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Microbiome Applications for Sustainable food systems through Technologies and EnteRprise


Project Website online

Project Website online

First version of curatedFoodMetagenomicData from publicly available data

First version of curatedFoodMetagenomicData from publicly available data

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The food-gut axis: lactic acid bacteria and their link to food, the gut microbiome and human health

Author(s): Francesca De Filippis, Edoardo Pasolli, Danilo Ercolini
Published in: FEMS Microbiology Reviews, Issue 44/4, 2020, Page(s) 454-489, ISSN 0168-6445
DOI: 10.1093/femsre/fuaa015

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

Author(s): Aaron M. Walsh, Guerrino Macori, Kieran N. Kilcawley, Paul D. Cotter
Published in: Nature Food, Issue 1/8, 2020, Page(s) 500-510, ISSN 2662-1355
DOI: 10.1038/s43016-020-0129-3

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

Author(s): 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
Published in: Cell Host & Microbe, Issue 26/5, 2019, Page(s) 666-679.e7, ISSN 1931-3128
DOI: 10.1016/j.chom.2019.08.018

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

Author(s): Sander Wuyts, Nicola Segata
Published in: Genome Biology, Issue 20/1, 2019, ISSN 1474-760X
DOI: 10.1186/s13059-019-1714-3

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

Author(s): Aoife J. McHugh, Conor Feehily, Mark A. Fenelon, David Gleeson, Colin Hill, Paul D. Cotter
Published in: mSystems, Issue 5/2, 2020, ISSN 2379-5077
DOI: 10.1128/msystems.00226-20

Detecting contamination in viromes using ViromeQC

Author(s): Moreno Zolfo, Federica Pinto, Francesco Asnicar, Paolo Manghi, Adrian Tett, Frederic D. Bushman, Nicola Segata
Published in: Nature Biotechnology, Issue 37/12, 2019, Page(s) 1408-1412, ISSN 1087-0156
DOI: 10.1038/s41587-019-0334-5

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

Author(s): 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
Published in: Nature Communications, Issue 11/1, 2020, ISSN 2041-1723
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

Author(s): 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
Published in: Genome Biology, Issue 20/1, 2019, ISSN 1474-760X
DOI: 10.1186/s13059-019-1923-9

Large-scale genome-wide analysis links lactic acid bacteria from food with the gut microbiome

Author(s): Edoardo Pasolli, Francesca De Filippis, Italia E. Mauriello, Fabio Cumbo, Aaron M. Walsh, John Leech, Paul D. Cotter, Nicola Segata, Danilo Ercolini
Published in: Nature Communications, Issue 11/1, 2020, ISSN 2041-1723
DOI: 10.1038/s41467-020-16438-8

Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations

Author(s): 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
Published in: Genome Biology, Issue 21/1, 2020, ISSN 1474-760X
DOI: 10.1186/s13059-020-02042-y

Analysis of Health Benefits Conferred by Lactobacillus Species from Kefir

Author(s): Conor Slattery, Paul D. Cotter, Paul W. O’Toole
Published in: Nutrients, Issue 11/6, 2019, Page(s) 1252, ISSN 2072-6643
DOI: 10.3390/nu11061252

Multiple levels of the unknown in microbiome research

Author(s): Andrew Maltez Thomas, Nicola Segata
Published in: BMC Biology, Issue 17/1, 2019, ISSN 1741-7007
DOI: 10.1186/s12915-019-0667-z