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Illuminating Functional Networks and Keystone Species in the Gut

Total Cost €


EC-Contrib. €






 FunKeyGut project word cloud

Explore the words cloud of the FunKeyGut project. It provides you a very rough idea of what is the project "FunKeyGut" about.

function    competing    associating    treatments    outstanding    mass    certain    unknown    infection    environment    functional    isotope    diet    network    webs    species    rationally    shape    human    food    identity    prebiotic    gut    provides    community    ideally    health    vital    exists    illuminate    immune    microspectroscopy    interactions    intimate    play    though    designed    microbial    networks    form    suited    spectrometry    rumonicoccus    elucidated    reveal    protect    unravel    stable    bromii    ultimately    live    ideal    probiotic    revealed    disease    nanosims    largely    sequencing    compounds    enteropathogen    dietary    ion    symbiosis    breakdown    keystone    services    metabolic    training    exclusively    microbes    microbiota    catalogue    thought    manipulating    intriguing    cooperating    microbiome    vitamin    raman    links    secondary    organisms    native    labeling    complexity    communities    discoveries    situ    diverse    uniquely   

Project "FunKeyGut" data sheet

The following table provides information about the project.


Organization address
city: WIEN
postcode: 1010

contact info
title: n.a.
name: n.a.
surname: n.a.
function: n.a.
email: n.a.
telephone: n.a.
fax: n.a.

 Coordinator Country Austria [AT]
 Project website
 Total cost 1˙498˙279 €
 EC max contribution 1˙498˙279 € (100%)
 Programme 1. H2020-EU.1.1. (EXCELLENT SCIENCE - European Research Council (ERC))
 Code Call ERC-2016-STG
 Funding Scheme ERC-STG
 Starting year 2017
 Duration (year-month-day) from 2017-04-01   to  2022-03-31


Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    UNIVERSITAT WIEN AT (WIEN) coordinator 1˙498˙279.00


 Project objective

We live in an intimate symbiosis with our gut microbiota, which provides us services such as vitamin production, breakdown of dietary compounds, and immune training. Sequencing-based approaches that have been applied to catalogue the gut microbiota have revealed intriguing discoveries associating the microbiome with diet and disease. The next outstanding challenge is to unravel the many activities and interactions that define gut microbiota function.

The gut microbiota is a diverse community of cooperating and competing microbes. These interactions form a network that links organisms with each other and their environment. Interactions in such a “functional network” are based partially, though not exclusively, on food webs. Certain “keystone species”, such as Rumonicoccus bromii, are thought to play a major role in these networks. Though some evidence exists for the presence of keystone species, their identity and activity remains largely unknown. As keystone species are vital to networks they are ideal targets for manipulating the gut microbiota to improve metabolic health and protect against enteropathogen infection.

Given the complexity of the gut microbiota, networks can only be elucidated directly in the native community. This project aims to identify functional networks and keystone species in the human gut using novel approaches that are uniquely and ideally suited for studying microbial activity in complex communities. Using state-of-the-art methods such as stable isotope labeling, Raman microspectroscopy, and secondary ion mass spectrometry (NanoSIMS) we will illuminate functional networks in situ. This will allow us to identify what factors shape gut microbiota activity, reveal important food webs, and ultimately use network knowledge to target the microbiota with prebiotic/probiotic treatments rationally designed to promote health.


year authors and title journal last update
List of publications.
2019 Alessandra Riva, Orest Kuzyk, Erica Forsberg, Gary Siuzdak, Carina Pfann, Craig Herbold, Holger Daims, Alexander Loy, Benedikt Warth, David Berry
A fiber-deprived diet disturbs the fine-scale spatial architecture of the murine colon microbiome
published pages: , ISSN: 2041-1723, DOI: 10.1038/s41467-019-12413-0
Nature Communications 10/1 2019-12-16
2019 Simone Herp, Sandrine Brugiroux, Debora Garzetti, Diana Ring, Lara M. Jochum, Markus Beutler, Claudia Eberl, Saib Hussain, Steffi Walter, Roman G. Gerlach, Hans J. Ruscheweyh, Daniel Huson, Mikael E. Sellin, Emma Slack, Buck Hanson, Alexander Loy, John F. Baines, Philipp Rausch, Marijana Basic, André Bleich, David Berry, Bärbel Stecher
Mucispirillum schaedleri Antagonizes Salmonella Virulence to Protect Mice against Colitis
published pages: 681-694.e8, ISSN: 1931-3128, DOI: 10.1016/j.chom.2019.03.004
Cell Host & Microbe 25/5 2019-12-16
2019 Gomes, Oudot, Macià, Foito, Carregosa, Stewart, Van de Wiele, Berry, Motilva, Brenner, dos Santos
Berry-Enriched Diet in Salt-Sensitive Hypertensive Rats: Metabolic Fate of (Poly)Phenols and the Role of Gut Microbiota
published pages: 2634, ISSN: 2072-6643, DOI: 10.3390/nu11112634
Nutrients 11/11 2019-12-16
2019 Kang Soo Lee, Márton Palatinszky, Fátima C. Pereira, Jen Nguyen, Vicente I. Fernandez, Anna J. Mueller, Filippo Menolascina, Holger Daims, David Berry, Michael Wagner, Roman Stocker
An automated Raman-based platform for the sorting of live cells by functional properties
published pages: 1035-1048, ISSN: 2058-5276, DOI: 10.1038/s41564-019-0394-9
Nature Microbiology 4/6 2019-12-16
2017 Jesse P. Harrison, David Berry
Vibrational Spectroscopy for Imaging Single Microbial Cells in Complex Biological Samples
published pages: , ISSN: 1664-302X, DOI: 10.3389/fmicb.2017.00675
Frontiers in Microbiology 8 2019-10-08

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