Advanced toolbox for rapid and cost-effective functional metagenomic screening - microbiology meets microfluidics.

Project Information

METAFLUIDICS

Grant agreement ID: 685474

DOI 10.3030/685474

Project closed

EC signature date 2 May 2016

Start date 1 June 2016

End date 30 November 2020

Funded under

• INDUSTRIAL LEADERSHIP - Leadership in enabling and industrial technologies – Biotechnology

Total cost € 8 808 363,00

EU contribution € 8 808 363,00

Coordinated by

UNIVERSIDAD AUTONOMA DE MADRID
Spain

Deliverables

Websites, patent fillings, videos etc. (4)

Website
Visual identity package
Scientific publications or patents
Posts, press releases and news items

Other (1)

Final version of software solution

Documents, reports (5)

Publishable summary
Certifications for biosafety, GMO manipulation, animal experimentation

Certifications for biosafety, GMO manipulation, animal experimentation facilities and personnel

Quality assurance form for deliverables and exchanged materials
Documentation and instructional materials of software solution
Standards document and revisions

Publications

Book chapters (14)

Cecembia

Author(s): Albuquerque Luciana; Rainey Fred; Egas Conceiçao; Froufe Hugo; Raposo Pedro; Da Costa, S, Milton
Published in: Bergey's Manual of Systematics of Archaea and Bacteria, Issue 6, 2018
Publisher: John Wiley & Sons, Inc.
DOI: 10.5281/zenodo.3458277

Albidovulum

Author(s): Albuquerque Luciana; Froufre Hugo; Conceiçao Egas; Rainy Fred; Da Costa, S
Published in: Whitman, WB (Ed), Bergey's Manual of Systematics of Archaea and Bacteria, Issue 9, 2018
Publisher: John Wiley & Sons, Inc.
DOI: 10.5281/zenodo.3458176

Meiothermus

Author(s): Albuquerque Luciana; Rainey Fred; Da Costa, S
Published in: Bergey's Manual of Systematics of Archaea and Bacteria, Issue 8, 2018
Publisher: John Wiley & Sons, Inc.
DOI: 10.5281/zenodo.3458314

Pullulanibacillus

Author(s): Albuquerque Luciana; Tiago Igor; Veríssimo António; Da Costa, S, Milton
Published in: Bergey's Manual of Systematics of Archaea and Bacteria, Issue 9, 2019
Publisher: John Wiley & Sons, Inc.
DOI: 10.5281/zenodo.3458514

Hydrotalea

Author(s): Albuquerque Luciana; Egas Conceição; Froufe Hugo; Da Costa, S
Published in: Bergey's Manual of Systematics of Archaea and Bacteria, Issue 7, 2019
Publisher: John Wiley & Sons, Inc.
DOI: 10.5281/zenodo.3458512

Tepidicella

Author(s): Albuquerque Luciana; Rainey Fred; Da Costa, S, Milton
Published in: Bergey's Manual of Systematics of Archaea and Bacteria, Issue 6, 2019
Publisher: John Wiley & Sons, Inc.
DOI: 10.5281/zenodo.3458506

Salirhabdus

Author(s): Albuquerque Luciana; Igor, Tiago; António, Veríssimo; Da Costa, S
Published in: Bergey's Manual of Systematics of Archaea and Bacteria, Issue 1, 2019
Publisher: John Wiley & Sons, Inc.
DOI: 10.5281/zenodo.3458495

Gaiella

Author(s): Albuquerque Luciana; Rainey Fred; Da Costa, S
Published in: Bergey's Manual of Systematics of Archaea and Bacteria, Issue 2, 2018
Publisher: John Wiley & Sons, Inc.
DOI: 10.5281/zenodo.3458297

Aquicella

Author(s): Albuquerque Luciana; Rainey, Fred; Da Costa, S
Published in: Bergey's Manual of Systematics of Archaea and Bacteria, Issue 13, 2018
Publisher: John Wiley & Sons, Inc.
DOI: 10.5281/zenodo.3458275

Rubritepida

Author(s): Albuquerque Luciana; Egas Conceiçao; Da Costa, S
Published in: Bergey's Manual of Systematics of Archaea and Bacteria, Issue 11, 2019
Publisher: John Wiley & Sons, Inc.
DOI: 10.5281/zenodo.3458332

Truepera

Author(s): Albuquerque Luciana; Rainey Fred; Da Costa, S
Published in: Bergey's Manual of Systematics of Archaea and Bacteria, Issue 6, 2018
Publisher: John Wiley & Sons, Inc.
DOI: 10.5281/zenodo.3458508

Tepidamorphus

Author(s): Albuquerque Luciana; Rainey Fred; Da Costa, S
Published in: Bergey's Manual of Systematics of Archaea and Bacteria, Issue 10, 2018
Publisher: John Wiley & Sons, Inc.
DOI: 10.5281/zenodo.3458498

Eliorea

Author(s): Da Costa, S; Albuquerque Luciana; Rainey Fred; Froufe Hugo; Roxo Inês; Raposo Pedro; Egas Conceiçao
Published in: Bergey's Manual of Systematics of Archaea and Bacteria, Issue 2, 2019
Publisher: John Wiley & Sons, Inc.
DOI: 10.5281/zenodo.3458286

Herminiimonas

Author(s): Albuquerque Luciana; Rainey Fred; Da Costa, S, Milton
Published in: Bergey's Manual of Systematics of Archaea and Bacteria, 2019
Publisher: John Wiley & Sons, Inc.
DOI: 10.5281/zenodo.3458306

Peer reviewed articles (25)

Investigating host-microbiome interactions by droplet based microfluidics

Author(s): Alexandra S. Tauzin, Mariana Rangel Pereira, Liisa D. Van Vliet, Pierre-Yves Colin, Elisabeth Laville, Jeremy Esque, Sandrine Laguerre, Bernard Henrissat, Nicolas Terrapon, Vincent Lombard, Marion Leclerc, Joël Doré, Florian Hollfelder, Gabrielle Potocki-Veronese
Published in: Microbiome, Issue 8/1, 2020, ISSN 2049-2618
Publisher: Springer Nature
DOI: 10.1186/s40168-020-00911-z

A Modular Vector Toolkit with a Tailored Set of Thermosensors To Regulate Gene Expression in Thermus thermophilus

Author(s): Carlos Verdú, Esther Sanchez, Carmen Ortega, Aurelio Hidalgo, José Berenguer, Mario Mencía
Published in: ACS Omega, Issue 4/11, 2019, Page(s) 14626-14632, ISSN 2470-1343
Publisher: American Chemical Society Publications (ACS Publications)
DOI: 10.1021/acsomega.9b02107

Investigating Host Microbiota Relationships Through Functional Metagenomics

Author(s): Elisabeth Laville, Josette Perrier, Nada Bejar, Marc Maresca, Jeremy Esque, Alexandra S. Tauzin, Emna Bouhajja, Marion Leclerc, Elodie Drula, Bernard Henrissat, Stephane Berdah, Eric Di Pasquale, Patrick Robe, Gabrielle Potocki-Veronese
Published in: Frontiers in Microbiology, Issue 10, 2019, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2019.01286

Complete Genome Sequence of Mycolicibacterium hassiacum DSM 44199.

Author(s): Alba Blesa; Eva Sacristán-Horcajada; José Berenguer; Mercedes Sánchez
Published in: Microbiology Resource Anouncements, Issue 3, 2019, Page(s) e01522-18, ISSN 2576-098X
Publisher: AMERICAN SOCIETY FOR MICROBIOLOGY
DOI: 10.1128/mra.01522-18

Developing robust protein analysis profiles to identify bacterial acid phosphatases in genomes and metagenomic libraries

Author(s): Zulema Udaondo, Estrella Duque, Abdelali Daddaoua, Carlos Caselles, Amalia Roca, Paloma Pizarro‐Tobias, Juan L. Ramos
Published in: Environmental Microbiology, Issue 22/8, 2020, Page(s) 3561-3571, ISSN 1462-2912
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/1462-2920.15138

Novel Genes Involved in Resistance to Both Ultraviolet Radiation and Perchlorate From the Metagenomes of Hypersaline Environments

Author(s): María Lamprecht-Grandío, Marta Cortesão, Salvador Mirete, Macarena Benguigui de la Cámara, Carolina G. de Figueras, Danilo Pérez-Pantoja, Joseph John White, María Eugenia Farías, Ramon Rosselló-Móra, José Eduardo González-Pastor
Published in: Frontiers in Microbiology, Issue 11, 2020, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2020.00453

Harvesting of Prebiotic Fructooligosaccharides by Nonbeneficial Human Gut Bacteria

Author(s): Zhi Wang, Alexandra S. Tauzin, Elisabeth Laville, Pietro Tedesco, Fabien Létisse, Nicolas Terrapon, Pascale Lepercq, Myriam Mercade, Gabrielle Potocki-Veronese
Published in: mSphere, Issue 5/1, 2020, ISSN 2379-5042
Publisher: American Society for Microbiology
DOI: 10.1128/msphere.00771-19

Effect of design geometry, exposure energy, cytophilic molecules, cell type and load in fabrication of single-cell arrays using micro-contact printing

Author(s): Swapnil Vilas Bhujbal, Maren Dekov, Vegar Ottesen, Karen Dunker, Rahmi Lale, Marit Sletmoen
Published in: Scientific Reports, Issue 10/1, 2020, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-020-72080-w

In Vitro Synthesis and Crystallization of β-1,4-Mannan

Author(s): Florent Grimaud, Sandra Pizzut-Serin, Laurence Tarquis, Simon Ladevèze, Sandrine Morel, Jean-Luc Putaux, Gabrielle Potocki-Veronese
Published in: Biomacromolecules, Issue 20/2, 2018, Page(s) 846-853, ISSN 1525-7797
Publisher: American Chemical Society
DOI: 10.1021/acs.biomac.8b01457

Analysis of the diversity of the glycoside hydrolase family 130 in mammal gut microbiomes reveals a novel mannoside-phosphorylase function

Author(s): Ao Li, Elisabeth Laville, Laurence Tarquis, Vincent Lombard, David Ropartz, Nicolas Terrapon, Bernard Henrissat, David Guieysse, Jeremy Esque, Julien Durand, Diego P. Morgavi, Gabrielle Potocki-Veronese
Published in: Microbial Genomics, Issue 6/10, 2020, ISSN 2057-5858
Publisher: Microbiology Society
DOI: 10.1099/mgen.0.000404

Use of photoswitchable fluorescent proteins for droplet-based microfluidic screening

Author(s): Adilya Dagkesamanskaya, Krzysztof Langer, Alexandra S. Tauzin, Catherine Rouzeau, Delphine Lestrade, Gabrielle Potocki-Veronese, Laurent Boitard, Jérôme Bibette, Jean Baudry, Denis Pompon, Véronique Anton-Leberre
Published in: Journal of Microbiological Methods, Issue 147, 2018, Page(s) 59-65, ISSN 0167-7012
Publisher: Elsevier BV
DOI: 10.1016/j.mimet.2018.03.001

Mechanisms and Regulation of Extracellular DNA Release and Its Biological Roles in Microbial Communities

Author(s): Alejandra L. Ibáñez de Aldecoa, Olga Zafra, José E. González-Pastor
Published in: Frontiers in Microbiology, Issue 8, 2017, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2017.01390

Role of Archaeal HerA Protein in the Biology of the Bacterium Thermus thermophilus

Author(s): Alba Blesa, Nieves Quintans, Ignacio Baquedano, Carlos Mata, José Castón, José Berenguer
Published in: Genes, Issue 8/5, 2017, Page(s) 130, ISSN 2073-4425
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/genes8050130

Into the Thermus Mobilome: Presence, Diversity and Recent Activities of Insertion Sequences Across Thermus spp.

Author(s): Alba Blesa, Mercedes Sánchez, Eva Sacristán-Horcajada, Sandra González-de la Fuente, Ramón Peiró, José Berenguer
Published in: Microorganisms, Issue 7/1, 2019, Page(s) 25, ISSN 2076-2607
Publisher: MDPI
DOI: 10.3390/microorganisms7010025

Raineya orbicola gen. nov., sp. nov. a slightly thermophilic bacterium of the phylum Bacteroidetes and the description of Raineyaceae fam. nov.

Author(s): Luciana Albuquerque, Ana Rita M. Polónia, Cristina Barroso, Hugo J. C. Froufe, Olga Lage, Alexandre Lobo-da-Cunha, Conceição Egas, Milton S. da Costa
Published in: International Journal of Systematic and Evolutionary Microbiology, Issue 68/4, 2018, Page(s) 982-989, ISSN 1466-5026
Publisher: Society for General Microbiology
DOI: 10.1099/ijsem.0.002556

Vibrio communities in scleractinian corals differ according to health status and geographic location in the Mediterranean Sea

Author(s): Esther Rubio-Portillo, Juan F. Gago, Manuel Martínez-García, Luigi Vezzulli, Ramon Rosselló-Móra, Josefa Antón, Alfonso A. Ramos-Esplá
Published in: Systematic and Applied Microbiology, Issue 41/2, 2018, Page(s) 131-138, ISSN 0723-2020
Publisher: Elsevier BV
DOI: 10.1016/j.syapm.2017.11.007

Biogeographic Differences in the Microbiome and Pathobiome of the Coral Cladocora caespitosa in the Western Mediterranean Sea

Author(s): Esther Rubio-Portillo, Diego K. Kersting, Cristina Linares, Alfonso A. Ramos-Esplá, Josefa Antón
Published in: Frontiers in Microbiology, Issue 9, 2018, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2018.00022

Discovery of carbamate degrading enzymes by functional metagenomics

Author(s): Lisa Ufarté, Elisabeth Laville, Sophie Duquesne, Diego Morgavi, Patrick Robe, Christophe Klopp, Angeline Rizzo, Sandra Pizzut-Serin, Gabrielle Potocki-Veronese
Published in: PLOS ONE, Issue 12/12, 2017, Page(s) e0189201, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0189201

Hierarchical Control of Nitrite Respiration by Transcription Factors Encoded within Mobile Gene Clusters of Thermus thermophilus

Author(s): Laura Alvarez, Nieves G. Quintáns, Alba Blesa, Ignacio Baquedano, Mario Mencía, Carlos Bricio, José Berenguer
Published in: Genes, Issue 8/12, 2017, Page(s) 361, ISSN 2073-4425
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/genes8120361

Solimicrobium silvestre gen. nov., sp. nov., isolated from alpine forest soil

Author(s): Rosa Margesin, Luciana Albuquerque, De-Chao Zhang, Hugo J. C. Froufe, Rita Severino, Inês Roxo, Conceição Egas, Milton S. da Costa
Published in: International Journal of Systematic and Evolutionary Microbiology, Issue 68/8, 2018, Page(s) 2491-2498, ISSN 1466-5026
Publisher: Society for General Microbiology
DOI: 10.1099/ijsem.0.002861

Transfer of Meiothermus chliarophilus (Tenreiro et al.1995) Nobre et al. 1996, Meiothermus roseus Ming et al. 2016, Meiothermus terrae Yu et al. 2014 and Meiothermus timidus Pires et al. 2005, to Calidithermus gen. nov., as Calidithermus chliarophilus comb. nov., Calidithermus roseus comb. nov., Calidithermus terrae comb. nov. and Calidithermus timidus comb. nov., respectively, and emended descrip

Author(s): Pedro Raposo, Tomeu Viver, Luciana Albuquerque, Hugo Froufe, Cristina Barroso, Conceição Egas, Ramon Rosselló-Móra, Milton S. da Costa
Published in: International Journal of Systematic and Evolutionary Microbiology, Issue 69/4, 2019, Page(s) 1060-1069, ISSN 1466-5026
Publisher: Society for General Microbiology
DOI: 10.1099/ijsem.0.003270

High‐quality draft genome sequence of Gaiella occulta isolated from a 150 meter deep mineral water borehole and comparison with the genome sequences of other deep‐branching lineages of the phylum Actinobacteria

Author(s): Rita Severino, Hugo J. C. Froufe, Cristina Barroso, Luciana Albuquerque, Alexandre Lobo‐da‐Cunha, Milton S. da Costa, Conceição Egas
Published in: MicrobiologyOpen, 2019, Page(s) e840, ISSN 2045-8827
Publisher: John Wiley and Sons Inc.
DOI: 10.1002/mbo3.840

Are in vivo selections on the path to extinction?

Author(s): Berenguer, José; Mencía, Mario; Hidalgo, Aurelio
Published in: Microbial Biotechnology, Issue 1, 2017, Page(s) 46-49, ISSN 1751-7915
Publisher: Wiley
DOI: 10.1111/1751-7915.12490

Virulence as a Side Effect of Interspecies Interaction in Vibrio Coral Pathogens.

Author(s): Josefa Antón; Andrés Mauricio Caraballo-Rodríguez; Forest Rohwer; Ana B. Martin-Cuadrado; Esther Rubio-Portillo; Esther Rubio-Portillo; Pieter C. Dorrestein
Published in: mBio, Issue 1, 2020, ISSN 2150-7511
Publisher: American Society for Microbiology
DOI: 10.1128/mbio.00201-20

Comparative genome sequence analysis of several species in the genus Tepidimonas and the description of a novel species Tepidimonas charontis sp. nov.

Author(s): Luciana Albuquerque, Nadine Castelhano, Pedro Raposo, Hugo J. C. Froufe, Igor Tiago, Rita Severino, Inês Roxo, Inês Gregório, Cristina Barroso, Conceição Egas, Milton S. da Costa
Published in: International Journal of Systematic and Evolutionary Microbiology, Issue 70/3, 2020, Page(s) 1596-1604, ISSN 1466-5026
Publisher: Society for General Microbiology
DOI: 10.1099/ijsem.0.003942

Thesis and dissertations (1)

Análisis del Pangenoma de Pseudomonas putida

Author(s): Udaondo Domínguez, Zulema
Published in: Issue 1, 2016
Publisher: Universidad de Granada

Intellectual Property Rights

Patent (3)

PLANT GROWTH PROMOTING MICROORGANISM AND ENZYMES FOR SOIL BIOGENIC CYCLES

Application/Publication number: 18 382861
Date: 2018-11-28
Applicant(s): BIOILIBERIS RESEARCH AND DEVELOPMENT SL

STRAINS CAPABLE OF PRODUCING PLANT GROWTH-STIMULATING COMPOUNDS

Application/Publication number: 18 382933
Date: 2018-12-17
Applicant(s): BIOILIBERIS RESEARCH AND DEVELOPMENT SL

MODULATION OF GENE EXPRESSION

Application/Publication number: 20 18058227
Date: 2018-03-29