Evolution of pro- and eukaryotic commensals within the human gut

Project Information

EPYC

Grant agreement ID: 948219

DOI

10.3030/948219

EC signature date 20 January 2021

Start date 1 February 2021

End date 31 July 2026

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 1 499 993,00

EU contribution

€ 1 499 993,00

Coordinated by

QUADRAM INSTITUTE BIOSCIENCE
United Kingdom

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Deliverables

Open Research Data Pilot (1)

Data Management Plan (DMP)

Data Management Plan DMP

Publications

Peer reviewed articles (27)

Structure and function of the soil microbiome underlying N2O emissions from global wetlands

Author(s): Mohammad Bahram, Mikk Espenberg, Jaan Pärn, Laura Lehtovirta-Morley, Sten Anslan, Kuno Kasak, Urmas Kõljalg, Jaan Liira, Martin Maddison, Mari Moora, Ülo Niinemets, Maarja Öpik, Meelis Pärtel, Kaido Soosaar, Martin Zobel, Falk Hildebrand, Leho Tedersoo, Ülo Mander
Published in: Nature Communications, Issue 20411723, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-29161-3

adhesiomeR: a tool for Escherichia coli adhesin classification and analysis

Author(s): Katarzyna Sidorczuk, Michał Burdukiewicz, Klara Cerk, Joachim Fritscher, Robert A. Kingsley, Peter Schierack, Falk Hildebrand, Rafał Kolenda
Published in: BMC Genomics, Issue 25, 2024, ISSN 1471-2164
Publisher: BioMed Central
DOI: 10.1186/s12864-024-10525-6

Microbiota Dysbiosis and Gut Barrier Dysfunction Associated with Non-Alcoholic Fatty Liver Disease Are Modulated by a Specific Metabolic Cofactors’ Combination

Author(s): Sergio Quesada-Vázquez; Caitlin Bone; Shikha Saha; Iris Triguero; Marina Colom-Pellicer; Gerard Aragonès; Falk Hildebrand; Josep M. del Bas; Antoni Caimari; Naiara Beraza; Xavier Escoté
Published in: International Journal of Molecular Sciences, Issue 1, 2022, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms232213675

Dispersal strategies shape persistence and evolution of human gut bacteria

Author(s): Falk Hildebrand, Toni I. Gossmann, Clemence Frioux, Ezgi Ozkurt, Pernille Neve Myers, Pamela Ferretti, Michael Kuhn, Mohammad Bahram, Henrik Bjørn Nielsen, Peer Bork
Published in: Cell Host & Microbe, Issue 19313128, 2021, ISSN 1931-3128
Publisher: Cell Press
DOI: 10.1016/j.chom.2021.05.008

KSGP 3.1: improved taxonomic annotation of Archaea communities using LotuS2, the genome taxonomy database and RNAseq data

Author(s): Alastair Grant, Abdullah Aleidan, Charli S Davies, Solomon C Udochi, Joachim Fritscher, Mohammad Bahram, Falk Hildebrand
Published in: ISME Communications, Issue 5, 2025, ISSN 2730-6151
Publisher: Oxford University Press (OUP)
DOI: 10.1093/ismeco/ycaf094

Regulation of intestinal senescence during cholestatic liver disease modulates barrier function and liver disease progression

Author(s): Mar Moreno-Gonzalez, Katherine Hampton, Paula Ruiz, Gemma Beasy, Falk SP. Nagies, Aimee Parker, James Lazenby, Caitlin Bone, Ane Alava-Arteaga, Meha Patel, Charlotte Hellmich, Pablo Luri-Martin, Ece Silan, Mark Philo, David Baker, Simon M. Rushbrook, Falk Hildebrand, Stuart A. Rushworth, Naiara Beraza
Published in: JHEP Reports, Issue 6, 2024, Page(s) 101159, ISSN 2589-5559
Publisher: Elsevier BV
DOI: 10.1016/j.jhepr.2024.101159

Gut microbiota dysbiosis in Parkinson disease: A systematic review and pooled analysis

Author(s): Sven Kleine Bardenhorst; Emanuele Cereda; Marco Severgnini; Michela Barichella; Gianni Pezzoli; Ali Keshavarzian; Alessandro Desideri; Daniele Pietrucci; Velma T. E. Aho; Filip Scheperjans; Falk Hildebrand; Severin Weis; Markus Egert; André Karch; Marius Vital; Nicole Rübsamen
Published in: European Journal of Neurology, Issue 1, 2023, ISSN 1468-1331
Publisher: Wiley
DOI: 10.1111/ene.15671

Global functional spectrum of soil bacterial communities

Author(s): Gabin Piton; Steven Allison; Mohammad Bahram; Falk Hildebrand; Jennifer Martiny; Kathleen K. Treseder; Adam Martiny
Published in: Nature Microbiology, Issue 2, 2023, ISSN 2058-5276
Publisher: Spring Nature
DOI: 10.1038/s41564-023-01465-0

LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis

Author(s): Ezgi Özkurt, Joachim Fritscher, Nicola Soranzo, Duncan Y. K. Ng, Robert P. Davey, Mohammad Bahram, Falk Hildebrand
Published in: BMC Microbiome, Issue 20492618, 2022, ISSN 2049-2618
Publisher: Springer Nature
DOI: 10.1186/s40168-022-01365-1

Enrichment of gut microbiome strains for cultivation-free genome sequencing using droplet microfluidics

Author(s): Anna Pryszlak; Tobias Wenzel; Kiley West Seitz; Falk Hildebrand; Ece Kartal; Marco Raffaele Cosenza; Vladimir Benes; Peer Bork; Christoph A. Merten
Published in: Cell Reports Methods, Issue 26672375, 2022, ISSN 2667-2375
Publisher: Cell Press
DOI: 10.1016/j.crmeth.2021.100137

Glacier melt-down changes habitat characteristics and unique microbial community composition and physiology in alpine lake sediments

Author(s): Julia Kleinteich, Kurt Hanselmann, Falk Hildebrand, Andreas Kappler, Christiane Zarfl
Published in: FEMS Microbiology Ecology, Issue 01686496, 2022, ISSN 0168-6496
Publisher: Blackwell
DOI: 10.1093/femsec/fiac075

Pervasive associations between dark septate endophytic fungi with tree root and soil microbiomes across Europe

Author(s): Tarquin Netherway, Jan Bengtsson, Franz Buegger, Joachim Fritscher, Jane Oja, Karin Pritsch, Falk Hildebrand, Eveline J. Krab, Mohammad Bahram
Published in: Nature Communications, 2024, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-023-44172-4

Benchmark of Data Processing Methods and Machine Learning Models for Gut Microbiome-Based Diagnosis of Inflammatory Bowel Disease

Author(s): Ryszard Kubinski, Jean-Yves Djamen-Kepaou, Timur Zhanabaev, Alex Hernandez-Garcia, Stefan Bauer, Falk Hildebrand, Tamas Korcsmaros, Sani Karam, Prévost Jantchou, Kamran Kafi, Ryan D. Martin
Published in: Frontiers in Genetics, Issue 16648021, 2022, ISSN 1664-8021
Publisher: Frontiers Media
DOI: 10.3389/fgene.2022.784397

Population-level impacts of antibiotic usage on the human gut microbiome

Author(s): Kihyun Lee, Sebastien Raguideau, Kimmo Sirén, Francesco Asnicar, Fabio Cumbo, Falk Hildebrand, Nicola Segata , Chang-Jun Cha, Christopher Quince
Published in: Nature Communications, 2023, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-023-36633-7

Enterosignatures define common bacterial guilds in the human gut microbiome

Author(s): Clemence Frioux, Rebecca Ansorge, Ezgi Ozkurt, Chabname Ghassemi Nedjad, Joachim Fritscher, Christopher Quince, Sebastian M. Waszak, Falk Hildebrand
Published in: Cell Host & Microbe, 2023, ISSN 1931-3128
Publisher: Cell Press
DOI: 10.1016/j.chom.2023.05.024

A prebiotic dietary pilot intervention restores faecal metabolites and may be neuroprotective in Parkinson’s Disease

Author(s): Janis Rebecca Bedarf, Stefano Romano, Silke Sophie Heinzmann, Anthony Duncan, Maria H. Traka, Duncan Ng, Daniella Segovia-Lizano, Marie-Christine Simon, Arjan Narbad, Ullrich Wüllner, Falk Hildebrand
Published in: npj Parkinson's Disease, Issue 11, 2025, Page(s) npj Parkinson's Disease, ISSN 2373-8057
Publisher: Springer Science and Business Media LLC
DOI: 10.1038/s41531-025-00885-5

Ecological insights into the microbiology of food using metagenomics and its potential surveillance applications

Author(s): Samuel J. Bloomfield, Falk Hildebrand, Aldert L. Zomer, Raphaëlle Palau, Alison E. Mather
Published in: Microbial Genomics, Issue 11, 2025, ISSN 2057-5858
Publisher: Microbiology Society
DOI: 10.1099/mgen.0.001337

A single dietary factor, daily consumption of a fermented beverage, can modulate the gut microbiome within the same ethnic community

Author(s): Santanu Das; Ezgi Özkurt; Tulsi Kumari Joishy; Dibyayan Deb; Ashis K. Mukherjee; Falk Hildebrand; Mojibur R. Khan
Published in: mSystems, Issue 1, 2023, ISSN 2379-5077
Publisher: ASM
DOI: 10.1101/2023.01.18.524612

Reply to: Microbial dark matter could add uncertainties to metagenomic trait estimations

Author(s): Gabin Piton, Steven D. Allison, Mohammad Bahram, Falk Hildebrand, Jennifer B. H. Martiny, Kathleen K. Treseder, Adam C. Martiny
Published in: Nature Microbiology, Issue 9, 2024, Page(s) 1431-1433, ISSN 2058-5276
Publisher: Springer Science and Business Media LLC
DOI: 10.1038/s41564-024-01688-9

IL-17RA signaling provides dual tumor-suppressor function during late-stage colorectal carcinogenesis

Author(s): Dominic Denk, Mallika Ramakrishnan, Claire Conche, Charles Pallangyo, Marina Pesic, Fatih Ceteci, Kilian B. Kennel, Asude C. Kirisözü, Esther Engel, Kathleen Mohs, Birgit Ritter, Angeles Macias Pardo, Ezgi Özkurt, Falk Hildebrand, Ari Waisman, Melek C. Arkan, Florian R. Greten
Published in: Immunity, Issue 58, 2025, Page(s) 701-715.e8, ISSN 1074-7613
Publisher: Cell Press
DOI: 10.1016/j.immuni.2025.02.005

A single dietary factor, daily consumption of a fermented beverage, can modulate the gut bacteria and fecal metabolites within the same ethnic community

Author(s): Santanu Das, Ezgi Özkurt, Tulsi Kumari Joishy, Ashis K. Mukherjee, Falk Hildebrand, Mojibur R. Khan
Published in: mSystems, Issue 8, 2024, ISSN 2379-5077
Publisher: American Society for Microbiology
DOI: 10.1128/msystems.00745-23

Potential therapeutic implications of histidine catabolism by the gut microbiota in NAFLD patients with morbid obesity

Author(s): Sergio Quesada-Vazquez Anna Castells-Nobau, Jessica Latorre, Nuria Oliveras-Canellas, Irene Puig-Parnau, Noemi Tejera, Yaiza Tobajas, Julio Baudin, Falk Hildebrand, Naiara Beraza, Remy Burcelin, Laura Martinez-Gili, Julien Chilloux, Marc-Emmanuel Dumas, Massimo Federici,Lesley Hoyles, Antoni Caimari, Josep M. del Bas, Xavier Escote, Jose-Manuel Fernandez-Real
Published in: Cell Reports Medicine, 2023, ISSN 2666-3791
Publisher: Elsevier
DOI: 10.1016/j.xcrm.2023.101341

Microbial composition and dynamics in environmental samples from a ready-to-eat food production facility with a long-term colonisation of Listeria monocytogenes

Author(s): Diaz Maria, Heather Aird, Thanh Le Viet, Ana Victoria Gutierrez, Nasmille Larke-Mejia, Oleksii Omelchenko, Lluis Moragues-Solanas, Joachim Fritscher, Nicolle Som, Jim McLauchlin, Falk Hildebrand, Frieda Jørgensen, Matthew Gilmour
Published in: Food Microbiology, 2024, ISSN 0740-0020
Publisher: Academic Press
DOI: 10.21203/rs.3.rs-3910281/v1

Community‐scale models of microbiomes: Articulating metabolic modelling and metagenome sequencing

Author(s): Klara Cerk; Pablo Ugalde‐Salas; Chabname Ghassemi Nedjad; Maxime Lecomte; Coralie Muller; David J. Sherman; Falk Hildebrand; Simon Labarthe; Clémence Frioux
Published in: Microbial Biotechnology, 2024, ISSN 1751-7915
Publisher: Wiley
DOI: 10.1111/1751-7915.14396

Ultra-resolution Metagenomics: When Enough Is Not Enough.

Author(s): Falk Hildebrand
Published in: mSystems, Issue 00219193, 2022, ISSN 0021-9193
Publisher: American Society for Microbiology
DOI: 10.1128/msystems.00881-21

Metagenomic analyses of gut microbiome composition and function with age in a wild bird; little change, except increased transposase gene abundance

Author(s): Chuen Zhang Lee, Sarah F Worsley, Charli S Davies, Ece Silan, Terry Burke, Jan Komdeur, Falk Hildebrand, Hannah L Dugdale, David S Richardson
Published in: ISME Communications, Issue 5, 2025, ISSN 2730-6151
Publisher: Oxford University Press (OUP)
DOI: 10.1093/ismeco/ycaf008

Genomic evidence of symbiotic adaptations in fungus-associated bacteria

Author(s): Daniyal Gohar, Kadri Põldmaa, Mari Pent, Saleh Rahimlou, Klara Cerk, Duncan Y.K. Ng, Falk Hildebrand, Mo Bahram
Published in: iScience, Issue 28, 2025, Page(s) 112253, ISSN 2589-0042
Publisher: Elsevier BV
DOI: 10.1016/j.isci.2025.112253