Complex microbiomes are part of the food we eat and influence our own microbiome, but their diversity remains largely unexplored. Here, we generated the open access curatedFoodMetagenomicData (cFMD) resource by integrating 1,950 newly sequenced and 583 public food metagenomes. We produced 10,899 metagenome-assembled genomes spanning 1,036 prokaryotic and 108 eukaryotic species-level genome bins (SGBs), including 320 previously undescribed taxa. Food SGBs displayed significant microbial diversity within and between food categories. Extension to >20,000 human metagenomes revealed that food SGBs accounted on average for 3% of the adult gut microbiome. Strain-level analysis highlighted potential instances of food-to-gut transmission and intestinal colonization (e.g., Lacticaseibacillus paracasei) as well as SGBs with divergent genomic structures in food and humans (e.g., Streptococcus gallolyticus and Limosilactobabillus mucosae). The cFMD expands our knowledge on food microbiomes, their r...
Complex microbiomes are part of the food we eat and influence our own microbiome, but their diversity remains largely unexplored. Here, we generated the open access curatedFoodMetagenomicData (cFMD) resource by integrating 1,950 newly sequenced and 583 public food metagenomes. We produced 10,899 metagenome-assembled genomes spanning 1,036 prokaryotic and 108 eukaryotic species-level genome bins (SGBs), including 320 previously undescribed taxa. Food SGBs displayed significant microbial diversity within and between food categories. Extension to >20,000 human metagenomes revealed that food SGBs accounted on average for 3% of the adult gut microbiome. Strain-level analysis highlighted potential instances of food-to-gut transmission and intestinal colonization (e.g., Lacticaseibacillus paracasei) as well as SGBs with divergent genomic structures in food and humans (e.g., Streptococcus gallolyticus and Limosilactobabillus mucosae). The cFMD expands our knowledge on food microbiomes, their role in shaping the human microbiome, and supports future uses of metagenomics for food quality, safety, and authentication.
Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome / Carlino, Niccolò; Blanco-Míguez, Aitor; Punčochář, Michal; Mengoni, Claudia; Pinto, Federica; Tatti, Alessia; Manghi, Paolo; Armanini, Federica; Avagliano, Michele; Barcenilla, Coral; Breselge, Samuel; Cabrera-Rubio, Raul; Calvete-Torre, Inés; Coakley, Mairéad; Cobo-Díaz, José F.; De Filippis, Francesca; Dey, Hrituraj; Leech, John; Klaassens, Eline S.; Knobloch, Stephen; O'Neil, Dominic; Quijada, Narciso M.; Sabater, Carlos; Skírnisdóttir, Sigurlaug; Valentino, Vincenzo; Walsh, Liam; Alvarez-Ordóñez, Avelino; Alvarez, Pablo; Antonielli, Livio; Arendt, Elke; Armanini, Federica; Aubry, Aurelie; Baelum, Jacob; Barcenilla, Coral; Belanche, Alejandro; Benavent-Gil, Yaiza; Blake, Tony; Blanco-Míguez, Aitor; Bongoni, Radhika; Boyer, Mickael; Brennan, Fiona; Breselge, Samuel; Briem, Helgi; Butler, Derek; Calvete-Torre, Inés; Carballo, Omar Cristobal; Cardinal, Mireille; Carlino, Niccolò; Chervaux, Christian; Chopin, Christine; Clotaire, Natallia; Coakley, Mairead; Cobo-Díaz, José Francisco; Codd, Jim; Conroy, Stephen; Corral-Jara, Karla Fabiola; Corral-Jara, Karla-Fabiola; Cotter, Paul D.; Coyne, Gerard; Coyne, Gerard; Creevey, Chris; Cuevas, Patricia D.; Curran, Brendan; Delgado, Susana; Derde, Liesbeth; Derrien, Muriel; Ercolini, Danilo; Exposito, Ruth Gomez; López Fernández, María Mercedes; De Filippis, Francesca; Fordham, Daniel; Galy, Hubert; Gavriilidou, Asimenia; Gunnarsson, Oddur; Hanson, Buck; Hermes, Gerben; Huang, Rongcai; Huws, Sharon; Ikoyi, Israel; Jaeger, Alice; Jeffery, Ian; Jérôme, Marc; Juan, Pierre-Alexandre; Kenny, David; Kers, Annelies; Khinouche, Karim-Franck; Kirwan, Stuart; Klaassens, Eline S.; Knobloch, Stephen; Kolbeinsson, Kristinn; Kolypczuk, Laetitia; Kostic, Tanja; Ledda, Fabio; Leech, John; Lehmann, Doerte; Leroi, Françoise; Lewis, Eva; Ley, Johanna; Lucic, Eva; Lynch, Kieran; Mace, Sabrina; MacLaren-Lee, Iain; Mahler de Sanchez, Lisa; Marchart, Juergen; Margolles, Abelardo; Marteinsson, Viggó Thór; Masetti, Giulia; Mcgovern, Fiona; Mchugh, Noirin; Mcloughlin, Steven; Meehan, Dara; Mølbak, Lars; Monin, Thomas; Moreno, Javier; Morgavi, Diego; Morrison, Steven; Müench, Steffen; Ramos Neves, Ana Rute; Neylon, Emma; Nyhan, Laura; O'Kelly, Rhona; O'Neil, Dominic; O'Toole, Paul; Ortiz-Chura, Abimael; Palma, Juan Manuel; Pasolli, Edoardo; Passerini, Delphine; Pastar, Milica; Pinto, Federica; Pirovano, Walter; Plans, Olga; Policht, Marion; Pop, Aurel; Pop, Bianca; Popova, Milka; Prieto, Miguel; Quijada, Narciso M.; Reiss, Antje; Romero, Pedro; Ruas-Madiedo, Patricia; Rubino, Francesco; Rubio, Raul Cabrera; Ruiz, Lorena; Ryan, Angela; Ryan, Clodagh; Sabater, Carlos; Sahin, Aylin; Salaun, Cecile; Santos, Fernanda Godoy; Schneider, Carolin; Segata, Nicola; Selberherr, Evelyne; Sessitsch, Angela; Skírnisdóttir, Sigurlaug; Smidt, Hauke; Smith, Paul; Sprenger-Haussels, Markus; Tapio, Ilma; Tap, Julien; Valentino, Vincenzo; Wagner, Martin; Walsh, Aaron; Walsh, Liam; Waters, Sinead M.; Willcocks, Spike; Yáñez-Ruiz, David R.; Yan, Tianhai; Yap, Min; Zannini, Emanuele; Zuliani, Véronique; Alvarez-Ordóñez, Avelino; Asnicar, Francesco; Fackelmann, Gloria; Heidrich, Vitor; Margolles, Abelardo; Marteinsson, Viggó Thór; Rota Stabelli, Omar; Wagner, Martin; Ercolini, Danilo; Cotter, Paul D.; Segata, Nicola; Pasolli, Edoardo. - In: CELL. - ISSN 0092-8674. - 187:20(2024), pp. 5775-5795.e15. [10.1016/j.cell.2024.07.039]
Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome
Carlino, Niccolò;Mengoni, Claudia;Pinto, Federica;Tatti, Alessia;Manghi, Paolo;Armanini, Federica;Dey, Hrituraj;Armanini, Federica;Carlino, Niccolò;Ledda, Fabio;Masetti, Giulia;Pasolli, Edoardo;Pinto, Federica;Segata, Nicola;Asnicar, Francesco;Fackelmann, Gloria;Heidrich, Vitor;Rota Stabelli, Omar;Segata, Nicola;Pasolli, Edoardo
2024-01-01
Abstract
Complex microbiomes are part of the food we eat and influence our own microbiome, but their diversity remains largely unexplored. Here, we generated the open access curatedFoodMetagenomicData (cFMD) resource by integrating 1,950 newly sequenced and 583 public food metagenomes. We produced 10,899 metagenome-assembled genomes spanning 1,036 prokaryotic and 108 eukaryotic species-level genome bins (SGBs), including 320 previously undescribed taxa. Food SGBs displayed significant microbial diversity within and between food categories. Extension to >20,000 human metagenomes revealed that food SGBs accounted on average for 3% of the adult gut microbiome. Strain-level analysis highlighted potential instances of food-to-gut transmission and intestinal colonization (e.g., Lacticaseibacillus paracasei) as well as SGBs with divergent genomic structures in food and humans (e.g., Streptococcus gallolyticus and Limosilactobabillus mucosae). The cFMD expands our knowledge on food microbiomes, their r...| File | Dimensione | Formato | |
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