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Project Newsletters MASTER newsletter, 2019 view View Master first newsletter MASTER newsletter, 2020 view View Master second newsletter
MASTER newsletter, 2021 view MASTER 3rd Newsletter MASTER newsletter, 2022 view MASTER 4th Newsletter
Public Deliverables First version of curated Food Metagenomic date from publicly available data view View Master first newsletter Project Website online view View Master second newsletter
Promotional materials MASTER general flyer view View Master first newsletter MASTER infographic view View Master first newsletter
Plant & Soil Microbiome Research Flyer_MASTER view View Master first newsletter Marine & Fish Microbiome Research Flyer_MASTER view View Master first newsletter
Rumen Microbiome Research Flyer_MASTER view View Master first newsletter Food and Health Research Flyer_MASTER view View Master first newsletter
Food Fermentations and Waste Streams Research Flyer_MASTER view View Master first newsletter Microbiome Technologies Research Flyer_MASTER view View Master first newsletter
MASTER Flyer - 2022 view View Master first newsletter MASTERing food chain microbiomes_Invite view View Master first newsletter
MASTER in the media Horizon Magazine article 2019 view View Master first newsletter Project Repository Journal article view View Master first newsletter
The science of fermented foods (podcast) view View Master first newsletter Phytobiomes Alliance Webinar 2020 view View Master first newsletter
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.

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Slattery, C., Cotter, P.D. and O'Toole, P.W. (2019) Analysis of health benefits conferred by Lactobacillus species from kefir. Nutrients, 11.

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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.

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Thomas, A.M. and Segata, N. (2019) Multiple levels of the unknown in microbiome research. BMC Biology, 17, 48.

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Wuyts, S. and Segata, N. (2019) At the forefront of the sequencing revolution-notes from the RNGS19 conference. Genome Biology, 20, 93.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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

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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.

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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.

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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

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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

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Barcenilla, C., Alvarez-Ordonez, A., Lopez, M., Alvseike, O., Prieto, M. (2022a) Microbiological safety and shelf-life of low-salt meat products-A Review. Foods 11. doi:10.3390/foods11152331

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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

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Huang, R., Romero, P., Belanche, A., Ungerfeld, E.M., Yanez-Ruiz, D., Morgavi, D.P., Popova, M. (2023) Evaluating the effect of phenolic compounds as hydrogen acceptors when ruminal methanogenesis is inhibited in vitro - Part 1. Dairy cows. Animal 17, 100788. doi: 10.1016/j.animal.2023.100788

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Jaeger, A., Sahin, A.W., Nyhan, L., Zannini, E., Arendt, E.K. (2023) Functional properties of Brewer's Spent Grain protein isolate: the missing piece in the plant protein portfolio. Foods 12. doi:10.3390/foods12040798

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Manghi, P., Blanco-Miguez, A., Manara, S., NabiNejad, A., Cumbo, F., Beghini, F., Armanini, F., Golzato, D., Huang, K.D., Thomas, A.M., Piccinno, G., Puncochar, M., Zolfo, M., Lesker, T.R., Bredon, M., Planchais, J., Glodt, J., Valles-Colomer, M., Koren, O., Pasolli, E., Asnicar, F., Strowig, T., Sokol, H., Segata, N. (2023) MetaPhlAn 4 profiling of unknown species-level genome bins improves the characterization of diet-associated microbiome changes in mice. Cell Reports 42, 112464. doi:10.1016/j.celrep.2023.112464

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Neylon, E., Nyhan, L., Zannini, E., Sahin, A.W., Arendt, E.K. (2023) From Waste to Taste: application of fermented spent rootlet ingredients in a bread system. Foods 12. doi:10.3390/foods12071549

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Neylon, E.N., Zannini, E., Monin, T., Muench, S., Sahin, A.W., Arendt, E.K. (2023) Food ingredients for the future: In-depth analysis of the effects of lactic acid bacteria fermentation on spent barley rootlets. Fermentation 9. doi:10.3390/fermentation9010078

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Romero, P., Huang, R., Jimenez, E., Palma-Hidalgo, J.M., Ungerfeld, E.M., Popova, M., Morgavi, D.P., Belanche, A., Yanez-Ruiz, D.R. (2023) Evaluating the effect of phenolic compounds as hydrogen acceptors when ruminal methanogenesis is inhibited in vitro - Part 2. Dairy goats. Animal 17, 100789. doi:10.1016/j.animal.2023.100789

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Tapio, M., Fischer, D., Mantysaari, P., Tapio, I. (2023) Rumen microbiota predicts feed efficiency of primiparous nordic red dairy cows. Microorganisms 11. doi:10.3390/microorganisms11051116

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Valentino, V., De Filippis, F., Sequino, G., Ercolini, D. (2023) Psychrotrophic bacteria equipped with virulence and colonization traits populate the ice cream manufacturing environment. Applied and Environmental Microbiology e0076523. doi:10.1128/aem.00765-23

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Walsh, A.M., Leech, J., Huttenhower, C., Delhomme-Nguyen, H., Crispie, F., Chervaux, C., Cotter, P.D. (2023) Integrated molecular approaches for fermented food microbiome research. FEMS Microbiology Reviews 47. doi:10.1093/femsre/fuad001

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