Microbiome Applications for Sustainable food systems through Technologies and EnteRprise

Livrables

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

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

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

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

Auteurs: Ines Calvete-Torre, Carlos Sabater, María José Antón, F. Javier Moreno, Sabino Riestra, Abelardo Margolles, Lorena Ruiz
Publié dans: Food Hydrocolloids. Volume, Numéro 133, 2022, Page(s) 107958, ISSN 1873-7137
Éditeur: 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

Auteurs: Francesca De Filippis, Edoardo Pasolli, Danilo Ercolini
Publié dans: FEMS Microbiology Reviews, Numéro 44/4, 2020, Page(s) 454-489, ISSN 0168-6445
Éditeur: Blackwell
DOI: 10.1093/femsre/fuaa015

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

Auteurs: Jaeger, A.; Arendt, E.K.; Zannini, E.; Sahin, A.W.
Publié dans: Fermentation, Numéro 6, 2020, Page(s) 123, ISSN 2311-5637
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/fermentation6040123

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

Auteurs: Francesca De Filippis, Vincenzo Valentino, Avelino Alvarez-Ordonez, Paul D. Cotter, Danilo Ercolini
Publié dans: Current Opinion in Food Science, Numéro 38, 2021, Page(s) 168-176, ISSN 2214-7993
Éditeur: 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

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

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

Auteurs: 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
Publié dans: NATURE BIOTECHNOLOGY, 2023, ISSN 1087-0156
Éditeur: Nature Publishing Group
DOI: 10.1038/s41587-023-01688-w

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

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

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

Auteurs: Carlos Sabater; Carlos Sabater; Lorena Ruiz; Lorena Ruiz; Susana Delgado; Susana Delgado; Patricia Ruas-Madiedo; Patricia Ruas-Madiedo; Abelardo Margolles; Abelardo Margolles
Publié dans: Frontiers in Microbiology, Numéro 11:581997, 2020, ISSN 1664-302X
Éditeur: Frontiers Media
DOI: 10.3389/fmicb.2020.581997

Prevotella diversity, niches and interactions with the human host

Auteurs: Adrian Tett, Edoardo Pasolli, Giulia Masetti, Danilo Ercolini & Nicola Segata
Publié dans: Nature Reviews in Microbiology, Numéro 19, 2021, Page(s) 585-599, ISSN 1740-1526
Éditeur: 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

Auteurs: Alice Jaeger, Emanuele Zannini, Aylin W. Sahin & Elke K. Arendt
Publié dans: Foods, Numéro 10(6), 2021, Page(s) 1389, ISSN 2304-8158
Éditeur: 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

Auteurs: Miroslav Ducic, Coral Barcenilla, Jose F. Cobo-Díaz, Mercedes Lopez, Avelino Alvarez-Ordoñez, Miguel Prieto
Publié dans: Food Research International, Numéro 163, 2023, ISSN 0963-9969
Éditeur: 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

Auteurs: 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.
Publié dans: Cell Reports, Numéro 42(5), 2023, Page(s) 112464, ISSN 2211-1247
Éditeur: Cell Press
DOI: 10.1016/j.celrep.2023.112464

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

Auteurs: Muñoz-Tamayo, R., Chagas, J.C., Ramin, M. and Krizsan, S.J.
Publié dans: Peer Community Journal, Numéro 1, 2021, Page(s) e7, ISSN 2804-3871
Éditeur: 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

Auteurs: Israel Ikoyi, Guylain Grange, John A. Finn & Fiona P. Brennan
Publié dans: European Journal of Soil Biology, Numéro 118 (Sept-Oct), 2023, ISSN 1164-5563
Éditeur: 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

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

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

Auteurs: Jérôme M., Passerini D., Chevalier F., Marchand L., Leroi F. and Macé S.
Publié dans: International Journal of Food Microbiology, Numéro 363, 2022, Page(s) 109504, ISSN 0168-1605
Éditeur: 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

Auteurs: 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
Publié dans: Microbiome, Numéro 9, 2021, Page(s) 204, ISSN 2049-2618
Éditeur: 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.

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

Bioinformatic approaches for studying the microbiome of fermented food

Auteurs: Walsh, L.H., Coakley, M., Walsh, A.M., O'Toole, P.W. and Cotter, P.D.
Publié dans: Critical Reviews in Microbiology, Numéro 26, 2022, Page(s) 1-33, ISSN 1040-841X
Éditeur: 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.

Auteurs: Alice Jaeger, Aylin W. Sahin, Laura Nyhan, Emanuele Zannini & Elke. K Arendt.
Publié dans: Fermentation, Numéro 10 (3), 2024, Page(s) 136, ISSN 2311-5637
Éditeur: 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

Auteurs: Narciso Martin Quijada, Monika Dzieciol, Stephan Schmitz-Esser, Martin Wagner, Evelyne Selberherr
Publié dans: Frontiers in Microbiology, 13:813480 (2022), Numéro 13, 2022, ISSN 1664-302X
Éditeur: Frontiers Media
DOI: 10.3389/fmicb.2022.813480

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

Auteurs: Juan Manuel Palma-Hidalgo, David R Yáñez-Ruiz, Elisabeth Jiménez, A Ignacio Martín-García, Alejandro Belanche
Publié dans: Frontiers in Veterinary Science, Numéro 8, 2021, Page(s) 706592, ISSN 2297-1769
Éditeur: 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

Auteurs: Huuki H, Tapio M, Mäntysaari P, Negussie E, Ahvenjärvi S, Vilkki J, Vanhatalo A and Tapio I
Publié dans: Frontiers in Microbiology, Numéro 13, 2022, Page(s) 983823, ISSN 1664-302X
Éditeur: 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

Auteurs: 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.
Publié dans: Genome Biology, Numéro 22, 2021, Page(s) 209, ISSN 1474-760X
Éditeur: 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.

Auteurs: Ahvenjärvi, S., Bayat, A.R., Toivanen, M., Mäntysaari, P., Tapio, I.
Publié dans: Scientific Reports., Numéro 14(1), 2024, Page(s) 613, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-024-51300-7

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

Auteurs: Coral Barcenilla, Miroslav Ducic, Mercedes López, Miguel Prieto, Avelino Álvarez-Ordóñez
Publié dans: Meat Science, Numéro 183, 2022, ISSN 0309-1740
Éditeur: Elsevier BV
DOI: 10.1016/j.meatsci.2021.108661

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

Auteurs: Milka Tapio, Daniel Fischer, Päivi Mäntysaari, Ilma Tapio
Publié dans: Microorganisms, Numéro 11(5), 2023, Page(s) 1116, ISSN 2076-2607
Éditeur: MDPI
DOI: 10.3390/microorganisms11051116

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

Auteurs: Davoudkhani, M., Rubino, F., Creevey, C.J., Ahvenjärvi, S., Bayat, A.R., Tapio, I., Belanche, A. & Muñoz-Tamayo, R.
Publié dans: PloS One, Numéro 19(3), 2024, Page(s) e0298930, ISSN 1932-6203
Éditeur: 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

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

Novel methods of microbiome analysis in the food industry

Auteurs: Sabater C, Cobo-Díaz JF, Álvarez-Ordóñez A, Ruas-Madiedo P, Ruiz L, Margolles A.
Publié dans: International Microbiology, Numéro 24, 2021, Page(s) 593-605, ISSN 1139-6709
Éditeur: 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.

Auteurs: Emma Neylon, Laura Nyhan, Emanuele Zannini, Thomas Monin, Steffen Muench, Aylin W. Sahin Elke K. Arendt.
Publié dans: Fermentation, Numéro 9, 78, 2023, ISSN 2311-5637
Éditeur: 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

Auteurs: Emma Neylon, Elke K. Arendt, Emanuele Zannini & Aylin W. Sahin
Publié dans: Foods, Numéro 10(7), 2021, Page(s) 1639, ISSN 2304-8158
Éditeur: 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

Auteurs: 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.
Publié dans: Gut, Numéro 70, 2021, Page(s) 1665-1674, ISSN 0017-5749
Éditeur: 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

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

Integrated molecular approaches for fermented food microbiome research

Auteurs: Aaron M Walsh, John Leech, Curtis Huttenhower, Hue Delhomme-Nguyen, Fiona Crispie, Christian Chervaux, Paul D. Cotter.
Publié dans: FEMS Microbiology Reviews, 2023, Page(s) 1-13, ISSN 0168-6445
Éditeur: 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

Auteurs: Emma Neylon, Elke K. Arendt, Emanuele Zannini & Aylin W. Sahin
Publié dans: Food Structure, Numéro 30:100225, 2021, ISSN 2213-3291
Éditeur: 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

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

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

Auteurs: Manara S, Selma-Royo M, Huang KD, Asnicar F, Armanini F, Blanco-Miguez A, Cumbo F, Golzato D, Manghi P, Pinto F, Valles-Colomer M, Amoroso L, Corrias MV, Ponzoni M, Raffaetà R, Cabrera-Rubio R, Olcina M, Pasolli E, Collado MC, Segata N.
Publié dans: Current Biology, 2023, ISSN 0960-9822
Éditeur: Cell Press
DOI: 10.1016/j.cub.2023.04.011

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

Auteurs: Neylon, E.; Nyhan, L.; Zannini, E.; Sahin, A.W.; Arendt, E.K.
Publié dans: Foods, Numéro 12, 2023, Page(s) 1549, ISSN 2304-8158
Éditeur: 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

Auteurs: Huang, R., Romero, P., Belanche, A., Ungerfeld, E. M., Yanez-Ruiz, D., Morgavi, D. P., Popova, M.
Publié dans: Animal, Numéro 17, 2023, Page(s) 5, ISSN 1751-732X
Éditeur: Elsevier
DOI: 10.1016/j.animal.2023.100788

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

Auteurs: Barcenilla C, Álvarez-Ordóñez A, López M, Alvseike O, Prieto M.
Publié dans: Foods, Numéro 11(15), 2022, Page(s) 2331, ISSN 2304-8158
Éditeur: MDPI
DOI: 10.3390/foods11152331

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

Auteurs: De Filippis, F., Pasolli, E. and Ercolini, D.
Publié dans: Current Biology, Numéro 30, 2020, Page(s) 1–12, ISSN 0960-9822
Éditeur: Cell Press
DOI: 10.1016/j.cub.2020.09.063

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

Auteurs: 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
Publié dans: eLife, 2021, ISSN 2050-084X
Éditeur: eLife Sciences Publications
DOI: 10.7554/elife.65088

Rootlets, a malting by-product with great potential.

Auteurs: Neylon, E., Arendt, E.K., Lynch, K.M., Zannini, E., Bazzoli, P., Monin, T., Sahin, A.W.
Publié dans: Fermentation, Numéro 6, 2020, Page(s) 117, ISSN 2311-5637
Éditeur: 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

Auteurs: Huuki, H., Vilkki, J., Vanhatalo, A. & Tapio, I.
Publié dans: Frontiers in Microbiology, Numéro 15, 2024, Page(s) 1353874, ISSN 1664-302X
Éditeur: 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.

Auteurs: 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.
Publié dans: International Journal of Food Microbiology, Numéro 403,110341, 2023, ISSN 0168-1605
Éditeur: Elsevier BV
DOI: 10.1016/j.ijfoodmicro.2023.110341

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

Auteurs: 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
Publié dans: Cell Host & Microbe, Numéro 26/5, 2019, Page(s) 666-679.e7, ISSN 1931-3128
Éditeur: Cell Press
DOI: 10.1016/j.chom.2019.08.018

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

Auteurs: Sander Wuyts, Nicola Segata
Publié dans: Genome Biology, Numéro 20/1, 2019, ISSN 1474-760X
Éditeur: Springer Nature (BioMed Central (BMC))
DOI: 10.1186/s13059-019-1714-3

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

Auteurs: Aoife J. McHugh, Conor Feehily, Mark A. Fenelon, David Gleeson, Colin Hill, Paul D. Cotter
Publié dans: mSystems, Numéro 5/2, 2020, ISSN 2379-5077
Éditeur: American Society for Microbiology (ASM)
DOI: 10.1128/msystems.00226-20

Detecting contamination in viromes using ViromeQC

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

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

Auteurs: 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
Publié dans: Nature Communications, Numéro 11/1, 2020, ISSN 2041-1723
Éditeur: 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

Auteurs: 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
Publié dans: Genome Biology, Numéro 20/1, 2019, ISSN 1474-760X
Éditeur: 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

Auteurs: Edoardo Pasolli, Francesca De Filippis, Italia E. Mauriello, Fabio Cumbo, Aaron M. Walsh, John Leech, Paul D. Cotter, Nicola Segata, Danilo Ercolini
Publié dans: Nature Communications, Numéro 11/1, 2020, ISSN 2041-1723
Éditeur: 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

Auteurs: 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
Publié dans: Genome Biology, Numéro 21/1, 2020, ISSN 1474-760X
Éditeur: BioMed Central
DOI: 10.1186/s13059-020-02042-y

Analysis of Health Benefits Conferred by Lactobacillus Species from Kefir

Auteurs: Conor Slattery, Paul D. Cotter, Paul W. O’Toole
Publié dans: Nutrients, Numéro 11/6, 2019, Page(s) 1252, ISSN 2072-6643
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/nu11061252

Multiple levels of the unknown in microbiome research

Auteurs: Andrew Maltez Thomas, Nicola Segata
Publié dans: BMC Biology, Numéro 17/1, 2019, ISSN 1741-7007
Éditeur: BioMed Central
DOI: 10.1186/s12915-019-0667-z

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

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

Outlook on next‐generation probiotics from the human gut

Auteurs: F. De Filippis, A. Esposito, D. Ercolini
Publié dans: Cellular and Molecular Life Sciences, Numéro 79, 2022, ISSN 1420-9071
Éditeur: 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

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

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

Auteurs: 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
Publié dans: Nature Medicine, Numéro 27, 2021, Page(s) 321-332, ISSN 1546-170X
Éditeur: 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

Auteurs: Huuki, H., Ahvenjärvi, S., Lidauer, P., Popova, M., Vilkki, J., Vanhatalo, A., & Tapio, I
Publié dans: Frontiers in Microbiology, 2022, Page(s) 3995, ISSN 1664-302X
Éditeur: 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.

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

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

Auteurs: Valentino, V., De Filippis, F., Sequino, G., Ercolini, D.
Publié dans: Applied and Environmental Microbiology, 2023, ISSN 0099-2240
Éditeur: 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.

Auteurs: Stephen Knobloch, Sigurlaug Skirnisdóttir, Marianne Dubois, Lucie Mayolle, Laetitia Kolypczuk, Françoise Leroi, Alexandra Leeper, Delphine Passerini, Viggó Þ. Marteinsson
Publié dans: FEMS Microbes, Numéro 5, 2024, Page(s) xtae011, ISSN 2633-6685
Éditeur: 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

Auteurs: Alice Jaeger, Aylin W. Sahin, Laura Nyhan, Emanuele Zannini & Elke. K Arendt
Publié dans: Fermentation, Numéro 10(1), 2024, Page(s) 54, ISSN 2311-5637
Éditeur: 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.

Auteurs: Liam H. Walsh, Mairéad Coakley, Aaron M. Walsh, Fiona Crispie, Paul W. O’Toole & Paul D. Cotter.
Publié dans: iScience, Numéro 26(10)108004, 2023, Page(s) 108004, ISSN 2589-0042
Éditeur: 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.

Auteurs: Smith PE, Waters SM, Kenny DA, Kirwan SF, Conroy S, Kelly AK.
Publié dans: Journal of Animal Science, Numéro 99, 2021, Page(s) skab275, ISSN 1525-3163
Éditeur: 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.

Auteurs: Alice Jaeger, Aylin W. Sahin, Laura Nyhan, Emanuele Zannini & Elke. K Arendt.
Publié dans: Foods, Numéro 12(4), 2023, Page(s) 798, ISSN 2304-8158
Éditeur: MDPI
DOI: 10.3390/foods12040798

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

Auteurs: Calvete-Torre I, Muñoz-Almagro N, Pacheco MT, Antón MJ, Dapena E, Ruiz L, Margolles A, Villamiel M, Moreno FJ
Publié dans: Carbohydrate Polymers, Numéro 264, 2021, Page(s) 117980, ISSN 0144-8617
Éditeur: 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

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

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

Auteurs: 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.,
Publié dans: Nature Protocols, 2024, ISSN 1750-2799
Éditeur: Springer Nature
DOI: 10.1038/s41596-023-00949-x

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

Auteurs: José F. Cobo-Díaz, Paloma González del Río, Avelino Álvarez-Ordóñez
Publié dans: Frontiers in Microbiology, Numéro 12, 2021, Page(s) 662144, ISSN 1664-302X
Éditeur: 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

Auteurs: Vincenzo Valentino, Giuseppina Sequino, José F. Cobo-Díaz, Avelino Álvarez-Ordóñez, Francesca De Filippis, Danilo Ercolini
Publié dans: Food Research International, Numéro 162, 2022, ISSN 1873-7145
Éditeur: 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

Auteurs: 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
Publié dans: BMC Medicine, Numéro 19, 2021, Page(s) 37, ISSN 1741-7015
Éditeur: BioMed Central
DOI: 10.1186/s12916-021-01913-w

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

Auteurs: 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
Publié dans: Microbiome, Numéro 8, 2020, Page(s) 164, ISSN 2049-2618
Éditeur: BioMed Central
DOI: 10.1186/s40168-020-00941-7

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

Auteurs: Knobloch Stephen, Skírnisdóttir Sigurlaug, Dubois Marianne, Kolypczuk Laetitia, Leroi Francoise, Leeper Alexandra, Passerini Delphine, Marteinsson Viggó
Publié dans: Frontiers In Microbiology, Numéro 13, 2022, Page(s) 912473, ISSN 1664-302X
Éditeur: 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.

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

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

Auteurs: Paul E. Smith; Sinéad M. Waters; David A. Kenny; Stuart F. Kirwan; Stephen Conroy; Alan K. Kelly
Publié dans: Animal Science Proceedings, Numéro 12 (1), 2021, Page(s) 18, ISSN 2772-283X
Éditeur: 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

Auteurs: O. Cristobal-Carballo, F. Godoy-Santos, J. Brans, S. Morrison, A. Aubry, S. Huws, E. Lewis and T. Yan
Publié dans: Animal Science Proceedings, Numéro 12(1), 2021, Page(s) 29, ISSN 2772-283X
Éditeur: 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

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

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