%0 Journal Article %T A European ECMM-ESCMID survey on goals and practices for mycobiota characterization using Next Generation Sequencing %+ Institut de recherche en santé, environnement et travail (Irset) %+ Centre de recherche Cardio-Thoracique de Bordeaux [Bordeaux] (CRCTB) %A Gangneux, Jean-Pierre %A Guegan, Hélène %A Vandenborght, Louise-Eva %A Buffet-Bataillon, Sylvie %A Enaud, Raphaël %A Delhaes, Laurence %Z The authors want to warmly acknowledge colleagues who accepted to answer to the survey: the ECMM‐ESCMID (ESGHAMI & EFISG) NGS study group (see Appendix 1). %< avec comité de lecture %@ 0933-7407 %J Mycoses %I Wiley %V 62 %N 12 %P 1096-1099 %8 2019 %D 2019 %R 10.1111/myc.12999 %M 31498487 %K Digestive tract infections %K Europe %K Lung infections %K Microbiota %K Mycobiota %K fungi %Z Life Sciences [q-bio]/Human health and pathology/Infectious diseases %Z Life Sciences [q-bio]/Microbiology and Parasitology/MycologyJournal articles %X Although substantial efforts have been made to investigate about the composition of the microbiota, fungi that constitute the mycobiota play a pivotal role in maintaining microbial communities and physiological processes in the body. Here, we conducted an international survey focusing on laboratory's current procedures regarding their goals and practices of mycobiota characterisation using NGS. A questionnaire was proposed to laboratories affiliated to working groups from ECMM (NGS study group) and ESCMID (ESGHAMI and EFISG study groups). Twenty-six questionnaires from 18 countries were received. The use of NGS to characterise the mycobiota was not in routine for most of the laboratories (N = 23, 82%), and the main reason of using NGS was primary to understand the pathophysiology of a dysbiosis (N = 20), to contribute to a diagnosis (N = 16) or to implement a therapeutic strategy (N = 12). Other reported reasons were to evaluate the exposome (environmental studies) (N = 10) or to investigate epidemics (N = 8). Sputum is the main sample studied, and cystic fibrosis represents a major disease studied via the analysis of pulmonary microbiota. No consensus has emerged for the choice of the targets with 18S, ITS1 and ITS2 used alternatively among the laboratories. Other answers are detailed in the manuscript. We report a photography of mycobiota analysis that may become a major tool in the near future. We can draw some conclusions on the diversity of approaches within the answers of the 27 laboratories and underline the need for standardisation. %G English %2 https://univ-rennes.hal.science/hal-02305001/document %2 https://univ-rennes.hal.science/hal-02305001/file/Gangneux_et_al-2019-A%20European%20ECMM%E2%80%90ESCMID%20survey%20on%20goals%20and%20practices.pdf %L hal-02305001 %U https://univ-rennes.hal.science/hal-02305001 %~ INSERM %~ UNIV-RENNES1 %~ UNIV-ANGERS %~ IFR140 %~ IRSET %~ STATS-UR1 %~ IRSET-SMS %~ IRSET-CCII %~ IRSET-TREC %~ IRSET-HIAEC %~ IRSET-SMLF %~ IRSET-ERD %~ IRSET-VCER %~ IRSET-NEED %~ IRSET-TNGC %~ UR1-UFR-SVE %~ UR1-HAL %~ UR1-SDV %~ IRSET-2 %~ TEST-UR-CSS %~ UNIV-RENNES %~ UR1-BIO-SA