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.

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

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.

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

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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.

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

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

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

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

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

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

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

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

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

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

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

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

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