Use of shotgun metagenomics for the identification of protozoa in the gut microbiota of healthy individuals from worldwide populations with various industrialization levels
| Autor: | Laure Ségurel, Eric Viscogliosi, Nausicaa Gantois, Alain Froment, Amandine Cian, Magali Chabé, Ana Lokmer |
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| Přispěvatelé: | Laure, Segurel, Eco-Anthropologie et Ethnobiologie (EAE), Muséum national d'Histoire naturelle (MNHN)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Patrimoines locaux, Environnement et Globalisation (PALOC), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU), This work was supported by the ANR MICROREGAL (ANR-15-CE02-0003), the Centre National de la Recherche Scientifique (LS) and the Institut Pasteur of Lille. AC was supported by a PhD fellowship from the University of Lille 2 and the Institut Pasteur of Lille., We wish to thank the 'Plateau Technique de Paléogénomique et Génétique Moléculaire (MNHN, site du Musée de l’Homme) for their technical help, Centre National de la Recherche Scientifique (CNRS)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP) |
| Jazyk: | angličtina |
| Rok vydání: | 2019 |
| Předmět: |
Male
MESH: Blastocystis/genetics [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics Phylogenetics and taxonomy Biochemistry Feces 0302 clinical medicine RNA Ribosomal 16S Peru MESH: Blastocystis/isolation & purification Cameroon Protozoans MESH: Middle Aged Eukaryota Genomics MESH: Peru/epidemiology Healthy Volunteers Nucleic acids Italy Medicine MESH: Cameroon/epidemiology Bioinformatics Science Zoology [SDV.MP.PRO]Life Sciences [q-bio]/Microbiology and Parasitology/Protistology MESH: Blastocystis/classification 03 medical and health sciences Genetics Humans Non-coding RNA MESH: Prevalence Aged MESH: DNA Ribosomal/genetics MESH: Humans MESH: Italy/epidemiology Organisms Entamoeba Biology and Life Sciences MESH: Adult Ribosomal RNA United States 030104 developmental biology Metagenomics Africa Protozoa MESH: Female 0301 basic medicine MESH: Feces/parasitology Gut flora MESH: United States/epidemiology Tanzania Geographical Locations Database and Informatics Methods MESH: Entamoeba/genetics MESH: Entamoeba/classification Prevalence MESH: Healthy Volunteers MESH: Aged Multidisciplinary biology Middle Aged Female Sequence Analysis Research Article Adult Cell biology Cellular structures and organelles 030231 tropical medicine [SDV.MP.PRO] Life Sciences [q-bio]/Microbiology and Parasitology/Protistology Research and Analysis Methods DNA Ribosomal MESH: Sequence Analysis DNA/methods parasitic diseases [SDV.BID.SPT] Life Sciences [q-bio]/Biodiversity/Systematics Phylogenetics and taxonomy MESH: Developed Countries Blastocystis Developed Countries MESH: Tanzania/epidemiology MESH: Gastrointestinal Tract/parasitology Sequence Analysis DNA biology.organism_classification MESH: RNA Ribosomal 16S/genetics Parasitic Protozoans MESH: Entamoeba/isolation & purification MESH: Male Gastrointestinal Tract MESH: Metagenomics/methods People and Places RNA Sequence Alignment Ribosomes |
| Zdroj: | PLoS ONE PLoS ONE, 2019, 14 (2), pp.e0211139. ⟨10.1371/journal.pone.0211139⟩ PLoS ONE, Public Library of Science, 2019, 14 (2), pp.e0211139. ⟨10.1371/journal.pone.0211139⟩ PLoS ONE, Vol 14, Iss 2, p e0211139 (2019) |
| ISSN: | 1932-6203 |
| DOI: | 10.1371/journal.pone.0211139 |
| Popis: | International audience; 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. |
| Databáze: | OpenAIRE |
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