Use of shotgun metagenomics for the ...
Type de document :
Compte-rendu et recension critique d'ouvrage
PMID :
Titre :
Use of shotgun metagenomics for the identification of protozoa in the gut microbiota of healthy individuals from worldwide populations with various industrialization levels
Auteur(s) :
Lokmer, Ana [Auteur]
Eco-Anthropologie et Ethnobiologie [EAE]
Cian, Amandine [Auteur]
Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 [CIIL]
Froment, Alain [Auteur]
Institut de Recherche pour le Développement [IRD]
Patrimoines locaux, Environnement et Globalisation [PALOC]
Gantois, Nausicaa [Auteur]
Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 [CIIL]
Viscogliosi, Eric [Auteur]
Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 [CIIL]
Chabé, Magali [Auteur]
Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 [CIIL]
Ségurel, Laure [Auteur correspondant]
Eco-Anthropologie et Ethnobiologie [EAE]
Eco-Anthropologie et Ethnobiologie [EAE]
Cian, Amandine [Auteur]
Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 [CIIL]
Froment, Alain [Auteur]
Institut de Recherche pour le Développement [IRD]
Patrimoines locaux, Environnement et Globalisation [PALOC]
Gantois, Nausicaa [Auteur]
Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 [CIIL]
Viscogliosi, Eric [Auteur]
Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 [CIIL]
Chabé, Magali [Auteur]
Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 [CIIL]
Ségurel, Laure [Auteur correspondant]
Eco-Anthropologie et Ethnobiologie [EAE]
Titre de la revue :
PLoS One
Pagination :
e0211139
Éditeur :
Public Library of Science
Date de publication :
2019-02
ISSN :
1932-6203
Discipline(s) HAL :
Sciences du Vivant [q-bio]/Microbiologie et Parasitologie/Protistologie
Sciences du Vivant [q-bio]/Biodiversité/Systématique, phylogénie et taxonomie
Sciences du Vivant [q-bio]/Biodiversité/Systématique, phylogénie et taxonomie
Résumé en anglais : [en]
Protozoa have long been considered undesirable residents of the human gut, but recent findings suggest that some of them may positively affect the gut ecosystem. To better understand the role and ecological dynamics of ...
Lire la suite >Protozoa have long been considered undesirable residents of the human gut, but recent findings suggest that some of them may positively affect the gut ecosystem. To better understand the role and ecological dynamics of these commensal and potentially beneficial protozoan symbionts, we need efficient methods to detect them, as well as accurate estimates of their prevalence across human populations. Metagenomics provides such an opportunity, allowing simultaneous detection of multiple symbionts in a single analytical procedure. In this study, we collected fecal samples of 68 individuals from three Cameroonian populations with different subsistence modes and compared metagenomics-based and targeted methods of detection for two common protozoan genera: Blastocystis and Ent-amoeba. In addition, we analyzed our data along with publicly available fecal metagenomes from various worldwide populations to explore the prevalence and association patterns of ten protozoan genera. Regarding the detection method, microscopy was much less sensitive than metagenomics for Entamoeba, whereas qPCR was at least as sensitive as meta-genomics for Blastocystis sp. However, metagenomics was more likely to detect co-colonizations by multiple subtypes. Out of the ten examined genera in 127 individuals from Cameroon, Tanzania, Peru, Italy or USA, only three (Blastocystis, Entamoeba and Entero-monas) had an overall prevalence exceeding 10%. All three genera were more common in less industrialized populations and their prevalence differed between continents and subsistence modes, albeit not in a straightforward manner. The majority (72.5%) of colonized individuals carried at least two protozoan species, indicating that mixed-species colonizations are common. In addition, we detected only positive and no negative association patterns between different protozoa. Despite the pitfalls of the metagenomic approach, ranging from the availability of good-quality sequencing data to the lack of standard analytical procedures, we demonstrated its utility in simultaneous detection of multiple protozoan genera, and especially its ability to efficiently detect mixed-species colonizations. Our study corroborates and expands prevalence results previously obtained for Blastocystis sp. and provides novel data for Entamoeba spp. and several other protozoan genera. Furthermore, it indicates that multiple protozoa are common residents of the healthy human gut worldwide.Lire moins >
Lire la suite >Protozoa have long been considered undesirable residents of the human gut, but recent findings suggest that some of them may positively affect the gut ecosystem. To better understand the role and ecological dynamics of these commensal and potentially beneficial protozoan symbionts, we need efficient methods to detect them, as well as accurate estimates of their prevalence across human populations. Metagenomics provides such an opportunity, allowing simultaneous detection of multiple symbionts in a single analytical procedure. In this study, we collected fecal samples of 68 individuals from three Cameroonian populations with different subsistence modes and compared metagenomics-based and targeted methods of detection for two common protozoan genera: Blastocystis and Ent-amoeba. In addition, we analyzed our data along with publicly available fecal metagenomes from various worldwide populations to explore the prevalence and association patterns of ten protozoan genera. Regarding the detection method, microscopy was much less sensitive than metagenomics for Entamoeba, whereas qPCR was at least as sensitive as meta-genomics for Blastocystis sp. However, metagenomics was more likely to detect co-colonizations by multiple subtypes. Out of the ten examined genera in 127 individuals from Cameroon, Tanzania, Peru, Italy or USA, only three (Blastocystis, Entamoeba and Entero-monas) had an overall prevalence exceeding 10%. All three genera were more common in less industrialized populations and their prevalence differed between continents and subsistence modes, albeit not in a straightforward manner. The majority (72.5%) of colonized individuals carried at least two protozoan species, indicating that mixed-species colonizations are common. In addition, we detected only positive and no negative association patterns between different protozoa. Despite the pitfalls of the metagenomic approach, ranging from the availability of good-quality sequencing data to the lack of standard analytical procedures, we demonstrated its utility in simultaneous detection of multiple protozoan genera, and especially its ability to efficiently detect mixed-species colonizations. Our study corroborates and expands prevalence results previously obtained for Blastocystis sp. and provides novel data for Entamoeba spp. and several other protozoan genera. Furthermore, it indicates that multiple protozoa are common residents of the healthy human gut worldwide.Lire moins >
Langue :
Anglais
Vulgarisation :
Non
Projet ANR :
Source :
Fichiers
- https://hal.archives-ouvertes.fr/hal-02120849/document
- Accès libre
- Accéder au document
- https://hal.archives-ouvertes.fr/hal-02120849/document
- Accès libre
- Accéder au document
- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6364966/pdf
- Accès libre
- Accéder au document
- https://hal.archives-ouvertes.fr/hal-02120849/document
- Accès libre
- Accéder au document
- document
- Accès libre
- Accéder au document
- Lokmer_2019_PLoSOne.pdf
- Accès libre
- Accéder au document
- Accès libre
- Accéder au document