Supplementary Materials Gut microbiota linked to

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We selected a random subset of 10,000 quality-filtered sequences per sample ... combination phyloseq,(McMurdie and Holmes, 2013) vegan,(Jari Oksanen, ... LEfSe criterion, i.e.: significant taxa had to differ between every pair of class values.
Supplementary Materials

Gut microbiota linked to sexual preference and HIV infection Marc Noguera-Julian

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1,3 1,3 1,2 1,3 , Muntsa Rocafort †, Yolanda Guillén , Javier Rivera , Maria Casadellà ,

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Piotr Nowak , Falk Hildebrand , Georg Zeller , Mariona Parera , Rocío Bellido , Cristina Rodríguez , Jorge Carrillo 8

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, Beatriz Mothe

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, Josep Coll , Isabel Bravo , Carla Estany , Cristina Herrero , Jorge

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Saz , Guillem Sirera , Ariadna Torrela , Jordi Navarro , Manel Crespo , Christian Brander Negredo

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, Julià Blanco

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, Francisco Guarner , Maria Luz Calle , Peer Bork

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Sönnerborg , Bonaventura Clotet

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, Roger Paredes*

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, Eugènia

, Anders

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irsiCaixa AIDS Research Institute, Ctra de Canyet s/n, 08916 Badalona, Catalonia, Spain. Universitat de Vic-Universitat Central de Catalunya, C. Sagrada Família 7, 08500 Vic, Catalonia, Spain. 3 Universitat Autònoma de Barcelona, 08193 Bellaterra, Catalonia, Spain. 4 Department of Medicine, Unit of Infectious Diseases, Karolinska University Hospital, Karolinska Institutet, Huddinge 141, 86 Stockholm, Sweden. 5 Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany. 6 HIV Unit & Lluita contra la SIDA Foundation, Hospital Universitari Germans Trias i Pujol, Ctra de Canyet s/n, 08916 Badalona, Catalonia, Spain. 7 ISGLOBAL, Carrer Rosselló, 132, 08036 Barcelona, Catalonia, Spain. 8 BCN Checkpoint, Carrer del Comte Borrell, 164, 08015 Barcelona, Catalonia, Spain. 9 Infectious Diseases Unit, Hospital Universitari Vall d’Hebrón, Passeig de la Vall d'Hebrón, 119-129, 08035 Barcelona, Catalonia, Spain. 10 Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain. 11 Digestive Diseases Department, Vall d’Hebrón Institute of Research, Hospital Universitari Vall d’Hebrón, Passeig de la Vall d'Hebrón, 119-129, 08035 Barcelona, Catalonia, Spain. 12 Max-Delbrück-Centre for Molecular Medicine, Robert-Rössle-Str. 10, 13092 Berlin, Germany. 13 Molecular Medicine Partnership Unit, EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany. 2

†!Contributed

equally to this work

* Corresponding author: Dr. Roger Paredes, HIV Unit and irsiCaixa AIDS Research Institute, Ctra de Canyet s/n, 08916 Badalona, Catalonia, Spain. Tel: + 34 93 465 6374 (Ext: 162) email: [email protected]

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Supplementary Methods HIV phenotype definitions To ensure that the study included a representative spectrum of different HIV-1 phenotypes, HIV-infected subjects had to belong to one of the following groups: (a) elite controllers, defined as subjects with HIV-1 RNA 10,000 copies/mL, nadir CD4+ T-cell counts>500 cells/mm and no ART exposure; (d) late 3

presenters, with CD4+ T-cell counts < 200 cells/mm at diagnosis and no ART exposure; (e) immune 3

discordant, maintaining HIV-1 RNA