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Project Newsletters	MASTER newsletter, 2019	view	MASTER newsletter, 2020	view
Project Newsletters	MASTER newsletter, 2021	view
Public Deliverables	First version of curated Food Metagenomic date from publicly available data	view	Project Website online	view
Promotional materials	MASTER general flyer	view	MASTER infographic	view
	Plant & Soil Microbiome Research Flyer_MASTER	view	Marine & Fish Microbiome Research Flyer_MASTER	view
	Rumen Microbiome Research Flyer_MASTER	view	Food and Health Research Flyer_MASTER	view
	Food Fermentations and Waste Streams Research Flyer_MASTER	view	Microbiome Technologies Research Flyer_MASTER	view
	MASTER Flyer - 2022	view
MASTER in the media	Horizon Magazine article 2019	view	Project Repository Journal article	view
MASTER in the media	The science of fermented foods (podcast)	view	Phytobiomes Alliance Webinar 2020	view
Scientific articles 2019	Manara, S., Asnicar, F., Beghini, F., Bazzani, D., Cumbo, F., Zolfo, M., Nigro, E., Karcher, N., Manghi, P., Metzger, M.I., Pasolli, E. and Segata, N. (2019) Microbial genomes from non-human primate gut metagenomes expand the primate-associated bacterial tree of life with over 1000 novel species. Genome Biology, 20, 299.	view	Slattery, C., Cotter, P.D. and O'Toole, P.W. (2019) *Analysis of health benefits conferred by Lactobacillus* species from kefir*. Nutrients*, 11.	view
	Tett, A., Huang, K.D., Asnicar, F., Fehlner-Peach, H., Pasolli, E., Karcher, N., Armanini, F., Manghi, P., Bonham, K., Zolfo, M., De Filippis, F., et al. (2019) *The Prevotella copri* complex comprises four distinct clades underrepresented in westernized populations*. Cell Host Microbe*, 26(5), 666-679.e7.	view	Thomas, A.M. and Segata, N. (2019) Multiple levels of the unknown in microbiome research. BMC Biology, 17, 48.	view
	Wuyts, S. and Segata, N. (2019) At the forefront of the sequencing revolution-notes from the RNGS19 conference. Genome Biology, 20, 93.	view	Zolfo, M., Pinto, F., Asnicar, F., Manghi, P., Tett, A., Bushman, F.D. and Segata, N. (2019) Detecting contamination in viromes using ViromeQC. Nature Biotechnology, 37, 1408-1412.	view
Scientific articles 2020	Asnicar, F., Thomas, A.M., Beghini, F., Mengoni, C., Manara, S., Manghi, P., Zhu, Q., Bolzan, M., Cumbo, F., May, U., et al. (2020) Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0. Nature Communications, 11, 2500.	view	Begrem, S., Ivaniuk, F., Gigout-Chevalier, F., Kolypczuk, L., Bonnetot, S., Leroi, F., Grovel, O., Delbarre-Ladrat, C., Passerini, D. (2020) *New insight into antimicrobial compounds from food and marine-sourced Carnobacterium* species through phenotype and genome analyses*. Microorganisms*, 8(7):1093.	view
	De Filippis, F., Pasolli, E. and Ercolini, D. (2020) The food-gut axis: lactic acid bacteria and their link to food, the gut microbiome and human health. FEMS Microbiology Reviews, 44(4), 454–489.	view	De Filippis, F., Pasolli, E. and Ercolini, D. (2020) Newly explored Faecalibacterium diversity is connected to age, lifestyle, geography, and disease. Current Biology, 30, 1–12.	view
	Karcher, N., Pasolli, E., Asnicar, F., Huang, K.D., Tett, A., Manara, S., Armanini, F., Bain, D., Duncan, S.H., Louis, P., et al. (2020) *Analysis of 1321 Eubacterium rectale* genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations*. Genome Biology*, 21, 138.	view	McHugh, A.J., Feehily, C., Fenelon, M.A., Gleeson, D., Hill, C. and Cotter, P.D. (2020) Tracking the dairy microbiota from farm bulk tank to skimmed milk powder. mSystems, 5.	view
	Pasolli, E., De Filippis, F., Mauriello, I.E., Cumbo, F., Walsh, A.M., Leech, J., Cotter, P.D., Segata, N. and Ercolini, D. (2020) Large-scale genome-wide analysis links lactic acid bacteria from food with the gut microbiome. Nature Communications, 11, 2610.	view	Sabater, C., Ruiz, L., Delgado, S., Ruas-Madiedo, P. and Margolles, A. (2020) Valorization of vegetable food waste and by-products through fermentation processes. Frontiers in Microbiology, 11:581997.	view
	Walsh, A.M., Macori, G., Kilcawley, K.N. and Cotter, P.D.(2020) Meta-analysis of cheese microbiomes highlights contributions to multiple aspects of quality. Nature Food, 1, 500–510.	view	Jaeger A., Arendt E.K., Zannini E and Sahin A.W. (2020) Brewer’s Spent Yeast (BSY), an Underutilized Brewing By-Product. Fermentation, 6, 123	view
	Neylon, E.; Arendt, E.K.; Lynch, K.M.; Zannini, E.; Bazzoli, P.; Monin, T.; Sahin, A.W. (2020) Rootlets, a Malting By-Product with Great Potential. Fermentation, 6, 117.	view	Mencia-Ares, O., Cabrera-Rubio, R., Cobo-Diaz, J.F., Alvarez-Ordonez, A., Gomez-Garcia, M., Puente, H., Cotter, P.D., Crispie, F., Carvajal, A., Rubio, P. and Arguello, H. (2020) Antimicrobial use and production system shape the fecal, environmental, and slurry resistomes of pig farms. Microbiome 8, 164. doi:10.1186/s40168-020-00941-7	view
Scientific articles 2021	Muñoz-Tamayo, R., Chagas, J.C., Ramin, M. and Krizsan, S.J. (2021) Modelling the impact of the macroalgae Asparagopsis taxiformis on rumen microbial fermentation and methane production. Peer Community Journal 1:e7. doi:10.24072/pcjournal.11	view	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., Hadjigeorgiou, G., Wolf, J., Ordovás, J.M., Gardner, C., Franks, P.W., Chan, A.T., Huttenhower, C., Spector, T.D. and Segata, N. (2021) Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals. Nature Medicine 27, 321–332. doi:10.1038/s41591-020-01183-8.	view
	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. and Berry, S.E. (2021) Blue poo: impact of gut transit time on the gut microbiome using a novel marker. Gut 70, 1665-1674. doi:10.1136/gutjnl-2020-323877	view	Beghini, F., McIver, L.J., Blanco-Miguez, A., Dubois, L., Asnicar, F., Maharjan, S., Mailyan, A., Manghi, P., Scholz, M., Thomas, A.M., Valles-Colomer, M., Weingart, G., Zhang, Y., Zolfo, M., Huttenhower, C., Franzosa, E.A. and Segata, N. (2021) Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. eLife 10. doi:10.7554/eLife.65088	view
	Belanche, A., Martin-Garcia, I., Jimenez, E., Jonsson, N.N. and Yanez-Ruiz, D.R. (2021) A novel ammoniation treatment of barley as a strategy to optimize rumen pH, feed degradability and microbial protein synthesis in sheep. Journal of the Science of Food and Agriculture 101, 5541-5549. doi:10.1002/jsfa.11205	view	Calvete-Torre, I., Munoz-Almagro, N., Pacheco, M.T., Anton, M.J., Dapena, E., Ruiz, L., Margolles, A., Villamiel, M. and Moreno, F.J. (2021) Apple pomaces derived from mono-varietal Asturian ciders production are potential source of pectins with appealing functional properties. Carbohydrate Polymers 264, 117980. doi:10.1016/j.carbpol.2021.117980	view
	Cobo-Diaz, J.F., Alvarez-Molina, A., Alexa, E.A., Walsh, C.J., Mencia-Ares, O., Puente-Gomez, P., Likotrafiti, E., Fernandez-Gomez, P., Prieto, B., Crispie, F., Ruiz, L., Gonzalez-Raurich, M., Lopez, M., Prieto, M., Cotter, P. and Alvarez-Ordonez, A. (2021) Microbial colonization and resistome dynamics in food processing environments of a newly opened pork cutting industry during 1.5 years of activity. Microbiome 9, 204. doi:10.1186/s40168-021-01131-9	view	Cobo-Diaz, J.F., Gonzalez Del Rio, P. and Alvarez-Ordonez, A. (2021) Whole resistome analysis in Campylobacter jejuni and Campylobacter coli genomes available in public repositories. Frontiers in Microbiology 12, 662144. doi:10.3389/fmicb.2021.662144	view
	De Filippis, F., Valentino, V., Alvarez-Ordonez, A., Cotter, P.D. and Ercolini, D. (2021) Environmental microbiome mapping as a strategy to improve quality and safety in the food industry. Current Opinion in Food Science 38, 168-176. doi:10.1016/j.cofs.2020.11.012	view	Jaeger, A., Zannini, E., Sahin, A.W. and Arendt, E.K. (2021) Barley protein properties, extraction and applications, with a focus on Brewers' Spent Grain protein. Foods 10. doi:10.3390/foods10061389	view
	Karcher, N., Nigro, E., Puncochar, M., Blanco-Miguez, A., Ciciani, M., Manghi, P., Zolfo, M., Cumbo, F., Manara, S., Golzato, D., Cereseto, A., Arumugam, M., Bui, T.P.N., Tytgat, H.L.P., Valles-Colomer, M., de Vos, W.M. and Segata, N. (2021) Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly. Genome Biology 22, 209. doi:10.1186/s13059-021-02427-7	view	McHugh, A.J., Yap, M., Crispie, F., Feehily, C., Hill, C. and Cotter, P.D. (2021) Microbiome-based environmental monitoring of a dairy processing facility highlights the challenges associated with low microbial-load samples. NPJ Science of Food 5, 4. doi:10.1038/s41538-021-00087-2	view
	Menni, C., Louca, P., Berry, S.E., Vijay, A., Astbury, S., Leeming, E.R., Gibson, R., Asnicar, F., Piccinno, G., Wolf, J., Davies, R., Mangino, M., Segata, N., Spector, T.D. and Valdes, A.M. (2021) High intake of vegetables is linked to lower white blood cell profile and the effect is mediated by the gut microbiome. BMC Medicine 19, 37. doi:10.1186/s12916-021-01913-w	view	Neylon, E., Arendt, E.K., Zannini, E. and Sahin, A.W. (2021) Fermentation as a tool to revitalise Brewers' Spent Grain and elevate techno-functional properties and nutritional value in high fibre bread. Foods 10. doi:10.3390/foods10071639	view
	Neylon, E., Arendt, E.K., Zannini, E. and Sahin, A.W. (2021) Fundamental study of the application of brewers spent grain and fermented brewers spent grain on the quality of pasta. Food Structure 30, 100225 doi:10.1016/j.foostr.2021.100225	view	Palma-Hidalgo, J.M., Yanez-Ruiz, D.R., Jimenez, E., Martin-Garcia, A.I. and Belanche, A. (2021) Presence of adult companion goats favors the rumen microbial and functional development in artificially reared kids. Frontiers in Veterinary Science 8, 706592. doi:10.3389/fvets.2021.706592	view
	Sabater, C., Calvete-Torre, I., Villamiel, M., Moreno, J.F., Margolles, A. and Ruiz, L. (2021) Vegetable waste and by-products to feed a healthy gut microbiota: Current evidence, machine learning and computational tools to design novel microbiome-targeted foods. Trends in Food Science & Technology 118, 399-417. doi:10.1016/j.tifs.2021.10.002	view	Sabater, C., Cobo-Diaz, J.F., Alvarez-Ordonez, A., Ruas-Madiedo, P., Ruiz, L. and Margolles, A. (2021) Novel methods of microbiome analysis in the food industry. International Microbiology 24, 593-605. doi:10.1007/s10123-021-00215-8	view
	Tett, A., Pasolli, E., Masetti, G., Ercolini, D. and Segata, N. (2021) Prevotella diversity, niches and interactions with the human host. Nature Reviews Microbiology 19, 585-599. doi:10.1038/s41579-021-00559-y	view	Smith, P.E., Waters, S.M., Kenny, D.A., Kirwan, S.F., Conroy, S. and Kelly, A.K. (2021) 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. Journal of Animal Science 99:11, skab275. doi:10.1093/jas/skab275	view
	Cristobal-Carballo, O., Godoy-Santos, F., Brans, J., Morrison, S., Aubry, A., Huws, S., Lewis, E. and Yan, T. (2021) 39. Dose-response effects of microalgae supplementation on feed intake and weight gain in finishing lambs. BSAS 2021 Conference ‘The Challenge of Change – The New Normal?’ Animal Science Proceedings 12(1):29. doi:10.1016/j.anscip.2021.03.040	view	Cristobal-Carballo, O., Godoy-Santos, F., Brans, J., Morrison, S., Aubry, A., Huws, S., Lewis, E. and Yan, T. (2021) 84. Effect of different levels of microalgae supplementation on methane emissions, ruminal fermentation, dietary digestibility and nitrogen retention in finishing lambs. BSAS 2021 Conference ‘The Challenge of Change – The New Normal?’ Animal Science Proceedings. 12(1):63. doi:10.1016/j.anscip.2021.03.085	view
	Smith, P.E., Waters, S.M., Kenny, D.A., Kirwan, S.F., Conroy, S., and Kelly, A.K. (2021) 28. The effect of phenotypically ranking beef cattle for residual methane output on daily methane emissions, intensity and animal productivity. BSAS 2021 Conference ‘The Challenge of Change – The New Normal?’ Animal Science Proceedings 12(1):18. doi:10.1016/j.anscip.2021.03.029	view
Scientific articles 2022	Barcenilla, C., Ducic, M., Lopez, M., Prieto, M. and Alvarez-Ordonez, A. (2022) Application of lactic acid bacteria for the biopreservation of meat products: A systematic review. Meat Science 183, 108661. doi:10.1016/j.meatsci.2021.108661	view	Huuki, H., Ahvenjärvi, S., Lidauer, P., Popova, M., Vilkki, J., Vanhatalo, A. and Tapio, I. (2022) Fresh rumen liquid inoculant enhances the rumen microbial community establishment in pre-weaned dairy calves. Frontiers in Microbiology 12. doi:10.3389/fmicb.2021.758395	view
	Jerome, M., Passerini, D., Chevalier, F., Marchand, L., Leroi, F. and Mace, S. (2022) Development of a rapid qPCR method to quantify lactic acid bacteria in cold-smoked salmon. International Journal of Food Microbiology 363, 109504. doi:10.1016/j.ijfoodmicro.2021.109504	view	Yap, M., Ercolini, D., Alvarez-Ordonez, A., O'Toole, P.W., O'Sullivan, O. and Cotter, P.D. (2022) Next-Generation Food Research: Use of meta-omic approaches for characterizing microbial communities along the food chain. Annual Review of Food Science and Technology 13:1, 361-384. doi:10.1146/annurev-food-052720-010751	view
	Calvete-Torre, I., Sabater, C., Antón, M.J., Moreno, F.J., Riestra, S., Margolles, A. and Ruiz, L. (2022) Prebiotic potential of apple pomace and pectins from different apple varieties: Modulatory effects on key target commensal microbial populations. Food Hydrocolloids 133, 107958. doi:10.1016/j.foodhyd.2022.107958	view	De Filippis, F., Esposito, A. and Ercolini, D. (2022) Outlook on next-generation probiotics from the human gut. Cellular and Molecular Life Sciences, 79. doi:10.1007/s00018-021-04080-6	view
	Huuki, H., Tapio, M., Mäntysaari, P., Negussie, E., Ahvenjärvi, S., Vilkki, J., Vanhatalo, A. and Tapio, I. (2022) Long-term effects of early-life rumen microbiota modulation on dairy cow production performance and methane emissions. Frontiers in Microbiology 13:983823. doi:10.3389/fmicb.2022.983823	view	Knobloch S., Skírnisdóttir, S., Dubois, M., Kolypczuk, L., Leroi, F., Leeper, A., Passerini, D. and Marteinsson, V. (2022) Impact of Putative probiotics on growth, behavior, and the gut microbiome of farmed Arctic Char (Salvelinus alpinus). Frontiers in Microbiology 13:912473. doi:10.3389/fmicb.2022.912473	view
	Martin Quijada, N., Dzieciol, M., Schmitz-Esser, S., Wagner, M., and Selberherr, E. (2022) Metatranscriptomic analyses unravel dynamic changes in the microbial and metabolic transcriptional profiles in artisanal Austrian hard-cheeses during ripening. Frontiers in Microbiology 13:813480. doi:10.3389/fmicb.2022.813480	view	Muñoz-Tamayo, R., Ruiz, B., Blavy, P., Giger-Reverdin, S., Sauvant, D., Williams, S.R.O. and Moate, P.J. (2022) Predicting the dynamics of enteric methane emissions based on intake kinetic patterns in dairy cows fed diets containing either wheat or corn. Animal Open Space 1,100003. doi:10.1016/j.anopes.2021.100003.	view
	Valentino, V., Sequino, G., Cobo-Díaz, J.F., Álvarez-Ordóñez, A., De Filippis, F. and Ercolini, D. (2022) Evidence of virulence and antibiotic resistance genes from the microbiome mapping in minimally processed vegetables producing facilities. Food Research International 162. doi:10.1016/j.foodres.2022.112202	view	Walsh, L.H., Coakley, M., Walsh, A.M., O'Toole, P.W. and Cotter, P.D. (2022) Bioinformatic approaches for studying the microbiome of fermented food. Critical Reviews in Microbiology 26:1-33. doi:10.1080/1040841X.2022.2132850	view

Scientific articles 2023	Ducic, M., Barcenilla, C., Cobo-Díaz, J.F., Lopez, M., Alvarez-Ordoñez, A. and Prieto, M. (2023) High pressure processing at the early stages of ripening enhances the safety and quality of dry fermented sausages elaborated with or without starter culture. Food Research International 163. doi:10.1016/j.foodres.2022.112162	view

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