All Stories

  1. TACTIC: hybrid denoising and clustering for robust 16S amplicon diversity estimates

    Article • October 2026, openRxiv

    Dr Ilias Lagkouvardos

  2. Reply - Letter to the editor: Subgroup associations should not be interpreted as modification of hydrolyzed formula effects in infants at risk of atopic disease

    Article • Clinical Nutrition ESPEN, September 2026, Elsevier

    Dr Ilias Lagkouvardos

  3. Mixed feeding and mode of birth modulate the effects of a hydrolyzed synbiotic formula on the gut microbiome in infants at risk of atopic disease

    Article • Clinical Nutrition ESPEN, August 2026, Elsevier

    Dr Ilias Lagkouvardos

  4. Global Archaeal Diversity Revealed Through Massive Data Integration: Uncovering Just Tip of Iceberg

    Article • Microorganisms, March 2025, MDPI AG

    Dr Ilias Lagkouvardos

  5. Circulating Bacterial DNA in Colorectal Cancer Patients: The Potential Role of Fusobacterium nucleatum

    Article • International Journal of Molecular Sciences, August 2024, MDPI AG

    Dr Ilias Lagkouvardos

  6. Exploring Gut Microbiome Composition and Circulating Microbial DNA Fragments in Patients with Stage II/III Colorectal Cancer: A Comprehensive Analysis

    Article • Cancers, May 2024, MDPI AG

    Dr Ilias Lagkouvardos

  7. Correction: Darier’s disease exhibits a unique cutaneous microbial dysbiosis associated with inflammation and body malodour

    Article • Microbiome, September 2023, Springer Science + Business Media

    Dr Ilias Lagkouvardos

  8. Persistent Dysbiosis, Parasite Rise and Growth Impairment in Aquacultured European Seabass after Oxytetracycline Treatment

    Article • Microorganisms, September 2023, MDPI AG

    Professor Konstantinos (Kostas) Kormas, Dr Ilias Lagkouvardos

  9. Darier’s disease exhibits a unique cutaneous microbial dysbiosis associated with inflammation and body malodour

    Article • Microbiome, July 2023, Springer Science + Business Media

    Dr Ilias Lagkouvardos

  10. Large-Scale Integration of Amplicon Data Reveals Massive Diversity within Saprospirales, Mostly Originating from Saline Environments

    Article • Microorganisms, July 2023, MDPI AG

    Dr Ilias Lagkouvardos

  11. Use of an Innovative Silage of Agro-Industrial Waste By-Products in Pig Nutrition: A Pilot Study of Its Effects on the Pig Gastrointestinal Microbiota

    Article • Microorganisms, June 2023, MDPI AG

    Dr Ilias Lagkouvardos

  12. Early life gut microbiota profiles linked to synbiotic formula effects: a randomized clinical trial in European infants

    Article • American Journal of Clinical Nutrition, February 2023, Elsevier

    Dr Ilias Lagkouvardos

  13. The Development of the Bacterial Community of Brown Trout (Salmo trutta) during Ontogeny

    Article • Microorganisms, January 2023, MDPI AG

    Dr Ilias Lagkouvardos

  14. An Insight into Goat Cheese: The Tales of Artisanal and Industrial Gidotyri Microbiota

    Article • Microorganisms, January 2023, MDPI AG

    Dr Ilias Lagkouvardos

  15. Investigating the implicit diversity of the Moraxellaceae family using the Taxonomy Informed Clustering (TIC) algorithm

    Article • January 2023, ScienceOpen

    Dr Ilias Lagkouvardos

  16. The “Crosstalk” between Microbiota and Metabolomic Profile of Kefalograviera Cheese after the Innovative Feeding Strategy of Dairy Sheep by Omega-3 Fatty Acids

    Article • Foods, October 2022, MDPI AG

    Dr Ilias Lagkouvardos, Professor Nikolaos S. Thomaidis

  17. Cronos: A Machine Learning Pipeline for Description and Predictive Modeling of Microbial Communities Over Time

    Article • Frontiers in Bioinformatics, August 2022, Frontiers

    Dr Ilias Lagkouvardos

  18. Namco: a microbiome explorer

    Article • Microbial Genomics, August 2022, Society for General Microbiology

    Dr Ilias Lagkouvardos

  19. DivCom: A Tool for Systematic Partition of Groups of Microbial Profiles Into Intrinsic Subclusters and Distance-Based Subgroup Comparisons

    Article • Frontiers in Bioinformatics, May 2022, Frontiers

    Dr Ilias Lagkouvardos

  20. Taxonomy Informed Clustering, an Optimized Method for Purer and More Informative Clusters in Diversity Analysis and Microbiome Profiling

    Article • Frontiers in Bioinformatics, April 2022, Frontiers

    Dr Ilias Lagkouvardos

  21. Namco: A microbiome explorer

    Article • December 2021, Cold Spring Harbor Laboratory Press

    Dr Ilias Lagkouvardos

  22. Seasonal dynamics in the number and composition of coliform bacteria in drinking water reservoirs

    Article • The Science of The Total Environment, September 2021, Elsevier

    Dr Ilias Lagkouvardos

  23. Handling of spurious sequences affects the outcome of high-throughput 16S rRNA gene amplicon profiling

    Article • ISME Communications, June 2021, Springer Science + Business Media

    Dr Ilias Lagkouvardos

  24. Alteration of Intestinal Microbiome of Clostridioides difficile-Infected Hamsters during the Treatment with Specific Cow Antibodies

    Article • Antibiotics, June 2021, MDPI AG

    Dr Ilias Lagkouvardos

  25. MiMiC: a bioinformatic approach for generation of synthetic communities from metagenomes

    Article • Microbial Biotechnology, June 2021, Wiley

    Dr Ilias Lagkouvardos

  26. Pre-digest of unprotected DNA by Benzonase improves the representation of living skin bacteria and efficiently depletes host DNA

    Article • Microbiome, May 2021, Springer Science + Business Media

    Dr Ilias Lagkouvardos

  27. Endophytic Bacterial Isolates From Halophytes Demonstrate Phytopathogen Biocontrol and Plant Growth Promotion Under High Salinity

    Article • Frontiers in Microbiology, May 2021, Frontiers

    Dr Ilias Lagkouvardos

  28. Correction to: Impact of Laparoscopic Sleeve Gastrectomy on Gut Permeability in Morbidly Obese Subjects

    Article • Obesity Surgery, April 2021, Springer Science + Business Media

    Dr Ilias Lagkouvardos

  29. Recent advances in culture-based gut microbiome research

    Article • International Journal of Medical Microbiology, April 2021, Elsevier

    Dr Ilias Lagkouvardos

  30. Processing Matters in Nutrient-Matched Laboratory Diets for Mice—Microbiome

    Article • Animals, March 2021, MDPI AG

    Dr Ilias Lagkouvardos

  31. Seasonal Dynamics in the Number and Composition of Coliform Bacteria in Drinking Water Reservoirs

    Article • February 2021, Cold Spring Harbor Laboratory Press

    Dr Ilias Lagkouvardos

  32. A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity

    Article • Nature Communications, December 2020, Springer Science + Business Media

    Dr Ilias Lagkouvardos

  33. Handling of Spurious Sequences Affects the Outcome of High-Throughput 16S rRNA Gene Amplicon Profiling

    Article • December 2020, Research Square

    Dr Ilias Lagkouvardos

  34. Infusion of donor feces affects the gut–brain axis in humans with metabolic syndrome

    Article • Molecular Metabolism, December 2020, Elsevier

    Dr Ilias Lagkouvardos

  35. Integrated microbiota and metabolite profiles link Crohn’s disease to sulfur metabolism

    Article • Nature Communications, August 2020, Springer Science + Business Media

    Dr Ilias Lagkouvardos

  36. A Novel Primer Mixture for GH48 Genes: Quantification and Identification of Truly Cellulolytic Bacteria in Biogas Fermenters

    Article • Microorganisms, August 2020, MDPI AG

    Dr Ilias Lagkouvardos

  37. Halophytic bacterial endophytome: a potential source of beneficial microbes for a sustainable agriculture

    Article • July 2020, Cold Spring Harbor Laboratory Press

    Dr Ilias Lagkouvardos, Dr David J Studholme

  38. Draft Genome Sequence of Paenibacillus polymyxa DSM 292, a Gram-Positive, Spore-Forming Soil Bacterium with High Biotechnological Potential

    Article • Microbiology Resource Announcements, March 2020, ASM Journals

    Dr Ilias Lagkouvardos

  39. An Integrated Metagenome Catalog Reveals New Insights into the Murine Gut Microbiome

    Article • Cell Reports, March 2020, Elsevier

    Dr Ilias Lagkouvardos

  40. Synbiotic-driven improvement of metabolic disturbances is associated with changes in the gut microbiome in diet-induced obese mice

    Article • Molecular Metabolism, April 2019, Elsevier

    Dr Ilias Lagkouvardos

  41. Impact of Laparoscopic Sleeve Gastrectomy on Gut Permeability in Morbidly Obese Subjects

    Article • Obesity Surgery, March 2019, Springer Science + Business Media

    Dr Ilias Lagkouvardos

  42. Sequence and cultivation study of Muribaculaceae reveals novel species, host preference, and functional potential of this yet undescribed family

    Article • Microbiome, February 2019, Springer Science + Business Media

    Dr Ilias Lagkouvardos

  43. An integrated metagenome catalog reveals novel insights into the murine gut microbiome

    Article • January 2019, Cold Spring Harbor Laboratory Press

    Dr Ilias Lagkouvardos

  44. Activated ATF6 Induces Intestinal Dysbiosis and Innate Immune Response to Promote Colorectal Tumorigenesis

    Article • Gastroenterology, November 2018, Elsevier

    Dr Ilias Lagkouvardos

  45. In-vivo shift of the microbiota in oral biofilm in response to frequent sucrose consumption

    Article • Scientific Reports, September 2018, Springer Science + Business Media

    Dr Ilias Lagkouvardos

  46. Increased Pancreatic Protease Activity in Response to Antibiotics Impairs Gut Barrier and Triggers Colitis

    Article • Cellular and Molecular Gastroenterology and Hepatology, January 2018, Elsevier

    Dr Ilias Lagkouvardos

  47. Short-Term Overfeeding with Dairy Cream Does Not Modify Gut Permeability, the Fecal Microbiota, or Glucose Metabolism in Young Healthy Men

    Article • Journal of Nutrition, January 2018, Elsevier

    Dr Ilias Lagkouvardos

  48. Randomized controlled trial on the impact of early-life intervention with bifidobacteria on the healthy infant fecal microbiota and metabolome

    Article • American Journal of Clinical Nutrition, November 2017, Elsevier

    Dr Ilias Lagkouvardos

  49. Determinants of postprandial plasma bile acid kinetics in human volunteers

    Article • AJP Gastrointestinal and Liver Physiology, October 2017, American Physiological Society

    Dr Ilias Lagkouvardos

  50. Effect of caloric restriction on gut permeability, inflammation markers, and fecal microbiota in obese women

    Article • Scientific Reports, September 2017, Springer Science + Business Media

    Dr Ilias Lagkouvardos

  51. Deciphering interactions between the gut microbiota and the immune system via microbial cultivation and minimal microbiomes

    Article • Immunological Reviews, August 2017, Wiley

    Thomas Clavel, Dr Ilias Lagkouvardos

  52. From complex gut communities to minimal microbiomes via cultivation

    Article • Current Opinion in Microbiology, August 2017, Elsevier

    Dr Ilias Lagkouvardos

  53. Cultured microbes represent a substantial fraction of the human and mouse gut microbiota

    Article • Gut Microbes, April 2017, Taylor & Francis

    Dr Ilias Lagkouvardos

  54. Rhea: a transparent and modular R pipeline for microbial profiling based on 16S rRNA gene amplicons

    Article • PeerJ, January 2017, PeerJ

    Dr Ilias Lagkouvardos

  55. Draft Genome of Scalindua rubra, Obtained from the Interface Above the Discovery Deep Brine in the Red Sea, Sheds Light on Potential Salt Adaptation Strategies in Anammox Bacteria

    Article • Microbial Ecology, January 2017, Springer Science + Business Media

    Prof. Dr. Bas E. Dutilh, Dr Ilias Lagkouvardos

  56. Dietary fat and gut microbiota interactions determine diet-induced obesity in mice

    Article • Molecular Metabolism, December 2016, Elsevier

    Dr Ilias Lagkouvardos

  57. Comparative genomics and physiology of the butyrate‐producing bacterium Intestinimonas butyriciproducens

    Article • Environmental Microbiology Reports, November 2016, Wiley

    Dr Bhawani Chamlagain, Dr Ilias Lagkouvardos

  58. Mining gut microbiome oligopeptides by functional metaproteome display

    Article • Scientific Reports, October 2016, Springer Science + Business Media

    Dr Ilias Lagkouvardos

  59. IMNGS: A comprehensive open resource of processed 16S rRNA microbial profiles for ecology and diversity studies

    Article • Scientific Reports, September 2016, Springer Science + Business Media

    Dr Ilias Lagkouvardos

  60. The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota

    Article • Nature Microbiology, August 2016, Springer Science + Business Media

    Dr Ilias Lagkouvardos

  61. Exclusive enteral nutrition in active pediatric Crohn disease: Effects on intestinal microbiota and immune regulation

    Article • Journal of Allergy and Clinical Immunology, August 2016, Elsevier

    Dr Ilias Lagkouvardos

  62. The mouse gut microbiome revisited: From complex diversity to model ecosystems

    Article • International Journal of Medical Microbiology, August 2016, Elsevier

    Dr Ilias Lagkouvardos

  63. Microbiome sequencing: challenges and opportunities for molecular medicine

    Article • Expert Review of Molecular Diagnostics, May 2016, Taylor & Francis

    Dr Ilias Lagkouvardos

  64. Oral versus intravenous iron replacement therapy distinctly alters the gut microbiota and metabolome in patients with IBD

    Article • Gut, February 2016, BMJ

    Dr Ilias Lagkouvardos

  65. Gut barrier impairment by high-fat diet in mice depends on housing conditions

    Article • Molecular Nutrition & Food Research, January 2016, Wiley

    Dr Ilias Lagkouvardos

  66. Cyanate as an energy source for nitrifiers

    Article • Nature, July 2015, Springer Science + Business Media

    Prof. Dr. Dr. h.c. Michael Wagner, Dr Ilias Lagkouvardos

  67. Surface-Associated Lipoproteins Link Enterococcus faecalis Virulence to Colitogenic Activity in IL-10-Deficient Mice Independent of Their Expression Levels

    Article • PLoS Pathogens, June 2015, PLOS

    Dr Ilias Lagkouvardos

  68. Gut metabolites and bacterial community networks during a pilot intervention study with flaxseeds in healthy adult men

    Article • Molecular Nutrition & Food Research, June 2015, Wiley

    Dr Ilias Lagkouvardos

  69. ARickettsialessymbiont of amoebae with ancient features

    Article • Environmental Microbiology, June 2015, Wiley

    Dr Ilias Lagkouvardos

  70. Physiological relevance of food grade microcapsules: Impact of milk protein based microcapsules on inflammation in mouse models for inflammatory bowel diseases

    Article • Molecular Nutrition & Food Research, May 2015, Wiley

    Dr Ilias Lagkouvardos

  71. Dysbiotic gut microbiota causes transmissible Crohn's disease-like ileitis independent of failure in antimicrobial defence

    Article • Gut, April 2015, BMJ

    Dr Ilias Lagkouvardos

  72. Murimonas intestini gen. nov., sp. nov., an acetate-producing bacterium of the family Lachnospiraceae isolated from the mouse gut

    Article • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, December 2014, Society for General Microbiology

    Dr Ilias Lagkouvardos

  73. Massive Expansion of Ubiquitination-Related Gene Families within the Chlamydiae

    Article • Molecular Biology and Evolution, July 2014, Oxford University Press (OUP)

    Dr Ilias Lagkouvardos

  74. Improved axenization method reveals complexity of symbiotic associations between bacteria and acanthamoebae

    Article • Environmental Microbiology Reports, April 2014, Wiley

    Dr Ilias Lagkouvardos

  75. The giant ciliate Zoothamnium niveum and its thiotrophic epibiont Candidatus Thiobios zoothamnicoli: a model system to study interspecies cooperation

    Article • Frontiers in Microbiology, April 2014, Frontiers

    Dr Ilias Lagkouvardos

  76. Life in an unusual intracellular niche: a bacterial symbiont infecting the nucleus of amoebae

    Article • The ISME Journal, February 2014, Springer Science + Business Media

    Dr Ilias Lagkouvardos

  77. Endospores of thermophilic bacteria as tracers of microbial dispersal by ocean currents

    Article • The ISME Journal, December 2013, Springer Science + Business Media

    Dr Ilias Lagkouvardos

  78. Signature Protein of the PVC Superphylum

    Article • Applied and Environmental Microbiology, November 2013, ASM Journals

    Dr Ilias Lagkouvardos

  79. Integrating metagenomic and amplicon databases to resolve the phylogenetic and ecological diversity of the Chlamydiae

    Article • The ISME Journal, August 2013, Springer Science + Business Media

    Dr Ilias Lagkouvardos

  80. Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling

    Article • Genome Biology, February 2013, Springer Science + Business Media

    Dr Jacob Lorenzo-Morales, Dr Ilias Lagkouvardos

  81. Interactions of Nitrifying Bacteria and Heterotrophs: Identification of a Micavibrio-Like Putative Predator of Nitrospira spp.

    Article • Applied and Environmental Microbiology, January 2013, ASM Journals

    Prof. Dr. Dr. h.c. Michael Wagner, Dr Ilias Lagkouvardos

  82. Depletion of Unwanted Nucleic Acid Templates by Selective Cleavage: LNAzymes, Catalytically Active Oligonucleotides Containing Locked Nucleic Acids, Open a New Window for Detecting Rare Microbial Community Members

    Article • Applied and Environmental Microbiology, December 2012, ASM Journals

    Dr Christiane Gruber-Dorninger, Prof. Dr. Dr. h.c. Michael Wagner, Dr Ilias Lagkouvardos