1
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Lokmer A, Alladi CG, Troudet R, Bacq-Daian D, Boland-Auge A, Latapie V, Deleuze JF, RajKumar RP, Shewade DG, Bélivier F, Marie-Claire C, Jamain S. Risperidone response in patients with schizophrenia drives DNA methylation changes in immune and neuronal systems. Epigenomics 2023; 15:21-38. [PMID: 36919681 DOI: 10.2217/epi-2023-0017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
Background: The choice of efficient antipsychotic therapy for schizophrenia relies on a time-consuming trial-and-error approach, whereas the social and economic burdens of the disease call for faster alternatives. Material & methods: In a search for predictive biomarkers of antipsychotic response, blood methylomes of 28 patients were analyzed before and 4 weeks into risperidone therapy. Results: Several CpGs exhibiting response-specific temporal dynamics were identified in otherwise temporally stable methylomes and noticeable global response-related differences were observed between good and bad responders. These were associated with genes involved in immunity, neurotransmission and neuronal development. Polymorphisms in many of these genes were previously linked with schizophrenia etiology and antipsychotic response. Conclusion: Antipsychotic response seems to be shaped by both stable and medication-induced methylation differences.
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Affiliation(s)
- Ana Lokmer
- Univ Paris Est Créteil, INSERM, IMRB, Translational Neuropsychiatry, Créteil, F-94000, France.,Fondation FondaMental, Créteil, F-94000, France
| | - Charanraj Goud Alladi
- Université de Paris, INSERM UMRS 1144, Optimisation Thérapeutique en Neuropsychopharmacologie (OTeN), Paris, F-75006, France
| | - Réjane Troudet
- Univ Paris Est Créteil, INSERM, IMRB, Translational Neuropsychiatry, Créteil, F-94000, France.,Fondation FondaMental, Créteil, F-94000, France
| | - Delphine Bacq-Daian
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, F-91057, France
| | - Anne Boland-Auge
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, F-91057, France
| | - Violaine Latapie
- Univ Paris Est Créteil, INSERM, IMRB, Translational Neuropsychiatry, Créteil, F-94000, France.,Fondation FondaMental, Créteil, F-94000, France
| | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, F-91057, France
| | - Ravi Philip RajKumar
- Department of Pharmacology, Jawaharlal Institute of Postgraduate Medical Education & Research, Puducherry, 605006, India
| | - Deepak Gopal Shewade
- Department of Psychiatry, Jawaharlal Institute of Postgraduate Medical Education & Research, Puducherry, 605006, India.,Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, F-91000, France
| | - Frank Bélivier
- Fondation FondaMental, Créteil, F-94000, France.,Université de Paris, INSERM UMRS 1144, Optimisation Thérapeutique en Neuropsychopharmacologie (OTeN), Paris, F-75006, France.,Hôpitaux Lariboisière-Fernand Widal, GHU APHP Nord, Département de Psychiatrie et de Médecine Addicto-logique, Paris, F-75010, France
| | - Cynthia Marie-Claire
- Université de Paris, INSERM UMRS 1144, Optimisation Thérapeutique en Neuropsychopharmacologie (OTeN), Paris, F-75006, France
| | - Stéphane Jamain
- Univ Paris Est Créteil, INSERM, IMRB, Translational Neuropsychiatry, Créteil, F-94000, France.,Fondation FondaMental, Créteil, F-94000, France
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Portet A, Toulza E, Lokmer A, Huot C, Duval D, Galinier R, Gourbal B. Experimental Infection of the Biomphalaria glabrata Vector Snail by Schistosoma mansoni Parasites Drives Snail Microbiota Dysbiosis. Microorganisms 2021; 9:microorganisms9051084. [PMID: 34070104 PMCID: PMC8158356 DOI: 10.3390/microorganisms9051084] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/01/2021] [Accepted: 05/04/2021] [Indexed: 02/07/2023] Open
Abstract
Host-parasite interaction can result in a strong alteration of the host-associated microbiota. This dysbiosis can affect the fitness of the host; can modify pathogen interaction and the outcome of diseases. Biomphalaria glabrata is the snail intermediate host of the trematode Schistosoma mansoni, the agent of human schistosomiasis, causing hundreds of thousands of deaths every year. Here, we present the first study of the snail bacterial microbiota in response to Schistosoma infection. We examined the interplay between B. glabrata, S. mansoni and host microbiota. Snails were infected and the microbiota composition was analysed by 16S rDNA amplicon sequencing approach. We demonstrated that the microbial composition of water did not affect the microbiota composition. Then, we characterised the Biomphalaria bacterial microbiota at the individual scale in both naive and infected snails. Sympatric and allopatric strains of parasites were used for infections and re-infections to analyse the modification or dysbiosis of snail microbiota in different host-parasite co-evolutionary contexts. Concomitantly, using RNAseq, we investigated the link between bacterial microbiota dysbiosis and snail anti-microbial peptide immune response. This work paves the way for a better understanding of snail/schistosome interaction and should have critical consequences in terms of snail control strategies for fighting schistosomiasis disease in the field.
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Affiliation(s)
- Anaïs Portet
- IHPE, University Montpellier, CNRS, Ifremer, University Perpignan Via Domitia, 66860 Perpignan, France; (A.P.); (E.T.); (C.H.); (D.D.); (R.G.)
| | - Eve Toulza
- IHPE, University Montpellier, CNRS, Ifremer, University Perpignan Via Domitia, 66860 Perpignan, France; (A.P.); (E.T.); (C.H.); (D.D.); (R.G.)
| | - Ana Lokmer
- Laboratory of Eco-Anthropology UMR 7206 CNRS-MNHN-Paris 7, 75005 Paris, France;
| | - Camille Huot
- IHPE, University Montpellier, CNRS, Ifremer, University Perpignan Via Domitia, 66860 Perpignan, France; (A.P.); (E.T.); (C.H.); (D.D.); (R.G.)
| | - David Duval
- IHPE, University Montpellier, CNRS, Ifremer, University Perpignan Via Domitia, 66860 Perpignan, France; (A.P.); (E.T.); (C.H.); (D.D.); (R.G.)
| | - Richard Galinier
- IHPE, University Montpellier, CNRS, Ifremer, University Perpignan Via Domitia, 66860 Perpignan, France; (A.P.); (E.T.); (C.H.); (D.D.); (R.G.)
| | - Benjamin Gourbal
- IHPE, University Montpellier, CNRS, Ifremer, University Perpignan Via Domitia, 66860 Perpignan, France; (A.P.); (E.T.); (C.H.); (D.D.); (R.G.)
- Correspondence:
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3
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Even G, Lokmer A, Rodrigues J, Audebert C, Viscogliosi E, Ségurel L, Chabé M. Changes in the Human Gut Microbiota Associated With Colonization by Blastocystis sp. and Entamoeba spp. in Non-Industrialized Populations. Front Cell Infect Microbiol 2021; 11:533528. [PMID: 33816323 PMCID: PMC8013780 DOI: 10.3389/fcimb.2021.533528] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 01/29/2021] [Indexed: 01/04/2023] Open
Abstract
Human gut microbial communities are mainly composed of bacteria, but also include fungi, viruses, archaea, and protozoa, whose role in the gut ecosystem has only recently begun to be recognized. For example, humans colonized by Blastocystis (a gut protozoan with controversial pathogenicity) host a more diverse bacterial microbiota than individuals not carrying it, suggesting that its presence may be beneficial for the host. In parallel, the presence of non-pathogenic Entamoeba spp. has been associated with an increased diversity and compositional shifts in the bacterial microbiota of healthy rural individuals in Cameroon. However, Entamoeba and Blastocystis, the two most prevalent human gut protozoa, have never been studied in the same individuals, preventing the study of their interaction. As Blastocystis is one of the few gut protozoa commonly found in industrialized populations, which are otherwise mostly devoid of gut eukaryotes, we need to focus on rural “traditional” populations, who harbor a higher diversity of gut eukaryotes (whether pathogenic or commensal) in order to study protozoa interactions in the gut ecosystem. To this end, we profiled the gut bacterial microbiota of 134 healthy Cameroonian adults using 16S rRNA gene amplicon sequencing data. Entamoeba and Blastocystis presence and co-occurrence pattern in the same individuals were determined using metagenomic shotgun data. We found that, when taking into account both protozoa jointly, Blastocystis was associated with both a higher richness and a higher evenness of the gut bacterial microbiota, while Entamoeba was associated only with a higher richness. We demonstrated a cumulative influence of these protozoa on bacterial microbiome diversity. Furthermore, while the abundance of several common taxa (for example, Ruminococcaceae, Coprococcus and Butyrivibrio) varied according to Blastocystis colonization, only a single Bacteroides amplicon sequence variant was found to be differentially abundant between Entamoeba-negative and Entamoeba-positive samples. Given the specific signature of each protozoan on the gut microbiota and the seemingly stronger association for Blastocystis, our results suggest that Blastocystis and Entamoeba interact with gut bacteria each in its own way, but experimental studies are needed to explore the precise mechanisms of these interactions.
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Affiliation(s)
- Gaël Even
- Gènes Diffusion, Douai, France.,PEGASE-Biosciences, Institut Pasteur de Lille, Lille, France
| | - Ana Lokmer
- UMR7206 Eco-Anthropologie, CNRS-MNHN-Université de Paris, Paris, France
| | - Jules Rodrigues
- UMR7206 Eco-Anthropologie, CNRS-MNHN-Université de Paris, Paris, France
| | - Christophe Audebert
- Gènes Diffusion, Douai, France.,PEGASE-Biosciences, Institut Pasteur de Lille, Lille, France
| | - Eric Viscogliosi
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Centre d'Infection et d'Immunité de Lille, Lille, France
| | - Laure Ségurel
- UMR7206 Eco-Anthropologie, CNRS-MNHN-Université de Paris, Paris, France.,Laboratoire de Biométrie et Biologie Evolutive UMR5558, CNRS - Université Lyon 1, Université de Lyon, Villeurbanne, France
| | - Magali Chabé
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Centre d'Infection et d'Immunité de Lille, Lille, France
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4
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Wegner KM, Lokmer A, John U. Genomic and Transcriptomic Differentiation of Independent Invasions of the Pacific Oyster Crassostrea gigas. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.567049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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5
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Dupont S, Lokmer A, Corre E, Auguet JC, Petton B, Toulza E, Montagnani C, Tanguy G, Pecqueur D, Salmeron C, Guillou L, Desnues C, La Scola B, Bou Khalil J, de Lorgeril J, Mitta G, Gueguen Y, Escoubas JM. Oyster hemolymph is a complex and dynamic ecosystem hosting bacteria, protists and viruses. Anim Microbiome 2020; 2:12. [PMID: 33499958 PMCID: PMC7807429 DOI: 10.1186/s42523-020-00032-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 04/14/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The impact of the microbiota on host fitness has so far mainly been demonstrated for the bacterial microbiome. We know much less about host-associated protist and viral communities, largely due to technical issues. However, all microorganisms within a microbiome potentially interact with each other as well as with the host and the environment, therefore likely affecting the host health. RESULTS We set out to explore how environmental and host factors shape the composition and diversity of bacterial, protist and viral microbial communities in the Pacific oyster hemolymph, both in health and disease. To do so, five oyster families differing in susceptibility to the Pacific oyster mortality syndrome were reared in hatchery and transplanted into a natural environment either before or during a disease outbreak. Using metabarcoding and shotgun metagenomics, we demonstrate that hemolymph can be considered as an ecological niche hosting bacterial, protist and viral communities, each of them shaped by different factors and distinct from the corresponding communities in the surrounding seawater. Overall, we found that hemolymph microbiota is more strongly shaped by the environment than by host genetic background. Co-occurrence network analyses suggest a disruption of the microbial network after transplantation into natural environment during both non-infectious and infectious periods. Whereas we could not identify a common microbial community signature for healthy animals, OsHV-1 μVar virus dominated the hemolymph virome during the disease outbreak, without significant modifications of other microbiota components. CONCLUSION Our study shows that oyster hemolymph is a complex ecosystem containing diverse bacteria, protists and viruses, whose composition and dynamics are primarily determined by the environment. However, all of these are also shaped by oyster genetic backgrounds, indicating they indeed interact with the oyster host and are therefore not only of transient character. Although it seems that the three microbiome components respond independently to environmental conditions, better characterization of hemolymph-associated viruses could change this picture.
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Affiliation(s)
- S Dupont
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Montpellier, Univ. Perpignan Via Domitia, 34095, Montpellier, France
| | - A Lokmer
- Coastal Ecology, Wadden Sea Station Sylt, Alfred Wegener Institute - Helmholtz Centre for Polar and Marine Research, List auf Sylt, Germany.,Current affiliation UMR 7206 Eco-anthropologie et Ethnologie, CNRS - MNHN Univ. Paris Diderot Sorbonne Paris Cité, Paris, France
| | - E Corre
- Sorbonne Université, CNRS, FR2424 ABiMS (Analysis and Bioanalysis for Marine Sciences), Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - J-C Auguet
- MARBEC, Université Montpellier, CNRS, IFREMER, IRD, CC093, place Eugène Bataillon, 34095, Montpellier, France
| | - B Petton
- Ifremer, LEMAR UMR 6539, 11 presqu'île du Vivier, 29840, Argenton-en-Landunvez, France
| | - E Toulza
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Montpellier, Univ. Perpignan Via Domitia, 34095, Montpellier, France
| | - C Montagnani
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Montpellier, Univ. Perpignan Via Domitia, 34095, Montpellier, France
| | - G Tanguy
- Sorbonne Université, CNRS, FR2424, Genomer, Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - D Pecqueur
- Observatoire Océanologique de Banyuls sur Mer, FR 3724, BioPIC, CNRS/SU, Avenue Pierre Fabre, 66650, Banyuls-sur-Mer, France
| | - C Salmeron
- Observatoire Océanologique de Banyuls sur Mer, FR 3724, BioPIC, CNRS/SU, Avenue Pierre Fabre, 66650, Banyuls-sur-Mer, France
| | - L Guillou
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - C Desnues
- Aix-Marseille Université, IRD 257, Assistance-Publique des Hôpitaux de Marseille, UMR Microbes, Evolution, Phylogeny and Infections (MEPHI), IHU Méditerranée Infection, 13005, Marseille, France.,Aix-Marseille Université, Université de Toulon, CNRS, IRD, Mediterranean Institute of Oceanography, UM 110, 13288, Marseille, France
| | - B La Scola
- Microbes, Evolution, Phylogeny and Infection (MEΦI), Aix-Marseille Université UM63, Institut de Recherche pour le Développement IRD 198, Assistance Publique - Hôpitaux de Marseille (AP-HM), Marseille, France.,Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, Marseille, France
| | - J Bou Khalil
- Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, Marseille, France
| | - J de Lorgeril
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Montpellier, Univ. Perpignan Via Domitia, 34095, Montpellier, France
| | - G Mitta
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Montpellier, Univ. Perpignan Via Domitia, 34095, Montpellier, France
| | - Y Gueguen
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Montpellier, Univ. Perpignan Via Domitia, 34095, Montpellier, France
| | - J-M Escoubas
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Montpellier, Univ. Perpignan Via Domitia, 34095, Montpellier, France.
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Lokmer A, Aflalo S, Amougou N, Lafosse S, Froment A, Tabe FE, Poyet M, Groussin M, Said-Mohamed R, Ségurel L. Response of the human gut and saliva microbiome to urbanization in Cameroon. Sci Rep 2020; 10:2856. [PMID: 32071424 PMCID: PMC7028744 DOI: 10.1038/s41598-020-59849-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 02/05/2020] [Indexed: 12/22/2022] Open
Abstract
Urban populations from highly industrialized countries are characterized by a lower gut bacterial diversity as well as by changes in composition compared to rural populations from less industrialized countries. To unveil the mechanisms and factors leading to this diversity loss, it is necessary to identify the factors associated with urbanization-induced shifts at a smaller geographical scale, especially in less industrialized countries. To do so, we investigated potential associations between a variety of dietary, medical, parasitological and socio-cultural factors and the gut and saliva microbiomes of 147 individuals from three populations along an urbanization gradient in Cameroon. We found that the presence of Entamoeba sp., a commensal gut protozoan, followed by stool consistency, were major determinants of the gut microbiome diversity and composition. Interestingly, urban individuals have retained most of their gut eukaryotic and bacterial diversity despite significant changes in diet compared to the rural areas, suggesting that the loss of bacterial microbiome diversity observed in industrialized areas is likely associated with medication. Finally, we observed a weak positive correlation between the gut and the saliva microbiome diversity and composition, even though the saliva microbiome is mainly shaped by habitat-related factors.
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Affiliation(s)
- Ana Lokmer
- UMR7206 Eco-anthropologie, CNRS - MNHN - Université de Paris, Paris, France.
| | - Sophie Aflalo
- UMR7206 Eco-anthropologie, CNRS - MNHN - Université de Paris, Paris, France
| | - Norbert Amougou
- UMR7206 Eco-anthropologie, CNRS - MNHN - Université de Paris, Paris, France
| | - Sophie Lafosse
- UMR7206 Eco-anthropologie, CNRS - MNHN - Université de Paris, Paris, France
| | - Alain Froment
- UMR7206 Eco-anthropologie, CNRS - MNHN - Université de Paris, Paris, France
| | - Francis Ekwin Tabe
- Faculté de Médecine et des Sciences Biomédicales - Université Yaoundé 1, Yaoundé, Cameroun
| | - Mathilde Poyet
- Department of Biological Engineering/Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA.,The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mathieu Groussin
- Department of Biological Engineering/Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA.,The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rihlat Said-Mohamed
- SAMRC/WITS Developmental Pathways for Health Research Unit, Department of Paediatrics, School of Clinical Medicine, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Laure Ségurel
- UMR7206 Eco-anthropologie, CNRS - MNHN - Université de Paris, Paris, France.
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7
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Lokmer A, Cian A, Froment A, Gantois N, Viscogliosi E, Chabé M, Ségurel L. Use of shotgun metagenomics for the identification of protozoa in the gut microbiota of healthy individuals from worldwide populations with various industrialization levels. PLoS One 2019; 14:e0211139. [PMID: 30726303 PMCID: PMC6364966 DOI: 10.1371/journal.pone.0211139] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 01/08/2019] [Indexed: 11/19/2022] Open
Abstract
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 Entamoeba. 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 metagenomics 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 Enteromonas) 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.
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Affiliation(s)
- Ana Lokmer
- UMR7206 Eco-anthropologie et Ethnobiologie, CNRS—MNHN—Univ Paris Diderot—Sorbonne Paris Cité, Paris, France
| | - Amandine Cian
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 –UMR 8204 –CIIL–Centre d’Infection et d’Immunité de Lille, Lille, France
| | - Alain Froment
- UMR7206 Eco-anthropologie et Ethnobiologie, CNRS—MNHN—Univ Paris Diderot—Sorbonne Paris Cité, Paris, France
| | - Nausicaa Gantois
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 –UMR 8204 –CIIL–Centre d’Infection et d’Immunité de Lille, Lille, France
| | - Eric Viscogliosi
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 –UMR 8204 –CIIL–Centre d’Infection et d’Immunité de Lille, Lille, France
| | - Magali Chabé
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 –UMR 8204 –CIIL–Centre d’Infection et d’Immunité de Lille, Lille, France
| | - Laure Ségurel
- UMR7206 Eco-anthropologie et Ethnobiologie, CNRS—MNHN—Univ Paris Diderot—Sorbonne Paris Cité, Paris, France
- * E-mail:
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8
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Feis ME, John U, Lokmer A, Luttikhuizen PC, Wegner KM. Dual transcriptomics reveals co-evolutionary mechanisms of intestinal parasite infections in blue mussels Mytilus edulis. Mol Ecol 2018; 27:1505-1519. [DOI: 10.1111/mec.14541] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 01/30/2018] [Accepted: 02/06/2018] [Indexed: 01/07/2023]
Affiliation(s)
- Marieke E. Feis
- Department Coastal Ecology; Wadden Sea Station Sylt; Alfred Wegener Institute; Helmholtz Centre for Polar and Marine Research; List/Sylt Germany
| | - Uwe John
- Department Ecological Chemistry; Alfred Wegener Institute; Helmholtz Centre for Polar and Marine Research; Bremerhaven Germany
- Helmholtz Institute for Functional Marine Biodiversity (HIFMB); Oldenburg Germany
| | - Ana Lokmer
- Department Coastal Ecology; Wadden Sea Station Sylt; Alfred Wegener Institute; Helmholtz Centre for Polar and Marine Research; List/Sylt Germany
| | - Pieternella C. Luttikhuizen
- NIOZ Royal Netherlands Institute for Sea Research; Department of Coastal Systems, and Utrecht University; Den Burg The Netherlands
| | - K. Mathias Wegner
- Department Coastal Ecology; Wadden Sea Station Sylt; Alfred Wegener Institute; Helmholtz Centre for Polar and Marine Research; List/Sylt Germany
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9
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Chabé M, Lokmer A, Ségurel L. Gut Protozoa: Friends or Foes of the Human Gut Microbiota? Trends Parasitol 2017; 33:925-934. [PMID: 28870496 DOI: 10.1016/j.pt.2017.08.005] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 07/17/2017] [Accepted: 08/11/2017] [Indexed: 12/18/2022]
Abstract
The importance of the gut microbiota for human health has sparked a strong interest in the study of the factors that shape its composition and diversity. Despite the growing evidence suggesting that helminths and protozoa significantly interact with gut bacteria, gut microbiome studies remain mostly focused on prokaryotes and on populations living in industrialized countries that typically have a low parasite burden. We argue that protozoa, like helminths, represent an important factor to take into account when studying the gut microbiome, and that their presence - especially considering their long coevolutionary history with humans - may be beneficial. From this perspective, we examine the relationship between the protozoa and their hosts, as well as their relevance for public health.
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Affiliation(s)
- Magali Chabé
- University of Lille, CNRS, Inserm, CHU de Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Centre d'Infection et d'Immunité de Lille, Lille, France
| | - Ana Lokmer
- UMR 7206 Eco-anthropologie et ethnobiologie, CNRS - MNHN - Paris Diderot University - Sorbonne Paris Cité, Paris, France
| | - Laure Ségurel
- UMR 7206 Eco-anthropologie et ethnobiologie, CNRS - MNHN - Paris Diderot University - Sorbonne Paris Cité, Paris, France.
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10
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Lokmer A, Goedknegt MA, Thieltges DW, Fiorentino D, Kuenzel S, Baines JF, Wegner KM. Spatial and Temporal Dynamics of Pacific Oyster Hemolymph Microbiota across Multiple Scales. Front Microbiol 2016; 7:1367. [PMID: 27630625 PMCID: PMC5006416 DOI: 10.3389/fmicb.2016.01367] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 08/18/2016] [Indexed: 01/09/2023] Open
Abstract
Unveiling the factors and processes that shape the dynamics of host associated microbial communities (microbiota) under natural conditions is an important part of understanding and predicting an organism's response to a changing environment. The microbiota is shaped by host (i.e., genetic) factors as well as by the biotic and abiotic environment. Studying natural variation of microbial community composition in multiple host genetic backgrounds across spatial as well as temporal scales represents a means to untangle this complex interplay. Here, we combined a spatially-stratified with a longitudinal sampling scheme within differentiated host genetic backgrounds by reciprocally transplanting Pacific oysters between two sites in the Wadden Sea (Sylt and Texel). To further differentiate contingent site from host genetic effects, we repeatedly sampled the same individuals over a summer season to examine structure, diversity and dynamics of individual hemolymph microbiota following experimental removal of resident microbiota by antibiotic treatment. While a large proportion of microbiome variation could be attributed to immediate environmental conditions, we observed persistent effects of antibiotic treatment and translocation suggesting that hemolymph microbial community dynamics is subject to within-microbiome interactions and host population specific factors. In addition, the analysis of spatial variation revealed that the within-site microenvironmental heterogeneity resulted in high small-scale variability, as opposed to large-scale (between-site) stability. Similarly, considerable within-individual temporal variability was in contrast with the overall temporal stability at the site level. Overall, our longitudinal, spatially-stratified sampling design revealed that variation in hemolymph microbiota is strongly influenced by site and immediate environmental conditions, whereas internal microbiome dynamics and oyster-related factors add to their long-term stability. The combination of small and large scale resolution of spatial and temporal observations therefore represents a crucial but underused tool to study host-associated microbiome dynamics.
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Affiliation(s)
- Ana Lokmer
- Coastal Ecology, Wadden Sea Station Sylt, Alfred Wegener Institute - Helmholtz Centre for Polar and Marine Research List auf Sylt, Germany
| | - M Anouk Goedknegt
- Department of Coastal Systems, Royal Netherlands Institute for Sea Research, Utrecht University Texel, Netherlands
| | - David W Thieltges
- Department of Coastal Systems, Royal Netherlands Institute for Sea Research, Utrecht University Texel, Netherlands
| | - Dario Fiorentino
- Coastal Ecology, Wadden Sea Station Sylt, Alfred Wegener Institute - Helmholtz Centre for Polar and Marine Research List auf Sylt, Germany
| | - Sven Kuenzel
- Max Planck Institute for Evolutionary Biology Plön, Germany
| | - John F Baines
- Max Planck Institute for Evolutionary BiologyPlön, Germany; Institute for Experimental Medicine, Christian-Albrechts-Universität zu KielKiel, Germany
| | - K Mathias Wegner
- Coastal Ecology, Wadden Sea Station Sylt, Alfred Wegener Institute - Helmholtz Centre for Polar and Marine Research List auf Sylt, Germany
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11
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Shama LNS, Mark FC, Strobel A, Lokmer A, John U, Mathias Wegner K. Transgenerational effects persist down the maternal line in marine sticklebacks: gene expression matches physiology in a warming ocean. Evol Appl 2016; 9:1096-1111. [PMID: 27695518 PMCID: PMC5039323 DOI: 10.1111/eva.12370] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Accepted: 01/28/2016] [Indexed: 12/25/2022] Open
Abstract
Transgenerational effects can buffer populations against environmental change, yet little is known about underlying mechanisms, their persistence or the influence of environmental cue timing. We investigated mitochondrial respiratory capacity (MRC) and gene expression of marine sticklebacks that experienced acute or developmental acclimation to simulated ocean warming (21°C) across three generations. Previous work showed that acute acclimation of grandmothers to 21°C led to lower (optimized) offspring MRCs. Here, developmental acclimation of mothers to 21°C led to higher, but more efficient offspring MRCs. Offspring with a 21°C × 17°C grandmother-mother environment mismatch showed metabolic compensation: their MRCs were as low as offspring with a 17°C thermal history across generations. Transcriptional analyses showed primarily maternal but also grandmaternal environment effects: genes involved in metabolism and mitochondrial protein biosynthesis were differentially expressed when mothers developed at 21°C, whereas 21°C grandmothers influenced genes involved in hemostasis and apoptosis. Genes involved in mitochondrial respiration all showed higher expression when mothers developed at 21° and lower expression in the 21°C × 17°C group, matching the phenotypic pattern for MRCs. Our study links transcriptomics to physiology under climate change, and demonstrates that mechanisms underlying transgenerational effects persist across multiple generations with specific outcomes depending on acclimation type and environmental mismatch between generations.
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Affiliation(s)
- Lisa N S Shama
- Coastal Ecology Section Alfred-Wegener-Institut Helmholtz-Zentrum für Polar-und Meeresforschung Wadden Sea Station Sylt Germany
| | - Felix C Mark
- Integrative Ecophysiology Section Alfred-Wegener-Institut Helmholtz-Zentrum für Polar-und Meeresforschung Bremerhaven Germany
| | - Anneli Strobel
- Integrative Ecophysiology Section Alfred-Wegener-Institut Helmholtz-Zentrum für Polar-und Meeresforschung Bremerhaven Germany; Man Society Environment (MGU) Department of Environmental Sciences University of Basel Switzerland
| | - Ana Lokmer
- Coastal Ecology Section Alfred-Wegener-Institut Helmholtz-Zentrum für Polar-und Meeresforschung Wadden Sea Station Sylt Germany
| | - Uwe John
- Ecological Chemistry Section Alfred-Wegener-Institut Helmholtz-Zentrum für Polar-und Meeresforschung Bremerhaven Germany
| | - K Mathias Wegner
- Coastal Ecology Section Alfred-Wegener-Institut Helmholtz-Zentrum für Polar-und Meeresforschung Wadden Sea Station Sylt Germany
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12
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Lokmer A, Kuenzel S, Baines JF, Wegner KM. The role of tissue-specific microbiota in initial establishment success of Pacific oysters. Environ Microbiol 2016; 18:970-87. [DOI: 10.1111/1462-2920.13163] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 11/27/2015] [Indexed: 12/26/2022]
Affiliation(s)
- Ana Lokmer
- Helmholtz Centre for Polar and Marine Research; Alfred Wegener Institute; Coastal Ecology; Wadden Sea Station Sylt; List Sylt Germany
| | - Sven Kuenzel
- Max Planck Institute for Evolutionary Biology; August-Thienemann-Strasse 2 D-24306 Plön Germany
| | - John F. Baines
- Max Planck Institute for Evolutionary Biology; August-Thienemann-Strasse 2 D-24306 Plön Germany
- Institute for Experimental Medicine; Christian-Albrechts-University of Kiel; Arnold-Heller-Strasse 3 D-24105 Kiel Germany
| | - Karl Mathias Wegner
- Helmholtz Centre for Polar and Marine Research; Alfred Wegener Institute; Coastal Ecology; Wadden Sea Station Sylt; List Sylt Germany
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13
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Lokmer A, Mathias Wegner K. Hemolymph microbiome of Pacific oysters in response to temperature, temperature stress and infection. ISME J 2015; 9:670-82. [PMID: 25180968 PMCID: PMC4331581 DOI: 10.1038/ismej.2014.160] [Citation(s) in RCA: 185] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 05/13/2014] [Accepted: 07/19/2014] [Indexed: 12/24/2022]
Abstract
Microbiota provide their hosts with a range of beneficial services, including defense from external pathogens. However, host-associated microbial communities themselves can act as a source of opportunistic pathogens depending on the environment. Marine poikilotherms and their microbiota are strongly influenced by temperature, but experimental studies exploring how temperature affects the interactions between both parties are rare. To assess the effects of temperature, temperature stress and infection on diversity, composition and dynamics of the hemolymph microbiota of Pacific oysters (Crassostrea gigas), we conducted an experiment in a fully-crossed, three-factorial design, in which the temperature acclimated oysters (8 or 22 °C) were exposed to temperature stress and to experimental challenge with a virulent Vibrio sp. strain. We monitored oyster survival and repeatedly collected hemolymph of dead and alive animals to determine the microbiome composition by 16s rRNA gene amplicon pyrosequencing. We found that the microbial dynamics and composition of communities in healthy animals (including infection survivors) were significantly affected by temperature and temperature stress, but not by infection. The response was mediated by changes in the incidence and abundance of operational taxonomic units (OTUs) and accompanied by little change at higher taxonomic levels, indicating dynamic stability of the hemolymph microbiome. Dead and moribund oysters, on the contrary, displayed signs of community structure disruption, characterized by very low diversity and proliferation of few OTUs. We can therefore link short-term responses of host-associated microbial communities to abiotic and biotic factors and assess the potential feedback between microbiota dynamics and host survival during disease.
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Affiliation(s)
- Ana Lokmer
- Helmholtz Centre for Polar and Marine Research, Alfred Wegener Institute, Coastal Ecology, Wadden Sea Station Sylt, List, Sylt, Germany
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Evolutionary Ecology of Marine Fishes, Kiel, Germany
| | - Karl Mathias Wegner
- Helmholtz Centre for Polar and Marine Research, Alfred Wegener Institute, Coastal Ecology, Wadden Sea Station Sylt, List, Sylt, Germany
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