N Segata

Publications (98)

Effect of Gluten-Free Diet on Gut Microbiota Composition in Patients with Celiac Disease and Non-Celiac Gluten/Wheat Sensitivity.

Nutrients

Avec: Giacomo Caio , Lisa Lungaro , Nicola Segata , Matteo Guarino , Giorgio Zoli , Umberto Volta , Roberto De Giorgio

SARS-CoV-2 from faeces to wastewater treatment: What do we know? A review.

The Science of the total environment

Avec: Paola Foladori , Francesca Cutrupi , Nicola Segata , Serena Manara , Federica Pinto , Francesca Malpei , Laura Bruni , Giuseppina La Rosa

How inoculation affects the development and the performances of microalgal-bacterial consortia treating real municipal wastewater.

Journal of environmental management

Avec: Serena Petrini , Paola Foladori , Francesco Beghini , Federica Armanini , Nicola Segata , Gianni Andreottola

Dental Implants with Anti-Biofilm Properties: A Pilot Study for Developing a New Sericin-Based Coating.

Materials (Basel, Switzerland)

Avec: Paolo Ghensi , Elia Bettio , Devid Maniglio , Emiliana Bonomi , Federico Piccoli , Silvia Gross , Patrizio Caciagli , Nicola Segata , Giandomenico Nollo , Francesco Tessarolo

A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity.

Nature communications

Avec: David Wylensek , Thomas C A Hitch , Thomas Riedel , Afrizal Afrizal , Neeraj Kumar , Esther Wortmann , Tianzhe Liu , Saravanan Devendran , Till R Lesker , Sara B Hernández , Viktoria Heine , Eva M Buhl , Paul M D'Agostino , Fabio Cumbo , Thomas Fischöder , Marzena Wyschkon , Torey Looft , Valeria R Parreira , Birte Abt , Heidi L Doden , Lindsey Ly , João M P Alves , Markus Reichlin , Krzysztof Flisikowski , Laura Navarro Suarez , Anthony P Neumann , Garret Suen , Tomas de Wouters , Sascha Rohn , Ilias Lagkouvardos , Emma Allen-Vercoe , Cathrin Spröer , Boyke Bunk , Anja J Taverne-Thiele , Marcel Giesbers , Jerry M Wells , Klaus Neuhaus , Angelika Schnieke , Felipe Cava , Nicola Segata , Lothar Elling , Till Strowig , Jason M Ridlon , Tobias A M Gulder , Jörg Overmann , Thomas Clavel

Ketogenic diet and ketone bodies enhance the anticancer effects of PD-1 blockade.

JCI insight

Avec: Gladys Ferrere , Maryam Tidjani Alou , Peng Liu , Anne-Gaëlle Goubet , Marine Fidelle , Oliver Kepp , Sylvère Durand , Valerio Iebba , Aurélie Fluckiger , Romain Daillère , Cassandra Thelemaque , Claudia Grajeda-Iglesias , Carolina Alves Costa Silva , Fanny Aprahamian , Déborah Lefevre , Liwei Zhao , Bernhard Ryffel , Emeline Colomba , Monica Arnedos , Damien Drubay , Conrad Rauber , Didier Raoult , Francesco Asnicar , Tim Spector , Nicola Segata , Lisa Derosa , Guido Kroemer , Laurence Zitvogel

Trial watch : the gut microbiota as a tool to boost the clinical efficacy of anticancer immunotherapy.

Oncoimmunology

Avec: Romain Daillère , Lisa Derosa , Mélodie Bonvalet , Nicola Segata , Bertrand Routy , Manuela Gariboldi , Eva Budinská , I Jolanda M De Vries , Alessio Gordon Naccarati , Valérie Zitvogel , Carlos Caldas , Lars Engstrand , Sibylle Loilbl , Jacques Fieschi , Lucie Heinzerling , Guido Kroemer , Laurence Zitvogel

Immune system and intestinal microbiota determine efficacy of androgen deprivation therapy against prostate cancer.

Journal for immunotherapy of cancer

Avec: Safae Terrisse , Anne-Gaelle Goubet , Kousuke Ueda , Andrew Maltez Thomas , Valentin Quiniou , Cassandra Thelemaque , Garett Dunsmore , Emmanuel Clave , Melissa Gamat-Huber , Satoru Yonekura , Gladys Ferrere , Conrad Rauber , Hang Phuong Pham , Jean-Eudes Fahrner , Eugenie Pizzato , Pierre Ly , Marine Fidelle , Marine Mazzenga , Carolina Alves Costa Silva , Federica Armanini , Federica Pinto , Francesco Asnicar , Romain Daillère , Lisa Derosa , Corentin Richard , Pierre Blanchard , Bertrand Routy , Stéphane Culine , Paule Opolon , Aymeric Silvin , Florent Ginhoux , Antoine Toubert , Nicola Segata , Douglas G McNeel , Karim Fizazi , Guido Kroemer , Laurence Zitvogel

Phylogenomics of Opsin Genes in Diptera Reveals Lineage-Specific Events and Contrasting Evolutionary Dynamics in Anopheles and Drosophila.

Genome biology and evolution

Avec: Roberto Feuda , Matthew Goulty , Nicola Zadra , Tiziana Gasparetti , Ezio Rosato , Davide Pisani , Annapaola Rizzoli , Nicola Segata , Lino Ometto , Omar Rota Stabelli

Microbiome characterization of alpine water springs for human consumption reveals site- and usage-specific microbial signatures.

Frontiers in microbiology

Avec: Renato Pedron , Alfonso Esposito , William Cozza , Massimo Paolazzi , Mario Cristofolini , Nicola Segata , Olivier Jousson

Exploring the relationship between social jetlag with gut microbial composition, diet and cardiometabolic health, in the ZOE PREDICT 1 cohort.

European journal of nutrition

Avec: Kate M Bermingham , Sophie Stensrud , Francesco Asnicar , Ana M Valdes , Paul W Franks , Jonathan Wolf , George Hadjigeorgiou , Richard Davies , Tim D Spector , Nicola Segata , Sarah E Berry , Wendy L Hall

Metabolomic and gut microbiome profiles across the spectrum of community-based COVID and non-COVID disease.

Scientific reports

Avec: Marc F Österdahl , Ronan Whiston , Carole H Sudre , Francesco Asnicar , Nathan J Cheetham , Aitor Blanco Miguez , Vicky Bowyer , Michela Antonelli , Olivia Snell , Liane Dos Santos Canas , Christina Hu , Jonathan Wolf , Cristina Menni , Michael Malim , Deborah Hart , Tim Spector , Sarah Berry , Nicola Segata , Katie Doores , Sebastien Ourselin , Emma L Duncan , Claire J Steves

MetaPhlAn 4 profiling of unknown species-level genome bins improves the characterization of diet-associated microbiome changes in mice.

Cell reports

Avec: Paolo Manghi , Aitor Blanco-Míguez , Serena Manara , Amir NabiNejad , Fabio Cumbo , Francesco Beghini , Federica Armanini , Davide Golzato , Kun D Huang , Andrew M Thomas , Gianmarco Piccinno , Michal Punčochář , Moreno Zolfo , Till R Lesker , Marius Bredon , Julien Planchais , Jeremy Glodt , Mireia Valles-Colomer , Omry Koren , Edoardo Pasolli , Francesco Asnicar , Till Strowig , Harry Sokol , Nicola Segata

Extension of the Segatella copri complex to 13 species with distinct large extrachromosomal elements and associations with host conditions.

Cell host & microbe

Avec: Aitor Blanco-Míguez , Eric J C Gálvez , Edoardo Pasolli , Francesca De Filippis , Lena Amend , Kun D Huang , Paolo Manghi , Till-Robin Lesker , Thomas Riedel , Linda Cova , Michal Punčochář , Andrew Maltez Thomas , Mireia Valles-Colomer , Isabel Schober , Thomas C A Hitch , Thomas Clavel , Sarah E Berry , Richard Davies , Jonathan Wolf , Tim D Spector , Jörg Overmann , Adrian Tett , Danilo Ercolini , Nicola Segata , Till Strowig

Maternal and food microbial sources shape the infant microbiome of a rural Ethiopian population.

Current biology : CB

Avec: Serena Manara , Marta Selma-Royo , Kun D Huang , Francesco Asnicar , Federica Armanini , Aitor Blanco-Miguez , Fabio Cumbo , Davide Golzato , Paolo Manghi , Federica Pinto , Mireia Valles-Colomer , Loredana Amoroso , Maria Valeria Corrias , Mirco Ponzoni , Roberta Raffaetà , Raul Cabrera-Rubio , Mari Olcina , Edoardo Pasolli , Maria Carmen Collado , Nicola Segata

Cardiometabolic health, diet and the gut microbiome: a meta-omics perspective.

Nature medicine

Avec: Mireia Valles-Colomer , Cristina Menni , Sarah E Berry , Ana M Valdes , Tim D Spector , Nicola Segata

The secondary bile acid isoursodeoxycholate correlates with post-prandial lipemia, inflammation, and appetite and changes post-bariatric surgery.

Cell reports. Medicine

Avec: Panayiotis Louca , Abraham S Meijnikman , Ana Nogal , Francesco Asnicar , Ilias Attaye , Amrita Vijay , Afroditi Kouraki , Alessia Visconti , Kari Wong , Sarah E Berry , Emily R Leeming , Olatz Mompeo , Francesca Tettamanzi , Andrei-Florin Baleanu , Mario Falchi , George Hadjigeorgiou , Jonathan Wolf , Yair I Z Acherman , Arnold W Van de Laar , Victor E A Gerdes , Gregory A Michelotti , Paul W Franks , Nicola Segata , Massimo Mangino , Tim D Spector , William J Bulsiewicz , Max Nieuwdorp , Ana M Valdes , Cristina Menni

A distinct Fusobacterium nucleatum clade dominates the colorectal cancer niche.

Nature

Avec: Martha Zepeda-Rivera , Samuel S Minot , Heather Bouzek , Hanrui Wu , Aitor Blanco-Míguez , Paolo Manghi , Dakota S Jones , Kaitlyn D LaCourse , Ying Wu , Elsa F McMahon , Soon-Nang Park , Yun K Lim , Andrew G Kempchinsky , Amy D Willis , Sean L Cotton , Susan C Yost , Ewa Sicinska , Joong-Ki Kook , Floyd E Dewhirst , Nicola Segata , Susan Bullman , Christopher D Johnston

Vitamin A carotenoids, but not retinoids, mediate the impact of a healthy diet on gut microbial diversity.

BMC medicine

Avec: Ana M Valdes , Panayiotis Louca , Alessia Visconti , Francesco Asnicar , Kate Bermingham , Ana Nogal , Kari Wong , Gregory A Michelotti , Jonathan Wolf , Nicola Segata , Tim D Spector , Sarah E Berry , Mario Falchi , Cristina Menni

Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome.

Cell

Avec: Niccolò Carlino , Aitor Blanco-Míguez , Michal Punčochář , Claudia Mengoni , Federica Pinto , Alessia Tatti , Paolo Manghi , Federica Armanini , Michele Avagliano , Coral Barcenilla , Samuel Breselge , Raul Cabrera-Rubio , Inés Calvete-Torre , Mairéad Coakley , José F Cobo-Díaz , Francesca De Filippis , Hrituraj Dey , John Leech , Eline S Klaassens , Stephen Knobloch , Dominic O'Neil , Narciso M Quijada , Carlos Sabater , Sigurlaug Skírnisdóttir , Vincenzo Valentino , Liam Walsh , Auteur inconnu , Avelino Alvarez-Ordóñez , Francesco Asnicar , Gloria Fackelmann , Vitor Heidrich , Abelardo Margolles , Viggó Thór Marteinsson , Omar Rota Stabelli , Martin Wagner , Danilo Ercolini , Paul D Cotter , Nicola Segata , Edoardo Pasolli

Faecal microbiota transplantation for the treatment of diarrhoea induced by tyrosine-kinase inhibitors in patients with metastatic renal cell carcinoma.

Nature communications

Avec: Gianluca Ianiro , Ernesto Rossi , Andrew M Thomas , Giovanni Schinzari , Luca Masucci , Gianluca Quaranta , Carlo Romano Settanni , Loris Riccardo Lopetuso , Federica Armanini , Aitor Blanco-Miguez , Francesco Asnicar , Clarissa Consolandi , Roberto Iacovelli , Maurizio Sanguinetti , Giampaolo Tortora , Antonio Gasbarrini , Nicola Segata , Giovanni Cammarota

A unified catalog of 204,938 reference genomes from the human gut microbiome.

Nature biotechnology

Avec: Alexandre Almeida , Stephen Nayfach , Miguel Boland , Francesco Strozzi , Martin Beracochea , Zhou Jason Shi , Katherine S Pollard , Ekaterina Sakharova , Donovan H Parks , Philip Hugenholtz , Nicola Segata , Nikos C Kyrpides , Robert D Finn

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

Nature communications

Avec: 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

Untargeted Metagenomic Investigation of the Airway Microbiome of Cystic Fibrosis Patients with Moderate-Severe Lung Disease.

Microorganisms

Avec: Giovanni Bacci , Giovanni Taccetti , Daniela Dolce , Federica Armanini , Nicola Segata , Francesca Di Cesare , Vincenzina Lucidi , Ersilia Fiscarelli , Patrizia Morelli , Rosaria Casciaro , Anna Negroni , Alessio Mengoni , Annamaria Bevivino

Endogenous murine microbiota member Faecalibaculum rodentium and its human homologue protect from intestinal tumour growth.

Nature microbiology

Avec: Elena Zagato , Chiara Pozzi , Alice Bertocchi , Tiziana Schioppa , Fabiana Saccheri , Silvia Guglietta , Bruno Fosso , Laura Melocchi , Giulia Nizzoli , Jacopo Troisi , Marinella Marzano , Bianca Oresta , Ilaria Spadoni , Koji Atarashi , Sara Carloni , Stefania Arioli , Giulia Fornasa , Francesco Asnicar , Nicola Segata , Simone Guglielmetti , Kenya Honda , Graziano Pesole , William Vermi , Giuseppe Penna , Maria Rescigno

Distinct Polysaccharide Utilization Profiles of Human Intestinal Prevotella copri Isolates.

Cell host & microbe

Avec: Hannah Fehlner-Peach , Cara Magnabosco , Varsha Raghavan , Jose U Scher , Adrian Tett , Laura M Cox , Claire Gottsegen , Aaron Watters , John D Wiltshire-Gordon , Nicola Segata , Richard Bonneau , Dan R Littman

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle.

Cell

Avec: Edoardo Pasolli , Francesco Asnicar , Serena Manara , Moreno Zolfo , Nicolai Karcher , Federica Armanini , Francesco Beghini , Paolo Manghi , Adrian Tett , Paolo Ghensi , Maria Carmen Collado , Benjamin L Rice , Casey DuLong , Xochitl C Morgan , Christopher D Golden , Christopher Quince , Curtis Huttenhower , Nicola Segata

Distinct Genetic and Functional Traits of Human Intestinal Prevotella copri Strains Are Associated with Different Habitual Diets.

Cell host & microbe

Avec: Francesca De Filippis , Edoardo Pasolli , Adrian Tett , Sonia Tarallo , Alessio Naccarati , Maria De Angelis , Erasmo Neviani , Luca Cocolin , Marco Gobbetti , Nicola Segata , Danilo Ercolini

Strong oral plaque microbiome signatures for dental implant diseases identified by strain-resolution metagenomics.

NPJ biofilms and microbiomes

Avec: Paolo Ghensi , Paolo Manghi , Moreno Zolfo , Federica Armanini , Edoardo Pasolli , Mattia Bolzan , Alberto Bertelle , Federico Dell'Acqua , Ester Dellasega , Romina Waldner , Francesco Tessarolo , Cristiano Tomasi , Nicola Segata

High intake of vegetables is linked to lower white blood cell profile and the effect is mediated by the gut microbiome.

BMC medicine

Avec: Cristina Menni , Panayiotis Louca , Sarah E Berry , Amrita Vijay , Stuart Astbury , Emily R Leeming , Rachel Gibson , Francesco Asnicar , Gianmarco Piccinno , Jonathan Wolf , Richard Davies , Massimo Mangino , Nicola Segata , Tim D Spector , Ana M Valdes

Sulfoquinovose is a select nutrient of prominent bacteria and a source of hydrogen sulfide in the human gut.

The ISME journal

Avec: Buck T Hanson , K Dimitri Kits , Jessica Löffler , Anna G Burrichter , Alexander Fiedler , Karin Denger , Benjamin Frommeyer , Craig W Herbold , Thomas Rattei , Nicolai Karcher , Nicola Segata , David Schleheck , Alexander Loy

Metagenomic analysis of ancient dental calculus reveals unexplored diversity of oral archaeal Methanobrevibacter.

Microbiome

Avec: Lena Granehäll , Kun D Huang , Adrian Tett , Paolo Manghi , Alice Paladin , Niall O'Sullivan , Omar Rota-Stabelli , Nicola Segata , Albert Zink , Frank Maixner

Meal-induced inflammation: postprandial insights from the Personalised REsponses to DIetary Composition Trial (PREDICT) study in 1000 participants.

The American journal of clinical nutrition

Avec: Mohsen Mazidi , Ana M Valdes , Jose M Ordovas , Wendy L Hall , Joan C Pujol , Jonathan Wolf , George Hadjigeorgiou , Nicola Segata , Naveed Sattar , Robert Koivula , Tim D Spector , Paul W Franks , Sarah E Berry

Prevotella diversity, niches and interactions with the human host.

Nature reviews. Microbiology

Avec: Adrian Tett , Edoardo Pasolli , Giulia Masetti , Danilo Ercolini , Nicola Segata

Reconstruction of ancient microbial genomes from the human gut.

Nature

Avec: Marsha C Wibowo , Zhen Yang , Maxime Borry , Alexander Hübner , Kun D Huang , Braden T Tierney , Samuel Zimmerman , Francisco Barajas-Olmos , Cecilia Contreras-Cubas , Humberto García-Ortiz , Angélica Martínez-Hernández , Jacob M Luber , Philipp Kirstahler , Tre Blohm , Francis E Smiley , Richard Arnold , Sonia A Ballal , Sünje Johanna Pamp , Julia Russ , Frank Maixner , Omar Rota-Stabelli , Nicola Segata , Karl Reinhard , Lorena Orozco , Christina Warinner , Meradeth Snow , Steven LeBlanc , Aleksandar D Kostic

Intestinal Akkermansia muciniphila predicts clinical response to PD-1 blockade in patients with advanced non-small-cell lung cancer.

Nature medicine

Avec: Lisa Derosa , Bertrand Routy , Andrew Maltez Thomas , Valerio Iebba , Gerard Zalcman , Sylvie Friard , Julien Mazieres , Clarisse Audigier-Valette , Denis Moro-Sibilot , François Goldwasser , Carolina Alves Costa Silva , Safae Terrisse , Melodie Bonvalet , Arnaud Scherpereel , Hervé Pegliasco , Corentin Richard , François Ghiringhelli , Arielle Elkrief , Antoine Desilets , Felix Blanc-Durand , Fabio Cumbo , Aitor Blanco , Romain Boidot , Sandy Chevrier , Romain Daillère , Guido Kroemer , Laurie Alla , Nicolas Pons , Emmanuelle Le Chatelier , Nathalie Galleron , Hugo Roume , Agathe Dubuisson , Nicole Bouchard , Meriem Messaoudene , Damien Drubay , Eric Deutsch , Fabrice Barlesi , David Planchard , Nicola Segata , Stéphanie Martinez , Laurence Zitvogel , Jean-Charles Soria , Benjamin Besse

Metagenomic and metabolomic remodeling in nonagenarians and centenarians and its association with genetic and socioeconomic factors.

Nature aging

Avec: Qian Xu , Chunyan Wu , Qi Zhu , Renyuan Gao , Jianquan Lu , Mireia Valles-Colomer , Jian Zhu , Fang Yin , Linsheng Huang , Lulu Ding , Xiaohui Zhang , Yonghui Zhang , Xiao Xiong , Miaomiao Bi , Xiang Chen , Yefei Zhu , Lin Liu , Yongqiang Liu , Yongshen Chen , Jian Fan , Yan Sun , Jun Wang , Zhan Cao , Chunsun Fan , S Dusko Ehrlich , Nicola Segata , Nan Qin , Huanlong Qin

Association of a Mediterranean Diet With Outcomes for Patients Treated With Immune Checkpoint Blockade for Advanced Melanoma.

JAMA oncology

Avec: Laura A Bolte , Karla A Lee , Johannes R Björk , Emily R Leeming , Marjo J E Campmans-Kuijpers , Jacco J de Haan , Arnau Vich Vila , Andrew Maltez-Thomas , Nicola Segata , Ruth Board , Mark Harries , Paul Lorigan , Elisabeth G E de Vries , Paul Nathan , Rudolf Fehrmann , Véronique Bataille , Tim D Spector , Geke A P Hospers , Rinse K Weersma

Spatial and temporal dynamics of West Nile virus between Africa and Europe.

Nature communications

Avec: Giulia Mencattelli , Marie Henriette Dior Ndione , Andrea Silverj , Moussa Moise Diagne , Valentina Curini , Liana Teodori , Marco Di Domenico , Rassoul Mbaye , Alessandra Leone , Maurilia Marcacci , Alioune Gaye , ElHadji Ndiaye , Diawo Diallo , Massimo Ancora , Barbara Secondini , Valeria Di Lollo , Iolanda Mangone , Andrea Bucciacchio , Andrea Polci , Giovanni Marini , Roberto Rosà , Nicola Segata , Gamou Fall , Cesare Cammà , Federica Monaco , Mawlouth Diallo , Omar Rota-Stabelli , Oumar Faye , Annapaola Rizzoli , Giovanni Savini

Diet and gut microbial associations in irritable bowel syndrome according to disease subtype.

Gut microbes

Avec: Yiqing Wang , Wenjie Ma , Raaj Mehta , Long H Nguyen , Mingyang Song , David A Drew , Francesco Asnicar , Curtis Huttenhower , Nicola Segata , Jonathan Wolf , Tim Spector , Sarah Berry , Kyle Staller , Andrew T Chan

High dietary inflammatory index associates with inflammatory proteins in plasma.

Diabetology & metabolic syndrome

Avec: Elisa Mattavelli , Elisa Piperni , Francesco Asnicar , Laura Redaelli , Liliana Grigore , Fabio Pellegatta , Amir Nabinejad , Sabrina Tamburini , Nicola Segata , Alberico Luigi Catapano , Andrea Baragetti

Oncoimmunology

Avec: Marius Bredon , Camille Danne , Hang Phuong Pham , Pauline Ruffié , Alban Bessede , Nathalie Rolhion , Laura Creusot , Loic Brot , Iria Alonso , Philippe Langella , Lisa Derosa , Alexis B Cortot , Bertrand Routy , Laurence Zitvogel , Nicola Segata , Harry Sokol

Microbiome mapping in dairy industry reveals new species and genes for probiotic and bioprotective activities.

NPJ biofilms and microbiomes

Avec: Francesca De Filippis , Vincenzo Valentino , Min Yap , Raul Cabrera-Rubio , Coral Barcenilla , Niccolò Carlino , José F Cobo-Díaz , Narciso Martín Quijada , Inés Calvete-Torre , Patricia Ruas-Madiedo , Carlos Sabater , Giuseppina Sequino , Edoardo Pasolli , Martin Wagner , Abelardo Margolles , Nicola Segata , Avelino Álvarez-Ordóñez , Paul D Cotter , Danilo Ercolini

Gut microbiome diversity and composition is associated with hypertension in women.

Journal of hypertension

Avec: Panayiotis Louca , Ana Nogal , Philippa M Wells , Francesco Asnicar , Jonathan Wolf , Claire J Steves , Tim D Spector , Nicola Segata , Sarah E Berry , Ana M Valdes , Cristina Menni

Large scale genome reconstructions illuminate Wolbachia evolution.

Nature communications

Avec: Matthias Scholz , Davide Albanese , Kieran Tuohy , Claudio Donati , Nicola Segata , Omar Rota-Stabelli

Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals.

Nature medicine

Avec: Francesco Asnicar , Sarah E Berry , Ana M Valdes , Long H Nguyen , Gianmarco Piccinno , David A Drew , Emily Leeming , Rachel Gibson , Caroline Le Roy , Haya Al Khatib , Lucy Francis , Mohsen Mazidi , Olatz Mompeo , Mireia Valles-Colomer , Adrian Tett , Francesco Beghini , Léonard Dubois , Davide Bazzani , Andrew Maltez Thomas , Chloe Mirzayi , Asya Khleborodova , Sehyun Oh , Rachel Hine , Christopher Bonnett , Joan Capdevila , Serge Danzanvilliers , Francesca Giordano , Ludwig Geistlinger , Levi Waldron , Richard Davies , George Hadjigeorgiou , Jonathan Wolf , José M Ordovás , Christopher Gardner , Paul W Franks , Andrew T Chan , Curtis Huttenhower , Tim D Spector , Nicola Segata

Multiple levels of the unknown in microbiome research.

BMC biology

Avec: Andrew Maltez Thomas , Nicola Segata

Sociodemographic variation in the oral microbiome.

Annals of epidemiology

Avec: Audrey Renson , Heidi E Jones , Francesco Beghini , Nicola Segata , Christine P Zolnik , Mykhaylo Usyk , Thomas U Moody , Lorna Thorpe , Robert Burk , Levi Waldron , Jennifer B Dowd

Methicillin-resistant Staphylococcus aureus eradication in cystic fibrosis patients: A randomized multicenter study.

PloS one

Avec: Daniela Dolce , Stella Neri , Laura Grisotto , Silvia Campana , Novella Ravenni , Francesca Miselli , Erica Camera , Lucia Zavataro , Cesare Braggion , Ersilia V Fiscarelli , Vincenzina Lucidi , Lisa Cariani , Daniela Girelli , Nadia Faelli , Carla Colombo , Cristina Lucanto , Mariangela Lombardo , Giuseppe Magazzù , Antonella Tosco , Valeria Raia , Serena Manara , Edoardo Pasolli , Federica Armanini , Nicola Segata , Annibale Biggeri , Giovanni Taccetti

Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer.

Nature medicine

Avec: Jakob Wirbel , Paul Theodor Pyl , Ece Kartal , Konrad Zych , Alireza Kashani , Alessio Milanese , Jonas S Fleck , Anita Y Voigt , Albert Palleja , Ruby Ponnudurai , Shinichi Sunagawa , Luis Pedro Coelho , Petra Schrotz-King , Emily Vogtmann , Nina Habermann , Emma Niméus , Andrew M Thomas , Paolo Manghi , Sara Gandini , Davide Serrano , Sayaka Mizutani , Hirotsugu Shiroma , Satoshi Shiba , Tatsuhiro Shibata , Shinichi Yachida , Takuji Yamada , Levi Waldron , Alessio Naccarati , Nicola Segata , Rashmi Sinha , Cornelia M Ulrich , Hermann Brenner , Manimozhiyan Arumugam , Peer Bork , Georg Zeller

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

Nature communications

Avec: Edoardo Pasolli , Francesca De Filippis , Italia E Mauriello , Fabio Cumbo , Aaron M Walsh , John Leech , Paul D Cotter , Nicola Segata , Danilo Ercolini

Human postprandial responses to food and potential for precision nutrition.

Nature medicine

Avec: Sarah E Berry , Ana M Valdes , David A Drew , Francesco Asnicar , Mohsen Mazidi , Jonathan Wolf , Joan Capdevila , George Hadjigeorgiou , Richard Davies , Haya Al Khatib , Christopher Bonnett , Sajaysurya Ganesh , Elco Bakker , Deborah Hart , Massimo Mangino , Jordi Merino , Inbar Linenberg , Patrick Wyatt , Jose M Ordovas , Christopher D Gardner , Linda M Delahanty , Andrew T Chan , Nicola Segata , Paul W Franks , Tim D Spector

Reporting guidelines for human microbiome research: the STORMS checklist.

Nature medicine

Avec: Chloe Mirzayi , Audrey Renson , Auteur inconnu , Auteur inconnu , Fatima Zohra , Shaimaa Elsafoury , Ludwig Geistlinger , Lora J Kasselman , Kelly Eckenrode , Janneke van de Wijgert , Amy Loughman , Francine Z Marques , David A MacIntyre , Manimozhiyan Arumugam , Rimsha Azhar , Francesco Beghini , Kirk Bergstrom , Ami Bhatt , Jordan E Bisanz , Jonathan Braun , Hector Corrada Bravo , Gregory A Buck , Frederic Bushman , David Casero , Gerard Clarke , Maria Carmen Collado , Paul D Cotter , John F Cryan , Ryan T Demmer , Suzanne Devkota , Eran Elinav , Juan S Escobar , Jennifer Fettweis , Robert D Finn , Anthony A Fodor , Sofia Forslund , Andre Franke , Cesare Furlanello , Jack Gilbert , Elizabeth Grice , Benjamin Haibe-Kains , Scott Handley , Pamela Herd , Susan Holmes , Jonathan P Jacobs , Lisa Karstens , Rob Knight , Dan Knights , Omry Koren , Douglas S Kwon , Morgan Langille , Brianna Lindsay , Dermot McGovern , Alice C McHardy , Shannon McWeeney , Noel T Mueller , Luigi Nezi , Matthew Olm , Noah Palm , Edoardo Pasolli , Jeroen Raes , Matthew R Redinbo , Malte Rühlemann , R Balfour Sartor , Patrick D Schloss , Lynn Schriml , Eran Segal , Michelle Shardell , Thomas Sharpton , Ekaterina Smirnova , Harry Sokol , Justin L Sonnenburg , Sujatha Srinivasan , Louise B Thingholm , Peter J Turnbaugh , Vaibhav Upadhyay , Ramona L Walls , Paul Wilmes , Takuji Yamada , Georg Zeller , Mingyu Zhang , Ni Zhao , Liping Zhao , Wenjun Bao , Aedin Culhane , Viswanath Devanarayan , Joaquin Dopazo , Xiaohui Fan , Matthias Fischer , Wendell Jones , Rebecca Kusko , Christopher E Mason , Tim R Mercer , Susanna-Assunta Sansone , Andreas Scherer , Leming Shi , Shraddha Thakkar , Weida Tong , Russ Wolfinger , Christopher Hunter , Nicola Segata , Curtis Huttenhower , Jennifer B Dowd , Heidi E Jones , Levi Waldron

Impact of insufficient sleep on dysregulated blood glucose control under standardised meal conditions.

Diabetologia

Avec: Neli Tsereteli , Raphael Vallat , Juan Fernandez-Tajes , Linda M Delahanty , Jose M Ordovas , David A Drew , Ana M Valdes , Nicola Segata , Andrew T Chan , Jonathan Wolf , Sarah E Berry , Matthew P Walker , Timothy D Spector , Paul W Franks

Hallstatt miners consumed blue cheese and beer during the Iron Age and retained a non-Westernized gut microbiome until the Baroque period.

Current biology : CB

Avec: Frank Maixner , Mohamed S Sarhan , Kun D Huang , Adrian Tett , Alexander Schoenafinger , Stefania Zingale , Aitor Blanco-Míguez , Paolo Manghi , Jan Cemper-Kiesslich , Wilfried Rosendahl , Ulrike Kusebauch , Seamus R Morrone , Michael R Hoopmann , Omar Rota-Stabelli , Thomas Rattei , Robert L Moritz , Klaus Oeggl , Nicola Segata , Albert Zink , Hans Reschreiter , Kerstin Kowarik

Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly.

Genome biology

Avec: Nicolai Karcher , Eleonora Nigro , Michal Punčochář , Aitor Blanco-Míguez , Matteo Ciciani , Paolo Manghi , Moreno Zolfo , Fabio Cumbo , Serena Manara , Davide Golzato , Anna Cereseto , Manimozhiyan Arumugam , Thi Phuong Nam Bui , Hanne L P Tytgat , Mireia Valles-Colomer , Willem M de Vos , Nicola Segata

Critical Assessment of Metagenome Interpretation: the second round of challenges.

Nature methods

Avec: Fernando Meyer , Adrian Fritz , Zhi-Luo Deng , David Koslicki , Till Robin Lesker , Alexey Gurevich , Gary Robertson , Mohammed Alser , Dmitry Antipov , Francesco Beghini , Denis Bertrand , Jaqueline J Brito , C Titus Brown , Jan Buchmann , Aydin Buluç , Bo Chen , Rayan Chikhi , Philip T L C Clausen , Alexandru Cristian , Piotr Wojciech Dabrowski , Aaron E Darling , Rob Egan , Eleazar Eskin , Evangelos Georganas , Eugene Goltsman , Melissa A Gray , Lars Hestbjerg Hansen , Steven Hofmeyr , Pingqin Huang , Luiz Irber , Huijue Jia , Tue Sparholt Jørgensen , Silas D Kieser , Terje Klemetsen , Axel Kola , Mikhail Kolmogorov , Anton Korobeynikov , Jason Kwan , Nathan LaPierre , Claire Lemaitre , Chenhao Li , Antoine Limasset , Fabio Malcher-Miranda , Serghei Mangul , Vanessa R Marcelino , Camille Marchet , Pierre Marijon , Dmitry Meleshko , Daniel R Mende , Alessio Milanese , Niranjan Nagarajan , Jakob Nissen , Sergey Nurk , Leonid Oliker , Lucas Paoli , Pierre Peterlongo , Vitor C Piro , Jacob S Porter , Simon Rasmussen , Evan R Rees , Knut Reinert , Bernhard Renard , Espen Mikal Robertsen , Gail L Rosen , Hans-Joachim Ruscheweyh , Varuni Sarwal , Nicola Segata , Enrico Seiler , Lizhen Shi , Fengzhu Sun , Shinichi Sunagawa , Søren Johannes Sørensen , Ashleigh Thomas , Chengxuan Tong , Mirko Trajkovski , Julien Tremblay , Gherman Uritskiy , Riccardo Vicedomini , Zhengyang Wang , Ziye Wang , Zhong Wang , Andrew Warren , Nils Peder Willassen , Katherine Yelick , Ronghui You , Georg Zeller , Zhengqiao Zhao , Shanfeng Zhu , Jie Zhu , Ruben Garrido-Oter , Petra Gastmeier , Stephane Hacquard , Susanne Häußler , Ariane Khaledi , Friederike Maechler , Fantin Mesny , Simona Radutoiu , Paul Schulze-Lefert , Nathiana Smit , Till Strowig , Andreas Bremges , Alexander Sczyrba , Alice Carolyn McHardy

Recent genetic exchanges and admixture shape the genome and population structure of the zoonotic pathogen Cryptosporidium parvum.

Molecular ecology

Avec: Giulia I Corsi , Swapnil Tichkule , Anna Rosa Sannella , Paolo Vatta , Francesco Asnicar , Nicola Segata , Aaron R Jex , Cock van Oosterhout , Simone M Cacciò

Next steps after 15 stimulating years of human gut microbiome research.

Microbial biotechnology

Avec: Thomas Clavel , Hans-Peter Horz , Nicola Segata , Maria Vehreschild

Influence of microbiota-associated metabolic reprogramming on clinical outcome in patients with melanoma from the randomized adjuvant dendritic cell-based MIND-DC trial.

Nature communications

Avec: Carolina Alves Costa Silva , Gianmarco Piccinno , Déborah Suissa , Mélanie Bourgin , Gerty Schreibelt , Sylvère Durand , Roxanne Birebent , Marine Fidelle , Cissé Sow , Fanny Aprahamian , Paolo Manghi , Michal Punčochář , Francesco Asnicar , Federica Pinto , Federica Armanini , Safae Terrisse , Bertrand Routy , Damien Drubay , Alexander M M Eggermont , Guido Kroemer , Nicola Segata , Laurence Zitvogel , Lisa Derosa , Kalijn F Bol , I Jolanda M de Vries

Effects of a personalized nutrition program on cardiometabolic health: a randomized controlled trial.

Nature medicine

Avec: Kate M Bermingham , Inbar Linenberg , Lorenzo Polidori , Francesco Asnicar , Alberto Arrè , Jonathan Wolf , Fatema Badri , Hannah Bernard , Joan Capdevila , William J Bulsiewicz , Christopher D Gardner , Jose M Ordovas , Richard Davies , George Hadjigeorgiou , Wendy L Hall , Linda M Delahanty , Ana M Valdes , Nicola Segata , Tim D Spector , Sarah E Berry

An Empirical Dietary Pattern Associated with the Gut Microbial Features in Relation to Colorectal Cancer Risk.

Gastroenterology

Avec: Kai Wang , Chun-Han Lo , Raaj S Mehta , Long H Nguyen , Yiqing Wang , Wenjie Ma , Tomotaka Ugai , Hidetaka Kawamura , Satoko Ugai , Yasutoshi Takashima , Kosuke Mima , Kota Arima , Kazuo Okadome , Marios Giannakis , Cynthia L Sears , Jeffrey A Meyerhardt , Kimmie Ng , Nicola Segata , Jacques Izard , Eric B Rimm , Wendy S Garrett , Curtis Huttenhower , Edward L Giovannucci , Andrew T Chan , Shuji Ogino , Mingyang Song

Inter-facility characterization of bacteria in seafood processing plants: Exploring potential reservoirs of spoilage organisms and the resistome.

Heliyon

Avec: Karla Fabiola Corral-Jara , Sigurlaug Skírnisdóttir , Stephen Knobloch , Helgi Briem , José F Cobo-Díaz , Niccolò Carlino , Pauline Bergsten , Federica Armanini , Francesco Asnicar , Federica Pinto , Avelino Alvarez-Ordóñez , Nicola Segata , Viggó Þór Marteinsson

Birthmode and environment-dependent microbiota transmission dynamics are complemented by breastfeeding during the first year.

Cell host & microbe

Avec: Marta Selma-Royo , Léonard Dubois , Serena Manara , Federica Armanini , Raúl Cabrera-Rubio , Mireia Valles-Colomer , Sonia González , Anna Parra-Llorca , Ramon Escuriet , Lars Bode , Cecilia Martínez-Costa , Nicola Segata , Maria Carmen Collado

Custom scoring based on ecological topology of gut microbiota associated with cancer immunotherapy outcome.

Cell

Avec: Lisa Derosa , Valerio Iebba , Carolina Alves Costa Silva , Gianmarco Piccinno , Guojun Wu , Leonardo Lordello , Bertrand Routy , Naisi Zhao , Cassandra Thelemaque , Roxanne Birebent , Federica Marmorino , Marine Fidelle , Meriem Messaoudene , Andrew Maltez Thomas , Gerard Zalcman , Sylvie Friard , Julien Mazieres , Clarisse Audigier-Valette , Denis Moro- Sibilot , François Goldwasser , Arnaud Scherpereel , Hervé Pegliasco , François Ghiringhelli , Nicole Bouchard , Cissé Sow , Ines Darik , Silvia Zoppi , Pierre Ly , Anna Reni , Romain Daillère , Eric Deutsch , Karla A Lee , Laura A Bolte , Johannes R Björk , Rinse K Weersma , Fabrice Barlesi , Lucas Padilha , Ana Finzel , Morten L Isaksen , Bernard Escudier , Laurence Albiges , David Planchard , Fabrice André , Chiara Cremolini , Stéphanie Martinez , Benjamin Besse , Liping Zhao , Nicola Segata , Jérôme Wojcik , Guido Kroemer , Laurence Zitvogel

Variability of strain engraftment and predictability of microbiome composition after fecal microbiota transplantation across different diseases.

Nature medicine

Avec: Gianluca Ianiro , Michal Punčochář , Nicolai Karcher , Serena Porcari , Federica Armanini , Francesco Asnicar , Francesco Beghini , Aitor Blanco-Míguez , Fabio Cumbo , Paolo Manghi , Federica Pinto , Luca Masucci , Gianluca Quaranta , Silvia De Giorgi , Giusi Desirè Sciumè , Stefano Bibbò , Federica Del Chierico , Lorenza Putignani , Maurizio Sanguinetti , Antonio Gasbarrini , Mireia Valles-Colomer , Giovanni Cammarota , Nicola Segata

The person-to-person transmission landscape of the gut and oral microbiomes.

Nature

Avec: Mireia Valles-Colomer , Aitor Blanco-Míguez , Paolo Manghi , Francesco Asnicar , Leonard Dubois , Davide Golzato , Federica Armanini , Fabio Cumbo , Kun D Huang , Serena Manara , Giulia Masetti , Federica Pinto , Elisa Piperni , Michal Punčochář , Liviana Ricci , Moreno Zolfo , Olivia Farrant , Adriana Goncalves , Marta Selma-Royo , Ana G Binetti , Jimmy E Becerra , Bei Han , John Lusingu , John Amuasi , Loredana Amoroso , Alessia Visconti , Claire M Steves , Mario Falchi , Michele Filosi , Adrian Tett , Anna Last , Qian Xu , Nan Qin , Huanlong Qin , Jürgen May , Daniel Eibach , Maria Valeria Corrias , Mirco Ponzoni , Edoardo Pasolli , Tim D Spector , Enrico Domenici , Maria Carmen Collado , Nicola Segata

Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4.

Nature biotechnology

Avec: Aitor Blanco-Míguez , Francesco Beghini , Fabio Cumbo , Lauren J McIver , Kelsey N Thompson , Moreno Zolfo , Paolo Manghi , Leonard Dubois , Kun D Huang , Andrew Maltez Thomas , William A Nickols , Gianmarco Piccinno , Elisa Piperni , Michal Punčochář , Mireia Valles-Colomer , Adrian Tett , Francesca Giordano , Richard Davies , Jonathan Wolf , Sarah E Berry , Tim D Spector , Eric A Franzosa , Edoardo Pasolli , Francesco Asnicar , Curtis Huttenhower , Nicola Segata

Snack quality and snack timing are associated with cardiometabolic blood markers: the ZOE PREDICT study.

European journal of nutrition

Avec: Kate M Bermingham , Anna May , Francesco Asnicar , Joan Capdevila , Emily R Leeming , Paul W Franks , Ana M Valdes , Jonathan Wolf , George Hadjigeorgiou , Linda M Delahanty , Nicola Segata , Tim D Spector , Sarah E Berry

A Fecal Metabolite Signature of Impaired Fasting Glucose: Results From Two Independent Population-Based Cohorts.

Diabetes

Avec: Ana Nogal , Francesca Tettamanzi , Qiuling Dong , Panayiotis Louca , Alessia Visconti , Colette Christiansen , Taylor Breuninger , Jakob Linseisen , Harald Grallert , Nina Wawro , Francesco Asnicar , Kari Wong , Andrei-Florin Baleanu , Gregory A Michelotti , Nicola Segata , Mario Falchi , Annette Peters , Paul W Franks , Vincenzo Bagnardi , Tim D Spector , Jordana T Bell , Christian Gieger , Ana M Valdes , Cristina Menni

Machine learning for microbiologists.

Nature reviews. Microbiology

Avec: Francesco Asnicar , Andrew Maltez Thomas , Andrea Passerini , Levi Waldron , Nicola Segata

Favorable subgingival plaque microbiome shifts are associated with clinical treatment for peri-implant diseases.

NPJ biofilms and microbiomes

Avec: Davide Bazzani , Vitor Heidrich , Paolo Manghi , Aitor Blanco-Miguez , Francesco Asnicar , Federica Armanini , Sara Cavaliere , Alberto Bertelle , Federico Dell'Acqua , Ester Dellasega , Romina Waldner , Daniela Vicentini , Mattia Bolzan , Cristiano Tomasi , Nicola Segata , Edoardo Pasolli , Paolo Ghensi

Longitudinal analysis of the gut microbiota during anti-PD-1 therapy reveals stable microbial features of response in melanoma patients.

Cell host & microbe

Avec: Angeli D G Macandog , Carlotta Catozzi , Mariaelena Capone , Amir Nabinejad , Padma P Nanaware , Shujing Liu , Smita Vinjamuri , Johanna A Stunnenberg , Serena Galiè , Maria Giovanna Jodice , Francesca Montani , Federica Armanini , Ester Cassano , Gabriele Madonna , Domenico Mallardo , Benedetta Mazzi , Salvatore Pece , Maria Tagliamonte , Vito Vanella , Massimo Barberis , Pier F Ferrucci , Christian U Blank , Marlene Bouvier , Miles C Andrews , Xiaowei Xu , Laura Santambrogio , Nicola Segata , Luigi Buonaguro , Emilia Cocorocchio , Paolo A Ascierto , Teresa Manzo , Luigi Nezi

At the forefront of the sequencing revolution-notes from the RNGS19 conference.

Genome biology

Avec: Sander Wuyts , Nicola Segata

Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.

Nature biotechnology

Avec: Evan Bolyen , Jai Ram Rideout , Matthew R Dillon , Nicholas A Bokulich , Christian C Abnet , Gabriel A Al-Ghalith , Harriet Alexander , Eric J Alm , Manimozhiyan Arumugam , Francesco Asnicar , Yang Bai , Jordan E Bisanz , Kyle Bittinger , Asker Brejnrod , Colin J Brislawn , C Titus Brown , Benjamin J Callahan , Andrés Mauricio Caraballo-Rodríguez , John Chase , Emily K Cope , Ricardo Da Silva , Christian Diener , Pieter C Dorrestein , Gavin M Douglas , Daniel M Durall , Claire Duvallet , Christian F Edwardson , Madeleine Ernst , Mehrbod Estaki , Jennifer Fouquier , Julia M Gauglitz , Sean M Gibbons , Deanna L Gibson , Antonio Gonzalez , Kestrel Gorlick , Jiarong Guo , Benjamin Hillmann , Susan Holmes , Hannes Holste , Curtis Huttenhower , Gavin A Huttley , Stefan Janssen , Alan K Jarmusch , Lingjing Jiang , Benjamin D Kaehler , Kyo Bin Kang , Christopher R Keefe , Paul Keim , Scott T Kelley , Dan Knights , Irina Koester , Tomasz Kosciolek , Jorden Kreps , Morgan G I Langille , Joslynn Lee , Ruth Ley , Yong-Xin Liu , Erikka Loftfield , Catherine Lozupone , Massoud Maher , Clarisse Marotz , Bryan D Martin , Daniel McDonald , Lauren J McIver , Alexey V Melnik , Jessica L Metcalf , Sydney C Morgan , Jamie T Morton , Ahmad Turan Naimey , Jose A Navas-Molina , Louis Felix Nothias , Stephanie B Orchanian , Talima Pearson , Samuel L Peoples , Daniel Petras , Mary Lai Preuss , Elmar Pruesse , Lasse Buur Rasmussen , Adam Rivers , Michael S Robeson , Patrick Rosenthal , Nicola Segata , Michael Shaffer , Arron Shiffer , Rashmi Sinha , Se Jin Song , John R Spear , Austin D Swafford , Luke R Thompson , Pedro J Torres , Pauline Trinh , Anupriya Tripathi , Peter J Turnbaugh , Sabah Ul-Hasan , Justin J J van der Hooft , Fernando Vargas , Yoshiki Vázquez-Baeza , Emily Vogtmann , Max von Hippel , William Walters , Yunhu Wan , Mingxun Wang , Jonathan Warren , Kyle C Weber , Charles H D Williamson , Amy D Willis , Zhenjiang Zech Xu , Jesse R Zaneveld , Yilong Zhang , Qiyun Zhu , Rob Knight , J Gregory Caporaso

Consumer Safety Considerations of Skin and Oral Microbiome Perturbation.

Clinical microbiology reviews

Avec: Andrew J McBain , Catherine A O'Neill , Alejandro Amezquita , Laura J Price , Karoline Faust , Adrian Tett , Nicola Segata , Jonathan R Swann , Adrian M Smith , Barry Murphy , Michael Hoptroff , Gordon James , Yugandhar Reddy , Anindya Dasgupta , Tom Ross , Iain L Chapple , William G Wade , Judith Fernandez-Piquer

Tobacco exposure associated with oral microbiota oxygen utilization in the New York City Health and Nutrition Examination Study.

Annals of epidemiology

Avec: Francesco Beghini , Audrey Renson , Christine P Zolnik , Ludwig Geistlinger , Mykhaylo Usyk , Thomas U Moody , Lorna Thorpe , Jennifer B Dowd , Robert Burk , Nicola Segata , Heidi E Jones , Levi Waldron

Gut Bacteria Composition Drives Primary Resistance to Cancer Immunotherapy in Renal Cell Carcinoma Patients.

European urology

Avec: Lisa Derosa , Bertrand Routy , Marine Fidelle , Valerio Iebba , Laurie Alla , Edoardo Pasolli , Nicola Segata , Aude Desnoyer , Filippo Pietrantonio , Gladys Ferrere , Jean-Eudes Fahrner , Emmanuelle Le Chatellier , Nicolas Pons , Nathalie Galleron , Hugo Roume , Connie P M Duong , Laura Mondragón , Kristina Iribarren , Mélodie Bonvalet , Safae Terrisse , Conrad Rauber , Anne-Gaëlle Goubet , Romain Daillère , Fabien Lemaitre , Anna Reni , Beatrice Casu , Maryam Tidjani Alou , Carolina Alves Costa Silva , Didier Raoult , Karim Fizazi , Bernard Escudier , Guido Kroemer , Laurence Albiges , Laurence Zitvogel

Cross-reactivity between tumor MHC class I-restricted antigens and an enterococcal bacteriophage.

Science (New York, N.Y.)

Avec: Aurélie Fluckiger , Romain Daillère , Mohamed Sassi , Barbara Susanne Sixt , Peng Liu , Friedemann Loos , Corentin Richard , Catherine Rabu , Maryam Tidjani Alou , Anne-Gaëlle Goubet , Fabien Lemaitre , Gladys Ferrere , Lisa Derosa , Connie P M Duong , Meriem Messaoudene , Andréanne Gagné , Philippe Joubert , Luisa De Sordi , Laurent Debarbieux , Sylvain Simon , Clara-Maria Scarlata , Maha Ayyoub , Belinda Palermo , Francesco Facciolo , Romain Boidot , Richard Wheeler , Ivo Gomperts Boneca , Zsofia Sztupinszki , Krisztian Papp , Istvan Csabai , Edoardo Pasolli , Nicola Segata , Carlos Lopez-Otin , Zoltan Szallasi , Fabrice Andre , Valerio Iebba , Valentin Quiniou , David Klatzmann , Jacques Boukhalil , Saber Khelaifia , Didier Raoult , Laurence Albiges , Bernard Escudier , Alexander Eggermont , Fathia Mami-Chouaib , Paola Nistico , François Ghiringhelli , Bertrand Routy , Nathalie Labarrière , Vincent Cattoir , Guido Kroemer , Laurence Zitvogel

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

Genome biology

Avec: 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

The Signal and the Noise: Characteristics of Antisense RNA in Complex Microbial Communities.

mSystems

Avec: Thomas Yssing Michaelsen , Jakob Brandt , Caitlin Margaret Singleton , Rasmus Hansen Kirkegaard , Johanna Wiesinger , Nicola Segata , Mads Albertsen

Longitudinal survey of microbiome associated with particulate matter in a megacity.

Genome biology

Avec: Nan Qin , Peng Liang , Chunyan Wu , Guanqun Wang , Qian Xu , Xiao Xiong , Tingting Wang , Moreno Zolfo , Nicola Segata , Huanlong Qin , Rob Knight , Jack A Gilbert , Ting F Zhu

Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea.

Nature communications

Avec: Qiyun Zhu , Uyen Mai , Wayne Pfeiffer , Stefan Janssen , Francesco Asnicar , Jon G Sanders , Pedro Belda-Ferre , Gabriel A Al-Ghalith , Evguenia Kopylova , Daniel McDonald , Tomasz Kosciolek , John B Yin , Shi Huang , Nimaichand Salam , Jian-Yu Jiao , Zijun Wu , Zhenjiang Z Xu , Kalen Cantrell , Yimeng Yang , Erfan Sayyari , Maryam Rabiee , James T Morton , Sheila Podell , Dan Knights , Wen-Jun Li , Curtis Huttenhower , Nicola Segata , Larry Smarr , Siavash Mirarab , Rob Knight

Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3.

eLife

Avec: Francesco Beghini , Lauren J McIver , Aitor Blanco-Míguez , Leonard Dubois , Francesco Asnicar , Sagun Maharjan , Ana Mailyan , Paolo Manghi , Matthias Scholz , Andrew Maltez Thomas , Mireia Valles-Colomer , George Weingart , Yancong Zhang , Moreno Zolfo , Curtis Huttenhower , Eric A Franzosa , Nicola Segata

Publisher Correction: Human postprandial responses to food and potential for precision nutrition.

Nature medicine

Shed Light in the DaRk LineagES of the Fungal Tree of Life-STRES.

Life (Basel, Switzerland)

Avec: Laura Selbmann , Zsigmond Benkő , Claudia Coleine , Sybren de Hoog , Claudio Donati , Irina Druzhinina , Tamás Emri , Cassie L Ettinger , Amy S Gladfelter , Anna A Gorbushina , Igor V Grigoriev , Martin Grube , Nina Gunde-Cimerman , Zsolt Ákos Karányi , Beatrix Kocsis , Tania Kubressoian , Ida Miklós , Márton Miskei , Lucia Muggia , Trent Northen , Monika Novak-Babič , Christa Pennacchio , Walter P Pfliegler , Istvàn Pòcsi , Valeria Prigione , Meritxell Riquelme , Nicola Segata , Julia Schumacher , Ekaterina Shelest , Katja Sterflinger , Donatella Tesei , Jana M U'Ren , Giovanna C Varese , Xabier Vázquez-Campos , Vania A Vicente , Emanuel M Souza , Polona Zalar , Allison K Walker , Jason E Stajich

Neonatal antibiotic exposure impairs child growth during the first six years of life by perturbing intestinal microbial colonization.

Nature communications

Avec: Atara Uzan-Yulzari , Olli Turta , Anna Belogolovski , Oren Ziv , Christina Kunz , Sarah Perschbacher , Hadar Neuman , Edoardo Pasolli , Aia Oz , Hila Ben-Amram , Himanshu Kumar , Helena Ollila , Anne Kaljonen , Erika Isolauri , Seppo Salminen , Hanna Lagström , Nicola Segata , Itai Sharon , Yoram Louzoun , Regina Ensenauer , Samuli Rautava , Omry Koren

Stool microRNA profiles reflect different dietary and gut microbiome patterns in healthy individuals.

Gut

Avec: Sonia Tarallo , Giulio Ferrero , Francesca De Filippis , Antonio Francavilla , Edoardo Pasolli , Valentina Panero , Francesca Cordero , Nicola Segata , Sara Grioni , Ruggero Gaetano Pensa , Barbara Pardini , Danilo Ercolini , Alessio Naccarati

Variation and transmission of the human gut microbiota across multiple familial generations.

Nature microbiology

Avec: Mireia Valles-Colomer , Rodrigo Bacigalupe , Sara Vieira-Silva , Shinya Suzuki , Youssef Darzi , Raul Y Tito , Takuji Yamada , Nicola Segata , Jeroen Raes , Gwen Falony

On the Origin and Propagation of the COVID-19 Outbreak in the Italian Province of Trento, a Tourist Region of Northern Italy.

Viruses

Avec: Luca Bianco , Mirko Moser , Andrea Silverj , Diego Micheletti , Giovanni Lorenzin , Lucia Collini , Mattia Barbareschi , Paolo Lanzafame , Nicola Segata , Massimo Pindo , Pietro Franceschi , Omar Rota-Stabelli , Annapaola Rizzoli , Paolo Fontana , Claudio Donati

Neuroblastoma is associated with alterations in gut microbiome composition subsequent to maternal microbial seeding.

EBioMedicine

Avec: Mireia Valles-Colomer , Paolo Manghi , Fabio Cumbo , Giulia Masetti , Federica Armanini , Francesco Asnicar , Aitor Blanco-Miguez , Federica Pinto , Michal Punčochář , Alberto Garaventa , Loredana Amoroso , Mirco Ponzoni , Maria Valeria Corrias , Nicola Segata

Microbial composition associated with biliary stents in patients undergoing pancreatic resection for cancer.

NPJ biofilms and microbiomes

Avec: Aitor Blanco-Míguez , Sara Carloni , Cindy Cardenas , Carola Conca Dioguardi , Luca Lambroia , Giovanni Capretti , Gennaro Nappo , Alessandro Fugazza , Antonio Capogreco , Federica Armanini , Francesco Asnicar , Leonard Dubois , Davide Golzato , Paolo Manghi , Federica Pinto , Cristina Scuderi , Erminia Casari , Marco Montorsi , Andrea Anderloni , Maria Rescigno , Alessandro Repici , Alessandro Zerbi , Clelia Peano , Sabrina Tamburini , Roberto Rusconi , Nicola Segata

Outer Membrane Vesicles From The Gut Microbiome Contribute to Tumor Immunity by Eliciting Cross-Reactive T Cells.

Frontiers in oncology

Avec: Michele Tomasi , Elena Caproni , Mattia Benedet , Ilaria Zanella , Sebastiano Giorgetta , Mattia Dalsass , Enrico König , Assunta Gagliardi , Laura Fantappiè , Alvise Berti , Silvia Tamburini , Lorenzo Croia , Gabriele Di Lascio , Erika Bellini , Silvia Valensin , Giada Licata , Guido Sebastiani , Francesco Dotta , Federica Armanini , Fabio Cumbo , Francesco Asnicar , Aitor Blanco-Míguez , Eliana Ruggiero , Nicola Segata , Guido Grandi , Alberto Grandi

Menopause is associated with postprandial metabolism, metabolic health and lifestyle: The ZOE PREDICT study.

EBioMedicine

Avec: Kate M Bermingham , Inbar Linenberg , Wendy L Hall , Kirstin Kadé , Paul W Franks , Richard Davies , Jonathan Wolf , George Hadjigeorgiou , Francesco Asnicar , Nicola Segata , JoAnn E Manson , Louise R Newson , Linda M Delahanty , Jose M Ordovas , Andrew T Chan , Tim D Spector , Ana M Valdes , Sarah E Berry

Population-level impacts of antibiotic usage on the human gut microbiome.

Nature communications

Avec: Kihyun Lee , Sebastien Raguideau , Kimmo Sirén , Francesco Asnicar , Fabio Cumbo , Falk Hildebrand , Nicola Segata , Chang-Jun Cha , Christopher Quince

A microbiota-modulated checkpoint directs immunosuppressive intestinal T cells into cancers.

Science (New York, N.Y.)

Avec: Marine Fidelle , Conrad Rauber , Carolina Alves Costa Silva , Ai-Ling Tian , Imran Lahmar , Anne-Laure Mallard de La Varende , Liwei Zhao , Cassandra Thelemaque , Isabelle Lebhar , Meriem Messaoudene , Eugenie Pizzato , Roxanne Birebent , Maxime Descartes Mbogning Fonkou , Silvia Zoppi , Anna Reni , Cécile Dalban , Marion Leduc , Gladys Ferrere , Sylvère Durand , Pierre Ly , Aymeric Silvin , Kevin Mulder , Charles-Antoine Dutertre , Florent Ginhoux , Satoru Yonekura , Maria Paula Roberti , Maryam Tidjani-Alou , Safae Terrisse , Jianzhou Chen , Oliver Kepp , Angela Schippers , Norbert Wagner , Javier Suárez-Gosálvez , Sebastian Kobold , Jean-Eudes Fahrner , Corentin Richard , Jacques Bosq , Leonardo Lordello , Giacomo Vitali , Nathalie Galleron , Benoît Quinquis , Emmanuelle Le Chatelier , Lucas Blanchard , Jean-Philippe Girard , Anne Jarry , Nadine Gervois , Emmanuelle Godefroy , Nathalie Labarrière , Ronald Koschny , Romain Daillère , Benjamin Besse , Caroline Truntzer , François Ghiringhelli , Nicolas Coatnoan , Vanessa Mhanna , David Klatzmann , Damien Drubay , Laurence Albiges , Andrew Maltez Thomas , Nicola Segata , François-Xavier Danlos , Aurélien Marabelle , Bertrand Routy , Lisa Derosa , Guido Kroemer , Laurence Zitvogel

Key determinants of success in fecal microbiota transplantation: From microbiome to clinic.

Cell host & microbe

Avec: Serena Porcari , Nicolas Benech , Mireia Valles-Colomer , Nicola Segata , Antonio Gasbarrini , Giovanni Cammarota , Harry Sokol , Gianluca Ianiro

Epidemiological and Evolutionary Analysis of West Nile Virus Lineage 2 in Italy.

Viruses

Avec: Giulia Mencattelli , Andrea Silverj , Federica Iapaolo , Carla Ippoliti , Liana Teodori , Annapia Di Gennaro , Valentina Curini , Luca Candeloro , Annamaria Conte , Andrea Polci , Daniela Morelli , Maria Gabriella Perrotta , Giovanni Marini , Roberto Rosà , Federica Monaco , Nicola Segata , Annapaola Rizzoli , Omar Rota-Stabelli , Giovanni Savini , West Nile Working Group

Réseau de co-auteurs

Nicola Segata 98 collaborations

Francesco Asnicar 40 collaborations

Federica Armanini 21 collaborations

Paolo Manghi 21 collaborations

Edoardo Pasolli 21 collaborations

Tim D Spector 18 collaborations

Jonathan Wolf 17 collaborations

Sarah E Berry 16 collaborations

Mireia Valles-Colomer 16 collaborations

Ana M Valdes 15 collaborations

Fabio Cumbo 13 collaborations

Francesco Beghini 12 collaborations

Aitor Blanco-Míguez 12 collaborations

Adrian Tett 12 collaborations

Andrew Maltez Thomas 11 collaborations

Curtis Huttenhower 11 collaborations

Serena Manara 10 collaborations

Federica Pinto 10 collaborations

Lisa Derosa 10 collaborations

Laurence Zitvogel 10 collaborations

Paul W Franks 10 collaborations

Moreno Zolfo 10 collaborations

Guido Kroemer 9 collaborations

Bertrand Routy 9 collaborations

George Hadjigeorgiou 9 collaborations

Richard Davies 9 collaborations

Kun D Huang 9 collaborations

Michal Punčochář 9 collaborations

Romain Daillère 8 collaborations

Omar Rota-Stabelli 8 collaborations

Carolina Alves Costa Silva 7 collaborations

Cristina Menni 7 collaborations

Danilo Ercolini 7 collaborations

Andrew T Chan 7 collaborations

Marine Fidelle 6 collaborations

Gianmarco Piccinno 6 collaborations

Francesca De Filippis 6 collaborations

Maria Carmen Collado 6 collaborations

Jose M Ordovas 6 collaborations

Levi Waldron 6 collaborations

Linda M Delahanty 6 collaborations

Gladys Ferrere 5 collaborations

Valerio Iebba 5 collaborations

Safae Terrisse 5 collaborations

Davide Golzato 5 collaborations

Panayiotis Louca 5 collaborations

Rob Knight 5 collaborations

Nicolai Karcher 5 collaborations

David A Drew 5 collaborations

Joan Capdevila 5 collaborations

Paolo Ghensi 4 collaborations

Till Strowig 4 collaborations

Cassandra Thelemaque 4 collaborations

Damien Drubay 4 collaborations

Conrad Rauber 4 collaborations

Corentin Richard 4 collaborations

Annapaola Rizzoli 4 collaborations

Kate M Bermingham 4 collaborations

Wendy L Hall 4 collaborations

Harry Sokol 4 collaborations

Aitor Blanco-Miguez 4 collaborations

Ana Nogal 4 collaborations

Alessia Visconti 4 collaborations

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Mario Falchi 4 collaborations

Massimo Mangino 4 collaborations

Paul D Cotter 4 collaborations

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None None 3 collaborations

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