PUBLICATIONS



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
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
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 View Master first newsletter 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 View Master first newsletter
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 View Master first newsletter 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 View Master first newsletter
Scientific articles 2021

 

Yap, M., Ercolini, D., Alvarez-Ordonez, A., O'Toole, P.W., O'Sullivan, O. and Cotter, P.D. (2021) Next-Generation Food Research: Use of meta-omic approaches for characterizing microbial communities along the food chain. Annual Review of Food Science and Technology doi:10.1146/annurev-food-052720-010751 view View Master first newsletter

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 View Master first newsletter 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 View Master first newsletter
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 View Master first newsletter 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 View Master first newsletter
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 View Master first newsletter 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 View Master first newsletter
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 View Master first newsletter 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 View Master first newsletter
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 View Master first newsletter 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 View Master first newsletter
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 View Master first newsletter
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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