Microbiome Applications for Sustainable food systems through Technologies and EnteRprise

Project Information

MASTER

Grant agreement ID: 818368

DOI 10.3030/818368

Project closed

EC signature date 10 October 2018

Start date 2 January 2019

End date 1 July 2023

Funded under

• SOCIETAL CHALLENGES - Food security, sustainable agriculture and forestry, marine, maritime and inland water research, and the bioeconomy

Total cost € 12 136 475,89

EU contribution € 10 950 171,90

Coordinated by

TEAGASC - AGRICULTURE AND FOOD DEVELOPMENT AUTHORITY
Ireland

Deliverables

Websites, patent fillings, videos etc. (6)

Project Website online
International Conference/webinar proceedings

International Conferencewebinar proceedings

Public version of the web portal with all SOPs and available produced data
Demonstration activities performed in at least 200 food companies
Dissemination, exploitation and communication plan

Dissemination exploitation and communication plan

First version of curatedFoodMetagenomicData from publicly available data

Other (3)

Final release of the pipelines for amplicon-based and metagenomics profiling
Updated version of foodGenVir database
Final version of curatedFoodMetagenomicData including all produced data

Documents, reports (2)

Report on the food, beverage and feed ingredients prototypes enriched with gut-health promoting bioactive components

Report on the food beverage and feed ingredients prototypes enriched with guthealth promoting bioactive components

SOPs for on-site, rapid microbiome screening on aquaculture farms and seawater samples

SOPs for onsite rapid microbiome screening on aquaculture farms and seawater samples

Publications

Peer reviewed articles (77)

Prebiotic potential of apple pomace and pectins from different apple varieties: Modulatory effects on key target commensal microbial populations.

Author(s): Ines Calvete-Torre, Carlos Sabater, María José Antón, F. Javier Moreno, Sabino Riestra, Abelardo Margolles, Lorena Ruiz
Published in: Food Hydrocolloids. Volume, Issue 133, 2022, Page(s) 107958, ISSN 1873-7137
Publisher: Elsevier,
DOI: 10.1016/j.foodhyd.2022.107958

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, Issue 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, Issue 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, Issue 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, Issue 13, 2022, Page(s) 1.1-1.24, ISSN 1941-1421
Publisher: Annual Reviews
DOI: 10.1146/annurev-food-052720-010751

Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4

Author(s): Blanco-Míguez, Aitor; Beghini, Francesco; Cumbo, Fabio; Mciver, Lauren J.; Thompson, Kelsey N.; Zolfo, Moreno; Manghi, Paolo; Dubois, Leonard; Huang, Kun D.; Thomas, Andrew Maltez; Nickols, William A.; Piccinno, Gianmarco; Piperni, Elisa; Punčochář, Michal; Valles-Colomer, Mireia; Tett, Adrian; Giordano, Francesca; Davies, Richard; Wolf, Jonathan; Berry, Sarah E.; Spector, Tim D.; Franzosa, Er
Published in: NATURE BIOTECHNOLOGY, 2023, ISSN 1087-0156
Publisher: Nature Publishing Group
DOI: 10.1038/s41587-023-01688-w

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, Issue 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, Issue 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, Issue 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, Issue 10(6), 2021, Page(s) 1389, ISSN 2304-8158
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/foods10061389

High pressure processing at the early stages of ripening enhances the safety and quality of dry fermented sausages elaborated with or without starter culture

Author(s): Miroslav Ducic, Coral Barcenilla, Jose F. Cobo-Díaz, Mercedes Lopez, Avelino Alvarez-Ordoñez, Miguel Prieto
Published in: Food Research International, Issue 163, 2023, ISSN 0963-9969
Publisher: Elsevier BV
DOI: 10.1016/j.foodres.2022.112162

MetaPhlAn 4 profiling of unknown species-level genome bins improves the characterization of diet-associated microbiome changes in mice

Author(s): Manghi P, Blanco-Míguez A, Manara S, NabiNejad A, Cumbo F, Beghini F, Armanini F, Golzato D, Huang KD, Thomas AM, Piccinno G, Punčochář M, Zolfo M, Lesker TR, Bredon M, Planchais J, Glodt J, Valles-Colomer M, Koren O, Pasolli E, Asnicar F, Strowig T, Sokol H, Segata N.
Published in: Cell Reports, Issue 42(5), 2023, Page(s) 112464, ISSN 2211-1247
Publisher: Cell Press
DOI: 10.1016/j.celrep.2023.112464

Modelling the impact of the macroalgae Asparagopsis taxiformis on rumen microbial fermentation and methane production

Author(s): Muñoz-Tamayo, R., Chagas, J.C., Ramin, M. and Krizsan, S.J.
Published in: Peer Community Journal, Issue 1, 2021, Page(s) e7, ISSN 2804-3871
Publisher: Peer Community In
DOI: 10.24072/pcjournal.11

Plant diversity enhanced nematode-based soil quality indices and changed soil nematode community structure in intensively-managed agricultural grasslands

Author(s): Israel Ikoyi, Guylain Grange, John A. Finn & Fiona P. Brennan
Published in: European Journal of Soil Biology, Issue 118 (Sept-Oct), 2023, ISSN 1164-5563
Publisher: Elsevier BV
DOI: 10.1016/j.ejsobi.2023.103542

Evaluation of the performance of a three-strains lactic acid bacteria cocktail for the control of Listeria monocytogenes on marinated lean pork

Author(s): Barcenilla, C., Puente, A., Cobo-Díaz, J.F., González-Raurich, M., López, M., Prieto, M., Álvarez-Ordóñez, A.
Published in: LWT - Food Science and Technology, Issue 200, 2024, Page(s) 116166, ISSN 0023-6438
Publisher: Academic Press
DOI: 10.1016/j.lwt.2024.116166

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, Issue 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, Issue 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, Issue 8(7), 2020, Page(s) 1093, ISSN 2076-2607
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/microorganisms8071093

Bioinformatic approaches for studying the microbiome of fermented food

Author(s): Walsh, L.H., Coakley, M., Walsh, A.M., O'Toole, P.W. and Cotter, P.D.
Published in: Critical Reviews in Microbiology, Issue 26, 2022, Page(s) 1-33, ISSN 1040-841X
Publisher: Taylor & Francis
DOI: 10.1080/1040841x.2022.2132850

Valorisation Process Using Lactic Acid Bacteria Fermentation Induces Significant Changes in the Physical and Functional Properties of Brewers Spent Yeast.

Author(s): Alice Jaeger, Aylin W. Sahin, Laura Nyhan, Emanuele Zannini & Elke. K Arendt.
Published in: Fermentation, Issue 10 (3), 2024, Page(s) 136, ISSN 2311-5637
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/fermentation10030136

Metatranscriptomic analyses unravel dynamic changes in the microbial and metabolic transcriptional profiles in artisanal Austrian hard-cheeses during ripening

Author(s): Narciso Martin Quijada, Monika Dzieciol, Stephan Schmitz-Esser, Martin Wagner, Evelyne Selberherr
Published in: Frontiers in Microbiology, 13:813480 (2022), Issue 13, 2022, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2022.813480

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, Issue 8, 2021, Page(s) 706592, ISSN 2297-1769
Publisher: Frontiers Media S.A.
DOI: 10.3389/fvets.2021.706592

Long-term effects of early-life rumen microbiota modulation on dairy cow production performance and methane emissions

Author(s): Huuki H, Tapio M, Mäntysaari P, Negussie E, Ahvenjärvi S, Vilkki J, Vanhatalo A and Tapio I
Published in: Frontiers in Microbiology, Issue 13, 2022, Page(s) 983823, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2022.983823

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, Issue 22, 2021, Page(s) 209, ISSN 1474-760X
Publisher: Springer Nature
DOI: 10.1186/s13059-021-02427-7

The effects of residual energy intake on nutrient use, methane emissions and microbial composition in dairy cows.

Author(s): Ahvenjärvi, S., Bayat, A.R., Toivanen, M., Mäntysaari, P., Tapio, I.
Published in: Scientific Reports., Issue 14(1), 2024, Page(s) 613, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-024-51300-7

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, Issue 183, 2022, ISSN 0309-1740
Publisher: Elsevier BV
DOI: 10.1016/j.meatsci.2021.108661

Rumen microbiota predicts feed efficiency of primiparous Nordic Red dairy cows.

Author(s): Milka Tapio, Daniel Fischer, Päivi Mäntysaari, Ilma Tapio
Published in: Microorganisms, Issue 11(5), 2023, Page(s) 1116, ISSN 2076-2607
Publisher: MDPI
DOI: 10.3390/microorganisms11051116

Integrating microbial abundance time series with fermentation dynamics of the rumen microbiome via mathematical modelling

Author(s): Davoudkhani, M., Rubino, F., Creevey, C.J., Ahvenjärvi, S., Bayat, A.R., Tapio, I., Belanche, A. & Muñoz-Tamayo, R.
Published in: PloS One, Issue 19(3), 2024, Page(s) e0298930, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0298930

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, Issue 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, Issue 24, 2021, Page(s) 593-605, ISSN 1139-6709
Publisher: Sociedad Espanola de Microbiologia
DOI: 10.1007/s10123-021-00215-8

Food ingredients for the future: In-depth analysis of the effects of lactic acid bacteria fermentation on spent barley rootlets.

Author(s): Emma Neylon, Laura Nyhan, Emanuele Zannini, Thomas Monin, Steffen Muench, Aylin W. Sahin Elke K. Arendt.
Published in: Fermentation, Issue 9, 78, 2023, ISSN 2311-5637
Publisher: MDPI
DOI: 10.3390/fermentation9010078

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, Issue 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, Issue 70, 2021, Page(s) 1665-1674, ISSN 0017-5749
Publisher: BMJ Publishing Group
DOI: 10.1136/gutjnl-2020-323877

Review: Towards the next-generation models of the rumen microbiome for enhancing predictive power and guiding sustainable production strategies

Author(s): Muñoz-Tamayo, R., Davoudkhani, M., Fakih, I., Robles-Rodriguez, C.E., Rubino, F., Creevey, C.J. & Forano, E
Published in: Animal, Issue 17(5), 2023, Page(s) 100984, ISSN 1751-732X
Publisher: Elsevier
DOI: 10.1016/j.animal.2023.100984

Integrated molecular approaches for fermented food microbiome research

Author(s): Aaron M Walsh, John Leech, Curtis Huttenhower, Hue Delhomme-Nguyen, Fiona Crispie, Christian Chervaux, Paul D. Cotter.
Published in: FEMS Microbiology Reviews, 2023, Page(s) 1-13, ISSN 0168-6445
Publisher: Blackwell
DOI: 10.1093/femsre/fuad001

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, Issue 30:100225, 2021, ISSN 2213-3291
Publisher: Elsevier BV
DOI: 10.1016/j.foostr.2021.100225

Evaluating the effect of phenolic compounds as hydrogen acceptors when ruminal methanogenesis is inhibited in vitro – Part 2. Dairy goats

Author(s): Romero, P., Huang, R., Jiménez, E., Palma-Hidalgo, J. M., Ungerfeld, E. M., Popova, M., Morgavi, D. P., Belanche, A., Yáñez-Ruiz, D. R.
Published in: Animal, Issue 17, 2023, Page(s) 5, ISSN 1751-732X
Publisher: Elsevier
DOI: 10.1016/j.animal.2023.100789

Maternal and food microbial sources shape the infant microbiome of a rural Ethiopian population

Author(s): Serena Manara 1, Marta Selma-Royo 2, Kun D Huang 1, Francesco Asnicar 1, Federica Armanini 1, Aitor Blanco-Miguez 1, Fabio Cumbo 1, Davide Golzato 1, Paolo Manghi 1, Federica Pinto 1, Mireia Valles-Colomer 1, Loredana Amoroso 3, Maria Valeria Corrias 4, Mirco Ponzoni 4, Roberta Raffaetà 5, Raul Cabrera-Rubio 6, Mari Olcina 7, Edoardo Pasolli 8, Maria Carmen Collado 9, Nicola Segata 10
Published in: current biology, 2023, ISSN 0960-9822
Publisher: Cell Press
DOI: 10.1016/j.cub.2023.04.011

From Waste to Taste: Application of Fermented Spent Rootlet Ingredients in a Bread System.

Author(s): Neylon, E.; Nyhan, L.; Zannini, E.; Sahin, A.W.; Arendt, E.K.
Published in: Foods, Issue 12, 2023, Page(s) 1549, ISSN 2304-8158
Publisher: MDPI
DOI: 10.3390/foods12071549

Evaluating the effect of phenolic compounds as hydrogen acceptors when ruminal methanogenesis is inhibited in vitro – Part 1. Dairy cows

Author(s): Huang, R., Romero, P., Belanche, A., Ungerfeld, E. M., Yanez-Ruiz, D., Morgavi, D. P., Popova, M.
Published in: Animal, Issue 17, 2023, Page(s) 5, ISSN 1751-732X
Publisher: Elsevier
DOI: 10.1016/j.animal.2023.100788

Microbiological safety and shelf-life of low-salt meat products-a review.

Author(s): Barcenilla C, Álvarez-Ordóñez A, López M, Alvseike O, Prieto M.
Published in: Foods, Issue 11(15), 2022, Page(s) 2331, ISSN 2304-8158
Publisher: MDPI
DOI: 10.3390/foods11152331

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, Issue 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, Issue 6, 2020, Page(s) 117, ISSN 2311-5637
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/fermentation6040117

Fecal microbiota colonization dynamics in dairy heifers associated with early-life rumen microbiota modulation and gut health

Author(s): Huuki, H., Vilkki, J., Vanhatalo, A. & Tapio, I.
Published in: Frontiers in Microbiology, Issue 15, 2024, Page(s) 1353874, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2024.1353874

Selection of lactic acid bacteria as biopreservation agents and optimization of their mode of application for the control of Listeria monocytogenes in ready-to-eat cooked meat products.

Author(s): Barcenilla, C., Puente, A., Cobo-Díaz, J.F., Alexa, E.A., García-Gutiérrez, E., O'Connor, P.M., Cotter, P.D., González-Raurich, M., López, M., Prieto, M., álvarez-Ordóñez, A.
Published in: International Journal of Food Microbiology, Issue 403,110341, 2023, ISSN 0168-1605
Publisher: Elsevier BV
DOI: 10.1016/j.ijfoodmicro.2023.110341

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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 17/1, 2019, ISSN 1741-7007
Publisher: BioMed Central
DOI: 10.1186/s12915-019-0667-z

Recent advances in enteric methane mitigation and the long road to sustainable ruminant production

Author(s): Roques, S., Martinez-Fernandez, G., Ramayo-Caldas, Y., Popova, M., Denman, S., Meale, S.J., Morgavi, D.P.
Published in: Annual Review of Animal Biosciences, Issue 12, 2024, Page(s) 321–343., ISSN 2165-8102
Publisher: Annual Reviews Inc.
DOI: 10.1146/annurev-animal-021022-024931

Outlook on next‐generation probiotics from the human gut

Author(s): F. De Filippis, A. Esposito, D. Ercolini
Published in: Cellular and Molecular Life Sciences, Issue 79, 2022, ISSN 1420-9071
Publisher: Springer Nature
DOI: 10.1007/s00018-021-04080-6

Predicting the dynamics of enteric methane emissions based on intake kinetic patterns in dairy cows fed diets containing either wheat or corn

Author(s): R. Muñoz-Tamayo, B. Ruiz, P. Blavy, S. Giger-Reverdin, D. Sauvant, S.R.O. Williams, P.J. Moate
Published in: Animal Open Space, Issue 1, 2022, Page(s) 100003, ISSN 2772-6940
Publisher: Elsevier
DOI: 10.1016/j.anopes.2021.100003

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, Issue 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, Issue 5(4), 2021, ISSN 2396-8370
Publisher: Springer Nature
DOI: 10.1038/s41538-021-00087-2

Psychrotrophic bacteria equipped with virulence and colonization traits populate ice-cream manufacture environment

Author(s): Valentino, V., De Filippis, F., Sequino, G., Ercolini, D.
Published in: Applied and Environmental Microbiology, 2023, ISSN 0099-2240
Publisher: American Society for Microbiology
DOI: 10.1128/aem.00765-23

The gut microbiome of farmed Arctic char (Salvelinus alpinus) is shaped by feeding stage and nutrient presence.

Author(s): Stephen Knobloch, Sigurlaug Skirnisdóttir, Marianne Dubois, Lucie Mayolle, Laetitia Kolypczuk, Françoise Leroi, Alexandra Leeper, Delphine Passerini, Viggó Þ. Marteinsson
Published in: FEMS Microbes, Issue 5, 2024, Page(s) xtae011, ISSN 2633-6685
Publisher: Oxford University Press
DOI: 10.1093/femsmc/xtae011

Lactic Acid Fermentation as a Valorising Agent for Brewer’s Spent Yeast—Improving the Sensory Quality and Nutritional Potential

Author(s): Alice Jaeger, Aylin W. Sahin, Laura Nyhan, Emanuele Zannini & Elke. K Arendt
Published in: Fermentation, Issue 10(1), 2024, Page(s) 54, ISSN 2311-5637
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/fermentation10010054

Analysis of the milk kefir pan-metagenome reveals four community types, core species, and associated metabolic pathways.

Author(s): Liam H. Walsh, Mairéad Coakley, Aaron M. Walsh, Fiona Crispie, Paul W. O’Toole & Paul D. Cotter.
Published in: iScience, Issue 26(10)108004, 2023, Page(s) 108004, ISSN 2589-0042
Publisher: Elselvier
DOI: 10.1016/j.isci.2023.108004

Effect of divergence in residual methane emissions on feed intake and efficiency, growth and carcass performance, and indices of rumen fermentation and methane emissions in finishing beef cattle.

Author(s): Smith PE, Waters SM, Kenny DA, Kirwan SF, Conroy S, Kelly AK.
Published in: Journal of Animal Science, Issue 99, 2021, Page(s) skab275, ISSN 1525-3163
Publisher: Oxford University Press
DOI: 10.1093/jas/skab275

Functional Properties of Brewer’s Spent Grain Protein Isolate: The Missing Piece in the Plant Protein Portfolio.

Author(s): Alice Jaeger, Aylin W. Sahin, Laura Nyhan, Emanuele Zannini & Elke. K Arendt.
Published in: Foods, Issue 12(4), 2023, Page(s) 798, ISSN 2304-8158
Publisher: MDPI
DOI: 10.3390/foods12040798

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, Issue 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, Issue 101(12), 2021, Page(s) 5541-5549, ISSN 0022-5142
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/jsfa.11205

Improved sampling and DNA extraction procedures for microbiome analysis in food processing environments.

Author(s): Barcenilla, C., Cobo-Diaz, J.F., De Filippis, F., Valentino, V., Cabrera Rubio, R., O’Neil, D., Mahler de Sanchez, L., Armanini, F., Carlino, N., Blanco-Míguez, A., Pinto, F., Calvete-Torre, I., Sabater, C., Delgado, S., Ruas-Madiedo, P., Quijada, N.M., Dzieciol, M., Skírnisdóttir, S., Knobloch, S., Puente, A., López, M., Prieto, M., Marteinsson, V.T., Wagner, M., Margolles, A., Segata, N.,
Published in: Nature Protocols, 2024, ISSN 1750-2799
Publisher: Springer Nature
DOI: 10.1038/s41596-023-00949-x

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, Issue 12, 2021, Page(s) 662144, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2021.662144

Evidence of virulence and antibiotic resistance genes from the microbiome mapping in minimally processed vegetables producing facilities

Author(s): Vincenzo Valentino, Giuseppina Sequino, José F. Cobo-Díaz, Avelino Álvarez-Ordóñez, Francesca De Filippis, Danilo Ercolini
Published in: Food Research International, Issue 162, 2022, ISSN 1873-7145
Publisher: Elsevier
DOI: 10.1016/j.foodres.2022.112202

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, Issue 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, Issue 8, 2020, Page(s) 164, ISSN 2049-2618
Publisher: BioMed Central
DOI: 10.1186/s40168-020-00941-7

Putative probiotics on growth, behavior, and the gut microbiome of farmed Arctic Char (Salvelinus alpinus)

Author(s): Knobloch Stephen, Skírnisdóttir Sigurlaug, Dubois Marianne, Kolypczuk Laetitia, Leroi Francoise, Leeper Alexandra, Passerini Delphine, Marteinsson Viggó
Published in: Frontiers In Microbiology, Issue 13, 2022, Page(s) 912473, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2022.912473

Kefir4All, a Citizen Science initiative to raise awareness of the roles that microbes play in food fermentation.

Author(s): Walsh, L.H., Breselge, S., Prado Martin, J.G., Coakley, M., Ferguson, E., Stapleton, A., Crispie, F., O’Toole, P.W. & Cotter, P.D.
Published in: Journal of Microbiology & Biology Education, 2024, ISSN 1935-7885
Publisher: ASM
DOI: 10.1128/jmbe.00155-23

Conference proceedings (3)

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, Issue 12 (1), 2021, Page(s) 18, ISSN 2772-283X
Publisher: Elsevier
DOI: 10.1016/j.anscip.2021.03.029

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, Issue 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, Issue 12 (1), 2021, Page(s) 63, ISSN 2772-283X
Publisher: Elsevier
DOI: 10.1016/j.anscip.2021.03.085