Cold Spring Harbor Laboratory Press

    Dr Thomas Sebastian Benedikt Schmidt

  51. Similarity of the dog and human gut microbiomes in gene content and response to diet

    Article • Microbiome, April 2018, Springer Science + Business Media

    Dr Thomas Sebastian Benedikt Schmidt

  52. The Human Gut Microbiome: From Association to Modulation

    Article • Cell, March 2018, Elsevier

    Dr Thomas Sebastian Benedikt Schmidt

  53. Preventive Trichuris suis ova (TSO) treatment protects immunocompetent rabbits from DSS colitis but may be detrimental under conditions of immunosuppression

    Article • Scientific Reports, November 2017, Nature

    Dr Thomas Sebastian Benedikt Schmidt

  54. MAPseq: highly efficient k-mer search with confidence estimates, for rRNA sequence analysis

    Article • Bioinformatics, August 2017, Oxford University Press (OUP)

    Dr Thomas Sebastian Benedikt Schmidt

  55. Effects of oral antibiotics and isotretinoin on the murine gut microbiota

    Article • International Journal of Antimicrobial Agents, July 2017, Elsevier

    Dr Thomas Sebastian Benedikt Schmidt

  56. MAPseq: Improved Speed, Accuracy And Consistency In Ribosomal RNA Sequence Analysis

    Article • April 2017, Cold Spring Harbor Laboratory Press

    Dr Thomas Sebastian Benedikt Schmidt

  57. A family of interaction-adjusted indices of community similarity

    Article • The ISME Journal, December 2016, Nature

    Dr Thomas Sebastian Benedikt Schmidt

  58. A Family of Interaction-Adjusted Indices of Community Similarity

    Article • February 2016, Cold Spring Harbor Laboratory Press

    Dr Thomas Sebastian Benedikt Schmidt

  59. Pseudo-transition Analysis Identifies the Key Regulators of Dynamic Metabolic Adaptations from Steady-State Data

    Article • Cell Systems, October 2015, Elsevier

    Dr Thomas Sebastian Benedikt Schmidt

  60. Limits to robustness and reproducibility in the demarcation of operational taxonomic units

    Article • Environmental Microbiology, September 2014, Wiley

    Dr Thomas Sebastian Benedikt Schmidt

  61. Analyses of dryland biological soil crusts highlight lichens as an important regulator of microbial communities

    Article • Biodiversity and Conservation, May 2014, Springer Science + Business Media

    Dr Thomas Sebastian Benedikt Schmidt

  62. Ecological Consistency of SSU rRNA-Based Operational Taxonomic Units at a Global Scale

    Article • PLoS Computational Biology, April 2014, PLOS

    Dr Thomas Sebastian Benedikt Schmidt

  63. Microbiota-Derived Hydrogen Fuels Salmonella Typhimurium Invasion of the Gut Ecosystem

    Article • Cell Host & Microbe, December 2013, Elsevier

    Dr Thomas Sebastian Benedikt Schmidt

  64. Grasp Detection from Human ECoG during Natural Reach-to-Grasp Movements

    Article • PLOS One, January 2013, PLOS

    Dr Thomas Sebastian Benedikt Schmidt