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Blasco G, Moreno-Navarrete JM, Rivero M, Pérez-Brocal V, Garre-Olmo J, Puig J, Daunis-I-Estadella P, Biarnés C, Gich J, Fernández-Aranda F, Alberich-Bayarri Á, Moya A, Pedraza S, Ricart W, López M, Portero-Otin M, Fernandez-Real JM. The Gut Metagenome Changes in Parallel to Waist Circumference, Brain Iron Deposition, and Cognitive Function. J Clin Endocrinol Metab 2017; 102:2962-2973. [PMID: 28591831 DOI: 10.1210/jc.2017-00133] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 05/30/2017] [Indexed: 02/07/2023]
Abstract
CONTEXT Microbiota perturbations seem to exert modulatory effects on emotional behavior, stress-, and pain-modulation systems in adult animals; however, limited information is available in humans. OBJECTIVE To study potential relationships among the gut metagenome, brain microstructure, and cognitive performance in middle-aged, apparently healthy, obese and nonobese subjects after weight changes. DESIGN This is a longitudinal study over a 2-year period. SETTING A tertiary public hospital. PATIENTS OR OTHER PARTICIPANTS Thirty-five (18 obese) apparently healthy subjects. INTERVENTION(S) Diet counseling was provided to all subjects. Obese subjects were followed every 6 months. MAIN OUTCOME MEASURE(S) Brain relaxometry (using magnetic resonance R2*), cognitive performance (by means of cognitive tests), and gut microbiome composition (shotgun). RESULTS R2* increased in both obese and nonobese subjects, independent of weight variations. Changes in waist circumference, but not in body mass index, were associated with brain iron deposition (R2*) in the striatum, amygdala, and hippocampus in parallel to visual-spatial constructional ability and circulating beta amyloid Aβ42 levels. These changes were linked to shifts in gut microbiome in which the relative abundance of bacteria belonging to Caldiserica and Thermodesulfobacteria phyla were reciprocally associated with raised R2* in different brain nuclei. Of note, the increase in bacteria belonging to Tenericutes phylum was parallel to decreased R2* gain in the striatum, serum Aβ42 levels, and spared visual-spatial constructional ability. Interestingly, metagenome functions associated with circulating and brain iron stores are involved in bacterial generation of siderophores. CONCLUSIONS Changes in the gut metagenome are associated longitudinally with cognitive function and brain iron deposition.
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Affiliation(s)
- Gerard Blasco
- Research Unit, Institute of Diagnostic Imaging (IDI), Parc Sanitari Pere Virgili, Barcelona 08023, Spain
- Medical Imaging, Girona Biomedical Research Institute (IDIBGI), Hospital Universitari Dr Josep Trueta, Girona 17007, Spain
| | - José Maria Moreno-Navarrete
- Department of Diabetes, Endocrinology and Nutrition (UDEN), Girona Biomedical Research Institute (IDIBGI), CIBER de la Fisiopatología de la Obesidad y la Nutrición (CIBERobn, CB06/03/0010), Instituto de Salud Carlos III (ISCIII), Girona 17007, Spain
- Department of Medicine, University of Girona, Girona 17007, Spain
| | - Mireia Rivero
- Neurology Department, Girona Biomedical Research Institute (IDIBGI), Hospital Universitari Dr Josep Trueta. Girona 17007, Spain
| | - Vicente Pérez-Brocal
- Genomics and Health Area of the Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO)-Salud Pública, Valencia 46020, Spain
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Valencia 46980, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid 28029, Spain
| | - Josep Garre-Olmo
- Research Group on Aging, Disability and Health, Girona Biomedical Research Institute (IDIBGI), Girona 17007, Spain
| | - Josep Puig
- Research Unit, Institute of Diagnostic Imaging (IDI), Parc Sanitari Pere Virgili, Barcelona 08023, Spain
- Medical Imaging, Girona Biomedical Research Institute (IDIBGI), Hospital Universitari Dr Josep Trueta, Girona 17007, Spain
| | - Pepus Daunis-I-Estadella
- Department of Computer Science, Applied Mathematics, and Statistics, University of Girona. Girona 17004, Spain
| | - Carles Biarnés
- Medical Imaging, Girona Biomedical Research Institute (IDIBGI), Hospital Universitari Dr Josep Trueta, Girona 17007, Spain
| | - Jordi Gich
- Department of Medicine, University of Girona, Girona 17007, Spain
| | - Fernando Fernández-Aranda
- Department of Psychiatry, University Hospital of Bellvitge, Bellvitge Biomedical ResearchInstitute (IDIBELL), CIBER Fisiopatología Obesidad y Nutrición (CIBERObn), Instituto Salud Carlos III, Barcelona 08908, Spain
| | - Ángel Alberich-Bayarri
- Biomedical Imaging Research Group (GIBI230), QUantitative Imaging Biomarkers In Medicine (QUIBIM SL), La Fe Polytechnics and University Hospital, La Fe Health ResearchInstitute, Valencia 46026, Spain
| | - Andrés Moya
- Genomics and Health Area of the Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO)-Salud Pública, Valencia 46020, Spain
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Valencia 46980, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid 28029, Spain
| | - Salvador Pedraza
- Medical Imaging, Girona Biomedical Research Institute (IDIBGI), Hospital Universitari Dr Josep Trueta, Girona 17007, Spain
| | - Wifredo Ricart
- Department of Diabetes, Endocrinology and Nutrition (UDEN), Girona Biomedical Research Institute (IDIBGI), CIBER de la Fisiopatología de la Obesidad y la Nutrición (CIBERobn, CB06/03/0010), Instituto de Salud Carlos III (ISCIII), Girona 17007, Spain
- Department of Medicine, University of Girona, Girona 17007, Spain
| | - Miguel López
- NeurObesity Group; Department of Physiology, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), University of Santiago de Compostela-Instituto de Investigación Sanitaria, Santiago de Compostela 15782, Spain
- CIBERObn, Santiago de Compostela 15706, Spain
| | - Manuel Portero-Otin
- Nutren Group, Department of Experimental Medicine, Lleida Biomedical Research Institute (IRBLleida) and Agroalimentary Science and Technology Park (PCiTAL)-University of Lleida, Lleida 25003, Spain
| | - José-Manuel Fernandez-Real
- Department of Diabetes, Endocrinology and Nutrition (UDEN), Girona Biomedical Research Institute (IDIBGI), CIBER de la Fisiopatología de la Obesidad y la Nutrición (CIBERobn, CB06/03/0010), Instituto de Salud Carlos III (ISCIII), Girona 17007, Spain
- Department of Medicine, University of Girona, Girona 17007, Spain
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Rojo D, Méndez-García C, Raczkowska BA, Bargiela R, Moya A, Ferrer M, Barbas C. Exploring the human microbiome from multiple perspectives: factors altering its composition and function. FEMS Microbiol Rev 2017; 41:453-478. [PMID: 28333226 PMCID: PMC5812509 DOI: 10.1093/femsre/fuw046] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 12/15/2016] [Indexed: 02/07/2023] Open
Abstract
Our microbiota presents peculiarities and characteristics that may be altered by multiple factors. The degree and consequences of these alterations depend on the nature, strength and duration of the perturbations as well as the structure and stability of each microbiota. The aim of this review is to sketch a very broad picture of the factors commonly influencing different body sites, and which have been associated with alterations in the human microbiota in terms of composition and function. To do so, first, a graphical representation of bacterial, fungal and archaeal genera reveals possible associations among genera affected by different factors. Then, the revision of sequence-based predictions provides associations with functions that become part of the active metabolism. Finally, examination of microbial metabolite contents and fluxes reveals whether metabolic alterations are a reflection of the differences observed at the level of population structure, and in the last step, link microorganisms to functions under perturbations that differ in nature and aetiology. The utilisation of complementary technologies and methods, with a special focus on metabolomics research, is thoroughly discussed to obtain a global picture of microbiota composition and microbiome function and to convey the urgent need for the standardisation of protocols.
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Affiliation(s)
- David Rojo
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, 28668 Madrid, Spain
| | | | - Beata Anna Raczkowska
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, 15-276 Bialystok, Poland
| | - Rafael Bargiela
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain
| | - Andrés Moya
- Foundation for the Promotion of Health and Biomedical Research in the Valencian Community Public Health (FISABIO), 46020 Valencia, Spain
- Network Research Center for Epidemiology and Public Health (CIBER-ESP), 28029 Madrid, Spain
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universidad de Valencia, Paterna, 46980 Valencia, Spain
- These authors contributed equally to this work
| | - Manuel Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain
- Corresponding author: Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain. Tel: (+34) 915854872; E-mail:
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, 28668 Madrid, Spain
- These authors contributed equally to this work
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Abstract
Our microbiome should be understood as one of the most complex components of the human body. The use of β-lactam antibiotics is one of the microbiome covariates that influence its composition. The extent to which our microbiota changes after an antibiotic intervention depends not only on the chemical nature of the antibiotic or cocktail of antibiotics used to treat specific infections, but also on the type of administration, duration and dose, as well as the level of resistance that each microbiota develops. We have begun to appreciate that not all bacteria within our microbiota are vulnerable or reactive to different antibiotic interventions, and that their influence on both microbial composition and metabolism may differ. Antibiotics are being used worldwide on a huge scale and the prescription of antibiotics is continuing to rise; however, their effects on our microbiota have been reported for only a limited number of them. This article presents a critical review of the antibiotics or antibiotic cocktails whose use in humans has been linked to changes in the composition of our microbial communities, with a particular focus on the gut, oral, respiratory, skin and vaginal microbiota, and on their molecular agents (genes, proteins and metabolites). We review the state of the art as of June 2016, and cover a total of circa 68 different antibiotics. The data herein are the first to compile information about the bacteria, fungi, archaea and viruses most influenced by the main antibiotic treatments prescribed nowadays.
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Affiliation(s)
- Manuel Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain.
| | | | - David Rojo
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Madrid, Spain
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Madrid, Spain
| | - Andrés Moya
- Foundation for the Promotion of Health and Biomedical Research in the Valencian Community Public Health (FISABIO), Valencia, Spain; Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain; Instituto Cavanilles de Biodiversidad y Biología Evolutiva (Universidad de Valencia), Valencia, Spain.
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Garcia-Nuñez M, Marti S, Puig C, Perez-Brocal V, Millares L, Santos S, Ardanuy C, Moya A, Liñares J, Monsó E. Bronchial microbiome, PA biofilm-forming capacity and exacerbation in severe COPD patients colonized by P. aeruginosa. Future Microbiol 2017; 12:379-392. [PMID: 28339291 DOI: 10.2217/fmb-2016-0127] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
AIM The bronchial microbiome of severe chronic obstructive pulmonary disease patients colonized by Pseudomonas aeruginosa was analyzed using 16S rRNA gene sequencing to identify differences related to biofilm-forming capacity. PATIENTS & METHODS Patient sputum samples from 21 patients were studied. RESULTS Statistically significant differences related to biofilm-forming capacity were only found for genera with relative abundances <1%, and Fusobacterium was over-represented when biofilm-forming capacity was high. Genera with relative abundances >50% which increased from baseline were observed in 10/14 exacerbations, but corresponded to Pseudomonas only in three episodes, while other pathogenic genera were identified in seven. CONCLUSION The bronchial microbiome shows differences according with P. aeruginosa biofilm-forming capacity. Pathogenic microorganisms other than P. aeruginosa cause a significant part of the exacerbations in colonized chronic obstructive pulmonary disease patients.
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Affiliation(s)
- Marian Garcia-Nuñez
- CIBER de Enfermedades Respiratorias (CIBERes), Instituto de Salud Carlos III, Madrid, Spain E-28029
- Department of Respiratory Medicine, Parc Taulí Hospital Universitari. Institut d'Investigació i Innovació Parc Taulí I3PT, Sabadell, Spain E-08208
- Fundació Institut d'Investigació Germans Trias i Pujol, Badalona, Spain E-08916
- Universitat Autonoma de Barcelona, Esfera UAB, Barcelona, Spain E-08193
| | - Sara Marti
- CIBER de Enfermedades Respiratorias (CIBERes), Instituto de Salud Carlos III, Madrid, Spain E-28029
- Microbiology Department, Hospital Universitari Bellvitge, Universitat de Barcelona-IDIBELL, Barcelona, Spain E-08908
| | - Carmen Puig
- CIBER de Enfermedades Respiratorias (CIBERes), Instituto de Salud Carlos III, Madrid, Spain E-28029
- Microbiology Department, Hospital Universitari Bellvitge, Universitat de Barcelona-IDIBELL, Barcelona, Spain E-08908
| | - Vicente Perez-Brocal
- Genomics & Health Area, Centro Superior de Investigación en Salud Pública - Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (CSISP-FISABIO), Valencia, Spain E-46020
- Department of Genetics, Institut Cavanilles de Biodiversitat i Biologia Evolutiva, (ICBiBE) Universitat de València, València, Spain E-46020
- CIBER Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain E-28029
| | - Laura Millares
- CIBER de Enfermedades Respiratorias (CIBERes), Instituto de Salud Carlos III, Madrid, Spain E-28029
- Department of Respiratory Medicine, Parc Taulí Hospital Universitari. Institut d'Investigació i Innovació Parc Taulí I3PT, Sabadell, Spain E-08208
- Fundació Institut d'Investigació Germans Trias i Pujol, Badalona, Spain E-08916
- Universitat Autonoma de Barcelona, Esfera UAB, Barcelona, Spain E-08193
| | - Salud Santos
- CIBER de Enfermedades Respiratorias (CIBERes), Instituto de Salud Carlos III, Madrid, Spain E-28029
- Department of Pulmonary Medicine, Hospital Universitari de Bellvitge, Institut d'Investigacions Biomèdiques de Bellvitge (IDIBELL), Universitat de Barcelona, Barcelona, Spain E-08908
| | - Carmen Ardanuy
- CIBER de Enfermedades Respiratorias (CIBERes), Instituto de Salud Carlos III, Madrid, Spain E-28029
- Microbiology Department, Hospital Universitari Bellvitge, Universitat de Barcelona-IDIBELL, Barcelona, Spain E-08908
| | - Andres Moya
- Genomics & Health Area, Centro Superior de Investigación en Salud Pública - Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (CSISP-FISABIO), Valencia, Spain E-46020
- Department of Genetics, Institut Cavanilles de Biodiversitat i Biologia Evolutiva, (ICBiBE) Universitat de València, València, Spain E-46020
- CIBER Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain E-28029
| | - Josefina Liñares
- CIBER de Enfermedades Respiratorias (CIBERes), Instituto de Salud Carlos III, Madrid, Spain E-28029
- Microbiology Department, Hospital Universitari Bellvitge, Universitat de Barcelona-IDIBELL, Barcelona, Spain E-08908
| | - Eduard Monsó
- CIBER de Enfermedades Respiratorias (CIBERes), Instituto de Salud Carlos III, Madrid, Spain E-28029
- Department of Respiratory Medicine, Parc Taulí Hospital Universitari. Institut d'Investigació i Innovació Parc Taulí I3PT, Sabadell, Spain E-08208
- Fundació Institut d'Investigació Germans Trias i Pujol, Badalona, Spain E-08916
- Universitat Autonoma de Barcelona, Esfera UAB, Barcelona, Spain E-08193
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Martí JM, Martínez-Martínez D, Rubio T, Gracia C, Peña M, Latorre A, Moya A, P. Garay C. Health and Disease Imprinted in the Time Variability of the Human Microbiome. mSystems 2017; 2:mSystems00144-16. [PMID: 28345059 PMCID: PMC5361781 DOI: 10.1128/msystems.00144-16] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [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: 09/26/2016] [Accepted: 02/16/2017] [Indexed: 02/07/2023] Open
Abstract
The animal microbiota (including the human microbiota) plays an important role in keeping the physiological status of the host healthy. Research seeks greater insight into whether changes in the composition and function of the microbiota are associated with disease. We analyzed published 16S rRNA and shotgun metagenomic sequencing (SMS) data pertaining to the gut microbiotas of 99 subjects monitored over time. Temporal fluctuations in the microbial composition revealed significant differences due to factors such as dietary changes, antibiotic intake, age, and disease. This article shows that a fluctuation scaling law can describe the temporal changes in the gut microbiota. This law estimates the temporal variability of the microbial population and quantitatively characterizes the path toward disease via a noise-induced phase transition. Estimation of the systemic parameters may be of clinical utility in follow-up studies and have more general applications in fields where it is important to know whether a given community is stable or not. IMPORTANCE The human microbiota correlates closely with the health status of its host. This article analyzes the microbial composition of several subjects under different conditions over time spans that ranged from days to months. Using the Langevin equation as the basis of our mathematical framework to evaluate microbial temporal stability, we proved that stable microbiotas can be distinguished from unstable microbiotas. This initial step will help us to determine how temporal microbiota stability is related to a subject's health status and to develop a more comprehensive framework that will provide greater insight into this complex system.
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Affiliation(s)
- Jose Manuel Martí
- Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
- Instituto de Física Corpuscular (IFIC), Valencia, Spain
| | - Daniel Martínez-Martínez
- Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
- Instituto de Física Corpuscular (IFIC), Valencia, Spain
- Cavanilles Institute of Biodiversity and Evolutionary Biology, Valencia, Spain
| | - Teresa Rubio
- Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
| | - César Gracia
- Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
- Instituto de Física Corpuscular (IFIC), Valencia, Spain
| | - Manuel Peña
- Instituto de Física Corpuscular (IFIC), Valencia, Spain
| | - Amparo Latorre
- Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
- FISABIO, Valencia, Spain
- Cavanilles Institute of Biodiversity and Evolutionary Biology, Valencia, Spain
- CIBER en Epidemiología y Salud Pública (CIBEResp), Madrid, Spain
| | - Andrés Moya
- Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
- FISABIO, Valencia, Spain
- Cavanilles Institute of Biodiversity and Evolutionary Biology, Valencia, Spain
- CIBER en Epidemiología y Salud Pública (CIBEResp), Madrid, Spain
| | - Carlos P. Garay
- Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
- Instituto de Física Corpuscular (IFIC), Valencia, Spain
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Serrano-Villar S, Vásquez-Domínguez E, Pérez-Molina JA, Sainz T, de Benito A, Latorre A, Moya A, Gosalbes MJ, Moreno S. HIV, HPV, and microbiota: partners in crime? AIDS 2017; 31:591-594. [PMID: 27922858 DOI: 10.1097/qad.0000000000001352] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Altered interplay between gut mucosa and dysbiotic bacteria during HIV infection seems to fuel chronic immune dysfunction and might explain the excess rates of human papillomavirus (HPV)-associated anal cancer in HIV-infected individuals. Here, we show in HIV-infected MSM undergoing screening for HPV-related cancer that specific fecal and mucosal bacteria are able to predict the existence of precancerous anal lesions. If confirmed, these bacterial biomarkers could be exploited either as diagnostic tools or therapeutic targets.
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Affiliation(s)
- Sergio Serrano-Villar
- aDepartment of Infectious Diseases, Hospital Universitario Ramón y Cajal, Facultad de Medicina, Universidad de Alcalá (IRYCIS), Madrid bUnidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública) y el Instituto Cavanilles de Biodiversidad y Biología Evolutiva (Universidad de Valencia), Valencia cDepartment of Pediatric Infectious Diseases, Hospital Universitario La Paz (IdiPAZ) dDepartment of Pathology, Hospital Universitario Ramón y Cajal eCIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain. *Santiago Moreno and María José Gosalbes contributed equally to this study
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Falgueras-Cano J, Carretero-Díaz JM, Moya A. Weighted fitness theory: an approach to symbiotic communities. Environ Microbiol Rep 2017; 9:44-46. [PMID: 28019707 DOI: 10.1111/1758-2229.12515] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 12/13/2016] [Indexed: 02/05/2023]
Affiliation(s)
- Javier Falgueras-Cano
- Laboratorio de Evolución Humana, Departamento de Historia, Geografía y Comunicación, Universidad de Burgos, Burgos, Spain
| | - José Miguel Carretero-Díaz
- Laboratorio de Evolución Humana, Departamento de Historia, Geografía y Comunicación, Universidad de Burgos, Burgos, Spain
- Centro Mixto UCM-ISCIII de Evolución y Comportamiento Humanos, Madrid, Spain
| | - Andrés Moya
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, València, Spain
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO), València, Spain
- CIBER en Epidemiología y Salud Pública (CIBEResp), Madrid, Spain
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Millares L, Bermudo G, Pérez-Brocal V, Domingo C, Garcia-Nuñez M, Pomares X, Moya A, Monsó E. The respiratory microbiome in bronchial mucosa and secretions from severe IgE-mediated asthma patients. BMC Microbiol 2017; 17:20. [PMID: 28103814 PMCID: PMC5248442 DOI: 10.1186/s12866-017-0933-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 01/13/2017] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The bronchial microbiome in chronic lung diseases presents an abnormal pattern, but its microbial composition and regional differences in severe asthma have not been sufficiently addressed. The aim of the study was to describe the bacterial community in bronchial mucosa and secretions of patients with severe chronic asthma chronically treated with corticosteroids in addition to usual care according to Global Initiative for Asthma. Bacterial community composition was obtained by 16S rRNA gene amplification and sequencing, and functional capabilities through PICRUSt. RESULTS Thirteen patients with severe asthma were included and provided 11 bronchial biopsies (BB) and 12 bronchial aspirates (BA) suitable for sequence analyses. Bacteroidetes, Firmicutes, Proteobacteria and Actinobacteria showed relative abundances (RAs) over 5% in BB, a cutoff that was reached by Streptococcus and Prevotella at genus level. Legionella genus attained a median RA of 2.7 (interquartile range 1.1-4.7) in BB samples. In BA a higher RA of Fusobacteria was found, when compared with BB [8.7 (5.9-11.4) vs 4.2 (0.8-7.5), p = 0.037], while the RA of Proteobacteria was lower in BA [4.3 (3.7-6.5) vs 17.1 (11.2-33.4), p = 0.005]. RA of the Legionella genus was also significantly lower in BA [0.004 (0.001-0.02) vs. 2.7 (1.1-4.7), p = 0.005]. Beta-diversity analysis confirmed the differences between the microbial communities in BA and BB (R2 = 0.20, p = 0.001, Adonis test), and functional analysis revealed also statistically significant differences between both types of sample on Metabolism, Cellular processes, Human diseases, Organismal systems and Genetic information processing pathways. CONCLUSIONS The microbiota in the bronchial mucosa of severe asthma has a specific pattern that is not accurately represented in bronchial secretions, which must be considered a different niche of bacteria growth.
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Affiliation(s)
- Laura Millares
- Fundació Parc Taulí, Parc Taulí 1, Edificio Santa Fe, planta baja, 08208, Sabadell, Barcelona, Spain.
- CIBER de Enfermedades Respiratorias, CIBERES, Madrid, Spain.
- Universitat Autònoma de Barcelona, Esfera UAB, Barcelona, Spain.
- Fundació Insitut d'Investigació Germans Trias i Pujol, Badalona, Spain.
| | - Guadalupe Bermudo
- Department of Respiratory Medicine, Hospital Universitari Parc Taulí, Sabadell, Spain
| | - Vicente Pérez-Brocal
- Genomics and Health Area, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Public Health), Valencia, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Evolutionary Genetics Unit, Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE), Universitat de València, Valencia, Spain
| | - Christian Domingo
- Department of Respiratory Medicine, Hospital Universitari Parc Taulí, Sabadell, Spain
- Department of Medicine, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Marian Garcia-Nuñez
- Fundació Parc Taulí, Parc Taulí 1, Edificio Santa Fe, planta baja, 08208, Sabadell, Barcelona, Spain
- CIBER de Enfermedades Respiratorias, CIBERES, Madrid, Spain
- Universitat Autònoma de Barcelona, Esfera UAB, Barcelona, Spain
- Fundació Insitut d'Investigació Germans Trias i Pujol, Badalona, Spain
| | - Xavier Pomares
- Department of Respiratory Medicine, Hospital Universitari Parc Taulí, Sabadell, Spain
| | - Andrés Moya
- Genomics and Health Area, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Public Health), Valencia, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Evolutionary Genetics Unit, Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE), Universitat de València, Valencia, Spain
| | - Eduard Monsó
- CIBER de Enfermedades Respiratorias, CIBERES, Madrid, Spain
- Universitat Autònoma de Barcelona, Esfera UAB, Barcelona, Spain
- Department of Medicine, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
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59
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Villar-García J, Güerri-Fernández R, Moya A, González A, Hernández JJ, Lerma E, Guelar A, Sorli L, Horcajada JP, Artacho A, D´Auria G, Knobel H. Impact of probiotic Saccharomyces boulardii on the gut microbiome composition in HIV-treated patients: A double-blind, randomised, placebo-controlled trial. PLoS One 2017; 12:e0173802. [PMID: 28388647 PMCID: PMC5384743 DOI: 10.1371/journal.pone.0173802] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [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: 11/09/2016] [Accepted: 02/22/2017] [Indexed: 02/07/2023] Open
Abstract
Dysbalance in gut microbiota has been linked to increased microbial translocation, leading to chronic inflammation in HIV-patients, even under effective HAART. Moreover, microbial translocation is associated with insufficient reconstitution of CD4+T cells, and contributes to the pathogenesis of immunologic non-response. In a double-blind, randomised, placebo-controlled trial, we recently showed that, compared to placebo, 12 weeks treatment with probiotic Saccharomyces boulardii significantly reduced plasma levels of bacterial translocation (Lipopolysaccharide-binding protein or LBP) and systemic inflammation (IL-6) in 44 HIV virologically suppressed patients, half of whom (n = 22) had immunologic non-response to antiretroviral therapy (<270 CD4+Tcells/μL despite long-term suppressed viral load). The aim of the present study was to investigate if this beneficial effect of the probiotic Saccharomyces boulardii is due to modified gut microbiome composition, with a decrease of some species associated with higher systemic levels of microbial translocation and inflammation. In this study, we used 16S rDNA gene amplification and parallel sequencing to analyze the probiotic impact on the composition of the gut microbiome (faecal samples) in these 44 patients randomized to receive oral supplementation with probiotic or placebo for 12 weeks. Compared to the placebo group, in individuals treated with probiotic we observed lower concentrations of some gut species, such as those of the Clostridiaceae family, which were correlated with systemic levels of bacterial translocation and inflammation markers. In a sub-study of these patients, we observed significantly higher parameters of microbial translocation (LBP, soluble CD14) and systemic inflammation in immunologic non-responders than in immunologic responders, which was correlated with a relative abundance of specific gut bacterial groups (Lachnospiraceae genus and Proteobacteria). Thus, in this work, we propose a new therapeutic strategy using the probiotic yeast S. boulardii to modify gut microbiome composition. Identifying pro-inflammatory species in the gut microbiome could also be a useful new marker of poor immune response and a new therapeutic target.
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Affiliation(s)
- Judit Villar-García
- Department of Infectious Diseases, Hospital del Mar, Barcelona, Spain
- IMIM (Hospital del Mar Medical Research Institute, Institut Hospital del Mar d'Investigacions Mediques), Barcelona, Spain
- Department of Medicine, Universitat Autònoma de Barcelona, Spain
- * E-mail:
| | - Robert Güerri-Fernández
- Department of Infectious Diseases, Hospital del Mar, Barcelona, Spain
- IMIM (Hospital del Mar Medical Research Institute, Institut Hospital del Mar d'Investigacions Mediques), Barcelona, Spain
- Department of Medicine, Universitat Autònoma de Barcelona, Spain
| | - Andrés Moya
- Joint Unit of Research in Genomics and Health, Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO) and Cavanilles Institute of Biodiversity and Evolutionary Biology (Universitat de València), València, Spain
- CIBER en Epidemiología y Salud Pública, Madrid, Spain
| | - Alicia González
- Department of Infectious Diseases, Hospital del Mar, Barcelona, Spain
- IMIM (Hospital del Mar Medical Research Institute, Institut Hospital del Mar d'Investigacions Mediques), Barcelona, Spain
| | | | - Elisabet Lerma
- Department of Infectious Diseases, Hospital del Mar, Barcelona, Spain
- IMIM (Hospital del Mar Medical Research Institute, Institut Hospital del Mar d'Investigacions Mediques), Barcelona, Spain
| | - Ana Guelar
- Department of Infectious Diseases, Hospital del Mar, Barcelona, Spain
- IMIM (Hospital del Mar Medical Research Institute, Institut Hospital del Mar d'Investigacions Mediques), Barcelona, Spain
| | - Luisa Sorli
- Department of Infectious Diseases, Hospital del Mar, Barcelona, Spain
- IMIM (Hospital del Mar Medical Research Institute, Institut Hospital del Mar d'Investigacions Mediques), Barcelona, Spain
| | - Juan P. Horcajada
- Department of Infectious Diseases, Hospital del Mar, Barcelona, Spain
- IMIM (Hospital del Mar Medical Research Institute, Institut Hospital del Mar d'Investigacions Mediques), Barcelona, Spain
- Department of Medicine, Universitat Autònoma de Barcelona, Spain
| | - Alejandro Artacho
- Joint Unit of Research in Genomics and Health, Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO) and Cavanilles Institute of Biodiversity and Evolutionary Biology (Universitat de València), València, Spain
| | - Giuseppe D´Auria
- Joint Unit of Research in Genomics and Health, Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO) and Cavanilles Institute of Biodiversity and Evolutionary Biology (Universitat de València), València, Spain
- CIBER en Epidemiología y Salud Pública, Madrid, Spain
| | - Hernando Knobel
- Department of Infectious Diseases, Hospital del Mar, Barcelona, Spain
- IMIM (Hospital del Mar Medical Research Institute, Institut Hospital del Mar d'Investigacions Mediques), Barcelona, Spain
- Department of Medicine, Universitat Autònoma de Barcelona, Spain
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60
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Gutiérrez-Preciado A, Vargas-Chávez C, Reyes-Prieto M, Ordoñez OF, Santos-García D, Rosas-Pérez T, Valdivia-Anistro J, Rebollar EA, Saralegui A, Moya A, Merino E, Farías ME, Latorre A, Souza V. The genomic sequence of Exiguobacterium chiriqhucha str. N139 reveals a species that thrives in cold waters and extreme environmental conditions. PeerJ 2017; 5:e3162. [PMID: 28439458 PMCID: PMC5399880 DOI: 10.7717/peerj.3162] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [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: 10/06/2016] [Accepted: 03/08/2017] [Indexed: 02/05/2023] Open
Abstract
We report the genome sequence of Exiguobacterium chiriqhucha str. N139, isolated from a high-altitude Andean lake. Comparative genomic analyses of the Exiguobacterium genomes available suggest that our strain belongs to the same species as the previously reported E. pavilionensis str. RW-2 and Exiguobacterium str. GIC 31. We describe this species and propose the chiriqhucha name to group them. 'Chiri qhucha' in Quechua means 'cold lake', which is a common origin of these three cosmopolitan Exiguobacteria. The 2,952,588-bp E. chiriqhucha str. N139 genome contains one chromosome and three megaplasmids. The genome analysis of the Andean strain suggests the presence of enzymes that confer E. chiriqhucha str. N139 the ability to grow under multiple environmental extreme conditions, including high concentrations of different metals, high ultraviolet B radiation, scavenging for phosphorous and coping with high salinity. Moreover, the regulation of its tryptophan biosynthesis suggests that novel pathways remain to be discovered, and that these pathways might be fundamental in the amino acid metabolism of the microbial community from Laguna Negra, Argentina.
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Affiliation(s)
- Ana Gutiérrez-Preciado
- Unidad de Genética Evolutiva, Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universidad de Valencia, Calle Catedrático José Beltrán Martínez, Paterna, Valencia, Spain
- Current affiliation: Ecologie Systématique Evolution, CNRS, AgroParisTech, Université Paris Sud (Paris XI), Orsay, France
| | - Carlos Vargas-Chávez
- Unidad de Genética Evolutiva, Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universidad de Valencia, Calle Catedrático José Beltrán Martínez, Paterna, Valencia, Spain
| | - Mariana Reyes-Prieto
- Unidad de Genética Evolutiva, Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universidad de Valencia, Calle Catedrático José Beltrán Martínez, Paterna, Valencia, Spain
| | - Omar F. Ordoñez
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas, Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Belgrano y Pasaje Caseros, San Miguel de Tucumán, Argentina
| | - Diego Santos-García
- Unidad de Genética Evolutiva, Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universidad de Valencia, Calle Catedrático José Beltrán Martínez, Paterna, Valencia, Spain
- Current affiliation: Department of Entomology, Hebrew University of Jerusalem, Rehovot, Israel
| | - Tania Rosas-Pérez
- Unidad de Genética Evolutiva, Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universidad de Valencia, Calle Catedrático José Beltrán Martínez, Paterna, Valencia, Spain
| | - Jorge Valdivia-Anistro
- Carrera de Biología, Faculta de Estudios Superiores Zaragoza, UNAM, Mexico City, Mexico
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México coyoacan, Mexico City, México
| | - Eria A. Rebollar
- Department of Biology, James Madison University, Harrisonburg, VI, United States of America
| | - Andrés Saralegui
- Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Andrés Moya
- Unidad de Genética Evolutiva, Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universidad de Valencia, Calle Catedrático José Beltrán Martínez, Paterna, Valencia, Spain
| | - Enrique Merino
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - María Eugenia Farías
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas, Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Belgrano y Pasaje Caseros, San Miguel de Tucumán, Argentina
| | - Amparo Latorre
- Unidad de Genética Evolutiva, Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universidad de Valencia, Calle Catedrático José Beltrán Martínez, Paterna, Valencia, Spain
| | - Valeria Souza
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México coyoacan, Mexico City, México
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61
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López-Labrador FX, Natividad-Sancho A, Pisareva M, Komissarov A, Salvatierra K, Fadeev A, Moya A, Grudinin M, Díez-Domingo J, Afanasieva O, Konovalova N, Sominina A, Puig-Barberà J. Genetic characterization of influenza viruses from influenza-related hospital admissions in the St. Petersburg and Valencia sites of the Global Influenza Hospital Surveillance Network during the 2013/14 influenza season. J Clin Virol 2016; 84:32-38. [PMID: 27690141 DOI: 10.1016/j.jcv.2016.09.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 09/06/2016] [Accepted: 09/19/2016] [Indexed: 02/07/2023]
Abstract
BACKGROUND Continuous surveillance for genetic changes in circulating influenza viruses is needed to guide influenza prevention and control. OBJECTIVES To compare intra-seasonal influenza genetic diversity of hemagglutinin in influenza A strains isolated from influenza hospital admissions collected at two distinct sites during the same season. STUDY DESIGN Comparative phylogenetic analysis of full-length hemagglutinin genes from 77 isolated influenza A viruses from the St. Petersburg, Russian Federation and Valencia, Spain sites of the Global Influenza Hospital Surveillance Network (GIHSN) during the 2013/14 season. RESULTS We found significant variability in A(H3N2) and A(H1N1)pdm09 viruses between the two sites, with nucleotide variation at antigenic positions much lower for A(H1N1)pdm09 than for A(H3N2) viruses. For A(H1N1)pdm09, antigenic sites differed by three to four amino acids from the vaccine strain, two of them common to all tested isolates. For A(H3N2) viruses, antigenic sites differed by six to nine amino acids from the vaccine strain, four of them common to all tested isolates. A fifth amino acid substitution in the antigenic sites of A(H3N2) defined a new clade, 3C.2. For both influenza A subtypes, pairwise amino acid distances between circulating viruses and vaccine strains were significantly higher at antigenic than at non-antigenic sites. Whereas A(H1N1)pdm09 viruses clustered with clade 6B and 94% of A(H3N2) with clade 3C.3, at both study sites A(H3N2) clade 3C.2 viruses emerged towards the end of the season, showing greater pairwise amino acid distances from the vaccine strain compared to the predominant clade 3C.3. CONCLUSIONS Influenza A antigenic variants differed between St. Petersburg and Valencia, and A(H3N2) clade 3C.2 viruses were characterized by more amino acid differences from the vaccine strain, especially at the antigenic sites.
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MESH Headings
- Adolescent
- Adult
- Aged
- Aged, 80 and over
- Child
- Child, Preschool
- Epidemiological Monitoring
- Female
- Genetic Variation
- Genome, Viral
- Global Health
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Humans
- Infant
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/isolation & purification
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/isolation & purification
- Influenza, Human/epidemiology
- Influenza, Human/virology
- Male
- Middle Aged
- Phylogeny
- RNA, Viral/genetics
- Russia/epidemiology
- Seasons
- Sequence Analysis, DNA
- Spain/epidemiology
- Young Adult
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Affiliation(s)
- F Xavier López-Labrador
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Avda. de Catalunya, 21, 46020 Valencia, Spain; Joint Units of Infection and of Genomics and Health, FISABIO/Cavanilles Institute for Biodiversity and Evolutionary Biology, University of Valencia, Spain; Centro de Investigación Biomédica en Red de Epidemiología y Salud Publica (CIBER-ESP), Instituto de Salud Carlos III, Spain.
| | - Angels Natividad-Sancho
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Avda. de Catalunya, 21, 46020 Valencia, Spain.
| | - Maria Pisareva
- Research Institute of Influenza, Ministry of Health, Prof. Popov Str. 15/17, St. Petersburg, Russian Federation.
| | - Andrey Komissarov
- Research Institute of Influenza, Ministry of Health, Prof. Popov Str. 15/17, St. Petersburg, Russian Federation.
| | - Karina Salvatierra
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Avda. de Catalunya, 21, 46020 Valencia, Spain; Joint Units of Infection and of Genomics and Health, FISABIO/Cavanilles Institute for Biodiversity and Evolutionary Biology, University of Valencia, Spain.
| | - Artem Fadeev
- Research Institute of Influenza, Ministry of Health, Prof. Popov Str. 15/17, St. Petersburg, Russian Federation.
| | - Andrés Moya
- Joint Units of Infection and of Genomics and Health, FISABIO/Cavanilles Institute for Biodiversity and Evolutionary Biology, University of Valencia, Spain.
| | - Mikhail Grudinin
- Research Institute of Influenza, Ministry of Health, Prof. Popov Str. 15/17, St. Petersburg, Russian Federation.
| | - Javier Díez-Domingo
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Avda. de Catalunya, 21, 46020 Valencia, Spain.
| | - Olga Afanasieva
- Research Institute of Influenza, Ministry of Health, Prof. Popov Str. 15/17, St. Petersburg, Russian Federation.
| | - Nadezhda Konovalova
- Research Institute of Influenza, Ministry of Health, Prof. Popov Str. 15/17, St. Petersburg, Russian Federation.
| | - Anna Sominina
- Research Institute of Influenza, Ministry of Health, Prof. Popov Str. 15/17, St. Petersburg, Russian Federation.
| | - Joan Puig-Barberà
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Avda. de Catalunya, 21, 46020 Valencia, Spain.
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62
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Rossi M, Martínez-Martínez D, Amaretti A, Ulrici A, Raimondi S, Moya A. Mining metagenomic whole genome sequences revealed subdominant but constant Lactobacillus population in the human gut microbiota. Environ Microbiol Rep 2016; 8:399-406. [PMID: 27043715 DOI: 10.1111/1758-2229.12405] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 03/08/2016] [Indexed: 02/05/2023]
Abstract
The genus Lactobacillus includes over 215 species that colonize plants, foods, sewage and the gastrointestinal tract (GIT) of humans and animals. In the GIT, Lactobacillus population can be made by true inhabitants or by bacteria occasionally ingested with fermented or spoiled foods, or with probiotics. This study longitudinally surveyed Lactobacillus species and strains in the feces of a healthy subject through whole genome sequencing (WGS) data-mining, in order to identify members of the permanent or transient populations. In three time-points (0, 670 and 700 d), 58 different species were identified, 16 of them being retrieved for the first time in human feces. L. rhamnosus, L. ruminis, L. delbrueckii, L. plantarum, L. casei and L. acidophilus were the most represented, with estimated amounts ranging between 6 and 8 Log (cells g(-1) ), while the other were detected at 4 or 5 Log (cells g(-1) ). 86 Lactobacillus strains belonging to 52 species were identified. 43 seemingly occupied the GIT as true residents, since were detected in a time span of almost 2 years in all the three samples or in 2 samples separated by 670 or 700 d. As a whole, a stable community of lactobacilli was disclosed, with wide and understudied biodiversity.
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Affiliation(s)
- Maddalena Rossi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Daniel Martínez-Martínez
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain
- Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO), Valencia, Spain
- Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
| | - Alberto Amaretti
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Alessandro Ulrici
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Stefano Raimondi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Andrés Moya
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain
- Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO), Valencia, Spain
- Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
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63
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Serrano-Villar S, Rojo D, Martínez-Martínez M, Deusch S, Vázquez-Castellanos JF, Bargiela R, Sainz T, Vera M, Moreno S, Estrada V, Gosalbes MJ, Latorre A, Seifert J, Barbas C, Moya A, Ferrer M. Gut Bacteria Metabolism Impacts Immune Recovery in HIV-infected Individuals. EBioMedicine 2016; 8:203-216. [PMID: 27428431 PMCID: PMC4919658 DOI: 10.1016/j.ebiom.2016.04.033] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 04/01/2016] [Accepted: 04/25/2016] [Indexed: 02/07/2023] Open
Abstract
While changes in gut microbial populations have been described in human immuno-deficiency virus (HIV)-infected patients undergoing antiretroviral therapy (ART), the mechanisms underlying the contributions of gut bacteria and their molecular agents (metabolites and proteins) to immune recovery remain unexplored. To study this, we examined the active fraction of the gut microbiome, through examining protein synthesis and accumulation of metabolites inside gut bacteria and in the bloodstream, in 8 healthy controls and 29 HIV-infected individuals (6 being longitudinally studied). We found that HIV infection is associated to dramatic changes in the active set of gut bacteria simultaneously altering the metabolic outcomes. Effects were accentuated among immunological ART responders, regardless diet, subject characteristics, clinical variables other than immune recovery, the duration and type of ART and sexual preferences. The effect was found at quantitative levels of several molecular agents and active bacteria which were herein identified and whose abundance correlated with HIV immune pathogenesis markers. Although, we cannot rule out the possibility that some changes are partially a random consequence of the disease status, our data suggest that most likely reduced inflammation and immune recovery is a joint solution orchestrated by both the active fraction of the gut microbiota and the host.
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Affiliation(s)
- Sergio Serrano-Villar
- Department of Infectious Diseases, University Hospital Ramón y Cajal and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
| | - David Rojo
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Madrid, Spain
| | | | - Simon Deusch
- Institute of Animal Science, Universität Hohenheim, Stuttgart, Germany
| | - Jorge F Vázquez-Castellanos
- Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO) - Public Health, Valencia, Spain; Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
| | - Rafael Bargiela
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Talía Sainz
- Department of Pediatric Infectious Diseases, University Hospital La Paz, and La Paz Research Institute (IdiPAZ), Madrid, Spain
| | - Mar Vera
- Centro Sanitario Sandoval, Madrid, Spain
| | - Santiago Moreno
- Department of Infectious Diseases, University Hospital Ramón y Cajal and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
| | - Vicente Estrada
- HIV Unit, Department of Internal Medicine, University Hospital Clínico San Carlos, Madrid, Spain
| | - María José Gosalbes
- Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO) - Public Health, Valencia, Spain; Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
| | - Amparo Latorre
- Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO) - Public Health, Valencia, Spain; Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain; Instituto Cavanilles de Biodiversidad y Biología Evolutiva (Universidad de Valencia), Valencia, Spain
| | - Jana Seifert
- Institute of Animal Science, Universität Hohenheim, Stuttgart, Germany
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Madrid, Spain.
| | - Andrés Moya
- Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO) - Public Health, Valencia, Spain; Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain; Instituto Cavanilles de Biodiversidad y Biología Evolutiva (Universidad de Valencia), Valencia, Spain.
| | - Manuel Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain.
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64
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Oceguera-Figueroa A, Manzano-Marín A, Kvist S, Moya A, Siddall ME, Latorre A. Comparative Mitogenomics of Leeches (Annelida: Clitellata): Genome Conservation and Placobdella-Specific trnD Gene Duplication. PLoS One 2016; 11:e0155441. [PMID: 27176910 PMCID: PMC4866719 DOI: 10.1371/journal.pone.0155441] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [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: 10/29/2015] [Accepted: 04/28/2016] [Indexed: 02/07/2023] Open
Abstract
Mitochondrial DNA sequences, often in combination with nuclear markers and morphological data, are frequently used to unravel the phylogenetic relationships, population dynamics and biogeographic histories of a plethora of organisms. The information provided by examining complete mitochondrial genomes also enables investigation of other evolutionary events such as gene rearrangements, gene duplication and gene loss. Despite efforts to generate information to represent most of the currently recognized groups, some taxa are underrepresented in mitochondrial genomic databases. One such group is leeches (Annelida: Hirudinea: Clitellata). Herein, we expand our knowledge concerning leech mitochondrial makeup including gene arrangement, gene duplication and the evolution of mitochondrial genomes by adding newly sequenced mitochondrial genomes for three bloodfeeding species: Haementeria officinalis, Placobdella lamothei and Placobdella parasitica. With the inclusion of three new mitochondrial genomes of leeches, a better understanding of evolution for this organelle within the group is emerging. We found that gene order and genomic arrangement in the three new mitochondrial genomes is identical to previously sequenced members of Clitellata. Interestingly, within Placobdella, we recovered a genus-specific duplication of the trnD gene located between cox2 and atp8. We performed phylogenetic analyses using 12 protein-coding genes and expanded our taxon sampling by including GenBank sequences for 39 taxa; the analyses confirm the monophyletic status of Clitellata, yet disagree in several respects with other phylogenetic hypotheses based on morphology and analyses of non-mitochondrial data.
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Affiliation(s)
- Alejandro Oceguera-Figueroa
- Laboratorio de Helmintología, Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Coyoacán, 04510, Mexico City, Mexico
- Research Collaborator, Department of Invertebrate Zoology, Smithsonian Institution. National Museum of Natural History, Washington D. C., United States of America
| | - Alejandro Manzano-Marín
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Catedrático José Beltrán 2, 46008, Paterna, Valencia, Spain
| | - Sebastian Kvist
- Department of Natural History, Royal Ontario Museum, 100 Queen’s Park, Toronto, ON, M5S 2C6, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
| | - Andrés Moya
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Catedrático José Beltrán 2, 46008, Paterna, Valencia, Spain
- Área de Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Avenida de Catalunya 21, 46020, Valencia, Spain
| | - Mark E. Siddall
- Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, United States of America
| | - Amparo Latorre
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Catedrático José Beltrán 2, 46008, Paterna, Valencia, Spain
- Área de Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Avenida de Catalunya 21, 46020, Valencia, Spain
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Moya A, Ferrer M. Functional Redundancy-Induced Stability of Gut Microbiota Subjected to Disturbance. Trends Microbiol 2016; 24:402-413. [PMID: 26996765 DOI: 10.1016/j.tim.2016.02.002] [Citation(s) in RCA: 313] [Impact Index Per Article: 39.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 01/26/2016] [Accepted: 02/01/2016] [Indexed: 02/07/2023]
Abstract
The microbiota should be considered as just another component of the human epigenetic landscape. Thus, health is also a reflection of the diversity and composition of gut microbiota and its metabolic status. In defining host health, it remains unclear whether diversity is paramount, or whether greater weight is held by gut microbiota composition or mono- or multiple-functional capacity of the different taxa and the mechanisms involved. A network-biology approach may shed light on the key gut players acting to protect against, or promote, disorders or diseases. This could be achieved by integrating data on total and active species, proteins and molecules, and their association with host response. In this review, we discuss the utilization of top-down and bottom-up approaches, following a functional hierarchy perspective.
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Affiliation(s)
- Andrés Moya
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain; Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO), Valencia, Spain; Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain.
| | - Manuel Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
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Gosalbes MJ, Vázquez-Castellanos JF, Angebault C, Woerther PL, Ruppé E, Ferrús ML, Latorre A, Andremont A, Moya A. Carriage of Enterobacteria Producing Extended-Spectrum β-Lactamases and Composition of the Gut Microbiota in an Amerindian Community. Antimicrob Agents Chemother 2016; 60:507-14. [PMID: 26552974 PMCID: PMC4704183 DOI: 10.1128/aac.01528-15] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 10/29/2015] [Indexed: 02/07/2023] Open
Abstract
Epidemiological and individual risk factors for colonization by enterobacteria producing extended-spectrum beta-lactamases (E-ESBL) have been studied extensively, but whether such colonization is associated with significant changes in the composition of the rest of the microbiota is still unknown. To address this issue, we assessed in an isolated Amerindian Guianese community whether intestinal carriage of E-ESBL was associated with specificities in gut microbiota using metagenomic and metatranscriptomic approaches. While the richness of taxa of the active microbiota of carriers was similar to that of noncarriers, the taxa were less homogeneous. In addition, species of four genera, Desulfovibrio, Oscillospira, Parabacteroides, and Coprococcus, were significantly more abundant in the active microbiota of noncarriers than in the active microbiota of carriers, whereas such was the case only for species of Desulfovibrio and Oscillospira in the total microbiota. Differential genera in noncarrier microbiota could either be associated with resistance to colonization or be the consequence of the colonization by E-ESBL.
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Affiliation(s)
- María José Gosalbes
- Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública) y el Institut Cavanilles de Biodiversitat y Biología Evolutiva (Universitat de València), Valencia, Spain CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Jorge F Vázquez-Castellanos
- Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública) y el Institut Cavanilles de Biodiversitat y Biología Evolutiva (Universitat de València), Valencia, Spain CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Cécile Angebault
- EA 3964 Bacterial resistance in vivo, University Paris-Diderot Medical School and APHP, Paris, France
| | - Paul-Louis Woerther
- EA 3964 Bacterial resistance in vivo, University Paris-Diderot Medical School and APHP, Paris, France
| | - Etienne Ruppé
- EA 3964 Bacterial resistance in vivo, University Paris-Diderot Medical School and APHP, Paris, France
| | - María Loreto Ferrús
- Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública) y el Institut Cavanilles de Biodiversitat y Biología Evolutiva (Universitat de València), Valencia, Spain
| | - Amparo Latorre
- Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública) y el Institut Cavanilles de Biodiversitat y Biología Evolutiva (Universitat de València), Valencia, Spain CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Antoine Andremont
- EA 3964 Bacterial resistance in vivo, University Paris-Diderot Medical School and APHP, Paris, France
| | - Andrés Moya
- Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública) y el Institut Cavanilles de Biodiversitat y Biología Evolutiva (Universitat de València), Valencia, Spain CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
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Džunková M, D'Auria G, Xu H, Huang J, Duan Y, Moya A, Kelly CP, Chen X. The Monoclonal Antitoxin Antibodies (Actoxumab-Bezlotoxumab) Treatment Facilitates Normalization of the Gut Microbiota of Mice with Clostridium difficile Infection. Front Cell Infect Microbiol 2016; 6:119. [PMID: 27757389 PMCID: PMC5048712 DOI: 10.3389/fcimb.2016.00119] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 09/21/2016] [Indexed: 02/05/2023] Open
Abstract
Antibiotics have significant and long-lasting impacts on the intestinal microbiota and consequently reduce colonization resistance against Clostridium difficile infection (CDI). Standard therapy using antibiotics is associated with a high rate of disease recurrence, highlighting the need for novel treatment strategies that target toxins, the major virulence factors, rather than the organism itself. Human monoclonal antibodies MK-3415A (actoxumab-bezlotoxumab) to C. difficile toxin A and toxin B, as an emerging non-antibiotic approach, significantly reduced the recurrence of CDI in animal models and human clinical trials. Although the main mechanism of protection is through direct neutralization of the toxins, the impact of MK-3415A on gut microbiota and its restoration has not been examined. Using a CDI murine model, we compared the bacterial diversity of the gut microbiome of mice under different treatments including MK-3415A, vancomycin, or vancomycin combined with MK-3415A, sampled longitudinally. Here, we showed that C. difficile infection resulted in the prevalence of Enterobacter species. Sixty percent of mice in the vehicle group died after 2 days and their microbiome was almost exclusively formed by Enterobacter. MK-3415A treatment resulted in lower Enterobacter levels and restoration of Blautia, Akkermansia, and Lactobacillus which were the core components of the original microbiota. Vancomycin treatment led to significantly lower survival rate than the combo treatment of MK-3415A and vancomycin. Vancomycin treatment decreased bacterial diversity with predominant Enterobacter and Akkermansia, while Staphylococcus expanded after vancomycin treatment was terminated. In contrast, mice treated by vancomycin combined with MK-3415A also experienced decreased bacterial diversity during vancomycin treatment. However, these animals were able to recover their initial Blautia and Lactobacillus proportions, even though episodes of Staphylococcus overgrowth were detected by the end of the experiments. In conclusion, MK-3415A (actoxumab-bezlotoxumab) treatment facilitates normalization of the gut microbiota in CDI mice. It remains to be examined whether or not the prevention of recurrent CDI by the antitoxin antibodies observed in clinical trials occurs through modulation of microbiota.
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Affiliation(s)
- Mária Džunková
- Área de Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad ValencianaValencia, Spain
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de ValènciaValencia, Spain
- Centro de Investigación Biomédica en Red en Epidemoioloía y Salud PúblicaMadrid, Spain
| | - Giuseppe D'Auria
- Área de Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad ValencianaValencia, Spain
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de ValènciaValencia, Spain
- Centro de Investigación Biomédica en Red en Epidemoioloía y Salud PúblicaMadrid, Spain
| | - Hua Xu
- Division of Gastroenterology, Beth Israel Deaconess Medical Center, Harvard Medical SchoolBoston, MA, USA
| | - Jun Huang
- Division of Gastroenterology, Beth Israel Deaconess Medical Center, Harvard Medical SchoolBoston, MA, USA
| | - Yinghua Duan
- Division of Gastroenterology, Beth Israel Deaconess Medical Center, Harvard Medical SchoolBoston, MA, USA
| | - Andrés Moya
- Área de Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad ValencianaValencia, Spain
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de ValènciaValencia, Spain
- Centro de Investigación Biomédica en Red en Epidemoioloía y Salud PúblicaMadrid, Spain
| | - Ciarán P. Kelly
- Division of Gastroenterology, Beth Israel Deaconess Medical Center, Harvard Medical SchoolBoston, MA, USA
| | - Xinhua Chen
- Division of Gastroenterology, Beth Israel Deaconess Medical Center, Harvard Medical SchoolBoston, MA, USA
- *Correspondence: Xinhua Chen
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Pérez-Brocal V, García-López R, Nos P, Beltrán B, Moret I, Moya A. Metagenomic Analysis of Crohn's Disease Patients Identifies Changes in the Virome and Microbiome Related to Disease Status and Therapy, and Detects Potential Interactions and Biomarkers. Inflamm Bowel Dis 2015; 21:2515-32. [PMID: 26313691 DOI: 10.1097/mib.0000000000000549] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND The aim of this study was to survey the bacterial and viral communities in different types of samples from patients with Crohn's disease (CD) at different stages of the disease to relate their distribution with the origin and progression of this disorder. METHODS A total of 42 fecal samples and 15 biopsies from 20 patients with CD and 20 healthy control individuals were collected for bacterial 16S rRNA gene profiling and DNA/RNA virome metagenomic analysis through 454 pyrosequencing. Their composition, abundance, and diversity were analyzed, and comparisons of disease status, patient status, and sample origin were used to determine statistical differences between the groups. RESULTS Bacterial composition and relative abundance in new-onset patients with CD differed markedly from control individuals. Individual variability and sample origin had a stronger impact on viral communities than the disease, contrary to what was observed for bacterial populations although increased numbers of overrepresented viruses were observed in feces from patients with CD. Correlation-based networks were constructed to show potential relations between bacteria and between those and viruses. CONCLUSIONS The bacterial community reflects the disease status of individuals more accurately than their viral counterparts. However, numerous viral biomarkers specifically associated with CD disease were identified. Because viruses can modulate bacterial communities, the correlation networks between both communities constitute a step forward in unraveling their interactions under normal and CD disease conditions.
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Affiliation(s)
- Vicente Pérez-Brocal
- *Genomics and Health Area, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO)-Salud Pública, Valencia, Spain; †Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Paterna, Spain; ‡CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; §Servicio de Medicina Digestiva, Hospital Universitari i Politècnic La Fe, Valencia, Spain; ‖CIBER en Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, Spain; and ¶Servicio de Medicina Digestiva, Instituto de Investigación Sanitaria La Fe, Valencia, Spain
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Manzano-Marín A, Oceguera-Figueroa A, Latorre A, Jiménez-García LF, Moya A. Solving a Bloody Mess: B-Vitamin Independent Metabolic Convergence among Gammaproteobacterial Obligate Endosymbionts from Blood-Feeding Arthropods and the Leech Haementeria officinalis. Genome Biol Evol 2015; 7:2871-84. [PMID: 26454017 PMCID: PMC4684696 DOI: 10.1093/gbe/evv188] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/21/2015] [Indexed: 02/07/2023] Open
Abstract
Endosymbiosis is a common phenomenon in nature, especially between bacteria and insects, whose typically unbalanced diets are usually complemented by their obligate endosymbionts. While much interest and focus has been directed toward phloem-feeders like aphids and mealybugs, blood-feeders such as the Lone star tick (Amblyomma americanum), Glossina flies, and the human body louse (Pediculus humanus corporis) depend on obligate endosymbionts which complement their B-vitamin-deficient diets, and thus are required for growth and survival. Glossiphoniid leeches have also been found to harbor distinct endosymbionts housed in specialized organs. Here, we present the genome of the bacterial endosymbiont from Haementeria officinalis, first of a glossiphoniid leech. This as-yet-unnamed endosymbiont belongs to the Gammaproteobacteria, has a pleomorphic shape and is restricted to bacteriocytes. For this bacterial endosymbiont, we propose the name Candidatus Providencia siddallii. This symbiont possesses a highly reduced genome with high A+T content and a reduced set of metabolic capabilities, all of which are common characteristics of ancient obligate endosymbionts of arthropods. Its genome has retained many pathways related to the biosynthesis of B-vitamins, pointing toward a role in supplementing the blood-restricted diet of its host. Through comparative genomics against the endosymbionts of A. americanum, Glossina flies, and P. humanus corporis, we were able to detect a high degree of metabolic convergence among these four very distantly related endosymbiotic bacteria.
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Affiliation(s)
| | - Alejandro Oceguera-Figueroa
- Laboratorio de Helmintología, Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Distrito Federal, Mexico
| | - Amparo Latorre
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain Área de Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Valencia, Spain
| | - Luis F Jiménez-García
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Distrito Federal, Mexico
| | - Andres Moya
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain Área de Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Valencia, Spain
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70
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Mosele JI, Gosalbes MJ, Macià A, Rubió L, Vázquez-Castellanos JF, Jiménez Hernández N, Moya A, Latorre A, Motilva MJ. Effect of daily intake of pomegranate juice on fecal microbiota and feces metabolites from healthy volunteers. Mol Nutr Food Res 2015; 59:1942-53. [PMID: 26228065 DOI: 10.1002/mnfr.201500227] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 07/15/2015] [Accepted: 07/16/2015] [Indexed: 02/05/2023]
Abstract
SCOPE The purpose of the study was to evaluate the effect, regarding the metabolic and microbial profile of feces, of diet supplementation of healthy adults with pomegranate juice (PJ). METHODS AND RESULTS Twelve healthy adults were recruited to the study, which consisted of the intake of 200 mL/day of PJ during 4 weeks. Feces were collected before and after the supplementation with PJ. Metabolites (phenolic catabolites, short-chain fatty acids, and fecal steroids) and microbial profile were analyzed at baseline and at 4 weeks. Fecal phenolic metabolites, 3-phenylpropionic acid, catechol, hydroxytyrosol, and urolithin A, showed a significant increase in their concentration after supplementation with PJ. Among fecal steroids, parallel to the significant increase of cholesterol concentration, a significant decrease of coprostanol was observed. Although no significant changes in the microbiota profile were observed, different relationships between initial microbiota and the metabolites produced were found. Catechol showed positive and negative correlation with Oscillospora and Paraprevotella genera, respectively, and 3-phenylpropionic acid was positively correlated with Odoribacter genus. CONCLUSION Inclusion of PJ in the diet did not significantly alter the gut microbiota composition in healthy adults, but the individual bacterial composition could contribute to the generation of potential health-promoting phenolic metabolites.
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Affiliation(s)
- Juana I Mosele
- Food Technology Department, Agrotecnio Center, University of Lleida, Lleida, Spain
| | - María-José Gosalbes
- Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica (FISABIO-Salud Pública) y del Instituto Cavanilles de Biodiversidad y Biología Evolutiva (Universitat de València), València, Spain
- CIBERESP (Consorcio de Investigación Biomédica de Epidemiología y Salud Pública), Madrid, Spain
| | - Alba Macià
- Food Technology Department, Agrotecnio Center, University of Lleida, Lleida, Spain
| | - Laura Rubió
- Functional Nutrition, Oxidation and Cardiovascular Diseases Group (NFOC-Salut), Unit of Lipids and Atherosclerosis Research (URLA), Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Hospital Universitari Sant Joan, IISPV, Technological Center of Nutrition and Health (CTNS), Faculty of Medicine and Health Sciences, Universitat Rovira i Virgili, Reus, Spain
| | - Jorge F Vázquez-Castellanos
- Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica (FISABIO-Salud Pública) y del Instituto Cavanilles de Biodiversidad y Biología Evolutiva (Universitat de València), València, Spain
- CIBERESP (Consorcio de Investigación Biomédica de Epidemiología y Salud Pública), Madrid, Spain
| | - Nuria Jiménez Hernández
- Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica (FISABIO-Salud Pública) y del Instituto Cavanilles de Biodiversidad y Biología Evolutiva (Universitat de València), València, Spain
- CIBERESP (Consorcio de Investigación Biomédica de Epidemiología y Salud Pública), Madrid, Spain
| | - Andrés Moya
- Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica (FISABIO-Salud Pública) y del Instituto Cavanilles de Biodiversidad y Biología Evolutiva (Universitat de València), València, Spain
- CIBERESP (Consorcio de Investigación Biomédica de Epidemiología y Salud Pública), Madrid, Spain
| | - Amparo Latorre
- Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica (FISABIO-Salud Pública) y del Instituto Cavanilles de Biodiversidad y Biología Evolutiva (Universitat de València), València, Spain
- CIBERESP (Consorcio de Investigación Biomédica de Epidemiología y Salud Pública), Madrid, Spain
| | - María-José Motilva
- Food Technology Department, Agrotecnio Center, University of Lleida, Lleida, Spain
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Rojo D, Gosalbes MJ, Ferrari R, Pérez-Cobas AE, Hernández E, Oltra R, Buesa J, Latorre A, Barbas C, Ferrer M, Moya A. Clostridium difficile heterogeneously impacts intestinal community architecture but drives stable metabolome responses. ISME J 2015; 9:2206-20. [PMID: 25756679 PMCID: PMC4579473 DOI: 10.1038/ismej.2015.32] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 01/12/2015] [Accepted: 02/06/2015] [Indexed: 02/07/2023]
Abstract
Clostridium difficile-associated diarrhoea (CDAD) is caused by C. difficile toxins A and B and represents a serious emerging health problem. Yet, its progression and functional consequences are unclear. We hypothesised that C. difficile can drive major measurable metabolic changes in the gut microbiota and that a relationship with the production or absence of toxins may be established. We tested this hypothesis by performing metabolic profiling on the gut microbiota of patients with C. difficile that produced (n=6) or did not produce (n=4) toxins and on non-colonised control patients (n=6), all of whom were experiencing diarrhoea. We report a statistically significant separation (P-value <0.05) among the three groups, regardless of patient characteristics, duration of the disease, antibiotic therapy and medical history. This classification is associated with differences in the production of distinct molecules with presumptive global importance in the gut environment, disease progression and inflammation. Moreover, although severe impaired metabolite production and biological deficits were associated with the carriage of C. difficile that did not produce toxins, only previously unrecognised selective features, namely, choline- and acetylputrescine-deficient gut environments, characterised the carriage of toxin-producing C. difficile. Additional results showed that the changes induced by C. difficile become marked at the highest level of the functional hierarchy, namely the metabolic activity exemplified by the gut microbial metabolome regardless of heterogeneities that commonly appear below the functional level (gut bacterial composition). We discuss possible explanations for this effect and suggest that the changes imposed by CDAD are much more defined and predictable than previously thought.
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Affiliation(s)
- David Rojo
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Madrid, Spain
| | - María J Gosalbes
- Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO) and Instituto Cavanilles de Biodiversidad y Biología Evolutiva de la Universidad de Valencia, Valencia, Spain
- CIBER en Epidemiología y Salud Pública (CIBEResp), Madrid, Spain
| | - Rafaela Ferrari
- Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO) and Instituto Cavanilles de Biodiversidad y Biología Evolutiva de la Universidad de Valencia, Valencia, Spain
- CIBER en Epidemiología y Salud Pública (CIBEResp), Madrid, Spain
| | - Ana E Pérez-Cobas
- Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO) and Instituto Cavanilles de Biodiversidad y Biología Evolutiva de la Universidad de Valencia, Valencia, Spain
- CIBER en Epidemiología y Salud Pública (CIBEResp), Madrid, Spain
| | | | - Rosa Oltra
- Unidad Enfermedades Infecciosas, Servicio Medicina Interna, Hospital Clínico Universitario de Valencia-INCLIVA, Valencia, Spain
| | - Javier Buesa
- Departamento de Microbiología, Facultad de Medicina, Universidad de Valencia and Hospital Clínico Universitario de Valencia-INCLIVA, Valencia, Spain
| | - Amparo Latorre
- Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO) and Instituto Cavanilles de Biodiversidad y Biología Evolutiva de la Universidad de Valencia, Valencia, Spain
- CIBER en Epidemiología y Salud Pública (CIBEResp), Madrid, Spain
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Madrid, Spain
| | - Manuel Ferrer
- CSIC, Institute of Catalysis, Madrid, Spain
- CSIC, Institute of Catalysis, Madrid 28049, Spain. E-mail:
| | - Andrés Moya
- Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO) and Instituto Cavanilles de Biodiversidad y Biología Evolutiva de la Universidad de Valencia, Valencia, Spain
- CIBER en Epidemiología y Salud Pública (CIBEResp), Madrid, Spain
- Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Valencia 46020, Spain. E-mail:
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Pérez-Cobas AE, Moya A, Gosalbes MJ, Latorre A. Colonization Resistance of the Gut Microbiota against Clostridium difficile. Antibiotics (Basel) 2015; 4:337-57. [PMID: 27025628 PMCID: PMC4790290 DOI: 10.3390/antibiotics4030337] [Citation(s) in RCA: 45] [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: 05/28/2015] [Accepted: 08/03/2015] [Indexed: 02/06/2023] Open
Abstract
Antibiotics strongly disrupt the human gut microbiota, which in consequence loses its colonization resistance capacity, allowing infection by opportunistic pathogens such as Clostridium difficile. This bacterium is the main cause of antibiotic-associated diarrhea and a current problem in developed countries, since its incidence and severity have increased during the last years. Furthermore, the emergence of antibiotic resistance strains has reduced the efficiency of the standard treatment with antibiotics, leading to a higher rate of relapses. Here, we review recent efforts focused on the impact of antibiotics in the gut microbiome and their relationship with C. difficile colonization, as well as, in the identification of bacteria and mechanisms involved in the protection against C. difficile infection. Since a healthy gut microbiota is able to avoid pathogen colonization, restoration of the gut microbiota seems to be the most promising approach to face C. difficile infection, especially for recurrent cases. Therefore, it would be possible to design probiotics for patients undergoing antimicrobial therapies in order to prevent or fight the expansion of the pathogen in the gut ecosystem.
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Affiliation(s)
- Ana Elena Pérez-Cobas
- Joint Research Unit of Foundation for the Promotion of Health and Biomedical Research of Valencian Region (FISABIO) and the Cavanilles Institute of Biodiversity and Evolutionary Biology (ICBiBE) of the University of Valencia, Valencia 46020, Spain.
- CIBER in Epidemiology and Public Health (CIBERESP), Madrid 28029, Spain.
| | - Andrés Moya
- Joint Research Unit of Foundation for the Promotion of Health and Biomedical Research of Valencian Region (FISABIO) and the Cavanilles Institute of Biodiversity and Evolutionary Biology (ICBiBE) of the University of Valencia, Valencia 46020, Spain.
- CIBER in Epidemiology and Public Health (CIBERESP), Madrid 28029, Spain.
| | - María José Gosalbes
- Joint Research Unit of Foundation for the Promotion of Health and Biomedical Research of Valencian Region (FISABIO) and the Cavanilles Institute of Biodiversity and Evolutionary Biology (ICBiBE) of the University of Valencia, Valencia 46020, Spain.
- CIBER in Epidemiology and Public Health (CIBERESP), Madrid 28029, Spain.
| | - Amparo Latorre
- Joint Research Unit of Foundation for the Promotion of Health and Biomedical Research of Valencian Region (FISABIO) and the Cavanilles Institute of Biodiversity and Evolutionary Biology (ICBiBE) of the University of Valencia, Valencia 46020, Spain.
- CIBER in Epidemiology and Public Health (CIBERESP), Madrid 28029, Spain.
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Campos M, Llorens C, Sempere JM, Futami R, Rodriguez I, Carrasco P, Capilla R, Latorre A, Coque TM, Moya A, Baquero F. A membrane computing simulator of trans-hierarchical antibiotic resistance evolution dynamics in nested ecological compartments (ARES). Biol Direct 2015; 10:41. [PMID: 26243297 PMCID: PMC4526193 DOI: 10.1186/s13062-015-0070-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 07/31/2015] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Antibiotic resistance is a major biomedical problem upon which public health systems demand solutions to construe the dynamics and epidemiological risk of resistant bacteria in anthropogenically-altered environments. The implementation of computable models with reciprocity within and between levels of biological organization (i.e. essential nesting) is central for studying antibiotic resistances. Antibiotic resistance is not just the result of antibiotic-driven selection but more properly the consequence of a complex hierarchy of processes shaping the ecology and evolution of the distinct subcellular, cellular and supra-cellular vehicles involved in the dissemination of resistance genes. Such a complex background motivated us to explore the P-system standards of membrane computing an innovative natural computing formalism that abstracts the notion of movement across membranes to simulate antibiotic resistance evolution processes across nested levels of micro- and macro-environmental organization in a given ecosystem. RESULTS In this article, we introduce ARES (Antibiotic Resistance Evolution Simulator) a software device that simulates P-system model scenarios with five types of nested computing membranes oriented to emulate a hierarchy of eco-biological compartments, i.e. a) peripheral ecosystem; b) local environment; c) reservoir of supplies; d) animal host; and e) host's associated bacterial organisms (microbiome). Computational objects emulating molecular entities such as plasmids, antibiotic resistance genes, antimicrobials, and/or other substances can be introduced into this framework and may interact and evolve together with the membranes, according to a set of pre-established rules and specifications. ARES has been implemented as an online server and offers additional tools for storage and model editing and downstream analysis. CONCLUSIONS The stochastic nature of the P-system model implemented in ARES explicitly links within and between host dynamics into a simulation, with feedback reciprocity among the different units of selection influenced by antibiotic exposure at various ecological levels. ARES offers the possibility of modeling predictive multilevel scenarios of antibiotic resistance evolution that can be interrogated, edited and re-simulated if necessary, with different parameters, until a correct model description of the process in the real world is convincingly approached. ARES can be accessed at http://gydb.org/ares.
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Affiliation(s)
- Marcelino Campos
- Department of Microbiology, Ramón y Cajal University Hospital, IRYCIS, Carretera de Colmenar Viejo, km. 9,100, 28034, Madrid, Spain.
- Department of Information Systems and Computation (DSIC), Polytechnic University of Valencia, Camino de Vera, 46022, Valencia, Spain.
| | - Carlos Llorens
- Biotechvana, Valencia, CEEI Building, Benjamin Franklin Av. 12, Valencia Technological Park, 46980, Paterna, Spain.
| | - José M Sempere
- Department of Information Systems and Computation (DSIC), Polytechnic University of Valencia, Camino de Vera, 46022, Valencia, Spain.
| | - Ricardo Futami
- Biotechvana, Valencia, CEEI Building, Benjamin Franklin Av. 12, Valencia Technological Park, 46980, Paterna, Spain.
| | - Irene Rodriguez
- Department of Microbiology, Ramón y Cajal University Hospital, IRYCIS, Carretera de Colmenar Viejo, km. 9,100, 28034, Madrid, Spain.
- Antibiotic Resistance and Bacterial Virulence Unit (HRYC-CSIC), associated to the Superior Council of Scientific Investigations (CSIC), Madrid, Spain.
- Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain.
| | - Purificación Carrasco
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, C/ Catedrático José Beltrán 2, 46980, Paterna, Valencia, Spain.
| | - Rafael Capilla
- Biotechvana, Valencia, CEEI Building, Benjamin Franklin Av. 12, Valencia Technological Park, 46980, Paterna, Spain.
| | - Amparo Latorre
- Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain.
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, C/ Catedrático José Beltrán 2, 46980, Paterna, Valencia, Spain.
- Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO) - Public Health, Avenida de Cataluña 21, 46020, Valencia, Spain.
| | - Teresa M Coque
- Department of Microbiology, Ramón y Cajal University Hospital, IRYCIS, Carretera de Colmenar Viejo, km. 9,100, 28034, Madrid, Spain.
- Antibiotic Resistance and Bacterial Virulence Unit (HRYC-CSIC), associated to the Superior Council of Scientific Investigations (CSIC), Madrid, Spain.
- Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain.
| | - Andres Moya
- Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain.
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, C/ Catedrático José Beltrán 2, 46980, Paterna, Valencia, Spain.
- Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO) - Public Health, Avenida de Cataluña 21, 46020, Valencia, Spain.
| | - Fernando Baquero
- Department of Microbiology, Ramón y Cajal University Hospital, IRYCIS, Carretera de Colmenar Viejo, km. 9,100, 28034, Madrid, Spain.
- Antibiotic Resistance and Bacterial Virulence Unit (HRYC-CSIC), associated to the Superior Council of Scientific Investigations (CSIC), Madrid, Spain.
- Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain.
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74
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Vázquez-Castellanos JF, Serrano-Villar S, Latorre A, Artacho A, Ferrús ML, Madrid N, Vallejo A, Sainz T, Martínez-Botas J, Ferrando-Martínez S, Vera M, Dronda F, Leal M, Del Romero J, Moreno S, Estrada V, Gosalbes MJ, Moya A. Altered metabolism of gut microbiota contributes to chronic immune activation in HIV-infected individuals. Mucosal Immunol 2015; 8:760-72. [PMID: 25407519 DOI: 10.1038/mi.2014.107] [Citation(s) in RCA: 209] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 10/06/2014] [Indexed: 02/07/2023]
Abstract
Altered interplay between gut mucosa and microbiota during treated HIV infection may possibly contribute to increased bacterial translocation and chronic immune activation, both of which are predictors of morbidity and mortality. Although a dysbiotic gut microbiota has recently been reported in HIV+ individuals, the metagenome gene pool associated with HIV infection remains unknown. The aim of this study is to characterize the functional gene content of gut microbiota in HIV+ patients and to define the metabolic pathways of this bacterial community, which is potentially associated with immune dysfunction. We determined systemic markers of innate and adaptive immunity in a cohort of HIV-infected individuals on successful antiretroviral therapy without comorbidities and in healthy non-HIV-infected subjects. Metagenome sequencing revealed an altered functional profile, with enrichment of the genes involved in various pathogenic processes, lipopolysaccharide biosynthesis, bacterial translocation, and other inflammatory pathways. In contrast, we observed depletion of genes involved in amino acid metabolism and energy processes. Bayesian networks showed significant interactions between the bacterial community, their altered metabolic pathways, and systemic markers of immune dysfunction. This study reveals altered metabolic activity of microbiota and provides novel insight into the potential host-microbiota interactions driving the sustained inflammatory state in successfully treated HIV-infected patients.
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Affiliation(s)
- J F Vázquez-Castellanos
- 1] Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública) y el Instituto Cavanilles de Biodiversitad y Biología Evolutiva (Universitat de València), Valencia, Spain [2] CIBER on Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - S Serrano-Villar
- Department of Infectious Diseases, University Hospital Ramón y Cajal-IRYCIS, Madrid, Spain
| | - A Latorre
- 1] Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública) y el Instituto Cavanilles de Biodiversitad y Biología Evolutiva (Universitat de València), Valencia, Spain [2] CIBER on Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - A Artacho
- Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública) y el Instituto Cavanilles de Biodiversitad y Biología Evolutiva (Universitat de València), Valencia, Spain
| | - M L Ferrús
- Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública) y el Instituto Cavanilles de Biodiversitad y Biología Evolutiva (Universitat de València), Valencia, Spain
| | - N Madrid
- Department of Infectious Diseases, University Hospital Ramón y Cajal-IRYCIS, Madrid, Spain
| | - A Vallejo
- Department of Infectious Diseases, University Hospital Ramón y Cajal-IRYCIS, Madrid, Spain
| | - T Sainz
- 1] Laboratory of Molecular Immune Biology, University Hospital Gregorio Marañón and Gregorio Marañón Research Institute, Madrid, Spain [2] CIBER on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain
| | - J Martínez-Botas
- 1] Department of Biochemistry, University Hospital Ramón y Cajal-IRYCIS, Madrid, Spain [2] CIBER on Obesity and Nutrition Pathophysiology (CIBEROBN), Madrid, Spain
| | - S Ferrando-Martínez
- 1] Laboratory of Molecular Immune Biology, University Hospital Gregorio Marañón and Gregorio Marañón Research Institute, Madrid, Spain [2] CIBER on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain [3] Laboratory of Immunovirology, Department of Infectious Diseases, Biomedicine Institute of Seville (IBIS), University Hospital Virgen del Rocío, Sevilla, Spain
| | - M Vera
- Centro Sandoval, Madrid, Spain
| | - F Dronda
- Department of Infectious Diseases, University Hospital Ramón y Cajal-IRYCIS, Madrid, Spain
| | - M Leal
- Laboratory of Immunovirology, Department of Infectious Diseases, Biomedicine Institute of Seville (IBIS), University Hospital Virgen del Rocío, Sevilla, Spain
| | | | - S Moreno
- Department of Infectious Diseases, University Hospital Ramón y Cajal-IRYCIS, Madrid, Spain
| | - V Estrada
- HIV Unit, Department of Internal Medicine, University Hospital Clínico San Carlos, Madrid, Spain
| | - M J Gosalbes
- 1] Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública) y el Instituto Cavanilles de Biodiversitad y Biología Evolutiva (Universitat de València), Valencia, Spain [2] CIBER on Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - A Moya
- 1] Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública) y el Instituto Cavanilles de Biodiversitad y Biología Evolutiva (Universitat de València), Valencia, Spain [2] CIBER on Epidemiology and Public Health (CIBERESP), Madrid, Spain
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75
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Álvarez-Canales G, Arellano-Álvarez G, González-Domenech CM, de la Cruz F, Moya A, Delaye L. Identification of Xenologs and Their Characteristic Low Expression Levels in the Cyanobacterium Synechococcus elongatus. J Mol Evol 2015; 80:292-304. [PMID: 26040248 DOI: 10.1007/s00239-015-9684-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 05/28/2015] [Indexed: 02/07/2023]
Abstract
Horizontal gene transfer (HGT) is a central process in prokaryotic evolution. Once a gene is introduced into a genome by HGT, its contribution to the fitness of the recipient cell depends in part on its expression level. Here we show that in Synechococcus elongatus PCC 7942, xenologs derived from non-cyanobacterial sources exhibited lower expression levels than native genes in the genome. In accord with our observation, xenolog codon adaptation indexes also displayed relatively low expression values. These results are in agreement with previous reports that suggested the relative neutrality of most xenologs. However, we also demonstrated that some of the xenologs detected participated in cellular functions, including iron starvation acclimation and nitrate reduction, which corroborate the role of HGT in bacterial adaptation. For example, the expression levels of some of the xenologs detected are known to increase under iron-limiting conditions. We interpreted the overall pattern as an indication that there is a selection pressure against high expression levels of xenologs. However, when a xenolog protein product confers a selective advantage, natural selection can further modulate its expression level to meet the requirements of the recipient cell. In addition, we show that ORFans did not exhibit significantly lower expression levels than native genes in the genome, which suggested an origin other than xenology.
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Affiliation(s)
- Gilberto Álvarez-Canales
- Departamento de Ingeniería Genética, CINVESTAV-Irapuato, Km. 9.6 Libramiento Norte, Carretera Irapuato-León, 36821, Irapuato, Guanajuato, Mexico
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76
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Rao Q, Rollat-Farnier PA, Zhu DT, Santos-Garcia D, Silva FJ, Moya A, Latorre A, Klein CC, Vavre F, Sagot MF, Liu SS, Mouton L, Wang XW. Genome reduction and potential metabolic complementation of the dual endosymbionts in the whitefly Bemisia tabaci. BMC Genomics 2015; 16:226. [PMID: 25887812 PMCID: PMC4438442 DOI: 10.1186/s12864-015-1379-6] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 02/21/2015] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The whitefly Bemisia tabaci is an important agricultural pest with global distribution. This phloem-sap feeder harbors a primary symbiont, "Candidatus Portiera aleyrodidarum", which compensates for the deficient nutritional composition of its food sources, and a variety of secondary symbionts. Interestingly, all of these secondary symbionts are found in co-localization with the primary symbiont within the same bacteriocytes, which should favor the evolution of strong interactions between symbionts. RESULTS In this paper, we analyzed the genome sequences of the primary symbiont Portiera and of the secondary symbiont Hamiltonella in the B. tabaci Mediterranean (MED) species in order to gain insight into the metabolic role of each symbiont in the biology of their host. The genome sequences of the uncultured symbionts Portiera and Hamiltonella were obtained from one single bacteriocyte of MED B. tabaci. As already reported, the genome of Portiera is highly reduced (357 kb), but has kept a number of genes encoding most essential amino-acids and carotenoids. On the other hand, Portiera lacks almost all the genes involved in the synthesis of vitamins and cofactors. Moreover, some pathways are incomplete, notably those involved in the synthesis of some essential amino-acids. Interestingly, the genome of Hamiltonella revealed that this secondary symbiont can not only provide vitamins and cofactors, but also complete the missing steps of some of the pathways of Portiera. In addition, some critical amino-acid biosynthetic genes are missing in the two symbiotic genomes, but analysis of whitefly transcriptome suggests that the missing steps may be performed by the whitefly itself or its microbiota. CONCLUSIONS These data suggest that Portiera and Hamiltonella are not only complementary but could also be mutually dependent to provide a full complement of nutrients to their host. Altogether, these results illustrate how functional redundancies can lead to gene losses in the genomes of the different symbiotic partners, reinforcing their inter-dependency.
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Affiliation(s)
- Qiong Rao
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, 310058, Hangzhou, China.
- School of Agriculture and Food Science, Zhejiang A & F University, 311300, Lin'an, Zhejiang, China.
| | - Pierre-Antoine Rollat-Farnier
- Université de Lyon, Université Lyon1, Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 558, 69622, Villeurbanne, Cedex, France.
- Inria Grenoble Rhône-Alpes, Grenoble, France.
| | - Dan-Tong Zhu
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, 310058, Hangzhou, China.
| | - Diego Santos-Garcia
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Valencia, Spain.
| | - Francisco J Silva
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Valencia, Spain.
- Unidad Mixta de Investigación en Genómica y Salud FISABIO-Salud Pública and Universitat de València, Valencia, Spain.
| | - Andrés Moya
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Valencia, Spain.
- Unidad Mixta de Investigación en Genómica y Salud FISABIO-Salud Pública and Universitat de València, Valencia, Spain.
| | - Amparo Latorre
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Valencia, Spain.
- Unidad Mixta de Investigación en Genómica y Salud FISABIO-Salud Pública and Universitat de València, Valencia, Spain.
| | - Cecilia C Klein
- Université de Lyon, Université Lyon1, Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 558, 69622, Villeurbanne, Cedex, France.
- Inria Grenoble Rhône-Alpes, Grenoble, France.
| | - Fabrice Vavre
- Université de Lyon, Université Lyon1, Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 558, 69622, Villeurbanne, Cedex, France.
| | - Marie-France Sagot
- Université de Lyon, Université Lyon1, Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 558, 69622, Villeurbanne, Cedex, France.
- Inria Grenoble Rhône-Alpes, Grenoble, France.
| | - Shu-Sheng Liu
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, 310058, Hangzhou, China.
| | - Laurence Mouton
- Université de Lyon, Université Lyon1, Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 558, 69622, Villeurbanne, Cedex, France.
| | - Xiao-Wei Wang
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, 310058, Hangzhou, China.
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Garcia-Nuñez M, Millares L, Pomares X, Ferrari R, Pérez-Brocal V, Gallego M, Espasa M, Moya A, Monsó E. Reply to "chronic obstructive pulmonary disease lung microbiota diversity may be mediated by age or inhaled corticosteroid use". J Clin Microbiol 2015; 53:1051. [PMID: 25700527 PMCID: PMC4390632 DOI: 10.1128/jcm.03358-14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Affiliation(s)
- Marian Garcia-Nuñez
- Fundació Parc Taulí, Sabadell/Badalona, Spain CIBER de Enfermedades Respiratorias, CIBERES, Bunyola, Spain Universitat Autònoma de Barcelona, Esfera UAB, Barcelona, Spain Fundació Institut d'Investigació Germans Trias i Pujol, Badalona, Spain
| | - Laura Millares
- Fundació Parc Taulí, Sabadell/Badalona, Spain CIBER de Enfermedades Respiratorias, CIBERES, Bunyola, Spain Universitat Autònoma de Barcelona, Esfera UAB, Barcelona, Spain Fundació Institut d'Investigació Germans Trias i Pujol, Badalona, Spain
| | - Xavier Pomares
- Universitat Autònoma de Barcelona, Esfera UAB, Barcelona, Spain Department of Respiratory Medicine, Hospital Universitari Parc Taulí, Sabadell, Spain
| | - Rafaela Ferrari
- Genomics and Health Area, Centro Superior de Investigación en Salud Pública, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (CSISP-FISABIO), Valencia, Spain Department of Genetics, Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE), Universitat de València, València, Spain
| | - Vicente Pérez-Brocal
- Genomics and Health Area, Centro Superior de Investigación en Salud Pública, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (CSISP-FISABIO), Valencia, Spain CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain Department of Genetics, Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE), Universitat de València, València, Spain
| | - Miguel Gallego
- Universitat Autònoma de Barcelona, Esfera UAB, Barcelona, Spain Department of Respiratory Medicine, Hospital Universitari Parc Taulí, Sabadell, Spain
| | - Mateu Espasa
- Department of Microbiology, Hospital Universitari Parc Taulí, Sabadell, Spain
| | - Andrés Moya
- Genomics and Health Area, Centro Superior de Investigación en Salud Pública, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (CSISP-FISABIO), Valencia, Spain CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain Department of Genetics, Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE), Universitat de València, València, Spain
| | - Eduard Monsó
- Fundació Parc Taulí, Sabadell/Badalona, Spain CIBER de Enfermedades Respiratorias, CIBERES, Bunyola, Spain Universitat Autònoma de Barcelona, Esfera UAB, Barcelona, Spain Department of Respiratory Medicine, Hospital Universitari Parc Taulí, Sabadell, Spain
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Abstract
Whiteflies are important agricultural insect pests, whose evolutionary success is related to a long-term association with a bacterial endosymbiont, Candidatus Portiera aleyrodidarum. To completely characterize this endosymbiont clade, we sequenced the genomes of three new Portiera strains covering the two extant whitefly subfamilies. Using endosymbiont and mitochondrial sequences we estimated the divergence dates in the clade and used these values to understand the molecular evolution of the endosymbiont coding sequences. Portiera genomes were maintained almost completely stable in gene order and gene content during more than 125 Myr of evolution, except in the Bemisia tabaci lineage. The ancestor had already lost the genetic information transfer autonomy but was able to participate in the synthesis of all essential amino acids and carotenoids. The time of divergence of the B. tabaci complex was much more recent than previous estimations. The recent divergence of biotypes B (MEAM1 species) and Q (MED species) suggests that they still could be considered strains of the same species. We have estimated the rates of evolution of Portiera genes, synonymous and nonsynonymous, and have detected significant differences among-lineages, with most Portiera lineages evolving very slowly. Although the nonsynonymous rates were much smaller than the synonymous, the genomic dN/dS ratios were similar, discarding selection as the driver of among-lineage variation. We suggest variation in mutation rate and generation time as the responsible factors. In conclusion, the slow evolutionary rates of Portiera may have contributed to its long-term association with whiteflies, avoiding its replacement by a novel and more efficient endosymbiont.
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Affiliation(s)
- Diego Santos-Garcia
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain
| | - Carlos Vargas-Chavez
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain
| | - Andrés Moya
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain Unidad Mixta de Investigación en Genómica y Salud, FISABIO-Salud Pública and Universitat de València, Spain
| | - Amparo Latorre
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain Unidad Mixta de Investigación en Genómica y Salud, FISABIO-Salud Pública and Universitat de València, Spain
| | - Francisco J Silva
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain Unidad Mixta de Investigación en Genómica y Salud, FISABIO-Salud Pública and Universitat de València, Spain
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79
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Rollat-Farnier PA, Santos-Garcia D, Rao Q, Sagot MF, Silva FJ, Henri H, Zchori-Fein E, Latorre A, Moya A, Barbe V, Liu SS, Wang XW, Vavre F, Mouton L. Two host clades, two bacterial arsenals: evolution through gene losses in facultative endosymbionts. Genome Biol Evol 2015; 7:839-55. [PMID: 25714744 PMCID: PMC5322557 DOI: 10.1093/gbe/evv030] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Bacterial endosymbiosis is an important evolutionary process in insects, which can harbor both obligate and facultative symbionts. The evolution of these symbionts is driven by evolutionary convergence, and they exhibit among the tiniest genomes in prokaryotes. The large host spectrum of facultative symbionts and the high diversity of strategies they use to infect new hosts probably impact the evolution of their genome and explain why they undergo less severe genomic erosion than obligate symbionts. Candidatus Hamiltonella defensa is suitable for the investigation of the genomic evolution of facultative symbionts because the bacteria are engaged in specific relationships in two clades of insects. In aphids, H. defensa is found in several species with an intermediate prevalence and confers protection against parasitoids. In whiteflies, H. defensa is almost fixed in some species of Bemisia tabaci, which suggests an important role of and a transition toward obligate symbiosis. In this study, comparisons of the genome of H. defensa present in two B. tabaci species (Middle East Asia Minor 1 and Mediterranean) and in the aphid Acyrthosiphon pisum revealed that they belong to two distinct clades and underwent specific gene losses. In aphids, it contains highly virulent factors that could allow protection and horizontal transfers. In whiteflies, the genome lost these factors and seems to have a limited ability to acquire genes. However it contains genes that could be involved in the production of essential nutrients, which is consistent with a primordial role for this symbiont. In conclusion, although both lineages of H. defensa have mutualistic interactions with their hosts, their genomes follow distinct evolutionary trajectories that reflect their phenotype and could have important consequences on their evolvability.
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Affiliation(s)
- Pierre-Antoine Rollat-Farnier
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université de Lyon, Université Lyon1, Villeurbanne, France BAMBOO Research Team, INRIA Grenoble, Rhône-Alpes, France
| | - Diego Santos-Garcia
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain
| | - Qiong Rao
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, China School of Agriculture and Food Science, Zhejiang Agriculture and Forestry University, Lin'an, Hangzhou, China
| | - Marie-France Sagot
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université de Lyon, Université Lyon1, Villeurbanne, France BAMBOO Research Team, INRIA Grenoble, Rhône-Alpes, France
| | - Francisco J Silva
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública) y el Instituto Cavanilles de Biodiversitad y Biología Evolutiva (Universitat de València), Valencia, Spain
| | - Hélène Henri
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université de Lyon, Université Lyon1, Villeurbanne, France
| | - Einat Zchori-Fein
- Department of Entomology, NeweYa'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Amparo Latorre
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública) y el Instituto Cavanilles de Biodiversitad y Biología Evolutiva (Universitat de València), Valencia, Spain
| | - Andrés Moya
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública) y el Instituto Cavanilles de Biodiversitad y Biología Evolutiva (Universitat de València), Valencia, Spain
| | - Valérie Barbe
- CEA/DSV/IG/Genoscope, 2 rue Gaston Cremieux, Evry, France
| | - Shu-Sheng Liu
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Xiao-Wei Wang
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Fabrice Vavre
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université de Lyon, Université Lyon1, Villeurbanne, France BAMBOO Research Team, INRIA Grenoble, Rhône-Alpes, France
| | - Laurence Mouton
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université de Lyon, Université Lyon1, Villeurbanne, France
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Millares L, Pérez-Brocal V, Ferrari R, Gallego M, Pomares X, García-Núñez M, Montón C, Capilla S, Monsó E, Moya A. Functional Metagenomics of the Bronchial Microbiome in COPD. PLoS One 2015; 10:e0144448. [PMID: 26632844 PMCID: PMC4669145 DOI: 10.1371/journal.pone.0144448] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 11/18/2015] [Indexed: 02/07/2023] Open
Abstract
The course of chronic obstructive pulmonary disease (COPD) is frequently aggravated by exacerbations, and changes in the composition and activity of the microbiome may be implicated in their appearance. The aim of this study was to analyse the composition and the gene content of the microbial community in bronchial secretions of COPD patients in both stability and exacerbation. Taxonomic data were obtained by 16S rRNA gene amplification and pyrosequencing, and metabolic information through shotgun metagenomics, using the Metagenomics RAST server (MG-RAST), and the PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) programme, which predict metagenomes from 16S data. Eight severe COPD patients provided good quality sputum samples, and no significant differences in the relative abundance of any phyla and genera were found between stability and exacerbation. Bacterial biodiversity (Chao1 and Shannon indexes) did not show statistical differences and beta-diversity analysis (Bray-Curtis dissimilarity index) showed a similar microbial composition in the two clinical situations. Four functional categories showed statistically significant differences with MG-RAST at KEGG level 2: in exacerbation, Cell growth and Death and Transport and Catabolism decreased in abundance [1.6 (0.2-2.3) vs 3.6 (3.3-6.9), p = 0.012; and 1.8 (0-3.3) vs 3.6 (1.8-5.1), p = 0.025 respectively], while Cancer and Carbohydrate Metabolism increased [0.8 (0-1.5) vs 0 (0-0.5), p = 0.043; and 7 (6.4-9) vs 5.9 (6.3-6.1), p = 0.012 respectively]. In conclusion, the bronchial microbiome as a whole is not significantly modified when exacerbation symptoms appear in severe COPD patients, but its functional metabolic capabilities show significant changes in several pathways.
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Affiliation(s)
- Laura Millares
- Fundació Parc Taulí, Sabadell, Spain
- CIBER de Enfermedades Respiratorias, CIBERES, Bunyola, Spain
- Universitat Autònoma de Barcelona, Esfera UAB, Barcelona, Spain
- Fundació Insitut d’Investigació Germans Trias i Pujol, Badalona, Spain
- * E-mail:
| | - Vicente Pérez-Brocal
- Genomics and Health Area, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Public Health), Valencia, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
- Evolutionary Genetics Unit, Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE), Universitat de València, Valencia, Spain
| | - Rafaela Ferrari
- Genomics and Health Area, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Public Health), Valencia, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
- Evolutionary Genetics Unit, Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE), Universitat de València, Valencia, Spain
| | - Miguel Gallego
- Department of Respiratory Medicine, Hospital Universitari Parc Taulí, Sabadell, Spain
| | - Xavier Pomares
- CIBER de Enfermedades Respiratorias, CIBERES, Bunyola, Spain
- Department of Respiratory Medicine, Hospital Universitari Parc Taulí, Sabadell, Spain
| | - Marian García-Núñez
- Fundació Parc Taulí, Sabadell, Spain
- CIBER de Enfermedades Respiratorias, CIBERES, Bunyola, Spain
- Universitat Autònoma de Barcelona, Esfera UAB, Barcelona, Spain
- Fundació Insitut d’Investigació Germans Trias i Pujol, Badalona, Spain
| | - Concepción Montón
- CIBER de Enfermedades Respiratorias, CIBERES, Bunyola, Spain
- Department of Respiratory Medicine, Hospital Universitari Parc Taulí, Sabadell, Spain
| | - Silvia Capilla
- Department of Microbiology, Hospital Universitari Parc Taulí, Sabadell, Spain
| | - Eduard Monsó
- CIBER de Enfermedades Respiratorias, CIBERES, Bunyola, Spain
- Universitat Autònoma de Barcelona, Esfera UAB, Barcelona, Spain
- Department of Respiratory Medicine, Hospital Universitari Parc Taulí, Sabadell, Spain
| | - Andrés Moya
- Genomics and Health Area, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Public Health), Valencia, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
- Evolutionary Genetics Unit, Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE), Universitat de València, Valencia, Spain
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Abstract
The sequence assembly of the human gut virome encounters several difficulties. A high proportion of human and bacterial matches is detected in purified viral samples. Viral DNA extraction results in a low DNA concentration, which does not reach the minimal limit required for sequencing library preparation. Therefore, the viromes are usually enriched by whole genome amplification (WGA), which is, however, prone to the development of chimeras and amplification bias. In addition, as there is a very wide diversity of gut viral species, very extensive sequencing efforts must be made for the assembling of whole viral genomes. We present an approach to improve human gut virome assembly by employing a more precise preparation of a viral sample before sequencing. Particles present in a virome previously filtered through 0.2 μm pores were further divided into groups in accordance with their size and DNA content by fluorescence activated cell sorting (FACS). One selected viral fraction was sequenced excluding the WGA step, so that unbiased sequences with high reliability were obtained. The DNA extracted from the 314 viral particles of the selected fraction was assembled into 34 contigs longer than 1,000 bp. This represents an increase to the number of assembled long contigs per sequenced Gb in comparison with other studies where non-fractioned viromes are sequenced. Seven of these contigs contained open reading frames (ORFs) with explicit matches to proteins related to bacteriophages. The remaining contigs also possessed uncharacterized ORFs with bacteriophage-related domains. When the particles that are present in the filtered viromes are sorted into smaller groups by FACS, large pieces of viral genomes can be recovered easily. This approach has several advantages over the conventional sequencing of non-fractioned viromes: non-viral contamination is reduced and the sequencing efforts required for viral assembly are minimized.
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Affiliation(s)
- Mária Džunková
- Área de Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana – Salud Pública, ValenciaSpain
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, ValenciaSpain
- CIBER en Epidemiología y Salud Pública, MadridSpain
| | - Giuseppe D’Auria
- Área de Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana – Salud Pública, ValenciaSpain
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, ValenciaSpain
- CIBER en Epidemiología y Salud Pública, MadridSpain
| | - Andrés Moya
- Área de Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana – Salud Pública, ValenciaSpain
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, ValenciaSpain
- CIBER en Epidemiología y Salud Pública, MadridSpain
- *Correspondence: Andrés Moya, Área de Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana – Salud Pública, Avenida de Cataluña 21, 46020 Valencia, Spain,
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82
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López-Madrigal S, Latorre A, Moya A, Gil R. The link between independent acquisition of intracellular gamma-endosymbionts and concerted evolution in Tremblaya princeps. Front Microbiol 2015; 6:642. [PMID: 26161080 PMCID: PMC4479817 DOI: 10.3389/fmicb.2015.00642] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [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: 03/30/2015] [Accepted: 06/12/2015] [Indexed: 02/05/2023] Open
Abstract
Many insect species establish mutualistic symbiosis with intracellular bacteria that complement their unbalanced diets. The betaproteobacterium "Candidatus Tremblaya" maintains an ancient symbiosis with mealybugs (Hemiptera: Pseudococcidae), which are classified in subfamilies Phenacoccinae and Pseudococcinae. Most Phenacoccinae mealybugs have "Candidatus Tremblaya phenacola" as their unique endosymbiont, while most Pseudococcinae mealybugs show a nested symbiosis (a bacterial symbiont placed inside another one) where every "Candidatus Tremblaya princeps" cell harbors several cells of a gammaproteobacterium. Genomic characterization of the endosymbiotic consortium from Planococcus citri, composed by "Ca. Tremblaya princeps" and "Candidatus Moranella endobia," unveiled several atypical features of the former's genome, including the concerted evolution of paralogous loci. Its comparison with the genome of "Ca. Tremblaya phenacola" PAVE, single endosymbiont of Phenacoccus avenae, suggests that the atypical reductive evolution of "Ca. Tremblaya princeps" could be linked to the acquisition of "Ca. Moranella endobia," which possess an almost complete set of genes encoding proteins involved in homologous recombination. In order to test this hypothesis, we performed comparative genomics between "Ca. Tremblaya phenacola" and "Ca. Tremblaya princeps" and searched for the co-occurrence of concerted evolution and homologous recombination genes in endosymbiotic consortia from four unexplored mealybug species, Dysmicoccus boninsis, Planococcus ficus, Pseudococcus longispinus, and Pseudococcus viburni. Our results support a link between concerted evolution and nested endosymbiosis.
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Affiliation(s)
- Sergio López-Madrigal
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de ValènciaValència, Spain
| | - Amparo Latorre
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de ValènciaValència, Spain
- Área de Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO) – Salud PúblicaValència, Spain
| | - Andrés Moya
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de ValènciaValència, Spain
- Área de Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO) – Salud PúblicaValència, Spain
| | - Rosario Gil
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de ValènciaValència, Spain
- *Correspondence: Rosario Gil, Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, C/Catedrático José Beltrán 2, 46980 Paterna, Valencia, Spain
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Reyes-Prieto M, Vargas-Chávez C, Latorre A, Moya A. SymbioGenomesDB: a database for the integration and access to knowledge on host-symbiont relationships. Database (Oxford) 2015; 2015:bav109. [PMID: 26607947 PMCID: PMC4659445 DOI: 10.1093/database/bav109] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 09/10/2015] [Indexed: 02/07/2023]
Abstract
Symbiotic relationships occur naturally throughout the tree of life, either in a commensal, mutualistic or pathogenic manner. The genomes of multiple organisms involved in symbiosis are rapidly being sequenced and becoming available, especially those from the microbial world. Currently, there are numerous databases that offer information on specific organisms or models, but none offer a global understanding on relationships between organisms, their interactions and capabilities within their niche, as well as their role as part of a system, in this case, their role in symbiosis. We have developed the SymbioGenomesDB as a community database resource for laboratories which intend to investigate and use information on the genetics and the genomics of organisms involved in these relationships. The ultimate goal of SymbioGenomesDB is to host and support the growing and vast symbiotic-host relationship information, to uncover the genetic basis of such associations. SymbioGenomesDB maintains a comprehensive organization of information on genomes of symbionts from diverse hosts throughout the Tree of Life, including their sequences, their metadata and their genomic features. This catalog of relationships was generated using computational tools, custom R scripts and manual integration of data available in public literature. As a highly curated and comprehensive systems database, SymbioGenomesDB provides web access to all the information of symbiotic organisms, their features and links to the central database NCBI. Three different tools can be found within the database to explore symbiosis-related organisms, their genes and their genomes. Also, we offer an orthology search for one or multiple genes in one or multiple organisms within symbiotic relationships, and every table, graph and output file is downloadable and easy to parse for further analysis. The robust SymbioGenomesDB will be constantly updated to cope with all the data being generated and included in major databases, in order to serve as an important, useful and timesaving tool. Database URL: http://symbiogenomesdb.uv.es.
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Affiliation(s)
- Mariana Reyes-Prieto
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Calle Catedrático José Beltrán 2, 46980 Paterna, València, Spain
| | - Carlos Vargas-Chávez
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Calle Catedrático José Beltrán 2, 46980 Paterna, València, Spain
| | - Amparo Latorre
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Calle Catedrático José Beltrán 2, 46980 Paterna, València, Spain, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO)-Salud Púbica, Avenida de Catalunya 21 46020, València, Spain and CIBER en Epidemiología y Salud Pública (CIBEResp), Madrid, Spain
| | - Andrés Moya
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Calle Catedrático José Beltrán 2, 46980 Paterna, València, Spain, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO)-Salud Púbica, Avenida de Catalunya 21 46020, València, Spain and CIBER en Epidemiología y Salud Pública (CIBEResp), Madrid, Spain
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84
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Garcia-Nuñez M, Millares L, Pomares X, Ferrari R, Pérez-Brocal V, Gallego M, Espasa M, Moya A, Monsó E. Severity-related changes of bronchial microbiome in chronic obstructive pulmonary disease. J Clin Microbiol 2014; 52:4217-23. [PMID: 25253795 PMCID: PMC4313290 DOI: 10.1128/jcm.01967-14] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Bronchial colonization by potentially pathogenic microorganisms (PPMs) is often demonstrated in chronic obstructive pulmonary disease (COPD), but culture-based techniques identify only a portion of the bacteria in mucosal surfaces. The aim of the study was to determine changes in the bronchial microbiome of COPD associated with the severity of the disease. The bronchial microbiome of COPD patients was analyzed by 16S rRNA gene amplification and pyrosequencing in sputum samples obtained during stable disease. Seventeen COPD patients were studied (forced expiratory volume in the first second expressed as a percentage of the forced vital capacity [FEV1%] median, 35.0%; interquartile range [IQR], 31.5 to 52.0), providing a mean of 4,493 (standard deviation [SD], 2,598) sequences corresponding to 47 operational taxonomic units (OTUs) (SD, 17) at a 97% identity level. Patients were dichotomized according to their lung function as moderate to severe when their FEV1% values were over the median and as advanced when FEV1% values were lower. The most prevalent phyla in sputum were Proteobacteria (44%) and Firmicutes (16%), followed by Actinobacteria (13%). A greater microbial diversity was found in patients with moderate-to-severe disease, and alpha diversity showed a statistically significant decrease in patients with advanced disease when assessed by Shannon (ρ = 0.528; P = 0.029, Spearman correlation coefficient) and Chao1 (ρ = 0.53; P = 0.028, Spearman correlation coefficient) alpha-diversity indexes. The higher severity that characterizes advanced COPD is paralleled by a decrease in the diversity of the bronchial microbiome, with a loss of part of the resident flora that is replaced by a more restricted microbiota that includes PPMs.
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Affiliation(s)
- Marian Garcia-Nuñez
- Fundació Parc Taulí, Sabadell/Badalona, Spain CIBER de Enfermedades Respiratorias (CIBERES), Bunyola, Spain Universitat Autonoma de Barcelona, Esfera (UAB), Barcelona, Spain Fundació Institut d'Investigació Germans Trias i Pujol, Badalona, Spain
| | - Laura Millares
- Fundació Parc Taulí, Sabadell/Badalona, Spain CIBER de Enfermedades Respiratorias (CIBERES), Bunyola, Spain Universitat Autonoma de Barcelona, Esfera (UAB), Barcelona, Spain Fundació Institut d'Investigació Germans Trias i Pujol, Badalona, Spain
| | - Xavier Pomares
- Universitat Autonoma de Barcelona, Esfera (UAB), Barcelona, Spain Department of Respiratory Medicine, Hospital Universitari Parc Taulí, Sabadell, Spain
| | - Rafaela Ferrari
- Genomics and Health Area, Centro Superior de Investigación en Salud Pública- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (CSISP-FISABIO), Valencia, Spain CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain Department of Genetics, Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE), Universitat de València, Valencia, Spain
| | - Vicente Pérez-Brocal
- Genomics and Health Area, Centro Superior de Investigación en Salud Pública- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (CSISP-FISABIO), Valencia, Spain CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain Department of Genetics, Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE), Universitat de València, Valencia, Spain
| | - Miguel Gallego
- Universitat Autonoma de Barcelona, Esfera (UAB), Barcelona, Spain Department of Respiratory Medicine, Hospital Universitari Parc Taulí, Sabadell, Spain
| | - Mateu Espasa
- Department of Microbiology, Hospital Universitari Parc Taulí, Sabadell, Spain
| | - Andrés Moya
- Genomics and Health Area, Centro Superior de Investigación en Salud Pública- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (CSISP-FISABIO), Valencia, Spain CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain Department of Genetics, Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE), Universitat de València, Valencia, Spain
| | - Eduard Monsó
- Fundació Parc Taulí, Sabadell/Badalona, Spain CIBER de Enfermedades Respiratorias (CIBERES), Bunyola, Spain Universitat Autonoma de Barcelona, Esfera (UAB), Barcelona, Spain Department of Respiratory Medicine, Hospital Universitari Parc Taulí, Sabadell, Spain
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85
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Novakova J, Džunková M, Musilova S, Vlkova E, Kokoska L, Moya A, D'Auria G. Selective growth-inhibitory effect of 8-hydroxyquinoline towards Clostridium difficile and Bifidobacterium longum subsp. longum in co-culture analysed by flow cytometry. J Med Microbiol 2014; 63:1663-1669. [PMID: 25298160 DOI: 10.1099/jmm.0.080796-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The major risk factor for Clostridium difficile infection (CDI) is the use of antibiotics owing to the disruption of the equilibrium of the host gut microbiota. To preserve the beneficial resident probiotic bacteria during infection treatment, the use of molecules with selective antibacterial activity enhances the efficacy by selectively removing C. difficile. One of them is the plant alkaloid 8-hydroxyquinoline (8HQ), which has been shown to selectively inhibit clostridia without repressing bifidobacteria. Selective antimicrobial activity is generally tested by culture techniques of individual bacterial strains. However, the main limitation of these techniques is the inability to describe differential growth dynamics of more bacterial strains in co-culture within the same experiment. In the present study, we combined fluorescent in situ hybridization and flow cytometry to describe the changes in active and non-active cells of a mixed culture formed by the opportunistic pathogen C. difficile CECT 531 and the beneficial Bifidobacterium longum subsp. longum CCMDMND BL1 after exposure to 8HQ. It was observed that without 8HQ, the proportion of both strains was almost equal, oscillating between 22.7 and 77.9 % during a time lapse of 12 h, whereas with 8HQ the proportion of active C. difficile decreased after 4 h, and persisted only between 8.8 and 17.5 %. In contrast, bifidobacterial growth was not disturbed by 8HQ. The results of this study showed the selective inhibitory effect of 8HQ on clostridial and bifidobacterial growth dynamics, and the potential of this compound for the development of selective agents to control CDIs.
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Affiliation(s)
- Jitka Novakova
- Department of Crop Sciences and Agroforestry, Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamycka 129, 165 21 Prague 6-Suchdol, Czech Republic
| | - Mária Džunková
- Joint Unit of Research in Genomics and Health, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO)-Salud Pública, Avenida de Catalunya 21, Valencia 46020, Spain
- Centro de Investigación en Red en Epidemiología y Salud Pública (CIBEResp), Melchor Fernández Almagro 3-5, 28029 Madrid, Spain
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, University of Valencia, c/Catedrático José Beltrán 2, 46980 Paterna, Valencia, Spain
| | - Sarka Musilova
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 21 Prague 6-Suchdol, Czech Republic
| | - Eva Vlkova
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 21 Prague 6-Suchdol, Czech Republic
| | - Ladislav Kokoska
- Department of Crop Sciences and Agroforestry, Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamycka 129, 165 21 Prague 6-Suchdol, Czech Republic
| | - Andrés Moya
- Centro de Investigación en Red en Epidemiología y Salud Pública (CIBEResp), Melchor Fernández Almagro 3-5, 28029 Madrid, Spain
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, University of Valencia, c/Catedrático José Beltrán 2, 46980 Paterna, Valencia, Spain
- Joint Unit of Research in Genomics and Health, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO)-Salud Pública, Avenida de Catalunya 21, Valencia 46020, Spain
| | - Giuseppe D'Auria
- Centro de Investigación en Red en Epidemiología y Salud Pública (CIBEResp), Melchor Fernández Almagro 3-5, 28029 Madrid, Spain
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, University of Valencia, c/Catedrático José Beltrán 2, 46980 Paterna, Valencia, Spain
- Joint Unit of Research in Genomics and Health, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO)-Salud Pública, Avenida de Catalunya 21, Valencia 46020, Spain
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González-Candelas F, Alma Bracho M, Comas I, d'Auria G, D Unková M, García R, Gosalbes MJ, Isaac S, Latorre A, López-Labrador FX, Patiño Galindo JÁ, Palero F, Pérez-Brocal V, Pérez-Cobas AE, Sánchez-Busó L, Silva FJ, Vázquez-Castellanos JF, Moya A. [Molecular epidemiology studies on the immigrant population in Spain]. Rev Esp Salud Publica 2014; 88:819-28. [PMID: 25418571 DOI: 10.4321/s1135-57272014000600013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Molecular epidemiology is a new scientific discipline which allows to integrate information on the genetic variation of infectious pathogens with their diffusion in a population and its subgroups including, for instance, resistance mutations to antibiotics and antiretrovirals. We present the results of an analysis of scientific publications that analyze the health status of the immigrant population in Spain from a molecular epidemiology perspective. METHODS We reviewed original articles published in 1998-2014 with the keywords "molecular epidemiology", "molecular typing", "sequencing", "immigrant", and "Spain". RESULTS From a total of 267 articles identified initially, only 50 passed through the established filters. Most of them (36) analyzed infections by Mycobacterium tuberculosis (3) and HIV (3), followed at a large distance by Staphylococcus aureus and hepatitis B virus. The main goal of these works was the typing of the pathogen and to determine the frequency of resistance mutations. CONCLUSION Is difficult to generalize the conclusions from the analyzed articles because most of them have a purely descriptive and quite restricted scope, considering the type and size of the samples studied. Several studies are focused on the most likely origin for the strains or variants of the pathogen but others also reveal transmissions from the local to the immigrant populations.
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87
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Santos-Garcia D, Silva FJ, Moya A, Latorre A. No exception to the rule: Candidatus Portiera aleyrodidarum cell wall revisited. FEMS Microbiol Lett 2014; 360:132-6. [PMID: 25196985 DOI: 10.1111/1574-6968.12595] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 09/02/2014] [Indexed: 02/05/2023] Open
Abstract
Many insect endosymbionts described so far are gram-negative bacteria. Primary endosymbionts are obligatory bacteria usually harboured by insects inside vacuoles in specialized cells called bacteriocytes. This combination produces a typical three-membrane system with one membrane derived from the insect vacuole and the other two from the bacterial gram-negative cell envelope, composed by the cell wall (the outer membrane plus the periplasmic space) and the plasma membrane (the inner membrane). For the last 21 years, the primary endosymbiont of whiteflies 'Candidatus Portiera aleyrodidarum' was considered an exception to this rule. Previous works stated that only two membranes were present, the vacuolar membrane and one of the two bacterial membranes. The absence of the cell wall was related to the special vertical transmission of the endosymbionts in whiteflies. In this work, we present electron microscopic studies showing a complete cell envelope in 'Ca. Portiera aleyrodidarum' from the whitefly Bemisia tabaci. Additionally, comparison of the inferred metabolism from the gene content did not show any difference in cell envelope biogenesis compared with the closely related three-membrane endosymbionts 'Candidatus Carsonella ruddii' and 'Candidatus Evansia muelleri' Xc1. Our results rule out the proposal that 'Ca. Portiera aleyrodidarum' is an exception to the three-membrane system.
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Affiliation(s)
- Diego Santos-Garcia
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Paterna, Spain
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88
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89
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García-López R, Moya A, Bagan JV, Pérez-Brocal V. Retrospective case-control study of viral pathogen screening in proliferative verrucous leukoplakia lesions. Clin Otolaryngol 2014; 39:272-80. [PMID: 25099922 DOI: 10.1111/coa.12291] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2014] [Indexed: 02/05/2023]
Abstract
OBJECTIVE This study aimed to survey the presence of known oncoviruses in oral biopsies from patients diagnosed with the aetiologically undetermined proliferative verrucous leukoplakia and compare results to those from milder oral leukoplakia (OL) cases, oral squamous cell carcinoma, a common outcome of the lesions of interest, and healthy controls. DESIGN Blind, retrospective, case-control study. SETTING A stomatology unit in an academic Hospital and a Public Health laboratory. PARTICIPANTS Forty patients were divided in four groups. Ten patients had been diagnosed with proliferative verrucous leukoplakia, 10 with OL and 10 with OSCC, and 10 were healthy subjects. MAIN OUTCOME MEASURES The presence or absence of oncovirus DNA was assayed with the amplification of viral genetic markers using PCR and subsequent gel electrophoresis confirmation. Amplified fragments were sequenced and identified bioinformatically. RESULTS No DNA from the herpesvirus, papillomavirus or polyomavirus species was detected in the samples. CONCLUSIONS No association between proliferative verrucous leukoplakia and target viruses was detected. A higher throughput viral metagenomic approach may prove valuable for future analyses, as it would not be restricted to a priori knowledge of potential targets.
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Affiliation(s)
- R García-López
- Área de Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO)-Salud Pública, Valencia, Spain; Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Valencia, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
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90
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Reyes-Prieto M, Oceguera-Figueroa A, Snell S, Negredo A, Barba E, Fernández L, Moya A, Latorre A. DNA barcodes reveal the presence of the introduced freshwater leech Helobdella europaea in Spain. Mitochondrial DNA 2014; 25:387-93. [PMID: 23885897 DOI: 10.3109/19401736.2013.809426] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Abstract We report the finding of the freshwater leech Helobdella europaea in Spain for the first time. Three leech specimens were found attached to the European pond turtle Emys orbicularis. Helobdella europaea is not a blood feeder and, like all members of the genus, feeds on the hemolymph of aquatic invertebrates including snails and worms. Despite the fact that the original geographical distribution or source population of this species is unknown, the close relationship between H. europaea and leeches of the "triserialis" series (sensu Sawyer, 1986) suggests a New World origin. Given its ability to invade and persist in new environments, this leech has been described as a new species by local taxonomists resulting in some nomenclatural problems. The presence of this introduced organism in Spain may represent serious obstacles to the current efforts to preserve endemic fauna and the potential negative impacts of this species in European environments should be investigated.
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Affiliation(s)
- Mariana Reyes-Prieto
- Laboratorio de Genética Evolutiva, Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universidad de Valencia , Paterna, Valencia , Spain
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91
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Santos-Garcia D, Latorre A, Moya A, Gibbs G, Hartung V, Dettner K, Kuechler SM, Silva FJ. Small but powerful, the primary endosymbiont of moss bugs, Candidatus Evansia muelleri, holds a reduced genome with large biosynthetic capabilities. Genome Biol Evol 2014; 6:1875-93. [PMID: 25115011 PMCID: PMC4122945 DOI: 10.1093/gbe/evu149] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Moss bugs (Coleorrhyncha: Peloridiidae) are members of the order Hemiptera, and like many hemipterans, they have symbiotic associations with intracellular bacteria to fulfill nutritional requirements resulting from their unbalanced diet. The primary endosymbiont of the moss bugs, Candidatus Evansia muelleri, is phylogenetically related to Candidatus Carsonella ruddii and Candidatus Portiera aleyrodidarum, primary endosymbionts of psyllids and whiteflies, respectively. In this work, we report the genome of Candidatus Evansia muelleri Xc1 from Xenophyes cascus, which is the only obligate endosymbiont present in the association. This endosymbiont possesses an extremely reduced genome similar to Carsonella and Portiera. It has crossed the borderline to be considered as an autonomous cell, requiring the support of the insect host for some housekeeping cell functions. Interestingly, in spite of its small genome size, Evansia maintains enriched amino acid (complete or partial pathways for ten essential and six nonessential amino acids) and sulfur metabolisms, probably related to the poor diet of the insect, based on bryophytes, which contains very low levels of nitrogenous and sulfur compounds. Several facts, including the congruence of host (moss bugs, whiteflies, and psyllids) and endosymbiont phylogenies and the retention of the same ribosomal RNA operon during genome reduction in Evansia, Portiera, and Carsonella, suggest the existence of an ancient endosymbiotic Halomonadaceae clade associated with Hemiptera. Three possible scenarios for the origin of these three primary endosymbiont genera are proposed and discussed.
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Affiliation(s)
- Diego Santos-Garcia
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain
| | - Amparo Latorre
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain
- Unidad Mixta de Investigación en Genómica y Salud (FISABIO-Salud Pública and Universitat de València), Spain
| | - Andrés Moya
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain
- Unidad Mixta de Investigación en Genómica y Salud (FISABIO-Salud Pública and Universitat de València), Spain
| | - George Gibbs
- School of Biological Science, Victoria University, Wellington, New Zealand
| | - Viktor Hartung
- Museum für Naturkunde, Leibniz-Institute for Research on Evolution and Biodiversity, Berlin, Germany
| | - Konrad Dettner
- Department of Animal Ecology II, University of Bayreuth, Germany
| | - Stefan Martin Kuechler
- Department of Animal Ecology II, University of Bayreuth, Germany
- *Corresponding author: E-mail: ;
| | - Francisco J. Silva
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain
- Unidad Mixta de Investigación en Genómica y Salud (FISABIO-Salud Pública and Universitat de València), Spain
- *Corresponding author: E-mail: ;
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92
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Patiño-Navarrete R, Piulachs MD, Belles X, Moya A, Latorre A, Peretó J. The cockroach Blattella germanica obtains nitrogen from uric acid through a metabolic pathway shared with its bacterial endosymbiont. Biol Lett 2014; 10:rsbl.2014.0407. [PMID: 25079497 PMCID: PMC4126632 DOI: 10.1098/rsbl.2014.0407] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Uric acid stored in the fat body of cockroaches is a nitrogen reservoir mobilized in times of scarcity. The discovery of urease in Blattabacterium cuenoti, the primary endosymbiont of cockroaches, suggests that the endosymbiont may participate in cockroach nitrogen economy. However, bacterial urease may only be one piece in the entire nitrogen recycling process from insect uric acid. Thus, in addition to the uricolytic pathway to urea, there must be glutamine synthetase assimilating the released ammonia by the urease reaction to enable the stored nitrogen to be metabolically usable. None of the Blattabacterium genomes sequenced to date possess genes encoding for those enzymes. To test the host's contribution to the process, we have sequenced and analysed Blattella germanica transcriptomes from the fat body. We identified transcripts corresponding to all genes necessary for the synthesis of uric acid and its catabolism to urea, as well as for the synthesis of glutamine, asparagine, proline and glycine, i.e. the amino acids required by the endosymbiont. We also explored the changes in gene expression with different dietary protein levels. It appears that the ability to use uric acid as a nitrogen reservoir emerged in cockroaches after its age-old symbiotic association with bacteria.
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Affiliation(s)
- Rafael Patiño-Navarrete
- InstitutCavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, C/Catedràtic José Beltrán n° 2, Paterna 46980, Spain
| | - Maria-Dolors Piulachs
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas and Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta n° 37-49, Barcelona 08003, Spain
| | - Xavier Belles
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas and Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta n° 37-49, Barcelona 08003, Spain
| | - Andrés Moya
- InstitutCavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, C/Catedràtic José Beltrán n° 2, Paterna 46980, Spain
| | - Amparo Latorre
- InstitutCavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, C/Catedràtic José Beltrán n° 2, Paterna 46980, Spain
| | - Juli Peretó
- InstitutCavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, C/Catedràtic José Beltrán n° 2, Paterna 46980, Spain Departament de Bioquímica i Biologia Molecular, Universitat de València, Burjassot 46100, Spain
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93
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Millares L, Ferrari R, Gallego M, Garcia-Nuñez M, Pérez-Brocal V, Espasa M, Pomares X, Monton C, Moya A, Monsó E. Bronchial microbiome of severe COPD patients colonised by Pseudomonas aeruginosa. Eur J Clin Microbiol Infect Dis 2014; 33:1101-11. [PMID: 24449346 PMCID: PMC4042013 DOI: 10.1007/s10096-013-2044-0] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 12/20/2013] [Indexed: 02/07/2023]
Abstract
The bronchial microbiome in severe COPD during stability and exacerbation in patients chronically colonised by Pseudomonas aeruginosa (PA), has not been defined. Our objective was to determine the characteristics of the bronchial microbiome of severe COPD patients colonised and not colonised by P. aeruginosa and its changes during exacerbation. COPD patients with severe disease and frequent exacerbations were categorised according to chronic colonisation by P. aeruginosa. Sputum samples were obtained in stability and exacerbation, cultured, and analysed by 16S rRNA gene amplification and pyrosequencing. Sixteen patients were included, 5 of them showing chronic colonisation by P. aeruginosa. Pseudomonas genus had significantly higher relative abundance in stable colonised patients (p = 0.019), but no significant differences in biodiversity parameters were found between the two groups (Shannon, 3 (2-4) vs 3 (2-3), p = 0.699; Chao1, 124 (77-159) vs 140 (115-163), p = 0.364). In PA-colonised patients bronchial microbiome changed to a microbiome similar to non-PA-colonised patients during exacerbations. An increase in the relative abundance over 20 % during exacerbation was found for Streptococcus, Pseudomonas, Moraxella, Haemophilus, Neisseria, Achromobacter and Corynebacterium genera, which include recognised potentially pathogenic microorganisms, in 13 patients colonised and not colonised by P. aeruginosa with paired samples. These increases were not identified by culture in 5 out of 13 participants (38.5 %). Stable COPD patients with severe disease and PA-colonised showed a similar biodiversity to non-PA-colonised patients, with a higher relative abundance of Pseudomonas genus in bronchial secretions. Exacerbation in severe COPD patients showed the same microbial pattern, independently of previous colonisation by P. aeruginosa.
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Affiliation(s)
- L. Millares
- Fundació Parc Taulí, Sabadell, Spain
- CIBER de Enfermedades Respiratorias, CIBERES, Bunyola, Spain
- Universitat Autònoma de Barcelona, Esfera UAB, Barcelona, Spain
- Fundació Institut d’Investigació Germans Trias i Pujol, Badalona, Spain
| | - R. Ferrari
- Genomics and Health Area, Centro Superior de Investigación en Salud Pública—Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (CSISP-FISABIO), Valencia, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
- Department of Genetics, Institut Cavanilles de Biodiversitat i Biologia Evolutiva, (ICBiBE) Universitat de València, Valencia, Spain
| | - M. Gallego
- CIBER de Enfermedades Respiratorias, CIBERES, Bunyola, Spain
- Department of Respiratory Medicine, Hospital Universitari Parc Taulí, Sabadell, Spain
| | - M. Garcia-Nuñez
- Fundació Parc Taulí, Sabadell, Spain
- CIBER de Enfermedades Respiratorias, CIBERES, Bunyola, Spain
- Fundació Institut d’Investigació Germans Trias i Pujol, Badalona, Spain
| | - V. Pérez-Brocal
- Genomics and Health Area, Centro Superior de Investigación en Salud Pública—Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (CSISP-FISABIO), Valencia, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
- Department of Genetics, Institut Cavanilles de Biodiversitat i Biologia Evolutiva, (ICBiBE) Universitat de València, Valencia, Spain
| | - M. Espasa
- Department of Microbiology, Hospital Universitari Parc Taulí, Sabadell, Spain
| | - X. Pomares
- Department of Respiratory Medicine, Hospital Universitari Parc Taulí, Sabadell, Spain
| | - C. Monton
- Department of Respiratory Medicine, Hospital Universitari Parc Taulí, Sabadell, Spain
| | - A. Moya
- Genomics and Health Area, Centro Superior de Investigación en Salud Pública—Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (CSISP-FISABIO), Valencia, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
- Department of Genetics, Institut Cavanilles de Biodiversitat i Biologia Evolutiva, (ICBiBE) Universitat de València, Valencia, Spain
| | - E. Monsó
- CIBER de Enfermedades Respiratorias, CIBERES, Bunyola, Spain
- Universitat Autònoma de Barcelona, Esfera UAB, Barcelona, Spain
- Department of Respiratory Medicine, Hospital Universitari Parc Taulí, Sabadell, Spain
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94
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Carrasco P, Pérez-Cobas AE, van de Pol C, Baixeras J, Moya A, Latorre A. Succession of the gut microbiota in the cockroach Blattella germanica. Int Microbiol 2014; 17:99-109. [PMID: 26418854 DOI: 10.2436/20.1501.01.212] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 06/10/2014] [Indexed: 02/07/2023]
Abstract
The cockroach gut harbors a wide variety of microorganisms that, among other functions, collaborate in digestion and act as a barrier against pathogen colonization. Blattabacterium, a primary endosymbiont, lives in the fat body inside bacteriocytes and plays an important role in nitrogen recycling. Little is known about the mode of acquisition of gut bacteria or their ecological succession throughout the insect life cycle. Here we report on the bacterial taxa isolated from different developmental instars of the cockroach Blattella germanica. The bacterial load in the gut increased two orders of magnitude from the first to the second nymphal stage, coinciding with the incorporation of the majority of bacterial taxa, but remained similar thereafter. Pyrosequencing of the hypervariable regions V1-V3 of the 16S rRNA genes showed that the microbial composition differed significantly between adults and nymphs. Specifically, a succession was observed in which Fusobacterium accumulated with aging, while Bacteroides decreased. Blattabacterium was the only symbiont found in the ootheca, which makes the vertical transmission of gut bacteria an unlikely mode of acquisition. Scanning electron microscopy disclosed a rich bacterial biofilm in third instar nymphs, while filamentous structures were found exclusively in adults.
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Affiliation(s)
- Purificación Carrasco
- Institute of Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain
| | - Ana Elena Pérez-Cobas
- Genomics and Health Area, Foundation for the Health and Biomedical of the Community of Valencia, Valencia, Spain
| | - Claudia van de Pol
- Institute of Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain
| | - Joaquín Baixeras
- Institute of Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain
| | - Andrés Moya
- Institute of Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain
- Genomics and Health Area, Foundation for the Health and Biomedical of the Community of Valencia, Valencia, Spain
| | - Amparo Latorre
- Institute of Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain
- Genomics and Health Area, Foundation for the Health and Biomedical of the Community of Valencia, Valencia, Spain
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95
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D'Auria G, Džunková M, Moya A, Tomáška M, Kološta M, Kmet V. Genome Sequence of Lactobacillus plantarum 19L3, a Strain Proposed as a Starter Culture for Slovenska Bryndza Ovine Cheese. Genome Announc 2014; 2:2/2/e00292-14. [PMID: 24762933 PMCID: PMC3999490 DOI: 10.1128/genomea.00292-14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The genome sequence of Lactobacillus plantarum isolated from ovine cheese is presented here. This bacterium is proposed as a starter strain, named 19L3, for Slovenská bryndza cheese, a traditional Slovak cheese fulfilling European Food Safety Authority (EFSA) requirements.
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Affiliation(s)
| | | | | | | | | | - Vladimir Kmet
- Institute of Animal Physiology, Slovak Academy of Sciences, Košice, Slovakia
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96
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Encinas D, Garcillán-Barcia MP, Santos-Merino M, Delaye L, Moya A, de la Cruz F. Plasmid conjugation from proteobacteria as evidence for the origin of xenologous genes in cyanobacteria. J Bacteriol 2014; 196:1551-9. [PMID: 24509315 PMCID: PMC3993370 DOI: 10.1128/jb.01464-13] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Comparative genomics have shown that 5% of Synechococcus elongatus PCC 7942 genes are of probable proteobacterial origin. To investigate the role of interphylum conjugation in cyanobacterial gene acquisition, we tested the ability of a set of prototype proteobacterial conjugative plasmids (RP4, pKM101, R388, R64, and F) to transfer DNA from Escherichia coli to S. elongatus. A series of BioBrick-compatible, mobilizable shuttle vectors was developed. These vectors were based on the putative origin of replication of the Synechococcus resident plasmid pANL. Not only broad-host-range plasmids, such as RP4 and R388, but also narrower-host-range plasmids, such as pKM101, all encoding MPFT-type IV secretion systems, were able to transfer plasmid DNA from E. coli to S. elongatus by conjugation. Neither MPFF nor MPFI could be used as interphylum DNA delivery agents. Reciprocally, pANL-derived cointegrates could be introduced in E. coli by electroporation, where they conferred a functional phenotype. These results suggest the existence of potentially ample channels of gene flow between proteobacteria and cyanobacteria and point to MPFT-based interphylum conjugation as a potential mechanism to explain the proteobacterial origin of a majority of S. elongatus xenologous genes.
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Affiliation(s)
- David Encinas
- Instituto de Biomedicina y Biotecnología de Cantabria IBBTEC, CSIC–Universidad de Cantabria-SODERCAN, Santander, Spain
| | - M. Pilar Garcillán-Barcia
- Instituto de Biomedicina y Biotecnología de Cantabria IBBTEC, CSIC–Universidad de Cantabria-SODERCAN, Santander, Spain
| | - María Santos-Merino
- Instituto de Biomedicina y Biotecnología de Cantabria IBBTEC, CSIC–Universidad de Cantabria-SODERCAN, Santander, Spain
| | - Luis Delaye
- Departamento de Ingeniería Genética CINVESTAV-Irapuato, Irapuato, Guanajuato, Mexico
| | - Andrés Moya
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Valencia, Spain
| | - Fernando de la Cruz
- Instituto de Biomedicina y Biotecnología de Cantabria IBBTEC, CSIC–Universidad de Cantabria-SODERCAN, Santander, Spain
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Santos-Garcia D, Rollat-Farnier PA, Beitia F, Zchori-Fein E, Vavre F, Mouton L, Moya A, Latorre A, Silva FJ. The genome of Cardinium cBtQ1 provides insights into genome reduction, symbiont motility, and its settlement in Bemisia tabaci. Genome Biol Evol 2014; 6:1013-30. [PMID: 24723729 PMCID: PMC4007549 DOI: 10.1093/gbe/evu077] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Many insects harbor inherited bacterial endosymbionts. Although some of them are not strictly essential and are considered facultative, they can be a key to host survival under specific environmental conditions, such as parasitoid attacks, climate changes, or insecticide pressures. The whitefly Bemisia tabaci is at the top of the list of organisms inflicting agricultural damage and outbreaks, and changes in its distribution may be associated to global warming. In this work, we have sequenced and analyzed the genome of Cardinium cBtQ1, a facultative bacterial endosymbiont of B. tabaci and propose that it belongs to a new taxonomic family, which also includes Candidatus Amoebophilus asiaticus and Cardinium cEper1, endosymbionts of amoeba and wasps, respectively. Reconstruction of their last common ancestors' gene contents revealed an initial massive gene loss from the free-living ancestor. This was followed in Cardinium by smaller losses, associated with settlement in arthropods. Some of these losses, affecting cofactor and amino acid biosynthetic encoding genes, took place in Cardinium cBtQ1 after its divergence from the Cardinium cEper1 lineage and were related to its settlement in the whitefly and its endosymbionts. Furthermore, the Cardinium cBtQ1 genome displays a large proportion of transposable elements, which have recently inactivated genes and produced chromosomal rearrangements. The genome also contains a chromosomal duplication and a multicopy plasmid, which harbors several genes putatively associated with gliding motility, as well as two other genes encoding proteins with potential insecticidal activity. As gene amplification is very rare in endosymbionts, an important function of these genes cannot be ruled out.
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Affiliation(s)
- Diego Santos-Garcia
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain
| | - Pierre-Antoine Rollat-Farnier
- Université de Lyon, Université Lyon1, Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Villeurbanne, France
- BAMBOO Research team, INRIA Grenoble, Rhône-Alpes, France
| | - Francisco Beitia
- Instituto Valenciano de Investigaciones Agrarias, Unidad Asociada de Entomología IVIA/CIB-CSIC, Valencia, Spain
| | - Einat Zchori-Fein
- Department of Entomology, Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Fabrice Vavre
- Université de Lyon, Université Lyon1, Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Villeurbanne, France
- BAMBOO Research team, INRIA Grenoble, Rhône-Alpes, France
| | - Laurence Mouton
- Université de Lyon, Université Lyon1, Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Villeurbanne, France
| | - Andrés Moya
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain
- Unidad Mixta de Investigación en Genómica y Salud (FISABIO-Salud Pública and Universitat de València), Valencia, Spain
| | - Amparo Latorre
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain
- Unidad Mixta de Investigación en Genómica y Salud (FISABIO-Salud Pública and Universitat de València), Valencia, Spain
- *Corresponding author: E-mail: ;
| | - Francisco J. Silva
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain
- Unidad Mixta de Investigación en Genómica y Salud (FISABIO-Salud Pública and Universitat de València), Valencia, Spain
- *Corresponding author: E-mail: ;
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Matas M, Picornell A, Cifuentes C, Payeras A, Homar F, González-Candelas F, López-Labrador FX, Moya A, Ramon C, Castro JA. Relating the outcome of HCV infection and different host SNP polymorphisms in a Majorcan population coinfected with HCV-HIV and treated with pegIFN-RBV. Int Microbiol 2014; 17:11-20. [PMID: 25296442 DOI: 10.2436/20.1501.01.203] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Hepatitis C virus (HCV) is one of the major causes of chronic hepatitis, cirrhosis, and hepatocellular carcinoma, and the development of HCV-related disease is accelerated in individuals coinfected with human immunodeficiency-1 virus (HIV). In the present study, we correlated different host single-nucleotide polymorphisms (SNPs) in the IL28B, CTLA4, LDLr, and HFE genes and mitochondrial DNA (mtDNA) haplogroups with the outcome of HCV infection and the response to pegylated-interferon plus ribavirin (pegIFN-RBV) treatment. Our study population consisted of 63 Majorcan patients coinfected with HCV and HIV and 59 anonymous unrelated controls. Whereas the population frequency of IL28B alleles was similar to that found in a North-American cohort of European descent, the frequency of the rs12979860 C allele was lower than that determined in other cohorts from Spain. The frequencies of CTLA4 and LDLr polymorphisms were comparable to those reported in other populations. Significant differences between cases and control cohorts occurred only for the H63D mutation of the HFE gene. There were no other differences in the frequencies of other polymorphisms or mtDNA haplogroups. The IL28B rs12979860 CC genotype was shown to be associated with a rapid virological response, and the spontaneous viral clearance rate for HCV was higher in patients with the CTLA4+49 G allele. There was no relationship between SNPs in the LDLr and HFE genes and mtDNA haplogroups and the response to treatment. Our results suggest that the host genetic background plays a significant role in the pegIFN-RBV response of patients coinfected with HCV and HIV.
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Reyes-Prieto M, Latorre A, Moya A. Scanty microbes, the 'symbionelle' concept. Environ Microbiol 2014; 16:335-8. [PMID: 23968559 DOI: 10.1111/1462-2920.12220] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 07/11/2013] [Accepted: 07/18/2013] [Indexed: 02/05/2023]
Affiliation(s)
- Mariana Reyes-Prieto
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Calle Catedrático Agustín Escardino 9, 46980, Paterna, València, Spain
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Abstract
Whole genome analysis based on next generation sequencing (NGS) now represents an affordable framework in public health systems. Robust analytical pipelines of genomic data provides in short laps of time (hours) information about taxonomy, comparative genomics (pan-genome) and single polymorphisms profiles. Pathogenic organisms of interest can be tracked at the genomic level, allowing monitoring at one-time several variables including: epidemiology, pathogenicity, resistance to antibiotics, virulence, persistence factors, mobile elements and adaptation features. Such information can be obtained not only at large spectra, but also at the "local" level, such as in the event of a recurrent or emergency outbreak. This paper reviews the state of the art in infection diagnostics in the context of modern NGS methodologies. We describe how actuation protocols in a public health environment will benefit from a "streaming approach" (pipeline). Such pipeline would NGS data quality assessment, data mining for comparative analysis, searching differential genetic features, such as virulence, resistance persistence factors and mutation profiles (SNPs and InDels) and formatted "comprehensible" results. Such analytical protocols will enable a quick response to the needs of locally circumscribed outbreaks, providing information on the causes of resistance and genetic tracking elements for rapid detection, and monitoring actuations for present and future occurrences.
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Affiliation(s)
- Giuseppe D'Auria
- Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública), Avenida de Cataluña 21, 46020 Valencia, Spain.
| | | | - Andrés Moya
- Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública), Avenida de Cataluña 21, 46020 Valencia, Spain.
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