Microbiome Applications for Sustainable food systems through Technologies and EnteRprise

Rezultaty

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

Publikacje

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

Autorzy: Ines Calvete-Torre, Carlos Sabater, María José Antón, F. Javier Moreno, Sabino Riestra, Abelardo Margolles, Lorena Ruiz
Opublikowane w: Food Hydrocolloids. Volume, Numer 133, 2022, Strona(/y) 107958, ISSN 1873-7137
Wydawca: 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

Autorzy: Francesca De Filippis, Edoardo Pasolli, Danilo Ercolini
Opublikowane w: FEMS Microbiology Reviews, Numer 44/4, 2020, Strona(/y) 454-489, ISSN 0168-6445
Wydawca: Blackwell
DOI: 10.1093/femsre/fuaa015

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

Autorzy: Jaeger, A.; Arendt, E.K.; Zannini, E.; Sahin, A.W.
Opublikowane w: Fermentation, Numer 6, 2020, Strona(/y) 123, ISSN 2311-5637
Wydawca: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/fermentation6040123

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

Autorzy: Francesca De Filippis, Vincenzo Valentino, Avelino Alvarez-Ordonez, Paul D. Cotter, Danilo Ercolini
Opublikowane w: Current Opinion in Food Science, Numer 38, 2021, Strona(/y) 168-176, ISSN 2214-7993
Wydawca: 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

Autorzy: Yap, M., Ercolini, D., Álvarez-Ordóñez, A., O'Toole, P.W., O'Sullivan, O., Cotter, P.D.
Opublikowane w: Annu Rev Food Sci Technol, Numer 13, 2022, Strona(/y) 1.1-1.24, ISSN 1941-1421
Wydawca: Annual Reviews
DOI: 10.1146/annurev-food-052720-010751

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

Autorzy: 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
Opublikowane w: NATURE BIOTECHNOLOGY, 2023, ISSN 1087-0156
Wydawca: Nature Publishing Group
DOI: 10.1038/s41587-023-01688-w

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

Autorzy: Aaron M. Walsh, Guerrino Macori, Kieran N. Kilcawley, Paul D. Cotter
Opublikowane w: Nature Food, Numer 1/8, 2020, Strona(/y) 500-510, ISSN 2662-1355
Wydawca: Springer Nature
DOI: 10.1038/s43016-020-0129-3

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

Autorzy: Carlos Sabater; Carlos Sabater; Lorena Ruiz; Lorena Ruiz; Susana Delgado; Susana Delgado; Patricia Ruas-Madiedo; Patricia Ruas-Madiedo; Abelardo Margolles; Abelardo Margolles
Opublikowane w: Frontiers in Microbiology, Numer 11:581997, 2020, ISSN 1664-302X
Wydawca: Frontiers Media
DOI: 10.3389/fmicb.2020.581997

Prevotella diversity, niches and interactions with the human host

Autorzy: Adrian Tett, Edoardo Pasolli, Giulia Masetti, Danilo Ercolini & Nicola Segata
Opublikowane w: Nature Reviews in Microbiology, Numer 19, 2021, Strona(/y) 585-599, ISSN 1740-1526
Wydawca: 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

Autorzy: Alice Jaeger, Emanuele Zannini, Aylin W. Sahin & Elke K. Arendt
Opublikowane w: Foods, Numer 10(6), 2021, Strona(/y) 1389, ISSN 2304-8158
Wydawca: 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

Autorzy: Miroslav Ducic, Coral Barcenilla, Jose F. Cobo-Díaz, Mercedes Lopez, Avelino Alvarez-Ordoñez, Miguel Prieto
Opublikowane w: Food Research International, Numer 163, 2023, ISSN 0963-9969
Wydawca: 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

Autorzy: 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.
Opublikowane w: Cell Reports, Numer 42(5), 2023, Strona(/y) 112464, ISSN 2211-1247
Wydawca: Cell Press
DOI: 10.1016/j.celrep.2023.112464

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

Autorzy: Muñoz-Tamayo, R., Chagas, J.C., Ramin, M. and Krizsan, S.J.
Opublikowane w: Peer Community Journal, Numer 1, 2021, Strona(/y) e7, ISSN 2804-3871
Wydawca: 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

Autorzy: Israel Ikoyi, Guylain Grange, John A. Finn & Fiona P. Brennan
Opublikowane w: European Journal of Soil Biology, Numer 118 (Sept-Oct), 2023, ISSN 1164-5563
Wydawca: 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

Autorzy: Barcenilla, C., Puente, A., Cobo-Díaz, J.F., González-Raurich, M., López, M., Prieto, M., Álvarez-Ordóñez, A.
Opublikowane w: LWT - Food Science and Technology, Numer 200, 2024, Strona(/y) 116166, ISSN 0023-6438
Wydawca: Academic Press
DOI: 10.1016/j.lwt.2024.116166

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

Autorzy: Jérôme M., Passerini D., Chevalier F., Marchand L., Leroi F. and Macé S.
Opublikowane w: International Journal of Food Microbiology, Numer 363, 2022, Strona(/y) 109504, ISSN 0168-1605
Wydawca: 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

Autorzy: 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
Opublikowane w: Microbiome, Numer 9, 2021, Strona(/y) 204, ISSN 2049-2618
Wydawca: 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.

Autorzy: Begrem, S., Ivaniuk, F., Gigout-Chevalier, F., Kolypczuk, L., Bonnetot, S., Leroi, F., Grovel, O., Delbarre-Ladrat, C., Passerini, D.
Opublikowane w: Microorganisms, Numer 8(7), 2020, Strona(/y) 1093, ISSN 2076-2607
Wydawca: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/microorganisms8071093

Bioinformatic approaches for studying the microbiome of fermented food

Autorzy: Walsh, L.H., Coakley, M., Walsh, A.M., O'Toole, P.W. and Cotter, P.D.
Opublikowane w: Critical Reviews in Microbiology, Numer 26, 2022, Strona(/y) 1-33, ISSN 1040-841X
Wydawca: 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.

Autorzy: Alice Jaeger, Aylin W. Sahin, Laura Nyhan, Emanuele Zannini & Elke. K Arendt.
Opublikowane w: Fermentation, Numer 10 (3), 2024, Strona(/y) 136, ISSN 2311-5637
Wydawca: 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

Autorzy: Narciso Martin Quijada, Monika Dzieciol, Stephan Schmitz-Esser, Martin Wagner, Evelyne Selberherr
Opublikowane w: Frontiers in Microbiology, 13:813480 (2022), Numer 13, 2022, ISSN 1664-302X
Wydawca: Frontiers Media
DOI: 10.3389/fmicb.2022.813480

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

Autorzy: Juan Manuel Palma-Hidalgo, David R Yáñez-Ruiz, Elisabeth Jiménez, A Ignacio Martín-García, Alejandro Belanche
Opublikowane w: Frontiers in Veterinary Science, Numer 8, 2021, Strona(/y) 706592, ISSN 2297-1769
Wydawca: 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

Autorzy: Huuki H, Tapio M, Mäntysaari P, Negussie E, Ahvenjärvi S, Vilkki J, Vanhatalo A and Tapio I
Opublikowane w: Frontiers in Microbiology, Numer 13, 2022, Strona(/y) 983823, ISSN 1664-302X
Wydawca: 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

Autorzy: 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.
Opublikowane w: Genome Biology, Numer 22, 2021, Strona(/y) 209, ISSN 1474-760X
Wydawca: 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.

Autorzy: Ahvenjärvi, S., Bayat, A.R., Toivanen, M., Mäntysaari, P., Tapio, I.
Opublikowane w: Scientific Reports., Numer 14(1), 2024, Strona(/y) 613, ISSN 2045-2322
Wydawca: Nature Publishing Group
DOI: 10.1038/s41598-024-51300-7

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

Autorzy: Coral Barcenilla, Miroslav Ducic, Mercedes López, Miguel Prieto, Avelino Álvarez-Ordóñez
Opublikowane w: Meat Science, Numer 183, 2022, ISSN 0309-1740
Wydawca: Elsevier BV
DOI: 10.1016/j.meatsci.2021.108661

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

Autorzy: Milka Tapio, Daniel Fischer, Päivi Mäntysaari, Ilma Tapio
Opublikowane w: Microorganisms, Numer 11(5), 2023, Strona(/y) 1116, ISSN 2076-2607
Wydawca: MDPI
DOI: 10.3390/microorganisms11051116

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

Autorzy: Davoudkhani, M., Rubino, F., Creevey, C.J., Ahvenjärvi, S., Bayat, A.R., Tapio, I., Belanche, A. & Muñoz-Tamayo, R.
Opublikowane w: PloS One, Numer 19(3), 2024, Strona(/y) e0298930, ISSN 1932-6203
Wydawca: 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

Autorzy: Sabater C, Calvete-Torre I, Villamiel M, Moreno FJ, Margolles A, Ruiz L.
Opublikowane w: Trends in Food Science & Technology, Numer 118, 2021, Strona(/y) 399-417, ISSN 0924-2244
Wydawca: Elsevier BV
DOI: 10.1016/j.tifs.2021.10.002

Novel methods of microbiome analysis in the food industry

Autorzy: Sabater C, Cobo-Díaz JF, Álvarez-Ordóñez A, Ruas-Madiedo P, Ruiz L, Margolles A.
Opublikowane w: International Microbiology, Numer 24, 2021, Strona(/y) 593-605, ISSN 1139-6709
Wydawca: 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.

Autorzy: Emma Neylon, Laura Nyhan, Emanuele Zannini, Thomas Monin, Steffen Muench, Aylin W. Sahin Elke K. Arendt.
Opublikowane w: Fermentation, Numer 9, 78, 2023, ISSN 2311-5637
Wydawca: 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

Autorzy: Emma Neylon, Elke K. Arendt, Emanuele Zannini & Aylin W. Sahin
Opublikowane w: Foods, Numer 10(7), 2021, Strona(/y) 1639, ISSN 2304-8158
Wydawca: 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

Autorzy: 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.
Opublikowane w: Gut, Numer 70, 2021, Strona(/y) 1665-1674, ISSN 0017-5749
Wydawca: 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

Autorzy: Muñoz-Tamayo, R., Davoudkhani, M., Fakih, I., Robles-Rodriguez, C.E., Rubino, F., Creevey, C.J. & Forano, E
Opublikowane w: Animal, Numer 17(5), 2023, Strona(/y) 100984, ISSN 1751-732X
Wydawca: Elsevier
DOI: 10.1016/j.animal.2023.100984

Integrated molecular approaches for fermented food microbiome research

Autorzy: Aaron M Walsh, John Leech, Curtis Huttenhower, Hue Delhomme-Nguyen, Fiona Crispie, Christian Chervaux, Paul D. Cotter.
Opublikowane w: FEMS Microbiology Reviews, 2023, Strona(/y) 1-13, ISSN 0168-6445
Wydawca: 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

Autorzy: Emma Neylon, Elke K. Arendt, Emanuele Zannini & Aylin W. Sahin
Opublikowane w: Food Structure, Numer 30:100225, 2021, ISSN 2213-3291
Wydawca: 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

Autorzy: Romero, P., Huang, R., Jiménez, E., Palma-Hidalgo, J. M., Ungerfeld, E. M., Popova, M., Morgavi, D. P., Belanche, A., Yáñez-Ruiz, D. R.
Opublikowane w: Animal, Numer 17, 2023, Strona(/y) 5, ISSN 1751-732X
Wydawca: Elsevier
DOI: 10.1016/j.animal.2023.100789

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

Autorzy: 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.
Opublikowane w: Current Biology, 2023, ISSN 0960-9822
Wydawca: Cell Press
DOI: 10.1016/j.cub.2023.04.011

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

Autorzy: Neylon, E.; Nyhan, L.; Zannini, E.; Sahin, A.W.; Arendt, E.K.
Opublikowane w: Foods, Numer 12, 2023, Strona(/y) 1549, ISSN 2304-8158
Wydawca: 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

Autorzy: Huang, R., Romero, P., Belanche, A., Ungerfeld, E. M., Yanez-Ruiz, D., Morgavi, D. P., Popova, M.
Opublikowane w: Animal, Numer 17, 2023, Strona(/y) 5, ISSN 1751-732X
Wydawca: Elsevier
DOI: 10.1016/j.animal.2023.100788

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

Autorzy: Barcenilla C, Álvarez-Ordóñez A, López M, Alvseike O, Prieto M.
Opublikowane w: Foods, Numer 11(15), 2022, Strona(/y) 2331, ISSN 2304-8158
Wydawca: MDPI
DOI: 10.3390/foods11152331

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

Autorzy: De Filippis, F., Pasolli, E. and Ercolini, D.
Opublikowane w: Current Biology, Numer 30, 2020, Strona(/y) 1–12, ISSN 0960-9822
Wydawca: Cell Press
DOI: 10.1016/j.cub.2020.09.063

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

Autorzy: 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
Opublikowane w: eLife, 2021, ISSN 2050-084X
Wydawca: eLife Sciences Publications
DOI: 10.7554/elife.65088

Rootlets, a malting by-product with great potential.

Autorzy: Neylon, E., Arendt, E.K., Lynch, K.M., Zannini, E., Bazzoli, P., Monin, T., Sahin, A.W.
Opublikowane w: Fermentation, Numer 6, 2020, Strona(/y) 117, ISSN 2311-5637
Wydawca: 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

Autorzy: Huuki, H., Vilkki, J., Vanhatalo, A. & Tapio, I.
Opublikowane w: Frontiers in Microbiology, Numer 15, 2024, Strona(/y) 1353874, ISSN 1664-302X
Wydawca: 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.

Autorzy: 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.
Opublikowane w: International Journal of Food Microbiology, Numer 403,110341, 2023, ISSN 0168-1605
Wydawca: Elsevier BV
DOI: 10.1016/j.ijfoodmicro.2023.110341

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

Autorzy: 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
Opublikowane w: Cell Host & Microbe, Numer 26/5, 2019, Strona(/y) 666-679.e7, ISSN 1931-3128
Wydawca: Cell Press
DOI: 10.1016/j.chom.2019.08.018

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

Autorzy: Sander Wuyts, Nicola Segata
Opublikowane w: Genome Biology, Numer 20/1, 2019, ISSN 1474-760X
Wydawca: Springer Nature (BioMed Central (BMC))
DOI: 10.1186/s13059-019-1714-3

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

Autorzy: Aoife J. McHugh, Conor Feehily, Mark A. Fenelon, David Gleeson, Colin Hill, Paul D. Cotter
Opublikowane w: mSystems, Numer 5/2, 2020, ISSN 2379-5077
Wydawca: American Society for Microbiology (ASM)
DOI: 10.1128/msystems.00226-20

Detecting contamination in viromes using ViromeQC

Autorzy: Moreno Zolfo, Federica Pinto, Francesco Asnicar, Paolo Manghi, Adrian Tett, Frederic D. Bushman, Nicola Segata
Opublikowane w: Nature Biotechnology, Numer 37/12, 2019, Strona(/y) 1408-1412, ISSN 1087-0156
Wydawca: Nature Publishing Group
DOI: 10.1038/s41587-019-0334-5

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

Autorzy: 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
Opublikowane w: Nature Communications, Numer 11/1, 2020, ISSN 2041-1723
Wydawca: 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

Autorzy: 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
Opublikowane w: Genome Biology, Numer 20/1, 2019, ISSN 1474-760X
Wydawca: 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

Autorzy: Edoardo Pasolli, Francesca De Filippis, Italia E. Mauriello, Fabio Cumbo, Aaron M. Walsh, John Leech, Paul D. Cotter, Nicola Segata, Danilo Ercolini
Opublikowane w: Nature Communications, Numer 11/1, 2020, ISSN 2041-1723
Wydawca: 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

Autorzy: 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
Opublikowane w: Genome Biology, Numer 21/1, 2020, ISSN 1474-760X
Wydawca: BioMed Central
DOI: 10.1186/s13059-020-02042-y

Analysis of Health Benefits Conferred by Lactobacillus Species from Kefir

Autorzy: Conor Slattery, Paul D. Cotter, Paul W. O’Toole
Opublikowane w: Nutrients, Numer 11/6, 2019, Strona(/y) 1252, ISSN 2072-6643
Wydawca: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/nu11061252

Multiple levels of the unknown in microbiome research

Autorzy: Andrew Maltez Thomas, Nicola Segata
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Recent advances in enteric methane mitigation and the long road to sustainable ruminant production

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Outlook on next‐generation probiotics from the human gut

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

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

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

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

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

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

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

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

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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.

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

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

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

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

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

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

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

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

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

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

Autorzy: Walsh, L.H., Breselge, S., Prado Martin, J.G., Coakley, M., Ferguson, E., Stapleton, A., Crispie, F., O’Toole, P.W. & Cotter, P.D.
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28. The effect of phenotypically ranking beef cattle for residual methane output on daily methane emissions, intensity and animal productivity

Autorzy: Paul E. Smith; Sinéad M. Waters; David A. Kenny; Stuart F. Kirwan; Stephen Conroy; Alan K. Kelly
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39. Dose-response effects of microalgae supplementation on feed intake and weight gain in finishing lambs

Autorzy: O. Cristobal-Carballo, F. Godoy-Santos, J. Brans, S. Morrison, A. Aubry, S. Huws, E. Lewis and T. Yan
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84. Effect of different levels of microalgae supplementation on methane emissions, ruminal fermentation, dietary digestibility and nitrogen retention in finishing lambs

Autorzy: O. Cristobal-Carballo, F. Godoy-Santos, J. Brans, S. Morrison, A. Aubry, S. Huws, E. Lewis and T. Yan
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