Microbiome Applications for Sustainable food systems through Technologies and EnteRprise

Deliverables

Dissemination, exploitation and communication plan

Dissemination exploitation and communication plan

First version of curatedFoodMetagenomicData from publicly available data

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Publications

The food-gut axis: lactic acid bacteria and their link to food, the gut microbiome and human health

Author(s): Francesca De Filippis, Edoardo Pasolli, Danilo Ercolini
Published in: FEMS Microbiology Reviews, 44/4, 2020, Page(s) 454-489, ISSN 0168-6445
Publisher: Blackwell
DOI: 10.1093/femsre/fuaa015

Brewers spent yeast (BSY), an underutilised brewing by-product.

Author(s): Jaeger, A.; Arendt, E.K.; Zannini, E.; Sahin, A.W.
Published in: Fermentation, 6, 2020, Page(s) 123, ISSN 2311-5637
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/fermentation6040123

Environmental microbiome mapping as a strategy to improve quality and safety in the food industry

Author(s): Francesca De Filippis, Vincenzo Valentino, Avelino Alvarez-Ordonez, Paul D. Cotter, Danilo Ercolini
Published in: Current Opinion in Food Science, 38, 2021, Page(s) 168-176, ISSN 2214-7993
Publisher: Elsevier BV
DOI: 10.1016/j.cofs.2020.11.012

Next-generation food research: Use of meta-omic approaches for characterizing microbial communities along the food chain

Author(s): Yap, M., Ercolini, D., Álvarez-Ordóñez, A., O'Toole, P.W., O'Sullivan, O., Cotter, P.D.
Published in: Annu Rev Food Sci Technol, 13, 2022, Page(s) 1.1-1.24, ISSN 1941-1421
Publisher: Annual Reviews
DOI: 10.1146/annurev-food-052720-010751

Meta-analysis of cheese microbiomes highlights contributions to multiple aspects of quality

Author(s): Aaron M. Walsh, Guerrino Macori, Kieran N. Kilcawley, Paul D. Cotter
Published in: Nature Food, 1/8, 2020, Page(s) 500-510, ISSN 2662-1355
Publisher: Springer Nature
DOI: 10.1038/s43016-020-0129-3

Valorization of Vegetable Food Waste and By-Products Through Fermentation Processes

Author(s): Carlos Sabater; Carlos Sabater; Lorena Ruiz; Lorena Ruiz; Susana Delgado; Susana Delgado; Patricia Ruas-Madiedo; Patricia Ruas-Madiedo; Abelardo Margolles; Abelardo Margolles
Published in: Frontiers in Microbiology, 11:581997, 2020, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2020.581997

Prevotella diversity, niches and interactions with the human host

Author(s): Adrian Tett, Edoardo Pasolli, Giulia Masetti, Danilo Ercolini & Nicola Segata
Published in: Nature Reviews in Microbiology, 19, 2021, Page(s) 585-599, ISSN 1740-1526
Publisher: Nature Publishing Group
DOI: 10.1038/s41579-021-00559-y

Barley protein properties, extraction and applications, with a focus on Brewer's Spent Grain Protein

Author(s): Alice Jaeger, Emanuele Zannini, Aylin W. Sahin & Elke K. Arendt
Published in: Foods, 10(6), 2021, Page(s) 1389, ISSN 2304-8158
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/foods10061389

Seasonality and geography have a greater influence than the use of chlorine-based cleaning agents on the microbiota of bulk tank raw milk.

Author(s): Yap, M., Gleeson, D., O'Toole, P.W., O'Sullivan, O. and Cotter, P.D.
Published in: Appl Environ Microbiol, 2021, ISSN 0099-2240
Publisher: American Society for Microbiology
DOI: 10.1128/aem.01081-21

Development of a rapid qPCR method to quantify lactic acid bacteria in cold-smoked salmon

Author(s): Jérôme M., Passerini D., Chevalier F., Marchand L., Leroi F. and Macé S.
Published in: International Journal of Food Microbiology, 363, 2022, Page(s) 109504, ISSN 0168-1605
Publisher: Elsevier BV
DOI: 10.1016/j.ijfoodmicro.2021.109504

Microbial colonization and resistome dynamics in food processing environments of a newly opened pork cutting industry during 1.5 years of activity

Author(s): José F. Cobo-Díaz, Adrián Alvarez-Molina, Elena A. Alexa, Calum J. Walsh, Oscar Mencía-Ares, Paula Puente-Gómez, Eleni Likotrafiti, Paula Fernández-Gómez, Bernardo Prieto, Fiona Crispie, Lorena Ruiz, Montserrat González-Raurich, Mercedes López, Miguel Prieto, Paul Cotter, Avelino Alvarez-Ordóñez
Published in: Microbiome, 9, 2021, Page(s) 204, ISSN 2049-2618
Publisher: BioMed Central
DOI: 10.1186/s40168-021-01131-9

New insight into antimicrobial compounds from food and marine-sourced Carnobacterium species through phenotype and genome analyses.

Author(s): Begrem, S., Ivaniuk, F., Gigout-Chevalier, F., Kolypczuk, L., Bonnetot, S., Leroi, F., Grovel, O., Delbarre-Ladrat, C., Passerini, D.
Published in: Microorganisms, 8(7), 2020, Page(s) 1093, ISSN 2076-2607
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/microorganisms8071093

Presence of adult companion goats favors the rumen microbial and functional development in artificially reared kids

Author(s): Juan Manuel Palma-Hidalgo, David R Yáñez-Ruiz, Elisabeth Jiménez, A Ignacio Martín-García, Alejandro Belanche
Published in: Frontiers in Veterinary Science, 8, 2021, Page(s) 706592, ISSN 2297-1769
Publisher: Frontiers Media S.A.
DOI: 10.3389/fvets.2021.706592

Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly

Author(s): Karcher, N., Nigro, E., Punčochář, M., Blanco-Míguez, A., Ciciani, M., Manghi, P., Zolfo, M., Cumbo, F., Manara, S., Golzato, D., Cereseto, A., Arumugam, M., Phuong Nam Bui, T.,. Tytgat H.L.P., Valles-Colomer, M., de Vos, W.M. & Segata, N.
Published in: Genome Biology, 22, 2021, Page(s) 209, ISSN 1474-760X
Publisher: Springer Nature
DOI: 10.1186/s13059-021-02427-7

Application of lactic acid bacteria for the biopreservation of meat products: A systematic review

Author(s): Coral Barcenilla, Miroslav Ducic, Mercedes López, Miguel Prieto, Avelino Álvarez-Ordóñez
Published in: Meat Science, 183, 2022, ISSN 0309-1740
Publisher: Elsevier BV
DOI: 10.1016/j.meatsci.2021.108661

Unraveling the emergence and population diversity of Listeria monocytogenes in a newly built meat facility through whole genome sequencing

Author(s): Adrián Alvarez-Molina, José F. Cobo-Díaz, Mercedes López, Miguel Prieto, María de Toro, Avelino Alvarez-Ordóñez
Published in: International Journal of Food Microbiology, 340, 2021, Page(s) 109043, ISSN 0168-1605
Publisher: Elsevier BV
DOI: 10.1016/j.ijfoodmicro.2021.109043

Vegetable waste and by-products to feed a healthy gut microbiota: current evidence, machine learning and computational tools to design novel microbiome-targeted foods

Author(s): Sabater C, Calvete-Torre I, Villamiel M, Moreno FJ, Margolles A, Ruiz L.
Published in: Trends in Food Science & Technology, 118, 2021, Page(s) 399-417, ISSN 0924-2244
Publisher: Elsevier BV
DOI: 10.1016/j.tifs.2021.10.002

Novel methods of microbiome analysis in the food industry

Author(s): Sabater C, Cobo-Díaz JF, Álvarez-Ordóñez A, Ruas-Madiedo P, Ruiz L, Margolles A.
Published in: International Microbiology, 24, 2021, Page(s) 593-605, ISSN 1139-6709
Publisher: Sociedad Espanola de Microbiologia
DOI: 10.1007/s10123-021-00215-8

Fermentation as a tool to revitalise brewer's spent grain and elevate techno-functional properties and nutritional value in high fibre bread

Author(s): Emma Neylon, Elke K. Arendt, Emanuele Zannini & Aylin W. Sahin
Published in: Foods, 10(7), 2021, Page(s) 1639, ISSN 2304-8158
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/foods10071639

Blue poo: impact of gut transit time on the gut microbiome using a novel marker , 70:1665-1674 (2021) BMJ Publishing Group; United Kingdom

Author(s): Asnicar, F., Leeming, E.R., Dimidi, E., Mazidi, M., Franks, P.W., Al Khatib, H., Valdes, A.M., Davies, R., Bakker, E., Francis, L., Chan, A., Gibson, R., Hadjigeorgiou, G., Wolf, J., Spector ,T.D., Segata, N. & Berry S.E.
Published in: Gut, 70, 2021, Page(s) 1665-1674, ISSN 0017-5749
Publisher: BMJ Publishing Group
DOI: 10.1136/gutjnl-2020-323877

Fundamental study of the application of brewers spent grain and fermented brewers spent grain on the quality of pasta

Author(s): Emma Neylon, Elke K. Arendt, Emanuele Zannini & Aylin W. Sahin
Published in: Food Structure, 30:100225, 2021, ISSN 2213-3291
Publisher: Elsevier BV
DOI: 10.1016/j.foostr.2021.100225

Newly explored Faecalibacterium diversity is connected to age, lifestyle, geography, and disease.

Author(s): De Filippis, F., Pasolli, E. and Ercolini, D.
Published in: Current Biology, 30, 2020, Page(s) 1–12, ISSN 0960-9822
Publisher: Cell Press
DOI: 10.1016/j.cub.2020.09.063

Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3

Author(s): Francesco Beghini, Lauren J McIver, Aitor Blanco-Míguez, Leonard Dubois, Francesco Asnicar, Sagun Maharjan, Ana Mailyan, Paolo Manghi, Matthias Scholz, Andrew Maltez Thomas, Mireia Valles-Colomer, George Weingart, Yancong Zhang, Moreno Zolfo, Curtis Huttenhower , Eric A Franzosa , Nicola Segata
Published in: eLife, 2021, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.65088

Rootlets, a malting by-product with great potential.

Author(s): Neylon, E., Arendt, E.K., Lynch, K.M., Zannini, E., Bazzoli, P., Monin, T., Sahin, A.W.
Published in: Fermentation, 6, 2020, Page(s) 117, ISSN 2311-5637
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/fermentation6040117

The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations

Author(s): Adrian Tett, Kun D. Huang, Francesco Asnicar, Hannah Fehlner-Peach, Edoardo Pasolli, Nicolai Karcher, Federica Armanini, Paolo Manghi, Kevin Bonham, Moreno Zolfo, Francesca De Filippis, Cara Magnabosco, Richard Bonneau, John Lusingu, John Amuasi, Karl Reinhard, Thomas Rattei, Fredrik Boulund, Lars Engstrand, Albert Zink, Maria Carmen Collado, Dan R. Littman, Daniel Eibach, Danilo Ercolini, Omar Ro
Published in: Cell Host & Microbe, 26/5, 2019, Page(s) 666-679.e7, ISSN 1931-3128
Publisher: Cell Press
DOI: 10.1016/j.chom.2019.08.018

At the forefront of the sequencing revolution—notes from the RNGS19 conference

Author(s): Sander Wuyts, Nicola Segata
Published in: Genome Biology, 20/1, 2019, ISSN 1474-760X
Publisher: Springer Nature (BioMed Central (BMC))
DOI: 10.1186/s13059-019-1714-3

Tracking the Dairy Microbiota from Farm Bulk Tank to Skimmed Milk Powder

Author(s): Aoife J. McHugh, Conor Feehily, Mark A. Fenelon, David Gleeson, Colin Hill, Paul D. Cotter
Published in: mSystems, 5/2, 2020, ISSN 2379-5077
Publisher: American Society for Microbiology (ASM)
DOI: 10.1128/msystems.00226-20

Detecting contamination in viromes using ViromeQC

Author(s): Moreno Zolfo, Federica Pinto, Francesco Asnicar, Paolo Manghi, Adrian Tett, Frederic D. Bushman, Nicola Segata
Published in: Nature Biotechnology, 37/12, 2019, Page(s) 1408-1412, ISSN 1087-0156
Publisher: Nature Publishing Group
DOI: 10.1038/s41587-019-0334-5

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0

Author(s): Francesco Asnicar, Andrew Maltez Thomas, Francesco Beghini, Claudia Mengoni, Serena Manara, Paolo Manghi, Qiyun Zhu, Mattia Bolzan, Fabio Cumbo, Uyen May, Jon G. Sanders, Moreno Zolfo, Evguenia Kopylova, Edoardo Pasolli, Rob Knight, Siavash Mirarab, Curtis Huttenhower, Nicola Segata
Published in: Nature Communications, 11/1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-16366-7

Microbial genomes from non-human primate gut metagenomes expand the primate-associated bacterial tree of life with over 1000 novel species

Author(s): Serena Manara, Francesco Asnicar, Francesco Beghini, Davide Bazzani, Fabio Cumbo, Moreno Zolfo, Eleonora Nigro, Nicolai Karcher, Paolo Manghi, Marisa Isabell Metzger, Edoardo Pasolli, Nicola Segata
Published in: Genome Biology, 20/1, 2019, ISSN 1474-760X
Publisher: Springer Nature (BioMed Central (BMC))
DOI: 10.1186/s13059-019-1923-9

Large-scale genome-wide analysis links lactic acid bacteria from food with the gut microbiome

Author(s): Edoardo Pasolli, Francesca De Filippis, Italia E. Mauriello, Fabio Cumbo, Aaron M. Walsh, John Leech, Paul D. Cotter, Nicola Segata, Danilo Ercolini
Published in: Nature Communications, 11/1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-16438-8

Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations

Author(s): Nicolai Karcher, Edoardo Pasolli, Francesco Asnicar, Kun D. Huang, Adrian Tett, Serena Manara, Federica Armanini, Debbie Bain, Sylvia H. Duncan, Petra Louis, Moreno Zolfo, Paolo Manghi, Mireia Valles-Colomer, Roberta Raffaetà, Omar Rota-Stabelli, Maria Carmen Collado, Georg Zeller, Daniel Falush, Frank Maixner, Alan W. Walker, Curtis Huttenhower, Nicola Segata
Published in: Genome Biology, 21/1, 2020, ISSN 1474-760X
Publisher: BioMed Central
DOI: 10.1186/s13059-020-02042-y

Analysis of Health Benefits Conferred by Lactobacillus Species from Kefir

Author(s): Conor Slattery, Paul D. Cotter, Paul W. O’Toole
Published in: Nutrients, 11/6, 2019, Page(s) 1252, ISSN 2072-6643
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/nu11061252

Multiple levels of the unknown in microbiome research

Author(s): Andrew Maltez Thomas, Nicola Segata
Published in: BMC Biology, 17/1, 2019, ISSN 1741-7007
Publisher: BioMed Central
DOI: 10.1186/s12915-019-0667-z

Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals

Author(s): Asnicar, F., Berry, S.E., Valdes, A.M., Nguyen, L.H., Piccinno, G., Drew, D.A., Leeming, E., Gibson, R., Le Roy, C., Khatib, H.A., Francis, L., Mazidi, M., Mompeo, O., Valles-Colomer, M., Tett, A., Beghini, F., Dubois, L., Bazzani, D., Thomas, A.M., Mirzayi, C., Khleborodova, A., Oh, S., Hine, R., Bonnett, C., Capdevila, J., Danzanvilliers, S., Giordano, F., Geistlinger, L., Waldron, L., Davies, R
Published in: Nature Medicine, 27, 2021, Page(s) 321-332, ISSN 1546-170X
Publisher: Springer Nature (Nature Research)
DOI: 10.1038/s41591-020-01183-8

Fresh rumen liquid inoculant enhances the rumen microbial community establishment in pre-weaned dairy calves

Author(s): Huuki, H., Ahvenjärvi, S., Lidauer, P., Popova, M., Vilkki, J., Vanhatalo, A., & Tapio, I
Published in: Frontiers in Microbiology, 2022, Page(s) 3995, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2021.758395

Microbiome-based environmental monitoring of a dairy processing facility highlights the challenges associated with low microbial-load samples.

Author(s): Aoife J. McHugh, Min Yap, Fiona Crispie, Conor Feehily, Colin Hill & Paul D. Cotter
Published in: NPJ: Science of Food, 5(4), 2021, ISSN 2396-8370
Publisher: Springer Nature
DOI: 10.1038/s41538-021-00087-2

Apple pomaces derived from mono-varietal Asturian ciders production are potential source of pectins with appealing functional properties

Author(s): Calvete-Torre I, Muñoz-Almagro N, Pacheco MT, Antón MJ, Dapena E, Ruiz L, Margolles A, Villamiel M, Moreno FJ
Published in: Carbohydrate Polymers, 264, 2021, Page(s) 117980, ISSN 0144-8617
Publisher: Pergamon Press Ltd.
DOI: 10.1016/j.carbpol.2021.117980

A novel ammoniation treatment of barley as a strategy to optimize rumen pH, feed degradability and microbial protein synthesis

Author(s): Alejandro Belanche, Ignacio Martín-García, Elisabeth Jiménez, Nicholas N Jonsson and David R Yañez-Ruiz
Published in: Journal of the Science of Food and Agriculture, 101(12), 2021, Page(s) 5541-5549, ISSN 0022-5142
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/jsfa.11205

Whole resistome analysis in Campylobacter jejuni and Campylobacter coli genomes available in public repositories

Author(s): José F. Cobo-Díaz, Paloma González del Río, Avelino Álvarez-Ordóñez
Published in: Frontiers in Microbiology, 12, 2021, Page(s) 662144, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2021.662144

High intake of vegetables is linked to lower white blood cell profile and the effect is mediated by the gut microbiome

Author(s): Cristina Menni, Panayiotis Louca, Sarah E. Berry, Amrita Vijay, Stuart Astbury, Emily R. Leeming, Rachel Gibson, Francesco Asnicar, Gianmarco Piccinno, Jonathan Wolf, Richard Davies, Massimo Mangino, Nicola Segata, Tim D. Spector & Ana M. Valdes
Published in: BMC Medicine, 19, 2021, Page(s) 37, ISSN 1741-7015
Publisher: BioMed Central
DOI: 10.1186/s12916-021-01913-w

Antimicrobial use and production system shape the fecal, environmental, and slurry resistomes of pig farms

Author(s): Oscar Mencía-Ares, Raúl Cabrera-Rubio, José Francisco Cobo-Díaz, Avelino Álvarez-Ordóñez , Manuel Gómez-García, Héctor Puente, Paul D. Cotter, Fiona Crispie, Ana Carvajal, Pedro Rubio and Héctor Argüello
Published in: Microbiome, 8, 2020, Page(s) 164, ISSN 2049-2618
Publisher: BioMed Central
DOI: 10.1186/s40168-020-00941-7

28. The effect of phenotypically ranking beef cattle for residual methane output on daily methane emissions, intensity and animal productivity

Author(s): Paul E. Smith; Sinéad M. Waters; David A. Kenny; Stuart F. Kirwan; Stephen Conroy; Alan K. Kelly
Published in: Animal Science Proceedings, 12 (1), 2021, Page(s) 18, ISSN 2772-283X
Publisher: Elsevier
DOI: 10.1016/j.anscip.2021.03.029

84 Effect of different levels of microalgae supplementation on methane emissions, ruminal fermentation, dietary digestibility and nitrogen retention in finishing lambs

Author(s): Omar Cristobal-Carballo; Fernanda Godoy-Santos; Steven Morrison; Sharon Huws; Johanna Brans; Aurelie Aubry; Eva Lewis; Tianhai Yan
Published in: Animal Science Proceedings, 12 (1), 2021, Page(s) 63, ISSN 2772-283X
Publisher: Elsevier
DOI: 10.1016/j.anscip.2021.03.085

39. Dose-response effects of microalgae supplementation on feed intake and weight gain in finishing lambs

Author(s): O. Cristobal-Carballo, F. Godoy-Santos, J. Brans, S. Morrison, A. Aubry, S. Huws, E. Lewis and T. Yan
Published in: Animal Science Proceedings, 12(1), 2021, Page(s) 29, ISSN 2772-283X
Publisher: Elsevier
DOI: 10.1016/j.anscip.2021.03.040

84. Effect of different levels of microalgae supplementation on methane emissions, ruminal fermentation, dietary digestibility and nitrogen retention in finishing lambs

Author(s): O. Cristobal-Carballo, F. Godoy-Santos, J. Brans, S. Morrison, A. Aubry, S. Huws, E. Lewis and T. Yan
Published in: Animal Science Proceedings, 12 (1), 2021, Page(s) 63, ISSN 2772-283X
Publisher: Elsevier
DOI: 10.1016/j.anscip.2021.03.085

80. Effect of breed and ruminal fraction on bacteria and archaea populations in sheep

Author(s): Steven McLoughlin, Charles Spillane, Frank Campion, Noel Claffey, Paul E. Smith, Michael G Diskin, and Sinead M. Waters
Published in: Animal Science Proceedings, 12 (1), 2021, Page(s) 59, ISSN 2772-283X
Publisher: Elsevier
DOI: 10.1016/j.anscip.2021.03.081

39. Dose-response effects of microalgae supplementation on feed intake and weight gain in finishing lambs

Author(s): Omar Cristobal-Carballo; Fernanda Godoy-Santos; Steven Morrison; Sharon Huws; Johanna Brans; Aurelie Aubry; Eva Lewis; Tianhai Yan
Published in: Animal Science Proceedings, 12 (1), 2021, Page(s) 29, ISSN 2772-283X
Publisher: Elsevier
DOI: 10.1016/j.anscip.2021.03.040

28. The effect of phenotypically ranking beef cattle for residual methane output on daily methane emissions, intensity and animal productivity

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