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Contreras-Rodriguez O, Arnoriaga-Rodríguez M, Miranda-Olivos R, Blasco G, Biarnés C, Puig J, Rivera-Pinto J, Calle ML, Pérez-Brocal V, Moya A, Coll C, Ramió-Torrentà L, Soriano-Mas C, Fernandez-Real JM. Obesity status and obesity-associated gut dysbiosis effects on hypothalamic structural covariance. Int J Obes (Lond) 2022; 46:30-38. [PMID: 34471225 PMCID: PMC8748191 DOI: 10.1038/s41366-021-00953-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 08/03/2021] [Accepted: 08/18/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND Functional connectivity alterations in the lateral and medial hypothalamic networks have been associated with the development and maintenance of obesity, but the possible impact on the structural properties of these networks remains largely unexplored. Also, obesity-related gut dysbiosis may delineate specific hypothalamic alterations within obese conditions. We aim to assess the effects of obesity, and obesity and gut-dysbiosis on the structural covariance differences in hypothalamic networks, executive functioning, and depressive symptoms. METHODS Medial (MH) and lateral (LH) hypothalamic structural covariance alterations were identified in 57 subjects with obesity compared to 47 subjects without obesity. Gut dysbiosis in the subjects with obesity was defined by the presence of high (n = 28) and low (n = 29) values in a BMI-associated microbial signature, and posthoc comparisons between these groups were used as a proxy to explore the role of obesity-related gut dysbiosis on the hypothalamic measurements, executive function, and depressive symptoms. RESULTS Structural covariance alterations between the MH and the striatum, lateral prefrontal, cingulate, insula, and temporal cortices are congruent with previously functional connectivity disruptions in obesity conditions. MH structural covariance decreases encompassed postcentral parietal cortices in the subjects with obesity and gut-dysbiosis, but increases with subcortical nuclei involved in the coding food-related hedonic information in the subjects with obesity without gut-dysbiosis. Alterations for the structural covariance of the LH in the subjects with obesity and gut-dysbiosis encompassed increases with frontolimbic networks, but decreases with the lateral orbitofrontal cortex in the subjects with obesity without gut-dysbiosis. Subjects with obesity and gut dysbiosis showed higher executive dysfunction and depressive symptoms. CONCLUSIONS Obesity-related gut dysbiosis is linked to specific structural covariance alterations in hypothalamic networks relevant to the integration of somatic-visceral information, and emotion regulation.
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Affiliation(s)
- O Contreras-Rodriguez
- Department of Psychiatry, Bellvitge University Hospital-IDIBELL, and CIBERSam-17 and CIBERObn (CB06/03/0034), Barcelona, Spain.
- Department of Radiology-Medical Imaging (IDI), Girona Biomedical Research Institute (IdIBGi), Josep Trueta University Hospital, Girona, Spain.
- Department of Psychiatry and Legal Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain.
- Health Institute Carlos III (ISCIII), Barcelona, Spain.
| | - M Arnoriaga-Rodríguez
- Health Institute Carlos III (ISCIII), Barcelona, Spain
- Department of Diabetes, Endocrinology and Nutrition-UDEN, and CIBERObn (CB06/03/0010), Girona, Spain
- Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain
| | - R Miranda-Olivos
- Department of Psychiatry, Bellvitge University Hospital-IDIBELL, and CIBERSam-17 and CIBERObn (CB06/03/0034), Barcelona, Spain
| | - G Blasco
- Department of Radiology-Medical Imaging (IDI), Girona Biomedical Research Institute (IdIBGi), Josep Trueta University Hospital, Girona, Spain
| | - C Biarnés
- Department of Radiology-Medical Imaging (IDI), Girona Biomedical Research Institute (IdIBGi), Josep Trueta University Hospital, Girona, Spain
| | - J Puig
- Department of Radiology-Medical Imaging (IDI), Girona Biomedical Research Institute (IdIBGi), Josep Trueta University Hospital, Girona, Spain
| | - J Rivera-Pinto
- IrsiCaixa AIDS Research Institute, Badalona, Spain
- Biosciences Department, Faculty of Sciences and Technology, University of Vic-Central University of Catalonia, VIC, Badalona, Spain
| | - M L Calle
- Biosciences Department, Faculty of Sciences and Technology, University of Vic-Central University of Catalonia, VIC, Badalona, Spain
| | - V Pérez-Brocal
- Department of Genomics and Health, Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO-Public Health), Valencia, Spain, and CIBEResp- CB06/02/0050, Madrid, Spain
| | - A Moya
- Department of Genomics and Health, Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO-Public Health), Valencia, Spain, and CIBEResp- CB06/02/0050, Madrid, Spain
- Institute for Integrative Systems Biology (I2SysBio), The University of Valencia and The Spanish National Research Council (CSIC-UVEG), Valencia, Spain
| | - C Coll
- Neuroimmunology and Multiple Sclerosis Unit, Department of Neurology, Girona Biomedical Research Institute (IdIBGi), Dr. Josep Trueta University Hospital, Girona, Spain
| | - L Ramió-Torrentà
- Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain
- Neuroimmunology and Multiple Sclerosis Unit, Department of Neurology, Girona Biomedical Research Institute (IdIBGi), Dr. Josep Trueta University Hospital, Girona, Spain
| | - C Soriano-Mas
- Department of Psychiatry, Bellvitge University Hospital-IDIBELL, and CIBERSam-17 and CIBERObn (CB06/03/0034), Barcelona, Spain
- Department of Psychobiology and Methodology of Health Sciences, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - J M Fernandez-Real
- Health Institute Carlos III (ISCIII), Barcelona, Spain.
- Department of Diabetes, Endocrinology and Nutrition-UDEN, and CIBERObn (CB06/03/0010), Girona, Spain.
- Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain.
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Arnoriaga-Rodríguez M, Mayneris-Perxachs J, Contreras-Rodríguez O, Burokas A, Ortega-Sanchez JA, Blasco G, Coll C, Biarnés C, Castells-Nobau A, Puig J, Garre-Olmo J, Ramos R, Pedraza S, Brugada R, Vilanova JC, Serena J, Barretina J, Gich J, Pérez-Brocal V, Moya A, Fernández-Real X, Ramio-Torrentà L, Pamplona R, Sol J, Jové M, Ricart W, Portero-Otin M, Maldonado R, Fernández-Real JM. Obesity-associated deficits in inhibitory control are phenocopied to mice through gut microbiota changes in one-carbon and aromatic amino acids metabolic pathways. Gut 2021; 70:2283-2296. [PMID: 33514598 PMCID: PMC8588299 DOI: 10.1136/gutjnl-2020-323371] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/16/2020] [Accepted: 01/08/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND Inhibitory control (IC) is critical to keep long-term goals in everyday life. Bidirectional relationships between IC deficits and obesity are behind unhealthy eating and physical exercise habits. METHODS We studied gut microbiome composition and functionality, and plasma and faecal metabolomics in association with cognitive tests evaluating inhibitory control (Stroop test) and brain structure in a discovery (n=156), both cross-sectionally and longitudinally, and in an independent replication cohort (n=970). Faecal microbiota transplantation (FMT) in mice evaluated the impact on reversal learning and medial prefrontal cortex (mPFC) transcriptomics. RESULTS An interplay among IC, brain structure (in humans) and mPFC transcriptomics (in mice), plasma/faecal metabolomics and the gut metagenome was found. Obesity-dependent alterations in one-carbon metabolism, tryptophan and histidine pathways were associated with IC in the two independent cohorts. Bacterial functions linked to one-carbon metabolism (thyX,dut, exodeoxyribonuclease V), and the anterior cingulate cortex volume were associated with IC, cross-sectionally and longitudinally. FMT from individuals with obesity led to alterations in mice reversal learning. In an independent FMT experiment, human donor's bacterial functions related to IC deficits were associated with mPFC expression of one-carbon metabolism-related genes of recipient's mice. CONCLUSION These results highlight the importance of targeting obesity-related impulsive behaviour through the induction of gut microbiota shifts.
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Affiliation(s)
- María Arnoriaga-Rodríguez
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain
- Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain
- CIBER Pathophysiology of Obesity and Nutrition (CIBEROBN), Madrid, Spain
- Deparment of Medical Sciences, Faculty of Medicine, University of Girona, Girona, Spain
| | - Jordi Mayneris-Perxachs
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain
- Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain
- CIBER Pathophysiology of Obesity and Nutrition (CIBEROBN), Madrid, Spain
| | - Oren Contreras-Rodríguez
- Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain
- Department of Psychiatry, Bellvitge University Hospital, Bellvitge Biomedical Research Institute (IDIBELL) and CIBERSAM, Barcelona, Spain
| | - Aurelijus Burokas
- Laboratory of Neuropharmacology, Deparment of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Present address: Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Juan-Antonio Ortega-Sanchez
- Laboratory of Neuropharmacology, Deparment of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Gerard Blasco
- Institute of Diagnostic Imaging (IDI)-Research Unit (IDIR), Parc Sanitari Pere Virgili, Barcelona, Spain
- Medical Imaging, Girona Biomedical Research Institute (IdibGi), Girona, Spain
| | - Claudia Coll
- Neuroimmunology and Multiple Sclerosis Unit, Deparment of Neurology, Dr. Josep Trueta University Hospital, Girona, Spain
| | - Carles Biarnés
- Medical Imaging, Girona Biomedical Research Institute (IdibGi), Girona, Spain
| | - Anna Castells-Nobau
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain
- Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain
- CIBER Pathophysiology of Obesity and Nutrition (CIBEROBN), Madrid, Spain
| | - Josep Puig
- Deparment of Medical Sciences, Faculty of Medicine, University of Girona, Girona, Spain
- Institute of Diagnostic Imaging (IDI)-Research Unit (IDIR), Parc Sanitari Pere Virgili, Barcelona, Spain
- Medical Imaging, Girona Biomedical Research Institute (IdibGi), Girona, Spain
| | - Josep Garre-Olmo
- Deparment of Medical Sciences, Faculty of Medicine, University of Girona, Girona, Spain
- Research Group on Aging, Health and Disability, Girona Biomedical Research Institute, Health Assistance Institute, Girona, Spain
| | - Rafel Ramos
- Deparment of Medical Sciences, Faculty of Medicine, University of Girona, Girona, Spain
- Institut Universitari d'Investigació en Atenció Primària Jordi Gol (IDIAP Jordi Gol), Barcelona, Catalonia, Spain
| | - Salvador Pedraza
- Deparment of Medical Sciences, Faculty of Medicine, University of Girona, Girona, Spain
- Medical Imaging, Girona Biomedical Research Institute (IdibGi), Girona, Spain
- Deparment of Radiology, Dr. Josep Trueta University Hospital, Girona, Spain
| | - Ramon Brugada
- Deparment of Medical Sciences, Faculty of Medicine, University of Girona, Girona, Spain
- Cardiovascular Genetics Center, CIBER-CV, Girona Biomedical Research Institute (IDIBGI), Dr. Josep Trueta University Hospital, Girona, Spain
- Biomedical Research Networking Center on Cardiovascular Diseases (CIBERCV), Madrid, Spain
- Deparment of Cardiology, Dr. Josep Trueta University Hospital, Girona, Spain
| | - Joan C Vilanova
- Deparment of Medical Sciences, Faculty of Medicine, University of Girona, Girona, Spain
- Medical Imaging, Girona Biomedical Research Institute (IdibGi), Girona, Spain
- Deparment of Radiology, Dr. Josep Trueta University Hospital, Girona, Spain
| | - Joaquín Serena
- Deparment of Medical Sciences, Faculty of Medicine, University of Girona, Girona, Spain
- Department of Neurology, Dr. Josep Trueta University Hospital, Girona Biomedical Research Institute (IDIBGI), Girona, Spain
| | - Jordi Barretina
- Girona Biomedical Research Institute (IdibGi), Dr. Josep Trueta University Hospital, Girona, Spain
| | - Jordi Gich
- Deparment of Medical Sciences, Faculty of Medicine, University of Girona, Girona, Spain
- Neurodegeneration and Neuroinflammation Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain
| | - Vicente Pérez-Brocal
- Joint Investigation Unit of FISABIO and I2Sysbio, University of València and CSIC, Valencia, Spain
- Biomedical Research Networking Center for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Andrés Moya
- Joint Investigation Unit of FISABIO and I2Sysbio, University of València and CSIC, Valencia, Spain
- Biomedical Research Networking Center for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Xavier Fernández-Real
- Institute of Mathematics, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Lluis Ramio-Torrentà
- Deparment of Medical Sciences, Faculty of Medicine, University of Girona, Girona, Spain
- Neuroimmunology and Multiple Sclerosis Unit, Deparment of Neurology, Dr. Josep Trueta University Hospital, Girona, Spain
- Department of Neurology, Dr. Josep Trueta University Hospital, Girona Biomedical Research Institute (IDIBGI), Girona, Spain
- Neurodegeneration and Neuroinflammation Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain
- Red Española de Esclerosis Múltiple (REEM), Madrid, Spain
| | - Reinald Pamplona
- Metabolic Physiopathology Research Group, Experimental Medicine Department, Lleida University-Lleida Biochemical Research Institute (UdL-IRBLleida), Lleida, Spain
| | - Joaquim Sol
- Metabolic Physiopathology Research Group, Experimental Medicine Department, Lleida University-Lleida Biochemical Research Institute (UdL-IRBLleida), Lleida, Spain
- Institut Català de la Salut, Atenció Primària, Lleida, Spain
- Research Support Unit Lleida, Fundació Institut Universitari per a la recerca a l'Atenció Primària de Salut Jordi Gol i Gurina (IDIAPJGol), Lleida, Spain
| | - Mariona Jové
- Metabolic Physiopathology Research Group, Experimental Medicine Department, Lleida University-Lleida Biochemical Research Institute (UdL-IRBLleida), Lleida, Spain
| | - Wifredo Ricart
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain
- Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain
- CIBER Pathophysiology of Obesity and Nutrition (CIBEROBN), Madrid, Spain
- Deparment of Medical Sciences, Faculty of Medicine, University of Girona, Girona, Spain
| | - Manuel Portero-Otin
- Metabolic Physiopathology Research Group, Experimental Medicine Department, Lleida University-Lleida Biochemical Research Institute (UdL-IRBLleida), Lleida, Spain
| | - Rafael Maldonado
- Laboratory of Neuropharmacology, Deparment of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Jose Manuel Fernández-Real
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain
- Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain
- CIBER Pathophysiology of Obesity and Nutrition (CIBEROBN), Madrid, Spain
- Deparment of Medical Sciences, Faculty of Medicine, University of Girona, Girona, Spain
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Falgueras-Cano J, Falgueras-Cano JA, Moya A. A Study of the Coevolution of Digital Organisms with an Evolutionary Cellular Automaton. Biology (Basel) 2021; 10:biology10111147. [PMID: 34827140 PMCID: PMC8614957 DOI: 10.3390/biology10111147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/04/2021] [Accepted: 11/05/2021] [Indexed: 02/07/2023]
Abstract
This paper presents an Evolutionary Cellular Automaton (ECA) that simulates the evolutionary dynamics of biological interactions by manipulating strategies of dispersion and associations between digital organisms. The parameterization of the different types of interaction and distribution strategies using configuration files generates easily interpretable results. In that respect, ECA is an effective instrument for measuring the effects of relative adaptive advantages and a good resource for studying natural selection. Although ECA works effectively in obtaining the expected results from most well-known biological interactions, some unexpected effects were observed. For example, organisms uniformly distributed in fragmented habitats do not favor eusociality, and mutualism evolved from parasitism simply by varying phenotypic flexibility. Finally, we have verified that natural selection represents a cost for the emergence of sex by destabilizing the stable evolutionary strategy of the 1:1 sex ratio after generating randomly different distributions in each generation.
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Affiliation(s)
- Javier Falgueras-Cano
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia and CSIC, 46980 Valencia, Spain
- Correspondence: (J.F.-C.); (A.M.)
| | | | - Andrés Moya
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia and CSIC, 46980 Valencia, Spain
- Genomics and Health Area, Foundation for the Promotion of Sanitary and Biomedical Research (FISABIO), 46020 Valencia, Spain
- Biomedical Research Centre Network of Epidemiology and Public Health (CIBEResp), 28029 Madrid, Spain
- Correspondence: (J.F.-C.); (A.M.)
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Stamilla A, Ruiz-Ruiz S, Artacho A, Pons J, Messina A, Lucia Randazzo C, Caggia C, Lanza M, Moya A. Analysis of the Microbial Intestinal Tract in Broiler Chickens during the Rearing Period. Biology (Basel) 2021; 10:biology10090942. [PMID: 34571819 PMCID: PMC8469170 DOI: 10.3390/biology10090942] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 09/16/2021] [Accepted: 09/17/2021] [Indexed: 02/07/2023]
Abstract
Gut microbiota contributes to animal health. However, identifying which microorganisms or associated functions are involved remains, still, difficult to assess. In the present study, the microbiota of healthy broiler chickens, under controlled diet and farm conditions, was investigated by 16S rRNA gene sequencing in four intestine segments and at four ages. In detail, 210 Ross-308 male chickens were raised according to the EU guidelines and fed on a commercial diet. The duodenum, jejunum, ileum, and caecum microbiota were analyzed at 11, 24, 35, and 46 days of life. Although the microbial composition was revealed as homogeneous 11 days after chicks hatched, it was found to be similar in the proximal intestine segments and different in ileum and caecum, where almost the same genera and species were detected with different relative abundances. Although changes during the later growth stage were revealed, each genus remained relatively unchanged. Lactobacillus mostly colonized the upper tract of the intestine, whereas the Escherichia/Shigella genus the ileum. Clostridium and Bacteroides genera were predominant in the caecum, where the highest richness of bacterial taxa was observed. We also analyze and discuss the predicted role of the microbiota for each intestine segment and its potential involvement in nutrient digestion and absorption.
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Affiliation(s)
- Alessandro Stamilla
- Dipartimento di Agricoltura, Alimentazione e Ambiente (Di3A), University of Catania, 95123 Catania, Italy; (A.S.); (C.L.R.); (C.C.); (M.L.)
| | - Susana Ruiz-Ruiz
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), 46020 València, Spain; (A.A.); (J.P.)
- Correspondence: (S.R.-R.); (A.M.)
| | - Alejandro Artacho
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), 46020 València, Spain; (A.A.); (J.P.)
| | - Javier Pons
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), 46020 València, Spain; (A.A.); (J.P.)
| | | | - Cinzia Lucia Randazzo
- Dipartimento di Agricoltura, Alimentazione e Ambiente (Di3A), University of Catania, 95123 Catania, Italy; (A.S.); (C.L.R.); (C.C.); (M.L.)
| | - Cinzia Caggia
- Dipartimento di Agricoltura, Alimentazione e Ambiente (Di3A), University of Catania, 95123 Catania, Italy; (A.S.); (C.L.R.); (C.C.); (M.L.)
| | - Massimiliano Lanza
- Dipartimento di Agricoltura, Alimentazione e Ambiente (Di3A), University of Catania, 95123 Catania, Italy; (A.S.); (C.L.R.); (C.C.); (M.L.)
| | - Andrés Moya
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), 46020 València, Spain; (A.A.); (J.P.)
- Instituto de Biología Integrativa de Sistemas (I2Sysbio), Universitat de València and Consejo Superior de Investigaciones Científicas (CSIC), 46980 València, Spain
- Correspondence: (S.R.-R.); (A.M.)
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Dinleyici M, Pérez-Brocal V, Arslanoglu S, Aydemir O, Sevuk Ozumut S, Tekin N, Vandenplas Y, Moya A, Dinleyici EC. Human Milk Virome Analysis: Changing Pattern Regarding Mode of Delivery, Birth Weight, and Lactational Stage. Nutrients 2021; 13:nu13061779. [PMID: 34071061 PMCID: PMC8224552 DOI: 10.3390/nu13061779] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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: 04/02/2021] [Revised: 05/15/2021] [Accepted: 05/17/2021] [Indexed: 02/07/2023] Open
Abstract
The human milk (HM) microbiota is a significant source of microbes that colonize the infant gut early in life. The aim of this study was to compare transient and mature HM virome compositions, and also possible changes related to the mode of delivery, gestational age, and weight for gestational age. Overall, in the 81 samples analyzed in this study, reads matching bacteriophages accounted for 79.5% (mainly Podoviridae, Myoviridae, and Siphoviridae) of the reads, far more abundant than those classified as eukaryotic viruses (20.5%, mainly Herpesviridae). In the whole study group of transient human milk, the most abundant families were Podoviridae and Myoviridae. In mature human milk, Podoviridae decreased, and Siphoviridae became the most abundant family. Bacteriophages were predominant in transient HM samples (98.4% in the normal spontaneous vaginal delivery group, 92.1% in the premature group, 89.9% in the C-section group, and 68.3% in the large for gestational age group), except in the small for gestational age group (only ~45% bacteriophages in transient HM samples). Bacteriophages were also predominant in mature HM; however, they were lower in mature HM than in transient HM (71.7% in the normal spontaneous vaginal delivery group, 60.8% in the C-section group, 56% in the premature group, and 80.6% in the large for gestational age group). Bacteriophages still represented 45% of mature HM in the small for gestational age group. In the transient HM of the normal spontaneous vaginal delivery group, the most abundant family was Podoviridae; however, in mature HM, Podoviridae became less prominent than Siphoviridae. Myoviridae was predominant in both transient and mature HM in the premature group (all C-section), and Podoviridae was predominant in transient HM, while Siphoviridae and Herpesviridae were predominant in mature HM. In the small for gestational age group, the most abundant taxa in transient HM were the family Herpesviridae and a species of the genus Roseolovirus. Bacteriophages constituted the major component of the HM virome, and we showed changes regarding the lactation period, preterm birth, delivery mode, and birth weight. Early in life, the HM virome may influence the composition of an infant's gut microbiome, which could have short- and long-term health implications. Further longitudinal mother-newborn pair studies are required to understand the effects of these variations on the composition of the HM and the infant gut virome.
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Affiliation(s)
- Meltem Dinleyici
- Department of Social Pediatrics, Faculty of Medicine, Eskisehir Osmangazi University, Eskisehir 26040, Turkey;
| | - Vicente Pérez-Brocal
- Genomics and Health Area, Foundation for the Promotion of Sanitary and Biomedical Research of Valencia Region (FISABIO-Public Health), 46020 Valencia, Spain; (V.P.-B.); (A.M.)
- CIBER in Epidemiology and Public Health (CIBEResp), 28029 Madrid, Spain
| | - Sertac Arslanoglu
- Division of Neonatology, Faculty of Medicine, Medeniyet University, Istanbul 34720, Turkey; (S.A.); (S.S.O.)
| | - Ozge Aydemir
- Division of Neonatology, Faculty of Medicine, Eskisehir Osmangazi University, Eskisehir 26040, Turkey; (O.A.); (N.T.)
| | - Sibel Sevuk Ozumut
- Division of Neonatology, Faculty of Medicine, Medeniyet University, Istanbul 34720, Turkey; (S.A.); (S.S.O.)
| | - Neslihan Tekin
- Division of Neonatology, Faculty of Medicine, Eskisehir Osmangazi University, Eskisehir 26040, Turkey; (O.A.); (N.T.)
| | - Yvan Vandenplas
- Department of Pediatrics, KidZ Health Castle, UZ Brussel, Vrije Unversiteit Brussel, 1050 Brussels, Belgium;
| | - Andrés Moya
- Genomics and Health Area, Foundation for the Promotion of Sanitary and Biomedical Research of Valencia Region (FISABIO-Public Health), 46020 Valencia, Spain; (V.P.-B.); (A.M.)
- CIBER in Epidemiology and Public Health (CIBEResp), 28029 Madrid, Spain
- Institute for Integrative Systems Biology (I2SysBio), The University of Valencia and The Spanish National Research Council (CSIC-UVEG), 46010 Valencia, Spain
| | - Ener Cagri Dinleyici
- Department of Pediatrics, Faculty of Medicine, Eskisehir Osmangazi University, Eskisehir 26040, Turkey
- Correspondence: ; Tel.: +90-222-239-29-79 (ext. 2722)
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Domínguez-Santos R, Pérez-Cobas AE, Cuti P, Pérez-Brocal V, García-Ferris C, Moya A, Latorre A, Gil R. Interkingdom Gut Microbiome and Resistome of the Cockroach Blattella germanica. mSystems 2021; 6:6/3/e01213-20. [PMID: 33975971 PMCID: PMC8125077 DOI: 10.1128/msystems.01213-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Cockroaches are intriguing animals with two coexisting symbiotic systems, an endosymbiont in the fat body, involved in nitrogen metabolism, and a gut microbiome whose diversity, complexity, role, and developmental dynamics have not been fully elucidated. In this work, we present a metagenomic approach to study Blattella germanica populations not treated, treated with kanamycin, and recovered after treatment, both naturally and by adding feces to the diet, with the aim of better understanding the structure and function of its gut microbiome along the development as well as the characterization of its resistome.IMPORTANCE For the first time, we analyze the interkingdom hindgut microbiome of this species, including bacteria, fungi, archaea, and viruses. Network analysis reveals putative cooperation between core bacteria that could be key for ecosystem equilibrium. We also show how antibiotic treatments alter microbiota diversity and function, while both features are restored after one untreated generation. Combining data from B. germanica treated with three antibiotics, we have characterized this species' resistome. It includes genes involved in resistance to several broad-spectrum antibiotics frequently used in the clinic. The presence of genetic elements involved in DNA mobilization indicates that they can be transferred among microbiota partners. Therefore, cockroaches can be considered reservoirs of antibiotic resistance genes (ARGs) and potential transmission vectors.
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Affiliation(s)
- Rebeca Domínguez-Santos
- Institute for Integrative Systems Biology (ISysBio), University of Valencia and CSIC, Valencia, Spain
| | | | - Paolo Cuti
- Institute for Integrative Systems Biology (ISysBio), University of Valencia and CSIC, Valencia, Spain
| | - Vicente Pérez-Brocal
- Genomics and Health Area, Foundation for the Promotion of Sanitary and Biomedical Research (FISABIO), Valencia, Spain
- Biomedical Research Center Network of Epidemiology and Public Health (CIBEResp), Madrid, Spain
| | - Carlos García-Ferris
- Institute for Integrative Systems Biology (ISysBio), University of Valencia and CSIC, Valencia, Spain
- Department of Biochemistry and Molecular Biology, University of Valencia, Valencia, Spain
| | - Andrés Moya
- Institute for Integrative Systems Biology (ISysBio), University of Valencia and CSIC, Valencia, Spain
- Genomics and Health Area, Foundation for the Promotion of Sanitary and Biomedical Research (FISABIO), Valencia, Spain
- Biomedical Research Center Network of Epidemiology and Public Health (CIBEResp), Madrid, Spain
| | - Amparo Latorre
- Institute for Integrative Systems Biology (ISysBio), University of Valencia and CSIC, Valencia, Spain
- Genomics and Health Area, Foundation for the Promotion of Sanitary and Biomedical Research (FISABIO), Valencia, Spain
- Biomedical Research Center Network of Epidemiology and Public Health (CIBEResp), Madrid, Spain
| | - Rosario Gil
- Institute for Integrative Systems Biology (ISysBio), University of Valencia and CSIC, Valencia, Spain
- Genomics and Health Area, Foundation for the Promotion of Sanitary and Biomedical Research (FISABIO), Valencia, Spain
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Serrano-Villar S, Talavera-Rodríguez A, Gosalbes MJ, Madrid N, Pérez-Molina JA, Elliott RJ, Navia B, Lanza VF, Vallejo A, Osman M, Dronda F, Budree S, Zamora J, Gutiérrez C, Manzano M, Vivancos MJ, Ron R, Martínez-Sanz J, Herrera S, Ansa U, Moya A, Moreno S. Fecal microbiota transplantation in HIV: A pilot placebo-controlled study. Nat Commun 2021; 12:1139. [PMID: 33602945 PMCID: PMC7892558 DOI: 10.1038/s41467-021-21472-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [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: 06/01/2020] [Accepted: 01/29/2021] [Indexed: 02/07/2023] Open
Abstract
Changes in the microbiota have been linked to persistent inflammation during treated HIV infection. In this pilot double-blind study, we study 30 HIV-infected subjects on antiretroviral therapy (ART) with a CD4/CD8 ratio < 1 randomized to either weekly fecal microbiota capsules or placebo for 8 weeks. Stool donors were rationally selected based on their microbiota signatures. We report that fecal microbiota transplantation (FMT) is safe, not related to severe adverse events, and attenuates HIV-associated dysbiosis. FMT elicits changes in gut microbiota structure, including significant increases in alpha diversity, and a mild and transient engraftment of donor's microbiota during the treatment period. The greater engraftment seems to be achieved by recent antibiotic use before FMT. The Lachnospiraceae and Ruminococcaceae families, which are typically depleted in people with HIV, are the taxa more robustly engrafted across time-points. In exploratory analyses, we describe a significant amelioration in the FMT group in intestinal fatty acid-binding protein (IFABP), a biomarker of intestinal damage that independently predicts mortality. Gut microbiota manipulation using a non-invasive and safe strategy of FMT delivery is feasible and deserves further investigation. Trial number: NCT03008941.
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Affiliation(s)
- Sergio Serrano-Villar
- Department of Infectious Diseases, Hospital Universitario Ramon y Cajal, and IRYCIS, Madrid, Spain.
| | | | - María José Gosalbes
- Area of Genomics and Health, FISABIO-Salud Pública, Valencia, Spain
- Centro de Investigación Biomédica en Red Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Nadia Madrid
- Department of Infectious Diseases, Hospital Universitario Ramon y Cajal, and IRYCIS, Madrid, Spain
| | - José A Pérez-Molina
- Department of Infectious Diseases, Hospital Universitario Ramon y Cajal, and IRYCIS, Madrid, Spain
| | | | - Beatriz Navia
- Department of Nutrition, Facultad de Farmacia, Universidad Complutense, Madrid, Spain
| | - Val F Lanza
- Bioinformatics Unit, Hospital Universitario Ramon y Cajal, IRYCIS, Madrid, Spain
| | - Alejandro Vallejo
- Department of Infectious Diseases, Hospital Universitario Ramon y Cajal, and IRYCIS, Madrid, Spain
| | | | - Fernando Dronda
- Department of Infectious Diseases, Hospital Universitario Ramon y Cajal, and IRYCIS, Madrid, Spain
| | | | - Javier Zamora
- Barts and the London School for Medicine and Dentistry. Queen Mary University of London, London, UK
| | - Carolina Gutiérrez
- Department of Infectious Diseases, Hospital Universitario Ramon y Cajal, and IRYCIS, Madrid, Spain
| | - Mónica Manzano
- Department of Nutrition, Facultad de Farmacia, Universidad Complutense, Madrid, Spain
| | - María Jesús Vivancos
- Department of Infectious Diseases, Hospital Universitario Ramon y Cajal, and IRYCIS, Madrid, Spain
| | - Raquel Ron
- Department of Infectious Diseases, Hospital Universitario Ramon y Cajal, and IRYCIS, Madrid, Spain
| | - Javier Martínez-Sanz
- Department of Infectious Diseases, Hospital Universitario Ramon y Cajal, and IRYCIS, Madrid, Spain
| | - Sabina Herrera
- Department of Infectious Diseases, Hospital Universitario Ramon y Cajal, and IRYCIS, Madrid, Spain
| | - Uxua Ansa
- Department of Infectious Diseases, Hospital Universitario Ramon y Cajal, and IRYCIS, Madrid, Spain
| | - Andrés Moya
- Area of Genomics and Health, FISABIO-Salud Pública, Valencia, Spain
- Institute for Integrative Systems Biology (I2SysBio), The University of Valencia and The Spanish National Research Council (CSIC)-UVEG), Valencia, Spain
| | - Santiago Moreno
- Department of Infectious Diseases, Hospital Universitario Ramon y Cajal, and IRYCIS, Madrid, Spain
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Debesa-Tur G, Pérez-Brocal V, Ruiz-Ruiz S, Castillejo A, Latorre A, Soto JL, Moya A. Metagenomic analysis of formalin-fixed paraffin-embedded tumor and normal mucosa reveals differences in the microbiome of colorectal cancer patients. Sci Rep 2021; 11:391. [PMID: 33432015 PMCID: PMC7801721 DOI: 10.1038/s41598-020-79874-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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: 08/31/2020] [Accepted: 12/14/2020] [Indexed: 02/06/2023] Open
Abstract
An increased risk of developing colorectal cancer (CRC) and other types of tumor is associated to Lynch syndrome (LS), an inherited condition caused by germline mutations in mismatch repair genes. We selected a cohort of LS patients that had developed CRC and had undergone surgical resection. Formalin-fixed paraffin embedded (FFPE) tissue blocks from matched colorectal and normal mucosa were used for genomic DNA extraction with a commercial kit and sequenced by high-throughput sequencing. A metagenomic approach enabled the taxonomic and functional identification of the microbial community and associated genes detected in the specimens. Slightly lower taxonomic diversity was observed in the tumor compared to the non-tumor tissue. Furthermore, the most remarkable differences between tumors and healthy tissue was the significant increase in the genus Fusobacterium in the former, in particular the species F. nucleatum, as well as Camplylobacter or Bacteroides fragilis, in accordance with previous studies of CRC. However, unlike prior studies, the present work is not based on directed detection by qPCR but instead uses a metagenomic approach to retrieve the whole bacterial community, and addresses the additional difficulty of using long-term stored FFPE samples.
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Affiliation(s)
- Gabriela Debesa-Tur
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO), Área de Genómica y Salud, Valencia, Spain
- Consorcio de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Vicente Pérez-Brocal
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO), Área de Genómica y Salud, Valencia, Spain
- Consorcio de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Susana Ruiz-Ruiz
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO), Área de Genómica y Salud, Valencia, Spain
- Consorcio de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Adela Castillejo
- Unidad de Genética Molecular, Hospital General Universitario de Elche, Alicante, Spain
- Departamento de Salud Elche, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO), Elche, Spain
| | - Amparo Latorre
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO), Área de Genómica y Salud, Valencia, Spain
- Consorcio de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Instituto de Biología Integrativa de Sistemas (I2Sysbio), Universitat de València and Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Valencia, Spain
| | - José Luis Soto
- Unidad de Genética Molecular, Hospital General Universitario de Elche, Alicante, Spain
- Departamento de Salud Elche, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO), Elche, Spain
| | - Andrés Moya
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO), Área de Genómica y Salud, Valencia, Spain.
- Consorcio de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.
- Instituto de Biología Integrativa de Sistemas (I2Sysbio), Universitat de València and Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Valencia, Spain.
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Becraft ED, Moya A. Editorial: Searching for the Boundaries of Microbial Speciation in a Rapidly Evolving World. Front Microbiol 2021; 12:808595. [PMID: 35003040 PMCID: PMC8733662 DOI: 10.3389/fmicb.2021.808595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 11/29/2021] [Indexed: 02/05/2023] Open
Affiliation(s)
- Eric Daniel Becraft
- Department of Biology, University of North Alabama, Florence, AL, United States
- *Correspondence: Eric Daniel Becraft
| | - Andrés Moya
- Institute for Integrative Systems Biology, University of Valencia and Spanish Research Council (CSIC), Valencia, Spain
- Foundation for the Promotion of Sanitary and Biomedical Research of Valencian Community (FISABIO), Valencia, Spain
- CIBER in Epidemiology and Public Health (CIBEResp), Madrid, Spain
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Reyes-Prieto M, Gil R, Llabrés M, Palmer-Rodríguez P, Moya A. The Metabolic Building Blocks of a Minimal Cell. Biology (Basel) 2020; 10:biology10010005. [PMID: 33374107 PMCID: PMC7824019 DOI: 10.3390/biology10010005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/18/2020] [Accepted: 12/21/2020] [Indexed: 02/07/2023]
Abstract
Defining the essential gene components for a system to be considered alive is a crucial step toward the synthesis of artificial life. Fifteen years ago, Gil and coworkers proposed the core of a putative minimal bacterial genome, which would provide the capability to achieve metabolic homeostasis, reproduce, and evolve to a bacterium in an ideally controlled environment. They also proposed a simplified metabolic chart capable of providing energy and basic components for a minimal living cell. For this work, we have identified the components of the minimal metabolic network based on the aforementioned studies, associated them to the KEGG database and, by applying the MetaDAG methodology, determined its Metabolic Building Blocks (MBB) and reconstructed its metabolic Directed Acyclic Graph (m-DAG). The reaction graph of this metabolic network consists of 80 compounds and 98 reactions, while its m-DAG has 36 MBBs. Additionally, we identified 12 essential reactions in the m-DAG that are critical for maintaining the connectivity of this network. In a similar manner, we reconstructed the m-DAG of JCVI-syn3.0, which is an artificially designed and manufactured viable cell whose genome arose by minimizing the one from Mycoplasma mycoides JCVI-syn1.0, and of "Candidatus Nasuia deltocephalinicola", the bacteria with the smallest natural genome known to date. The comparison of the m-DAGs derived from a theoretical, an artificial, and a natural genome denote slightly different lifestyles, with a consistent core metabolism. The MetaDAG methodology we employ uses homogeneous descriptors and identifiers from the KEGG database, so that comparisons between bacterial strains are not only easy but also suitable for many research fields. The modeling of m-DAGs based on minimal metabolisms can be the first step for the synthesis and manipulation of minimal cells.
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Affiliation(s)
- Mariana Reyes-Prieto
- Evolutionary Systems Biology of Symbionts, Institute for Integrative Systems Biology, University of Valencia and Spanish Research Council, Paterna, 46980 Valencia, Spain; (M.R.-P.); (R.G.)
- Sequencing and Bioinformatics Service, Foundation for the Promotion of Sanitary and Biomedical Research of the Valencia Region, 46020 Valencia, Spain
| | - Rosario Gil
- Evolutionary Systems Biology of Symbionts, Institute for Integrative Systems Biology, University of Valencia and Spanish Research Council, Paterna, 46980 Valencia, Spain; (M.R.-P.); (R.G.)
| | - Mercè Llabrés
- Department of Mathematics and Computer Science, University of Balearic Islands, 07122 Palma de Mallorca, Spain; (M.L.); (P.P.-R.)
| | - Pere Palmer-Rodríguez
- Department of Mathematics and Computer Science, University of Balearic Islands, 07122 Palma de Mallorca, Spain; (M.L.); (P.P.-R.)
| | - Andrés Moya
- Evolutionary Systems Biology of Symbionts, Institute for Integrative Systems Biology, University of Valencia and Spanish Research Council, Paterna, 46980 Valencia, Spain; (M.R.-P.); (R.G.)
- Genomic and Health Area, Foundation for the Promotion of Sanitary and Biomedical Research of the Valencia Region, 46020 Valencia, Spain
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública, 28029 Madrid, Spain
- Correspondence: ; Tel.: +34-963-543-480
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11
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Džunková M, Lipták R, Vlková B, Gardlík R, Čierny M, Moya A, Celec P. Salivary microbiome composition changes after bariatric surgery. Sci Rep 2020; 10:20086. [PMID: 33208788 PMCID: PMC7674438 DOI: 10.1038/s41598-020-76991-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 04/17/2020] [Accepted: 10/27/2020] [Indexed: 02/07/2023] Open
Abstract
Recent studies show that the salivary microbiome in subjects with obesity differ from those without obesity, but the mechanism of interaction between the salivary microbiome composition and body weight is unclear. Herein we investigate this relation by analyzing saliva samples from 35 adult patients with obesity undergoing bariatric surgery. Our aim was to describe salivary microbiome changes during body weight loss on an individual-specific level, and to elucidate the effect of bariatric surgery on the salivary microbiome which has not been studied before. Analysis of samples collected before and 1 day after surgery, as well as 3 and 12 months after surgery, showed that the salivary microbiome changed in all study participants, but these changes were heterogeneous. In the majority of participants proportions of Gemella species, Granulicatella elegans, Porphyromonas pasteri, Prevotella nanceiensis and Streptococcus oralis decreased, while Veillonella species, Megasphaera micronuciformis and Prevotella saliva increased. Nevertheless, we found participants deviating from this general trend which suggests that a variety of individual-specific factors influence the salivary microbiome composition more effectively than the body weight dynamics alone. The observed microbiome alternations could be related to dietary changes. Therefore, further studies should focus on association with altered taste preferences and potential oral health consequences.
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Affiliation(s)
- Mária Džunková
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Róbert Lipták
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, Bratislava, Slovakia
| | - Barbora Vlková
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, Bratislava, Slovakia
| | - Roman Gardlík
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, Bratislava, Slovakia
| | - Michal Čierny
- Department of Bariatric Surgery, Břeclav Hospital, Břeclav, Czech Republic
| | - Andrés Moya
- Department of Genomics and Health, Foundation for the Promotion of Sanitary and Biomedical Research of Valencian Community (FISABIO-Public Health), Valencia, Spain.
- CIBER in Epidemiology and Public Health (CIBEResp), Madrid, Spain.
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia and Spanish National Research Council (CSIC), Valencia, Spain.
| | - Peter Celec
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, Bratislava, Slovakia.
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Moya A, Oliver JL, Verdú M, Delaye L, Arnau V, Bernaola-Galván P, de la Fuente R, Díaz W, Gómez-Martín C, González FM, Latorre A, Lebrón R, Román-Roldán R. Driven progressive evolution of genome sequence complexity in Cyanobacteria. Sci Rep 2020; 10:19073. [PMID: 33149190 PMCID: PMC7643063 DOI: 10.1038/s41598-020-76014-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 05/09/2020] [Accepted: 10/22/2020] [Indexed: 02/07/2023] Open
Abstract
Progressive evolution, or the tendency towards increasing complexity, is a controversial issue in biology, which resolution entails a proper measurement of complexity. Genomes are the best entities to address this challenge, as they encode the historical information of a species' biotic and environmental interactions. As a case study, we have measured genome sequence complexity in the ancient phylum Cyanobacteria. To arrive at an appropriate measure of genome sequence complexity, we have chosen metrics that do not decipher biological functionality but that show strong phylogenetic signal. Using a ridge regression of those metrics against root-to-tip distance, we detected positive trends towards higher complexity in three of them. Lastly, we applied three standard tests to detect if progressive evolution is passive or driven-the minimum, ancestor-descendant, and sub-clade tests. These results provide evidence for driven progressive evolution at the genome-level in the phylum Cyanobacteria.
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Affiliation(s)
- Andrés Moya
- Institute of Integrative Systems Biology (I2Sysbio), University of València and Consejo Superior de Investigaciones Científicas (CSIC), 46980, Valencia, Spain.
- Foundation for the Promotion of Sanitary and Biomedical Research of Valencian Community (FISABIO), 46020, Valencia, Spain.
- CIBER in Epidemiology and Public Health, 28029, Madrid, Spain.
| | - José L Oliver
- Department of Genetics, Faculty of Sciences, University of Granada, 18071, Granada, Spain
- Laboratory of Bioinformatics, Institute of Biotechnology, Center of Biomedical Research, 18100, Granada, Spain
| | - Miguel Verdú
- Centro de Investigaciones sobre Desertificación, Consejo Superior de Investigaciones Científicas (CSIC), University of València and Generalitat Valenciana, 46113, Valencia, Spain
| | - Luis Delaye
- Department of Genetic Engineering, CINVESTAV, 36821, Irapuato, Mexico
| | - Vicente Arnau
- Institute of Integrative Systems Biology (I2Sysbio), University of València and Consejo Superior de Investigaciones Científicas (CSIC), 46980, Valencia, Spain
| | - Pedro Bernaola-Galván
- Department of Applied Physics II and Institute Carlos I for Theoretical and Computational Physics, University of Málaga, 29071, Málaga, Spain
| | - Rebeca de la Fuente
- Institute for Cross-Disciplinary Physics and Complex Systems (IFISC), Consejo Superior de Investigaciones Científicas (CSIC) and University of Balearic Islands, 07122, Palma de Mallorca, Spain
| | - Wladimiro Díaz
- Institute of Integrative Systems Biology (I2Sysbio), University of València and Consejo Superior de Investigaciones Científicas (CSIC), 46980, Valencia, Spain
| | - Cristina Gómez-Martín
- Department of Genetics, Faculty of Sciences, University of Granada, 18071, Granada, Spain
- Laboratory of Bioinformatics, Institute of Biotechnology, Center of Biomedical Research, 18100, Granada, Spain
| | | | - Amparo Latorre
- Institute of Integrative Systems Biology (I2Sysbio), University of València and Consejo Superior de Investigaciones Científicas (CSIC), 46980, Valencia, Spain
- Foundation for the Promotion of Sanitary and Biomedical Research of Valencian Community (FISABIO), 46020, Valencia, Spain
- CIBER in Epidemiology and Public Health, 28029, Madrid, Spain
| | - Ricardo Lebrón
- Department of Genetics, Faculty of Sciences, University of Granada, 18071, Granada, Spain
- Laboratory of Bioinformatics, Institute of Biotechnology, Center of Biomedical Research, 18100, Granada, Spain
| | - Ramón Román-Roldán
- Department of Applied Physics, University of Granada, 18071, Granada, Spain
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Pérez-Brocal V, Magne F, Ruiz-Ruiz S, Ponce CA, Bustamante R, Martin VS, Gutierrez M, Gatti G, Vargas SL, Moya A. Optimized DNA extraction and purification method for characterization of bacterial and fungal communities in lung tissue samples. Sci Rep 2020; 10:17377. [PMID: 33060634 PMCID: PMC7562954 DOI: 10.1038/s41598-020-74137-2] [Citation(s) in RCA: 5] [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: 03/19/2020] [Accepted: 07/28/2020] [Indexed: 02/07/2023] Open
Abstract
Human lungs harbor a scarce microbial community, requiring to develop methods to enhance the recovery of nucleic acids from bacteria and fungi, leading to a more efficient analysis of the lung tissue microbiota. Here we describe five extraction protocols including pre-treatment, bead-beating and/or Phenol:Chloroform:Isoamyl alcohol steps, applied to lung tissue samples from autopsied individuals. The resulting total DNA yield and quality, bacterial and fungal DNA amount and the microbial community structure were analyzed by qPCR and Illumina sequencing of bacterial 16S rRNA and fungal ITS genes. Bioinformatic modeling revealed that a large part of microbiome from lung tissue is composed of microbial contaminants, although our controls clustered separately from biological samples. After removal of contaminant sequences, the effects of extraction protocols on the microbiota were assessed. The major differences among samples could be attributed to inter-individual variations rather than DNA extraction protocols. However, inclusion of the bead-beater and Phenol:Chloroform:Isoamyl alcohol steps resulted in changes in the relative abundance of some bacterial/fungal taxa. Furthermore, inclusion of a pre-treatment step increased microbial DNA concentration but not diversity and it may contribute to eliminate DNA fragments from dead microorganisms in lung tissue samples, making the microbial profile closer to the actual one.
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Affiliation(s)
- Vicente Pérez-Brocal
- Department of Genomics and Health, Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO-Public Health), Avda. Cataluña 21, 46020, València, Spain
- CIBER in Epidemiology and Public Health (CIBEResp), Madrid, Spain
| | - Fabien Magne
- Microbiology and Mycology Program, Biomedical Sciences Institute (ICBM), University of Chile School of Medicine, Av. Independencia 1027, Independencia, Santiago, Chile.
| | - Susana Ruiz-Ruiz
- Department of Genomics and Health, Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO-Public Health), Avda. Cataluña 21, 46020, València, Spain
- CIBER in Epidemiology and Public Health (CIBEResp), Madrid, Spain
| | - Carolina A Ponce
- Microbiology and Mycology Program, Biomedical Sciences Institute (ICBM), University of Chile School of Medicine, Av. Independencia 1027, Independencia, Santiago, Chile
| | - Rebeca Bustamante
- Microbiology and Mycology Program, Biomedical Sciences Institute (ICBM), University of Chile School of Medicine, Av. Independencia 1027, Independencia, Santiago, Chile
| | | | | | - Gianna Gatti
- Médico Legal Institute of Chile, Santiago, Chile
| | - Sergio L Vargas
- Microbiology and Mycology Program, Biomedical Sciences Institute (ICBM), University of Chile School of Medicine, Av. Independencia 1027, Independencia, Santiago, Chile.
| | - Andrés Moya
- Department of Genomics and Health, Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO-Public Health), Avda. Cataluña 21, 46020, València, Spain.
- CIBER in Epidemiology and Public Health (CIBEResp), Madrid, Spain.
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia and Spanish National Research Council (CSIC), València, Spain.
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Arnoriaga-Rodríguez M, Mayneris-Perxachs J, Burokas A, Contreras-Rodríguez O, Blasco G, Coll C, Biarnés C, Miranda-Olivos R, Latorre J, Moreno-Navarrete JM, Castells-Nobau A, Sabater M, Palomo-Buitrago ME, Puig J, Pedraza S, Gich J, Pérez-Brocal V, Ricart W, Moya A, Fernández-Real X, Ramió-Torrentà L, Pamplona R, Sol J, Jové M, Portero-Otin M, Maldonado R, Fernández-Real JM. Obesity Impairs Short-Term and Working Memory through Gut Microbial Metabolism of Aromatic Amino Acids. Cell Metab 2020; 32:548-560.e7. [PMID: 33027674 DOI: 10.1016/j.cmet.2020.09.002] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 05/12/2020] [Accepted: 08/31/2020] [Indexed: 02/07/2023]
Abstract
The gut microbiome has been linked to fear extinction learning in animal models. Here, we aimed to explore the gut microbiome and memory domains according to obesity status. A specific microbiome profile associated with short-term memory, working memory, and the volume of the hippocampus and frontal regions of the brain differentially in human subjects with and without obesity. Plasma and fecal levels of aromatic amino acids, their catabolites, and vegetable-derived compounds were longitudinally associated with short-term and working memory. Functionally, microbiota transplantation from human subjects with obesity led to decreased memory scores in mice, aligning this trait from humans with that of recipient mice. RNA sequencing of the medial prefrontal cortex of mice revealed that short-term memory associated with aromatic amino acid pathways, inflammatory genes, and clusters of bacterial species. These results highlight the potential therapeutic value of targeting the gut microbiota for memory impairment, specifically in subjects with obesity.
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Affiliation(s)
- María Arnoriaga-Rodríguez
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain; Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain; Biomedical Research Networking Center for Physiopathology of Obesity and Nutrition (CIBEROBN), Madrid, Spain; Department of Medical Sciences, Faculty of Medicine, Girona University, Girona, Spain
| | - Jordi Mayneris-Perxachs
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain; Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain; Biomedical Research Networking Center for Physiopathology of Obesity and Nutrition (CIBEROBN), Madrid, Spain
| | - Aurelijus Burokas
- Laboratory of Neuropharmacology, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Oren Contreras-Rodríguez
- Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain; Psychiatry Department, Bellvitge University Hospital, Bellvitge Biomedical Research Institute (IDIBELL) and CIBERSAM, Barcelona, Spain
| | - Gerard Blasco
- Institute of Diagnostic Imaging (IDI)-Research Unit (IDIR), Parc Sanitari Pere Virgili, Barcelona, Spain; Medical Imaging, Girona Biomedical Research Institute (IdibGi), Girona, Spain
| | - Clàudia Coll
- Neuroimmunology and Multiple Sclerosis Unit, Department of Neurology, Dr. Josep Trueta University Hospital, Girona, Spain
| | - Carles Biarnés
- Institute of Diagnostic Imaging (IDI)-Research Unit (IDIR), Parc Sanitari Pere Virgili, Barcelona, Spain
| | - Romina Miranda-Olivos
- Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain; Psychiatry Department, Bellvitge University Hospital, Bellvitge Biomedical Research Institute (IDIBELL) and CIBERSAM, Barcelona, Spain
| | - Jèssica Latorre
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain; Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain; Biomedical Research Networking Center for Physiopathology of Obesity and Nutrition (CIBEROBN), Madrid, Spain
| | - José-Maria Moreno-Navarrete
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain; Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain; Biomedical Research Networking Center for Physiopathology of Obesity and Nutrition (CIBEROBN), Madrid, Spain; Department of Medical Sciences, Faculty of Medicine, Girona University, Girona, Spain
| | - Anna Castells-Nobau
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain; Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain; Biomedical Research Networking Center for Physiopathology of Obesity and Nutrition (CIBEROBN), Madrid, Spain
| | - Mònica Sabater
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain; Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain; Biomedical Research Networking Center for Physiopathology of Obesity and Nutrition (CIBEROBN), Madrid, Spain
| | - María Encarnación Palomo-Buitrago
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain; Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain
| | - Josep Puig
- Department of Medical Sciences, Faculty of Medicine, Girona University, Girona, Spain; Institute of Diagnostic Imaging (IDI)-Research Unit (IDIR), Parc Sanitari Pere Virgili, Barcelona, Spain; Medical Imaging, Girona Biomedical Research Institute (IdibGi), Girona, Spain
| | - Salvador Pedraza
- Department of Medical Sciences, Faculty of Medicine, Girona University, Girona, Spain; Medical Imaging, Girona Biomedical Research Institute (IdibGi), Girona, Spain; Department of Radiology, Dr. Josep Trueta University Hospital, Girona, Spain
| | - Jordi Gich
- Department of Medical Sciences, Faculty of Medicine, Girona University, Girona, Spain; Girona Neurodegeneration and Neuroinflammation Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain
| | - Vicente Pérez-Brocal
- Department of Genomics and Health, Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO-Public Health), Valencia, Spain; Biomedical Research Networking Center for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Wifredo Ricart
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain; Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain; Biomedical Research Networking Center for Physiopathology of Obesity and Nutrition (CIBEROBN), Madrid, Spain; Department of Medical Sciences, Faculty of Medicine, Girona University, Girona, Spain
| | - Andrés Moya
- Department of Genomics and Health, Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO-Public Health), Valencia, Spain; Biomedical Research Networking Center for Epidemiology and Public Health (CIBERESP), Madrid, Spain; Institute for Integrative Systems Biology (I2SysBio), University of Valencia and Spanish National Research Council (CSIC), Valencia, Spain
| | - Xavier Fernández-Real
- Institute of Mathematics, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Lluís Ramió-Torrentà
- Department of Medical Sciences, Faculty of Medicine, Girona University, Girona, Spain; Neuroimmunology and Multiple Sclerosis Unit, Department of Neurology, Dr. Josep Trueta University Hospital, Girona, Spain; Girona Neurodegeneration and Neuroinflammation Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain
| | - Reinald Pamplona
- Metabolic Pathophysiology Research Group, Lleida Biomedical Research Institute (IRBLleida)-Universitat de Lleida, Lleida, Spain
| | - Joaquim Sol
- Metabolic Pathophysiology Research Group, Lleida Biomedical Research Institute (IRBLleida)-Universitat de Lleida, Lleida, Spain
| | - Mariona Jové
- Metabolic Pathophysiology Research Group, Lleida Biomedical Research Institute (IRBLleida)-Universitat de Lleida, Lleida, Spain
| | - Manuel Portero-Otin
- Metabolic Pathophysiology Research Group, Lleida Biomedical Research Institute (IRBLleida)-Universitat de Lleida, Lleida, Spain
| | - Rafael Maldonado
- Laboratory of Neuropharmacology, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain; Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain.
| | - José Manuel Fernández-Real
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain; Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain; Biomedical Research Networking Center for Physiopathology of Obesity and Nutrition (CIBEROBN), Madrid, Spain; Department of Medical Sciences, Faculty of Medicine, Girona University, Girona, Spain.
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15
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Mayneris-Perxachs J, Arnoriaga-Rodríguez M, Luque-Córdoba D, Priego-Capote F, Pérez-Brocal V, Moya A, Burokas A, Maldonado R, Fernández-Real JM. Gut microbiota steroid sexual dimorphism and its impact on gonadal steroids: influences of obesity and menopausal status. Microbiome 2020; 8:136. [PMID: 32951609 PMCID: PMC7504665 DOI: 10.1186/s40168-020-00913-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [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] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 08/24/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Gonadal steroid hormones have been suggested as the underlying mechanism responsible for the sexual dimorphism observed in metabolic diseases. Animal studies have also evidenced a causal role of the gut microbiome and metabolic health. However, the role of sexual dimorphism in the gut microbiota and the potential role of the microbiome in influencing sex steroid hormones and shaping sexually dimorphic susceptibility to disease have been largely overlooked. Although there is some evidence of sex-specific differences in the gut microbiota diversity, composition, and functionality, the results are inconsistent. Importantly, most of these studies have not taken into account the gonadal steroid status. Therefore, we investigated the gut microbiome composition and functionality in relation to sex, menopausal status, and circulating sex steroids. RESULTS No significant differences were found in alpha diversity indices among pre- and post-menopausal women and men, but beta diversity differed among groups. The gut microbiota from post-menopausal women was more similar to men than to pre-menopausal women. Metagenome functional analyses revealed no significant differences between post-menopausal women and men. Gonadal steroids were specifically associated with these differences. Hence, the gut microbiota of pre-menopausal women was more enriched in genes from the steroid biosynthesis and degradation pathways, with the former having the strongest fold change among all associated pathways. Microbial steroid pathways also had significant associations with the plasma levels of testosterone and progesterone. In addition, a specific microbiome signature was able to predict the circulating testosterone levels at baseline and after 1-year follow-up. In addition, this microbiome signature could be transmitted from humans to antibiotic-induced microbiome-depleted male mice, being able to predict donor's testosterone levels 4 weeks later, implying that the microbiota profile of the recipient mouse was influenced by the donor's gender. Finally, obesity eliminated most of the differences observed among non-obese pre-menopausal women, post-menopausal women, and men in the gut microbiota composition (Bray-Curtis and weighted unifrac beta diversity), functionality, and the gonadal steroid status. CONCLUSIONS The present findings evidence clear differences in the gut microbial composition and functionality between men and women, which is eliminated by both menopausal and obesity status. We also reveal a tight link between the gut microbiota composition and the circulating levels of gonadal steroids, particularly testosterone. Video Abstract.
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Affiliation(s)
- Jordi Mayneris-Perxachs
- Department of Endocrinology, Diabetes and Nutrition, Departament de Ciències Mèdiques, Hospital of Girona "Dr JosepTrueta", Girona Biomedical Research Institute (IdibGi), University of Girona, Carretera de França s/n, 17007, Girona, Spain
- CIBERobn Pathophysiology of Obesity and Nutrition, Instituto de Salud Carlos III, Madrid, Spain
| | - María Arnoriaga-Rodríguez
- Department of Endocrinology, Diabetes and Nutrition, Departament de Ciències Mèdiques, Hospital of Girona "Dr JosepTrueta", Girona Biomedical Research Institute (IdibGi), University of Girona, Carretera de França s/n, 17007, Girona, Spain
- CIBERobn Pathophysiology of Obesity and Nutrition, Instituto de Salud Carlos III, Madrid, Spain
| | - Diego Luque-Córdoba
- Maimónides Institute of Biomedical Research (IMIBIC), Reina Sofía University Hospital, University of Cordoba, Cordoba, Spain
- CIBERfes Frailty and Healthy Aging, Instituto de Salud Carlos III, Madrid, Spain
| | - Feliciano Priego-Capote
- Maimónides Institute of Biomedical Research (IMIBIC), Reina Sofía University Hospital, University of Cordoba, Cordoba, Spain
- CIBERfes Frailty and Healthy Aging, Instituto de Salud Carlos III, Madrid, Spain
| | - Vicente Pérez-Brocal
- Department of Genomics and Health, Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO-Public Health), Valencia, Spain
- CIBER in Epidemiology and Public Health (CIBEResp), Madrid, Spain
| | - Andrés Moya
- Department of Genomics and Health, Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO-Public Health), Valencia, Spain
- CIBER in Epidemiology and Public Health (CIBEResp), Madrid, Spain
- Institute for Integrative Systems Biology (I2SysBio), The University of Valencia and The Spanish National Research Council (CSIC-UVEG), Valencia, Spain
| | - Aurelijus Burokas
- Laboratory of Neuropharmacology, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Present address: Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Rafael Maldonado
- Laboratory of Neuropharmacology, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - José-Manuel Fernández-Real
- Department of Endocrinology, Diabetes and Nutrition, Departament de Ciències Mèdiques, Hospital of Girona "Dr JosepTrueta", Girona Biomedical Research Institute (IdibGi), University of Girona, Carretera de França s/n, 17007, Girona, Spain.
- CIBERobn Pathophysiology of Obesity and Nutrition, Instituto de Salud Carlos III, Madrid, Spain.
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16
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Ibarra-Juarez LA, Burton MAJ, Biedermann PHW, Cruz L, Desgarennes D, Ibarra-Laclette E, Latorre A, Alonso-Sánchez A, Villafan E, Hanako-Rosas G, López L, Vázquez-Rosas-Landa M, Carrion G, Carrillo D, Moya A, Lamelas A. Evidence for Succession and Putative Metabolic Roles of Fungi and Bacteria in the Farming Mutualism of the Ambrosia Beetle Xyleborus affinis. mSystems 2020; 5:5/5/e00541-20. [PMID: 32934115 PMCID: PMC7498683 DOI: 10.1128/msystems.00541-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The bacterial and fungal community involved in ambrosia beetle fungiculture remains poorly studied compared to the famous fungus-farming ants and termites. Here we studied microbial community dynamics of laboratory nests, adults, and brood during the life cycle of the sugarcane shot hole borer, Xyleborus affinis We identified a total of 40 fungal and 428 bacterial operational taxonomic units (OTUs), from which only five fungi (a Raffaelea fungus and four ascomycete yeasts) and four bacterial genera (Stenotrophomonas, Enterobacter, Burkholderia, and Ochrobactrum) can be considered the core community playing the most relevant symbiotic role. Both the fungal and bacterial populations varied significantly during the beetle's life cycle. While the ascomycete yeasts were the main colonizers of the gallery early on, the Raffaelea and other filamentous fungi appeared after day 10, at the time when larval hatching happened. Regarding bacteria, Stenotrophomonas and Enterobacter dominated overall but decreased in foundresses and brood with age. Finally, inferred analyses of the putative metabolic capabilities of the bacterial microbiome revealed that they are involved in (i) degradation of fungal and plant polymers, (ii) fixation of atmospheric nitrogen, and (iii) essential amino acid, cofactor, and vitamin provisioning. Overall, our results suggest that yeasts and bacteria are more strongly involved in supporting the beetle-fungus farming symbiosis than previously thought.IMPORTANCE Ambrosia beetles farm their own food fungi within tunnel systems in wood and are among the three insect lineages performing agriculture (the others are fungus-farming ants and termites). In ambrosia beetles, primary ambrosia fungus cultivars have been regarded essential, whereas other microbes have been more or less ignored. Our KEGG analyses suggest so far unknown roles of yeasts and bacterial symbionts, by preparing the tunnel walls for the primary ambrosia fungi. This preparation includes enzymatic degradation of wood, essential amino acid production, and nitrogen fixation. The latter is especially exciting because if it turns out to be present in vivo in ambrosia beetles, all farming animals (including humans) are dependent on atmospheric nitrogen fertilization of their crops. As previous internal transcribed spacer (ITS) metabarcoding approaches failed on covering the primary ambrosia fungi, our 18S metabarcoding approach can also serve as a template for future studies on the ambrosia beetle-fungus symbiosis.
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Affiliation(s)
- L A Ibarra-Juarez
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A. C., Xalapa, México
| | - M A J Burton
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A. C., Xalapa, México
| | - P H W Biedermann
- Chair of Forest Entomology and Protection, University of Freiburg, Freiburg, Germany
| | - L Cruz
- Tropical Research and Education Center, University of Florida, Homestead, Florida, USA
| | - D Desgarennes
- Red de Biodiversidad y Sistemática, Instituto de Ecología A. C., Xalapa, México
| | - E Ibarra-Laclette
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A. C., Xalapa, México
| | - A Latorre
- Institute for Integrative Systems Biology (Universitat de València and CSIC), València, Spain
- Foundation for the Promotion of Sanitary and Biomedical Research in the Valencian Community (FISABIO), València, Spain
| | - A Alonso-Sánchez
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A. C., Xalapa, México
| | - E Villafan
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A. C., Xalapa, México
| | - G Hanako-Rosas
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A. C., Xalapa, México
| | - L López
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A. C., Xalapa, México
| | | | - G Carrion
- Red de Biodiversidad y Sistemática, Instituto de Ecología A. C., Xalapa, México
| | - D Carrillo
- Red de Biodiversidad y Sistemática, Instituto de Ecología A. C., Xalapa, México
| | - A Moya
- Institute for Integrative Systems Biology (Universitat de València and CSIC), València, Spain
- Foundation for the Promotion of Sanitary and Biomedical Research in the Valencian Community (FISABIO), València, Spain
| | - A Lamelas
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A. C., Xalapa, México
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17
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Allaw M, Manca ML, Caddeo C, Recio MC, Pérez-Brocal V, Moya A, Fernàndez-Busquets X, Manconi M. Advanced strategy to exploit wine-making waste by manufacturing antioxidant and prebiotic fibre-enriched vesicles for intestinal health. Colloids Surf B Biointerfaces 2020; 193:111146. [PMID: 32485579 DOI: 10.1016/j.colsurfb.2020.111146] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 04/30/2020] [Revised: 05/16/2020] [Accepted: 05/18/2020] [Indexed: 02/07/2023]
Abstract
Grape extract-loaded fibre-enriched vesicles, nutriosomes, were prepared by combining antioxidant extracts obtained from grape pomaces and a prebiotic, soluble fibre (Nutriose®FM06). The nutriosomes were small in size (from ∼140 to 260 nm), homogeneous (polydispersity index < 0.2) and highly negative (∼ -79 mV). The vesicles were highly stable during 12 months of storage at 25 °C. When diluted with warmed (37 °C) acidic medium (pH 1.2) of high ionic strength, the vesicles only displayed an increase of the mean diameter and a low release of the extract, which were dependent on Nutriose concentration. The formulations were highly biocompatible and able to protect intestinal cells (Caco-2) from oxidative stress damage. In vivo results underlined that the composition of mouse microbiota was not affected by the vesicular formulations. Overall results support the potential application of grape nutriosomes as an alternative strategy for the protection of the intestinal tract.
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Affiliation(s)
- Mohamad Allaw
- Dept. of Scienze della Vita e dell'Ambiente, Sezione di Scienze del Farmaco, University of Cagliari, Via Ospedale 72, 09124 Cagliari, Italy
| | - Maria Letizia Manca
- Dept. of Scienze della Vita e dell'Ambiente, Sezione di Scienze del Farmaco, University of Cagliari, Via Ospedale 72, 09124 Cagliari, Italy.
| | - Carla Caddeo
- Dept. of Scienze della Vita e dell'Ambiente, Sezione di Scienze del Farmaco, University of Cagliari, Via Ospedale 72, 09124 Cagliari, Italy
| | - Maria Carmen Recio
- Dept. of Pharmacology, Faculty of Pharmacy, University of Valencia, Avda Vicent Andrés Estellés sn, 46100 Burjassot-Valencia, Spain
| | - Vicente Pérez-Brocal
- Dept. of Genomics and Health, Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO-Public Health), Valencia, Spain; CIBER in Epidemiology and Public Health (CIBEResp), Madrid, Spain
| | - Andres Moya
- Dept. of Genomics and Health, Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO-Public Health), Valencia, Spain; CIBER in Epidemiology and Public Health (CIBEResp), Madrid, Spain; Institute for Integrative Systems Biology (I2SysBio), The University of Valencia and The Spanish National Research Council (CSIC)-UVEG), Valencia, Spain
| | - Xavier Fernàndez-Busquets
- Institute for Bioengineering of Catalonia, (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Barcelona Institute for Global Health (ISGlobal, Hospital Clínic-Universitat de Barcelona), Nanoscience and Nanotechnology Institute (IN2UB), University of Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Maria Manconi
- Dept. of Scienze della Vita e dell'Ambiente, Sezione di Scienze del Farmaco, University of Cagliari, Via Ospedale 72, 09124 Cagliari, Italy
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18
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Sainz T, Gosalbes MJ, Talavera A, Jimenez-Hernandez N, Prieto L, Escosa L, Guillén S, Ramos JT, Muñoz-Fernández MÁ, Moya A, Navarro ML, Mellado MJ, Serrano-Villar S. Effect of a Nutritional Intervention on the Intestinal Microbiota of Vertically HIV-Infected Children: The Pediabiota Study. Nutrients 2020; 12:nu12072112. [PMID: 32708743 PMCID: PMC7400861 DOI: 10.3390/nu12072112] [Citation(s) in RCA: 5] [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: 06/29/2020] [Revised: 07/08/2020] [Accepted: 07/10/2020] [Indexed: 02/07/2023] Open
Abstract
AIMS The gut microbiota exerts a critical influence in the immune system. The gut microbiota of human virus immunodeficiency (HIV)-infected children remains barely explored. We aimed to characterize the fecal microbiota in vertically HIV-infected children and to explore the effects of its modulation with a symbiotic nutritional intervention. METHODS a pilot, double blind, randomized placebo-controlled study including HIV-infected children who were randomized to receive a nutritional supplementation including prebiotics and probiotics or placebo for four weeks. HIV-uninfected siblings were recruited as controls. The V3-V4 region of the 16S rRNA gene was sequenced in fecal samples. RESULTS 22 HIV-infected children on antiretroviral therapy (ART) and with viral load (VL) <50/mL completed the follow-up period. Mean age was 11.4 ± 3.4 years, eight (32%) were male. Their microbiota showed reduced alpha diversity compared to controls and distinct beta diversity at the genus level (Adonis p = 0.042). Patients showed decreased abundance of commensals Faecalibacterium and an increase in Prevotella, Akkermansia and Escherichia. The nutritional intervention shaped the microbiota towards the control group, without a clear directionality. CONCLUSIONS Vertical HIV infection is characterized by changes in gut microbiota structure, distinct at the compositional level from the findings reported in adults. A short nutritional intervention attenuated bacterial dysbiosis, without clear changes at the community level. SUMMARY In a group of 24 vertically HIV-infected children, in comparison to 11 uninfected controls, intestinal dysbiosis was observed despite effective ART. Although not fully effective to restore the microbiota, a short intervention with pre/probiotics attenuated bacterial dysbiosis.
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Affiliation(s)
- Talía Sainz
- Servicio de Pediatría, Hospital Universitario La Paz and IdiPAZ, 28046 Madrid, Spain; (L.E.); (M.J.M.)
- Red de Investigación CoRISpe integrada en la Red en Infectología Pediátrica (RITIP), 28046 Madrid, Spain; (L.P.); (S.G.); (J.T.R.); (M.L.N.)
- Correspondence: ; Tel.: +34-917277201
| | - María José Gosalbes
- Área Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica (FISABIO), 46010 Valencia, Spain; (M.J.G.); (N.J.-H.); (A.M.)
- CIBER en Epidemiología y Salud Pública, 28029 Madrid, Spain
| | - Alba Talavera
- Bioinformatics Unit, Hospital Universitario Ramón y Cajal and IRYCIS, 28034 Madrid, Spain;
| | - Nuria Jimenez-Hernandez
- Área Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica (FISABIO), 46010 Valencia, Spain; (M.J.G.); (N.J.-H.); (A.M.)
- CIBER en Epidemiología y Salud Pública, 28029 Madrid, Spain
| | - Luis Prieto
- Red de Investigación CoRISpe integrada en la Red en Infectología Pediátrica (RITIP), 28046 Madrid, Spain; (L.P.); (S.G.); (J.T.R.); (M.L.N.)
- Servicio de Pediatría, Hospital 12 de Octubre and I+12, 28041 Madrid, Spain
| | - Luis Escosa
- Servicio de Pediatría, Hospital Universitario La Paz and IdiPAZ, 28046 Madrid, Spain; (L.E.); (M.J.M.)
- Red de Investigación CoRISpe integrada en la Red en Infectología Pediátrica (RITIP), 28046 Madrid, Spain; (L.P.); (S.G.); (J.T.R.); (M.L.N.)
| | - Sara Guillén
- Red de Investigación CoRISpe integrada en la Red en Infectología Pediátrica (RITIP), 28046 Madrid, Spain; (L.P.); (S.G.); (J.T.R.); (M.L.N.)
- Servicio de Pediatría, Hospital de Getafe, 28901 Madrid, Spain
| | - José Tomás Ramos
- Red de Investigación CoRISpe integrada en la Red en Infectología Pediátrica (RITIP), 28046 Madrid, Spain; (L.P.); (S.G.); (J.T.R.); (M.L.N.)
- Spain Servicio de Pediatría, Hospital Clinico San Carlos and UCM, 28040 Madrid, Spain
| | - María Ángeles Muñoz-Fernández
- Laboratorio InmunoBiología Molecular, Sección Inmunología, Hospital General Universitario Gregorio Marañón and Spanish HIV HGM BioBank, Madrid Spain, Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 28007 Madrid, Spain;
| | - Andrés Moya
- Área Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica (FISABIO), 46010 Valencia, Spain; (M.J.G.); (N.J.-H.); (A.M.)
- CIBER en Epidemiología y Salud Pública, 28029 Madrid, Spain
- Instituto de Biología Integrativa de Sistemas, Universidad de Valencia, 46003 Valencia, Spain
| | - Maria Luisa Navarro
- Red de Investigación CoRISpe integrada en la Red en Infectología Pediátrica (RITIP), 28046 Madrid, Spain; (L.P.); (S.G.); (J.T.R.); (M.L.N.)
- Servicio de Pediatría, Hospital General Universitario Gregorio Marañón, 28007 Madrid, Spain
| | - María José Mellado
- Servicio de Pediatría, Hospital Universitario La Paz and IdiPAZ, 28046 Madrid, Spain; (L.E.); (M.J.M.)
- Red de Investigación CoRISpe integrada en la Red en Infectología Pediátrica (RITIP), 28046 Madrid, Spain; (L.P.); (S.G.); (J.T.R.); (M.L.N.)
| | - Sergio Serrano-Villar
- Servicio de Enfermedades Infecciosas, Hospital Universitario Ramón y Cajal and IRYCIS, 28034 Madrid, Spain;
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Méndez-Pérez R, García-López R, Bautista-López JSBL, Vázquez-Castellanos J, Alvarez-González C, Peña-Marín E, Baltierra-Trejo E, Adams-Schroeder R, Domínguez-Rodríguez V, Melgar-Valdés C, Martínez-García R, Moya A, Gómez-Cruz R. High-throughput sequencing of the 16S rRNA gene to analyze the gut microbiome in juvenile and adult tropical gar (Atractosteus tropicus). Lat Am J Aquat Res 2020. [DOI: 10.3856/vol48-issue3-fulltext-2419] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Tropical gar (Atractosteus tropicus) is freshwater and estuarine fish, inhabiting the Earth since the Mesozoic era and undergoing limited physiological variation ever since. Besides its recognized cultural andscientific relevance, the species has seen remarkable growth in its economic impact due to pisciculture. In this study, we present the first report of the whole taxonomic composition of microbial communities in gut contents in juveniles and adults of A. tropicus, by sex and origin (wild and cultivated). For this study, 508 genera were identified, with the most and least abundant being Cetobacterium and Paludibacter, respectively. Fusobacteria, Proteobacteria, Firmicutes, and Bacteroidetes phyla are the core gut microbiome of A. tropicus juvenile and adult by sex and origin. Deinococcus-Thermus phylum sequence was only identified in wild-type males. In the phylogenetic trees reconstruction Lactococcus lactis strains CAU929 and CAU6600, Cp6 and CAU9951,Cetobacterium strain H69, Aeromonas hydrophila strain P5 and WR-5-3-2, Aeromonas sobria strain CP DC28 and Aeromonas hydrophila were identified, some of them with probiotic potential within the three dominant phyla in core gut microbiome in A. tropicus adults, especially in wild-type organisms. Myroides genus was recognized in microbiota gut of the cultivated juvenile A. tropicus. Nevertheless, Alpha diversity indicated that the highest gut microbiota abundance and richness is found in cultivated juvenile and wild-type adult A. tropicus female, rather than adult wild-type males and the least gut microbiota abundance and richness is found in a cultivated adult of A. tropicus for both sexes.
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20
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González-Serrano F, Pérez-Cobas AE, Rosas T, Baixeras J, Latorre A, Moya A. The Gut Microbiota Composition of the Moth Brithys crini Reflects Insect Metamorphosis. Microb Ecol 2020; 79:960-970. [PMID: 31796995 DOI: 10.1007/s00248-019-01460-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 11/04/2019] [Indexed: 02/07/2023]
Abstract
Lepidoptera is a highly diverse insect order with major importance in agriculture as many species are considered pests. The role of the gut microbiota in insect physiology is still poorly understood, despite the research undertaken in recent years. Furthermore, Lepidoptera are holometabolous insects and few studies have addressed the influence of the changes taking place on the gut microbiome composition and diversity during metamorphosis, especially in monophagous species. The V3-V4 region of the 16S rRNA gene was sequenced to investigate the microbiota composition and diversity of the monophagous moth Brithys crini during three different life stages: egg, larvae (midgut and hindgut), and adult (gut). Our results showed that the microbiota composition of B. crini was stage specific, indicating that the developmental stage is a main factor affecting the gut microbiome in composition and potential functions. Moreover, the diversity of the gut microbiome reflected the developmental process, since a drop in diversity occurred between the larval and the adult phase, when the intestine is completely renewed. In spite of the changes in the gut microbiota during metamorphosis, 29 genera were conserved throughout the three developmental stages, mainly belonging to the Proteobacteria phylum, which define the core microbiome of B. crini. These genera seem to contribute to host physiology by participating in food digestion, nutrition, and detoxification mechanisms.
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Affiliation(s)
- Francisco González-Serrano
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
- Institute for Integrative Systems Biology, University of València and Consejo Superior de Investigaciones Científicas, València, Spain
| | - Ana Elena Pérez-Cobas
- Institut Pasteur and Biologie des Bactéries Intracellulaires, Paris, France
- CNRS UMR 3525, 75724, Paris, France
| | - Tania Rosas
- Institute for Integrative Systems Biology, University of València and Consejo Superior de Investigaciones Científicas, València, Spain
| | - Joaquín Baixeras
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, University of València, València, Spain
| | - Amparo Latorre
- Institute for Integrative Systems Biology, University of València and Consejo Superior de Investigaciones Científicas, València, Spain
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad València, (FISABIO), València, Spain
- CIBER en Epidemiología y Salud Pública (CIBEResp), Madrid, Spain
| | - Andrés Moya
- Institute for Integrative Systems Biology, University of València and Consejo Superior de Investigaciones Científicas, València, Spain.
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad València, (FISABIO), València, Spain.
- CIBER en Epidemiología y Salud Pública (CIBEResp), Madrid, Spain.
- Integrative Systems Biology Institute (I2Sysbio) University of València and Spanish Research Council (CSIC). c/ Catedrático Agustín Escardino Benlloch 9, 46980, Paterna, València, Spain.
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21
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Arnoriaga-Rodríguez M, Mayneris-Perxachs J, Burokas A, Pérez-Brocal V, Moya A, Portero-Otin M, Ricart W, Maldonado R, Fernández-Real JM. Gut bacterial ClpB-like gene function is associated with decreased body weight and a characteristic microbiota profile. Microbiome 2020; 8:59. [PMID: 32354351 PMCID: PMC7193372 DOI: 10.1186/s40168-020-00837-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [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] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 04/02/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND The chaperone ClpB, a bacterial protein, is a conformational antigen-mimetic of α-melanocyte-stimulating hormone (α-MSH) implicated in body weight regulation in mice. We here investigated the potential associations of gut bacterial ClpB-like gene function with obesity status and gut microbiota in humans. RESULTS Gut microbiota ClpB KEGG function was negatively associated with body mass index, waist circumference, and total fat mass (DEXA). The relative abundance (RA) of several phyla and families directly associated with ClpB was decreased in subjects with obesity. Specifically, the RA of Rikenellaceae, Clostridiaceae and not assigned Firmicutes were lower in subjects with obesity and positively associated with gut bacterial ClpB-like gene function (not assigned Firmicutes (r = 0.405, FDR = 2.93 × 10-2), Rikenellaceae (r = 0.217, FDR = 0.031), and Clostridiaceae (r = 0.239, FDR = 0.017)). The gut bacterial ClpB-like gene function was also linked to specific plasma metabolites (hippuric acid and 3-indolepropionic acid) and fecal lupeol. The α-MSH-like epitope similar to that of Escherichia coli ClpB was also identified in some sequences of those bacterial families. After fecal transplantation from humans to mice, the families that more contributed to ClpB-like gene function in humans were also associated with ClpB-like gene function in mice after adjusting for the donor's body mass index (not assigned Firmicutes (r = 0.621, p = 0.003), Prevotellaceae (r = 0.725, p = 4.1 × 10-7), Rikenellaceae (r = 0.702, p = 3.9 × 10-4), and Ruminococcaceae (r = 0.526, p = 0.014)). Clostridiaceae (r = - 0.445, p = 0.038) and Prevotellaceae RA (r = - 0.479, p = 0.024) and were also negatively associated with weight gain in mice. The absolute abundance (AA) of Prevotellaceae in mice was also positively associated with the gut bacterial ClpB-like gene function in mice. DESeq2 identified species of Prevotellaceae, both negatively associated with mice' weight gain and positively with gut bacterial ClpB-like gene function. CONCLUSIONS In summary, gut bacterial ClpB-like gene function is associated with obesity status, a specific gut microbiota composition and a plasma metabolomics profile in humans that could be partially transplanted to mice. Video Abstract.
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Affiliation(s)
- María Arnoriaga-Rodríguez
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Carretera de França s/n, 17007, Girona, Spain
- Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Madrid, Spain
- Department of Medical Sciences, Faculty of Medicine, University of Girona, Girona, Spain
| | - Jordi Mayneris-Perxachs
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Carretera de França s/n, 17007, Girona, Spain
- Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Madrid, Spain
| | - Aurelijus Burokas
- Laboratory of Neuropharmacology, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Present address: Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257, Vilnius, Lithuania
| | - Vicente Pérez-Brocal
- Department of Genomics and Health, Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO-Public Health), Valencia, Spain
- Biomedical Research Networking Center for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Andrés Moya
- Department of Genomics and Health, Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO-Public Health), Valencia, Spain
- Biomedical Research Networking Center for Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia, Spanish National Research Council (CSIC-UVEG), Valencia, Spain
| | - Manuel Portero-Otin
- Metabolic Pathophysiology Research Group, Lleida Biomedical Research Institute (IRBLleida), Universitat de Lleida, Lleida, Spain
| | - Wifredo Ricart
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Carretera de França s/n, 17007, Girona, Spain
- Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Madrid, Spain
- Department of Medical Sciences, Faculty of Medicine, University of Girona, Girona, Spain
| | - Rafael Maldonado
- Laboratory of Neuropharmacology, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - José-Manuel Fernández-Real
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Carretera de França s/n, 17007, Girona, Spain.
- Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain.
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Madrid, Spain.
- Department of Medical Sciences, Faculty of Medicine, University of Girona, Girona, Spain.
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22
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Dinleyici M, Pérez-Brocal V, Arslanoglu S, Aydemir O, Ozumut SS, Tekin N, Vandenplas Y, Moya A, Dinleyici EC. Human milk mycobiota composition: relationship with gestational age, delivery mode, and birth weight. Benef Microbes 2020; 11:151-162. [PMID: 31990220 DOI: 10.3920/bm2019.0158] [Citation(s) in RCA: 12] [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: 02/05/2023]
Abstract
Intestinal and human milk microbiota studies during infancy have shown variations according to geographical location, delivery mode, gestational age, and mother-related factors during pregnancy. In this study, we performed metagenomic mycobiota analyses of 44 transient and mature human milk among five different groups: mothers of normal spontaneous delivery-term (NS-T), caesarean delivery-term (CS-T), premature (PT), small for gestational age (SGA), and large for gestational age (LGA) infants. Fungi were detected in 80 out of the 88 samples. Regarding the number of observed fungal species, the NS-T group was more homogeneous (less variable) comparing the other groups (P<0.05). In the transient human milk samples, the most abundant species were Saccharomyces cerevisiae (33.3%) and Aspergillus glaucus (27.4%). While A. glaucus (33.7%) was second most abundant species in mature milk, S. cerevisiae disappeared (P<0.01) and Penicillium rubens became the most abundant species (35.5%) (P<0.05). Among the NS-T group, the most abundant species was Malassezia globosa in both transient and mature milk. In contrast, S. cerevisiae was the most abundant species in transient human milk (45.0%) in the CS-T group, but it disappeared in mature milk (P<0.01). In transient milk, M. globosa was only represented 6.0-9.0% of taxa in the PT, SGA, and LGA groups (P<0.05). In transient and mature milk in the PT, SGA and LGA groups, the most abundant species were A. glaucus and P. rubens. In mature milk samples, P. rubens is more abundant in CS-T group, PT group and LGA group, than the NS-T groups (P<0.05 for all). Although fungi constitute only a very small part of the human milk microbiome, we observed some changes that the human milk mycobiota composition varies in caesarean delivery, premature, SGA and LGA groups, comparing the normal spontaneous delivery, as well as differences between transient and mature human milk.
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Affiliation(s)
- M Dinleyici
- Eskisehir Osmangazi University Faculty of Medicine, Department of Pediatrics, Eskisehir 26480, Turkey
- Eskisehir Osmangazi University Faculty of Medicine, Department of Social Pediatrics, Eskisehir 26480, Turkey
| | - V Pérez-Brocal
- Department of Genomics and Health, Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO-Public Health), Valencia, Spain
- CIBER in Epidemiology and Public Health (CIBEResp), Madrid, Spain
| | - S Arslanoglu
- Division of Neonatology, Department of Pediatrics, Istanbul Medeniyet University Faculty of Medicine, Istanbul, Turkey
| | - O Aydemir
- Eskisehir Osmangazi University Faculty of Medicine, Department of Pediatrics, Eskisehir 26480, Turkey
- Eskisehir Osmangazi University Faculty of Medicine, Division of Neonatology, Eskisehir 26480, Turkey
| | - S Sevuk Ozumut
- Division of Neonatology, Department of Pediatrics, Istanbul Medeniyet University Faculty of Medicine, Istanbul, Turkey
| | - N Tekin
- Eskisehir Osmangazi University Faculty of Medicine, Department of Pediatrics, Eskisehir 26480, Turkey
- Eskisehir Osmangazi University Faculty of Medicine, Division of Neonatology, Eskisehir 26480, Turkey
| | - Y Vandenplas
- UZ Brussel, Vrije Universiteit Brussel, Department of Pediatrics, Brussel, Belgium
| | - A Moya
- Department of Genomics and Health, Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO-Public Health), Valencia, Spain
- CIBER in Epidemiology and Public Health (CIBEResp), Madrid, Spain
- Institute for Integrative Systems Biology (I2SysBio), The University of Valencia and The Spanish National Research Council (CSIC-UVEG), Valencia, Spain
| | - E C Dinleyici
- Eskisehir Osmangazi University Faculty of Medicine, Department of Pediatrics, Eskisehir 26480, Turkey
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23
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Moreno-Arrones OM, Serrano-Villar S, Perez-Brocal V, Saceda-Corralo D, Morales-Raya C, Rodrigues-Barata R, Moya A, Jaen-Olasolo P, Vano-Galvan S. Analysis of the gut microbiota in alopecia areata: identification of bacterial biomarkers. J Eur Acad Dermatol Venereol 2020; 34:400-405. [PMID: 31419351 DOI: 10.1111/jdv.15885] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [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: 01/01/2019] [Accepted: 07/16/2019] [Indexed: 02/05/2023]
Abstract
BACKGROUND Alopecia areata is a T-cell-mediated autoimmune disease with an unknown etiopathogenesis. Gut microbiota has been revealed as a key modulator of systemic immunity. OBJECTIVE To determine whether patients affected by alopecia universalis present differences in gut bacteria composition compared with healthy controls and investigate possible bacterial biomarkers of the disease. METHODS We conducted a cross-sectional study that involved 15 patients affected by alopecia universalis and 15 controls. Gut microbiome of the study subjects was analysed by sequencing the 16SrRNA of stool samples. We searched for bacterial biomarkers of alopecia universalis using the linear discriminant analysis effect size (LEFse) tool. RESULTS In total, 30 study subjects (46.6% female; mean [SD] age, 40.1 [9.8] years) were enrolled. Neither alpha (Shannon diversity index 5.31 ± 0.43 vs. 5.03 ± 0.43, P 0.1) or beta diversity (ADONIS P value: 0.35) of gut microbiota showed statistically significant differences between cases and controls. In patients affected with alopecia, we found an enriched presence (LDA SCORE > 2) of Holdemania filiformis, Erysipelotrichacea, Lachnospiraceae, Parabacteroides johnsonii, Clostridiales vadin BB60 group, Bacteroides eggerthii and Parabacteroides distasonis. A predictive model based on the number of bacterial counts of Parabacteroides distasonis and Clostridiales vadin BB60 group correctly predicted disease status in 80% of patients (AUC 0.804 (0.633-0.976), P 0.004). CONCLUSION Alopecia universalis does not seem to affect broadly gut microbiota structure. Bacterial biomarkers found associated with the disease (Holdemania filiformis, Erysipelotrichacea, Lachnospiraceae, Parabacteroides johnsonii, Eggerthellaceae, Clostridiales vadin BB60 group, Bacteroides eggerthii and Parabacteroides distasonis) should be further studied as they could be involved in its pathophysiology or be used as diagnostic tools.
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Affiliation(s)
- O M Moreno-Arrones
- Dermatology Department, Hospital Universitario Ramón y Cajal, IRYCIS, Universidad de Alcalá, Madrid, Spain
| | - S Serrano-Villar
- Infectious Diseases Department, Ramon y Cajal Hospital, Madrid, Spain
| | - V Perez-Brocal
- Department of Genomics and Health, Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO-Public Health), València, Spain
- CIBER in Epidemiology and Public Health (CIBEResp), Madrid, Spain
| | - D Saceda-Corralo
- Dermatology Department, Hospital Universitario Ramón y Cajal, IRYCIS, Universidad de Alcalá, Madrid, Spain
| | | | - R Rodrigues-Barata
- Dermatology Department, Hospital Universitario Ramón y Cajal, IRYCIS, Universidad de Alcalá, Madrid, Spain
| | - A Moya
- Department of Genomics and Health, Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO-Public Health), València, Spain
- CIBER in Epidemiology and Public Health (CIBEResp), Madrid, Spain
- Institute for Integrative Systems Biology (I2SysBio), The University of Valencia and The Spanish National Research Council (CSIC)-UVEG), València, Spain
| | - P Jaen-Olasolo
- Dermatology Department, Hospital Universitario Ramón y Cajal, IRYCIS, Universidad de Alcalá, Madrid, Spain
| | - S Vano-Galvan
- Dermatology Department, Hospital Universitario Ramón y Cajal, IRYCIS, Universidad de Alcalá, Madrid, Spain
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Lamelas A, Desgarennes D, López-Lima D, Villain L, Alonso-Sánchez A, Artacho A, Latorre A, Moya A, Carrión G. The Bacterial Microbiome of Meloidogyne-Based Disease Complex in Coffee and Tomato. Front Plant Sci 2020; 11:136. [PMID: 32174936 PMCID: PMC7056832 DOI: 10.3389/fpls.2020.00136] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 01/29/2020] [Indexed: 02/05/2023]
Abstract
The Meloidogyne-based disease complexes (MDCs) are caused by the interaction of different root-knot nematode species and phytopathogenic fungi. These complexes are devastating several important crops worldwide including tomato and coffee. Despite their relevance, little is known about the role of the bacterial communities in the MDCs. In this study 16s rDNA gene sequencing was used to analyze the bacterial microbiome associated with healthy and infested roots, as well with females and eggs of Meloidogyne enterolobii and M. paranaensis, the causal agents of MDC in tomato and coffee, respectively. Each MDC pathosystems displayed a specific taxonomic diversity and relative abundances constituting a very complex system. The main bacterial drivers of the MDC infection process were identified for both crops at order level. While corky-root coffee samples presented an enrichment of Bacillales and Burkholderiales, the corcky-root tomato samples presented an enrichment on Saprospirales, Chthoniobacterales, Alteromonadales, and Xanthomonadales. At genus level, Nocardia was common to both systems, and it could be related to the development of tumor symptoms by altering both nematode and plant systems. Furthermore, we predicted the healthy metabolic profile of the roots microbiome and a shift that may result in an increment of activity of central metabolism and the presence of pathogenic genes in both crops.
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Affiliation(s)
- Araceli Lamelas
- Red de Estudios Moleculares Avanzados and Red de Biodiversidad y Sistemática, Instituto de Ecología A. C., Xalapa, Mexico
| | - Damaris Desgarennes
- Red de Estudios Moleculares Avanzados and Red de Biodiversidad y Sistemática, Instituto de Ecología A. C., Xalapa, Mexico
| | - Daniel López-Lima
- Red de Estudios Moleculares Avanzados and Red de Biodiversidad y Sistemática, Instituto de Ecología A. C., Xalapa, Mexico
| | | | - Alexandro Alonso-Sánchez
- Red de Estudios Moleculares Avanzados and Red de Biodiversidad y Sistemática, Instituto de Ecología A. C., Xalapa, Mexico
| | - 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, Valencia, Spain
| | - Amparo Latorre
- 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, Valencia, Spain
- CIBER en Epidemiología y Salud Pública, Madrid, Spain
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia, Spanish National Research Council (CSIC-UVEG), Valencia, 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, Valencia, Spain
- CIBER en Epidemiología y Salud Pública, Madrid, Spain
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia, Spanish National Research Council (CSIC-UVEG), Valencia, Spain
| | - Gloria Carrión
- Red de Estudios Moleculares Avanzados and Red de Biodiversidad y Sistemática, Instituto de Ecología A. C., Xalapa, Mexico
- *Correspondence: Gloria Carrión,
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Abstract
In this chapter, we describe how to use DarkHorse2.0 to search for xenologs in the genome of the cyanobacterium Synechococcus elongatus PCC 7942. DarkHorse is an implicit phylogenetic method that uses BLAST searches to identify proteins having close homologs of unexpected taxonomic affiliation. Once a set of putative xenologs are identified, Phylomizer is used to reconstruct phylogenetic trees. Phylomizer reproduces all the necessary steps to perform a basic phylogenetic analysis. The combined use of DarkHorse and Phylomizer allows the identification of genes incorporated into a given genome by HGT.
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Affiliation(s)
- Luis Delaye
- Departamento de Ingeniería Genética, CINVESTAV Irapuato, Irapuato, Guanajuato, México
| | - Carlos Vargas
- Institute of Integrative Systems Biology, University of València and CSIC, València, Spain
| | - Amparo Latorre
- Institute of Integrative Systems Biology, University of València and CSIC, València, Spain
- Joint Unit in Genomics and Health, FISABIO-Public Health - I2Sysbio, University of Valencia and CSIC, València, Spain
- CIBER in Epidemiology and Public Health, Madrid, Spain
| | - Andrés Moya
- Institute of Integrative Systems Biology, University of València and CSIC, València, Spain.
- Joint Unit in Genomics and Health, FISABIO-Public Health - I2Sysbio, University of Valencia and CSIC, València, Spain.
- CIBER in Epidemiology and Public Health, Madrid, Spain.
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Ruiz‐Ruiz S, Sanchez‐Carrillo S, Ciordia S, Mena MC, Méndez‐García C, Rojo D, Bargiela R, Zubeldia‐Varela E, Martínez‐Martínez M, Barbas C, Ferrer M, Moya A. Functional microbiome deficits associated with ageing: Chronological age threshold. Aging Cell 2020; 19:e13063. [PMID: 31730262 PMCID: PMC6974723 DOI: 10.1111/acel.13063] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [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: 06/17/2019] [Revised: 10/16/2019] [Accepted: 10/17/2019] [Indexed: 02/05/2023] Open
Abstract
Composition of the gut microbiota changes during ageing, but questions remain about whether age is also associated with deficits in microbiome function and whether these changes occur sharply or progressively. The ability to define these deficits in populations of different ages may help determine a chronological age threshold at which deficits occur and subsequently identify innovative dietary strategies for active and healthy ageing. Here, active gut microbiota and associated metabolic functions were evaluated using shotgun proteomics in three well-defined age groups consisting of 30 healthy volunteers, namely, ten infants, ten adults and ten elderly individuals. Samples from each volunteer at intervals of up to 6 months (n = 83 samples) were used for validation. Ageing gradually increases the diversity of gut bacteria that actively synthesize proteins, that is by 1.4-fold from infants to elderly individuals. An analysis of functional deficits consistently identifies a relationship between tryptophan and indole metabolism and ageing (p < 2.8e-8 ). Indeed, the synthesis of proteins involved in tryptophan and indole production and the faecal concentrations of these metabolites are directly correlated (r2 > .987) and progressively decrease with age (r2 > .948). An age threshold for a 50% decrease is observed ca. 11-31 years old, and a greater than 90% reduction is observed from the ages of 34-54 years. Based on recent investigations linking tryptophan with abundance of indole and other "healthy" longevity molecules and on the results from this small cohort study, dietary interventions aimed at manipulating tryptophan deficits since a relatively "young" age of 34 and, particularly, in the elderly are recommended.
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Affiliation(s)
- Susana Ruiz‐Ruiz
- Unidad Mixta de Investigación en Genómica y SaludFundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO) and Instituto de Biología Integrativa de SistemasUniversitat de València and Consejo Superior de Investigaciones Científicas (CSIC)ValènciaSpain
- CIBER en Epidemiología y Salud Pública (CIBERESP)MadridSpain
| | | | - Sergio Ciordia
- Unidad de ProteómicaCentro Nacional de BiotecnologíaConsejo Superior de Investigaciones Científicas (CSIC)MadridSpain
| | - María C. Mena
- Unidad de ProteómicaCentro Nacional de BiotecnologíaConsejo Superior de Investigaciones Científicas (CSIC)MadridSpain
| | - Celia Méndez‐García
- Instituto de CatálisisConsejo Superior de Investigaciones Científicas (CSIC)MadridSpain
| | - David Rojo
- Centro de Metabolómica y Bioanálisis (CEMBIO)Facultad de FarmaciaUniversidad CEU San Pablo, Campus MontepríncipeMadridSpain
| | - Rafael Bargiela
- Instituto de CatálisisConsejo Superior de Investigaciones Científicas (CSIC)MadridSpain
- Present address:
School of Natural ScienceBangor UniversityBangorUK
| | - Elisa Zubeldia‐Varela
- Centro de Metabolómica y Bioanálisis (CEMBIO)Facultad de FarmaciaUniversidad CEU San Pablo, Campus MontepríncipeMadridSpain
- Departamento de Ciencias Médicas BásicasFacultad de MedicinaUniversidad CEU San PabloMadridSpain
| | | | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO)Facultad de FarmaciaUniversidad CEU San Pablo, Campus MontepríncipeMadridSpain
| | - Manuel Ferrer
- Instituto de CatálisisConsejo Superior de Investigaciones Científicas (CSIC)MadridSpain
| | - Andrés Moya
- Unidad Mixta de Investigación en Genómica y SaludFundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO) and Instituto de Biología Integrativa de SistemasUniversitat de València and Consejo Superior de Investigaciones Científicas (CSIC)ValènciaSpain
- CIBER en Epidemiología y Salud Pública (CIBERESP)MadridSpain
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Jiménez-Hernández N, Serrano-Villar S, Domingo A, Pons X, Artacho A, Estrada V, Moya A, Gosalbes MJ. Modulation of Saliva Microbiota through Prebiotic Intervention in HIV-Infected Individuals. Nutrients 2019; 11:nu11061346. [PMID: 31208015 PMCID: PMC6627446 DOI: 10.3390/nu11061346] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 05/09/2019] [Revised: 06/07/2019] [Accepted: 06/12/2019] [Indexed: 02/07/2023] Open
Abstract
Human immunodeficiency virus (HIV) infection is characterized by an early depletion of the mucosal associated T helper (CD4+) cells that impair the host immunity and impact the oral and gut microbiomes. Although, the HIV-associated gut microbiota was studied in depth, few works addressed the dysbiosis of oral microbiota in HIV infection and, to our knowledge, no studies on intervention with prebiotics were performed. We studied the effect of a six-week-long prebiotic administration on the salivary microbiota in HIV patients and healthy subjects. Also, the co-occurrence of saliva microorganisms in the fecal bacteria community was explored. We assessed salivary and feces microbiota composition using deep 16S ribosomal RNA (rRNA) gene sequencing with Illumina methodology. At baseline, the different groups shared the same most abundant genera, but the HIV status had an impact on the saliva microbiota composition and diversity parameters. After the intervention with prebiotics, we found a drastic decrease in alpha diversity parameters, as well as a change of beta diversity, without a clear directionality toward a healthy microbiota. Interestingly, we found a differential response to the prebiotics, depending on the initial microbiota. On the basis of 100% identity clustering, we detected saliva sequences in the feces datasets, suggesting a drag of microorganisms from the upper to the lower gastrointestinal tract.
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Affiliation(s)
- Nuria Jiménez-Hernández
- Área de Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO), 46020 Valencia, Spain.
- CIBER en Epidemiología y Salud Pública, 28029 Madrid, Spain.
| | - Sergio Serrano-Villar
- Departamento de Enfermedades Infecciosas, Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain.
| | - Alba Domingo
- Área de Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO), 46020 Valencia, Spain.
| | - Xavier Pons
- Área de Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO), 46020 Valencia, Spain.
| | - Alejandro Artacho
- Área de Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO), 46020 Valencia, Spain.
| | - Vicente Estrada
- Unidad de Enfermedades Infecciosas/Medicina Interna, Hospital Clínico San Carlos-IdiSSC, Universidad Complutense, 28040 Madrid, Spain.
| | - Andrés Moya
- Área de Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO), 46020 Valencia, Spain.
- CIBER en Epidemiología y Salud Pública, 28029 Madrid, Spain.
- Instituto de Biología Integrativa de Sistemas, Universidad de Valencia y CSIC, 46980 Paterna, Valencia, Spain.
| | - María José Gosalbes
- Área de Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO), 46020 Valencia, Spain.
- CIBER en Epidemiología y Salud Pública, 28029 Madrid, Spain.
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Palomo-Buitrago ME, Sabater-Masdeu M, Moreno-Navarrete JM, Caballano-Infantes E, Arnoriaga-Rodríguez M, Coll C, Ramió L, Palomino-Schätzlein M, Gutiérrez-Carcedo P, Pérez-Brocal V, Simó R, Moya A, Ricart W, Herance JR, Fernández-Real JM. Glutamate interactions with obesity, insulin resistance, cognition and gut microbiota composition. Acta Diabetol 2019; 56:569-579. [PMID: 30888539 DOI: 10.1007/s00592-019-01313-w] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 02/21/2019] [Indexed: 02/07/2023]
Abstract
AIMS To investigate the interactions among fecal and plasma glutamate levels, insulin resistance cognition and gut microbiota composition in obese and non-obese subjects. METHODS Gut microbiota composition (shotgun) and plasma and fecal glutamate, glutamine and acetate (NMR) were analyzed in a pilot study of obese and non-obese subjects (n = 35). Neuropsychological tests [Trail making test A (TMT-A) and Trail making test B (TMT-B)] scores measured cognitive information about processing speed, mental flexibility and executive function. RESULTS Trail-making test score was significantly altered in obese compared with non-obese subjects. Fecal glutamate and glutamate/glutamine ratio tended to be lower among obese subjects while fecal glutamate/acetate ratio was negatively associated with BMI and TMT-A scores. Plasma glutamate/acetate ratio was negatively associated with TMT-B. The relative abundance (RA) of some bacterial families influenced glutamate levels, given the positive association of fecal glutamate/glutamine ratio with Corynebacteriaceae, Coriobacteriaceae and Burkholderiaceae RA. In contrast, Streptococaceae RA, that was significantly higher in obese subjects, negatively correlated with fecal glutamate/glutamine ratio. To close the circle, Coriobacteriaceae/Streptococaceae ratio and Corynebacteriaceae/Streptococaceae ratio were associated both with TMT-A scores and fecal glutamate/glutamine ratio. CONCLUSIONS Gut microbiota composition is associated with processing speed and mental flexibility in part through changes in fecal and plasma glutamate metabolism.
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Affiliation(s)
- María Encarnación Palomo-Buitrago
- Department of Diabetes, Endocrinology and Nutrition, Hospital of Girona "Dr Josep Trueta", Institut d'Investigació Biomèdica de Girona (IDIBGI), Avinguda de França s/n, 17007, Girona, Spain
| | - Mònica Sabater-Masdeu
- Department of Diabetes, Endocrinology and Nutrition, Hospital of Girona "Dr Josep Trueta", Institut d'Investigació Biomèdica de Girona (IDIBGI), Avinguda de França s/n, 17007, Girona, Spain
- CIBER de la Fisiopatología de la Obesidad y Nutrición (CIBERobn, CB06/03/010) and Instituto de Salud Carlos III (ISCIII), Girona, Spain
| | - Jose Maria Moreno-Navarrete
- Department of Diabetes, Endocrinology and Nutrition, Hospital of Girona "Dr Josep Trueta", Institut d'Investigació Biomèdica de Girona (IDIBGI), Avinguda de França s/n, 17007, Girona, Spain
- CIBER de la Fisiopatología de la Obesidad y Nutrición (CIBERobn, CB06/03/010) and Instituto de Salud Carlos III (ISCIII), Girona, Spain
| | - Estefanía Caballano-Infantes
- Department of Diabetes, Endocrinology and Nutrition, Hospital of Girona "Dr Josep Trueta", Institut d'Investigació Biomèdica de Girona (IDIBGI), Avinguda de França s/n, 17007, Girona, Spain
- CIBER de la Fisiopatología de la Obesidad y Nutrición (CIBERobn, CB06/03/010) and Instituto de Salud Carlos III (ISCIII), Girona, Spain
| | - María Arnoriaga-Rodríguez
- Department of Diabetes, Endocrinology and Nutrition, Hospital of Girona "Dr Josep Trueta", Institut d'Investigació Biomèdica de Girona (IDIBGI), Avinguda de França s/n, 17007, Girona, Spain
- CIBER de la Fisiopatología de la Obesidad y Nutrición (CIBERobn, CB06/03/010) and Instituto de Salud Carlos III (ISCIII), Girona, Spain
| | - Clàudia Coll
- Department of Neurology, Institut d'Investigació Biomèdica de Girona (IDIBGI), Hospital of Girona "Dr Josep Trueta", Girona, Spain
| | - Lluís Ramió
- Department of Neurology, Institut d'Investigació Biomèdica de Girona (IDIBGI), Hospital of Girona "Dr Josep Trueta", Girona, Spain
| | | | - Patricia Gutiérrez-Carcedo
- Medical Molecular Imaging Research Group, Vall d'Hebron Research Institute, Instituto de Salud Carlos III (ISCIII), CIBBIM-Nanomedicine, CIBER-bbn, Barcelona, Spain
| | - Vicente Pérez-Brocal
- Genomics and Health Area, Foundation for the Promotion of Sanitary and Biomedical Research (FISABIO), València, Spain
- CIBER de Epidemiology y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Rafael Simó
- Diabetes and Metabolism Research Unit, Vall d'Hebron Research Institute, Barcelona, Spain
- Department of Endocrinology, Vall d'Hebron Research Institute, Instituto de Salud Carlos III (ISCIII), CIBERDEM, Barcelona, Spain
| | - Andrés Moya
- Genomics and Health Area, Foundation for the Promotion of Sanitary and Biomedical Research (FISABIO), València, Spain
- CIBER de Epidemiology y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Wifredo Ricart
- Department of Diabetes, Endocrinology and Nutrition, Hospital of Girona "Dr Josep Trueta", Institut d'Investigació Biomèdica de Girona (IDIBGI), Avinguda de França s/n, 17007, Girona, Spain
- CIBER de la Fisiopatología de la Obesidad y Nutrición (CIBERobn, CB06/03/010) and Instituto de Salud Carlos III (ISCIII), Girona, Spain
| | - José Raúl Herance
- Medical Molecular Imaging Research Group, Vall d'Hebron Research Institute, Instituto de Salud Carlos III (ISCIII), CIBBIM-Nanomedicine, CIBER-bbn, Barcelona, Spain.
| | - José Manuel Fernández-Real
- Department of Diabetes, Endocrinology and Nutrition, Hospital of Girona "Dr Josep Trueta", Institut d'Investigació Biomèdica de Girona (IDIBGI), Avinguda de França s/n, 17007, Girona, Spain.
- CIBER de la Fisiopatología de la Obesidad y Nutrición (CIBERobn, CB06/03/010) and Instituto de Salud Carlos III (ISCIII), Girona, Spain.
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Ata B, Yildiz S, Turkgeldi E, Brocal VP, Dinleyici EC, Moya A, Urman B. The Endobiota Study: Comparison of Vaginal, Cervical and Gut Microbiota Between Women with Stage 3/4 Endometriosis and Healthy Controls. Sci Rep 2019; 9:2204. [PMID: 30778155 PMCID: PMC6379373 DOI: 10.1038/s41598-019-39700-6] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 01/30/2019] [Indexed: 02/07/2023] Open
Abstract
Dysbiosis in the genital tract or gut microbiome can be associated with endometriosis. We sampled vaginal, cervical and gut microbiota from 14 women with histology proven stage 3/4 endometriosis and 14 healthy controls. The V3 and V4 regions of the 16S rRNA gene were amplified following the 16S Metagenomic Sequencing Library Preparation. Despite overall similar vaginal, cervical and intestinal microbiota composition between stage 3/4 endometriosis group and controls, we observed differences at genus level. The complete absence of Atopobium in the vaginal and cervical microbiota of the stage 3/4 endometriosis group was noteworthy. In the cervical microbiota, Gardnerella, Streptococcus, Escherichia, Shigella, and Ureoplasma, all of which contain potentially pathogenic species, were increased in stage 3/4 endometriosis. More women in the stage 3/4 endometriosis group had Shigella/Escherichia dominant stool microbiome. Further studies can clarify whether the association is causal, and whether dysbiosis leads to endometriosis or endometriosis leads to dysbiosis.
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Affiliation(s)
- Baris Ata
- Department of Obstetrics and Gynecology, Koc University Faculty of Medicine, Istanbul, Turkey.
| | - Sule Yildiz
- Department of Obstetrics and Gynecology, Koc University Hospital, Istanbul, Turkey
| | - Engin Turkgeldi
- Department of Obstetrics and Gynecology, Koc University Hospital, Istanbul, Turkey
| | - Vicente Pérez Brocal
- Área de Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública), Valencia, Spain
| | - Ener Cagri Dinleyici
- Eskisehir Osmangazi University Faculty of Medicine, Department of Pediatrics, Eskisehir, Turkey
| | - Andrés Moya
- Área de Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública), Valencia, Spain
- Institute for Integrative Systems Biology, Universitat de València, Valencia, Spain
- CIBER en Epidemiología y Salud Pública (CIBEResp), Madrid, Spain
| | - Bulent Urman
- Department of Obstetrics and Gynecology, Koc University Faculty of Medicine, Istanbul, Turkey
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Campos M, Capilla R, Naya F, Futami R, Coque T, Moya A, Fernandez-Lanza V, Cantón R, Sempere JM, Llorens C, Baquero F. Simulating Multilevel Dynamics of Antimicrobial Resistance in a Membrane Computing Model. mBio 2019; 10:mBio.02460-18. [PMID: 30696743 PMCID: PMC6355984 DOI: 10.1128/mbio.02460-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [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] [Indexed: 02/07/2023] Open
Abstract
Membrane computing is a bio-inspired computing paradigm whose devices are the so-called membrane systems or P systems. The P system designed in this work reproduces complex biological landscapes in the computer world. It uses nested "membrane-surrounded entities" able to divide, propagate, and die; to be transferred into other membranes; to exchange informative material according to flexible rules; and to mutate and be selected by external agents. This allows the exploration of hierarchical interactive dynamics resulting from the probabilistic interaction of genes (phenotypes), clones, species, hosts, environments, and antibiotic challenges. Our model facilitates analysis of several aspects of the rules that govern the multilevel evolutionary biology of antibiotic resistance. We examined a number of selected landscapes where we predict the effects of different rates of patient flow from hospital to the community and vice versa, the cross-transmission rates between patients with bacterial propagules of different sizes, the proportion of patients treated with antibiotics, and the antibiotics and dosing found in the opening spaces in the microbiota where resistant phenotypes multiply. We also evaluated the selective strengths of some drugs and the influence of the time 0 resistance composition of the species and bacterial clones in the evolution of resistance phenotypes. In summary, we provide case studies analyzing the hierarchical dynamics of antibiotic resistance using a novel computing model with reciprocity within and between levels of biological organization, a type of approach that may be expanded in the multilevel analysis of complex microbial landscapes.IMPORTANCE The work that we present here represents the culmination of many years of investigation in looking for a suitable methodology to simulate the multihierarchical processes involved in antibiotic resistance. Everything started with our early appreciation of the different independent but embedded biological units that shape the biology, ecology, and evolution of antibiotic-resistant microorganisms. Genes, plasmids carrying these genes, cells hosting plasmids, populations of cells, microbial communities, and host's populations constitute a complex system where changes in one component might influence the other ones. How would it be possible to simulate such a complexity of antibiotic resistance as it occurs in the real world? Can the process be predicted, at least at the local level? A few years ago, and because of their structural resemblance to biological systems, we realized that membrane computing procedures could provide a suitable frame to approach these questions. Our manuscript describes the first application of this modeling methodology to the field of antibiotic resistance and offers a bunch of examples-just a limited number of them in comparison with the possible ones to illustrate its unprecedented explanatory power.
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Affiliation(s)
- Marcelino Campos
- Department of Microbiology, Ramón y Cajal University Hospital, IRYCIS, Madrid, Spain
- Department of Information Systems and Computation (DSIC), Universitat Politècnica de València, Valencia, Spain
- Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
| | | | | | | | - Teresa Coque
- Department of Microbiology, Ramón y Cajal University Hospital, IRYCIS, Madrid, Spain
- Antibiotic Resistance and Bacterial Virulence Unit (HRYC-CSIC), Superior Council of Scientific Research (CSIC), Madrid, Spain
- Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
| | - Andrés Moya
- Integrative Systems Biology Institute, University of Valencia and Spanish Research Council (CSIC), Paterna, Valencia, Spain
- Foundation for the Promotion of Sanitary and Biomedical Research in the Valencian Community (FISABIO), Valencia, Spain
| | - Val Fernandez-Lanza
- Department of Microbiology, Ramón y Cajal University Hospital, IRYCIS, Madrid, Spain
- Bioinformatics Support Unit, IRYCIS, Madrid, Spain
| | - Rafael Cantón
- Department of Microbiology, Ramón y Cajal University Hospital, IRYCIS, Madrid, Spain
- Antibiotic Resistance and Bacterial Virulence Unit (HRYC-CSIC), Superior Council of Scientific Research (CSIC), Madrid, Spain
- Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
| | - José M Sempere
- Department of Information Systems and Computation (DSIC), Universitat Politècnica de València, Valencia, Spain
| | | | - Fernando Baquero
- Department of Microbiology, Ramón y Cajal University Hospital, IRYCIS, Madrid, Spain
- Antibiotic Resistance and Bacterial Virulence Unit (HRYC-CSIC), Superior Council of Scientific Research (CSIC), Madrid, Spain
- Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
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Raimondi S, Luciani R, Sirangelo TM, Amaretti A, Leonardi A, Ulrici A, Foca G, D'Auria G, Moya A, Zuliani V, Seibert TM, Søltoft-Jensen J, Rossi M. Microbiota of sliced cooked ham packaged in modified atmosphere throughout the shelf life: Microbiota of sliced cooked ham in MAP. Int J Food Microbiol 2019; 289:200-208. [PMID: 30268907 DOI: 10.1016/j.ijfoodmicro.2018.09.017] [Citation(s) in RCA: 24] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 09/04/2018] [Accepted: 09/19/2018] [Indexed: 02/07/2023]
Abstract
Fourteen lots of cooked ham in modified atmosphere packaging (CH) were analyzed within a few days from packaging (S) and at the end of the shelf-life (E), after storage at 7 °C to simulate thermal abuse. Five more lots, rejected from the market because spoiled (R), were included in the study. Quality of the products was generally compromised during the shelf life, with only 4 lots remaining unaltered. Analysis of 16S rRNA gene amplicons resulted in 801 OTUs. S samples presented a higher diversity than E and R ones. At the beginning of the shelf life, Proteobacteria and Firmicutes dominated the microbiota, with Acinetobacter, Brochothrix, Carnobacterium, Lactobacillus, Prevotella, Pseudomonas, Psychrobacter, Weissella, Vibrio rumoiensis occurring frequently and/or abundantly. E and R samples were dominated by Firmicutes mostly ascribed to Lactobacillales. It is noteworthy the appearance of abundant Leuconostoc, negligible in S samples, in some E and R samples, while in other LAB were outnumbered by V. rumoiensis or Brochothrix thermosphacta. The microbiota of spoiled and R samples could not be clustered on the basis of specific defects (discoloration, presence of slime, sourness, and swollen packages) or supplemented additives. LAB population of S samples, averaging 2.9 log10(cfu/g), increased to 7.7 log10(cfu/g) in the E and R samples. Dominant cultivable LAB belonged to the species Lactobacillus sakei and Leuconostoc carnosum. The same biotypes ascribed to different species where often found in the corresponding S and R samples, and sometime in different batches provided from the same producer, suggesting a recurrent contamination from the plant of production. Consistently with growth of LAB, initial pH (6.26) dropped to 5.74 in E samples. Volatiles organic compound (VOCs) analysis revealed that ethanol was the major metabolite produced during the shelf life. The profile of volatile compounds got enriched with other molecules (e.g. 2-butanone, ethyl acetate, acetic acid, acetoin, butanoic acid, ethyl ester, butanoic acid, and 2,3-butanediol) mainly ascribed to microbial metabolism.
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Affiliation(s)
- Stefano Raimondi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Rosaria Luciani
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | | | - Alberto Amaretti
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy; BIOGEST - SITEIA, University of Modena and Reggio Emilia, Modena, Italy
| | - Alan Leonardi
- 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; BIOGEST - SITEIA, University of Modena and Reggio Emilia, Modena, Italy
| | - Giorgia Foca
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy; BIOGEST - SITEIA, University of Modena and Reggio Emilia, Modena, Italy
| | - Giuseppe D'Auria
- Servicio de Secuenciación y Bioinformática, Fundación para el Fomento de la Investigación Sanitaria y Biomédica (FISABIO), Valencia, Spain; Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Valencia, Spain
| | - Andrés Moya
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Valencia, Spain; Area de Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica (FISABIO), Valencia, Spain; Instituto de Biología Integrativa de Sistemas, Universitat de València, València, Spain
| | | | | | | | - Maddalena Rossi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy; BIOGEST - SITEIA, University of Modena and Reggio Emilia, Modena, Italy.
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32
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Serrano-Villar S, de Lagarde M, Vázquez-Castellanos J, Vallejo A, Bernadino JI, Madrid N, Matarranz M, Díaz-Santiago A, Gutiérrez C, Cabello A, Villar-García J, Blanco JR, Bisbal O, Sainz T, Moya A, Moreno S, Gosalbes MJ, Estrada V. Effects of Immunonutrition in Advanced Human Immunodeficiency Virus Disease: A Randomized Placebo-controlled Clinical Trial (Promaltia Study). Clin Infect Dis 2019; 68:120-130. [PMID: 29788075 DOI: 10.1093/cid/ciy414] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [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: 03/06/2018] [Accepted: 05/09/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND While nutritional interventions with prebiotics and probiotics seem to exert immunological effects, their clinical implications in human immunodeficiency virus (HIV)-infected subjects initiating antiretroviral therapy (ART) at advanced HIV disease remain unclear. METHODS This was a pilot multicenter randomized, placebo-controlled, double-blind study in which 78 HIV-infected, ART-naive subjects with <350 CD4 T cells/μL or AIDS were randomized to either daily PMT25341 (a mixture of synbiotics, omega-3/6 fatty acids and amino acids) or placebo for 48 weeks, each in combination with first-line ART. Primary endpoints were changes in CD4 T-cell counts and CD4/CD8 ratio from baseline to week 48 and safety. Secondary endpoints were changes in markers of T-cell activation, bacterial translocation, inflammation, and α and β microbiota diversity. RESULTS Fifty-nine participants completed the follow-up with a mean CD4+ T-cell count of 221 ± 108 cells/μL and mean CD4/CD8 ratio of 0.26 ± 0.19. PMT25341 was well tolerated, without grade 3-4 adverse effects attributable to the intervention. While most of the assessed biomarkers improved during the follow-up in both arms, PMT25341-treated subjects did not experience any significant change, compared to placebo-treated subjects, in mean CD4+ T-cell count change (278 vs 250 cells/μL, P = .474) or CD4/CD8 ratio change (0.30 vs 0.32, P = .854). Similarly, we did not detect differences between treatment arms in secondary endpoints. CONCLUSIONS In HIV-infected patients initiating ART at advanced disease, the clear immunological benefits of ART were not enhanced by this nutritional intervention targeting the gut-associated lymphoid tissue and microbiota. CLINICAL TRIALS REGISTRATION NCT00870363.
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Affiliation(s)
- Sergio Serrano-Villar
- Department of Infectious Diseases, Hospital Universitario Ramon y Cajal, Facultad de Medicina, Universidad de Alcalá, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid
| | | | | | - Alejandro Vallejo
- Department of Infectious Diseases, Hospital Universitario Ramon y Cajal, Facultad de Medicina, Universidad de Alcalá, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid
| | - José I Bernadino
- HIV Unit, Hospital Universitario La Paz, Instituto de Investigación Hospital Universitario La Paz (IdiPAZ), Madrid
| | - Nadia Madrid
- Department of Infectious Diseases, Hospital Universitario Ramon y Cajal, Facultad de Medicina, Universidad de Alcalá, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid
| | | | - Alberto Díaz-Santiago
- Department of Infectious Diseases, Hospital Universitario Ramon y Cajal, Facultad de Medicina, Universidad de Alcalá, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid
| | - Carolina Gutiérrez
- Department of Infectious Diseases, Hospital Universitario Ramon y Cajal, Facultad de Medicina, Universidad de Alcalá, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid
| | - Alfonso Cabello
- Infectious Diseases Division, Hospital Universitario Fundación Jiménez Díaz, Madrid
| | - Judit Villar-García
- Infectious Diseases Department, Hospital del Mar, Instituto Hospital del Mar de Investigaciones Médicas (IMIM), Barcelona
| | - José Ramón Blanco
- Department of Infectious Diseases, Hospital San Pedro - Centro de Investigación Biomédica de la Rioja (CIBIR), Logroño
| | - Otilia Bisbal
- HIV Unit, Hospital Universitario Doce de Octubre, Madrid
| | - Talía Sainz
- Pediatric Tropical and Infectious Diseases Department, Hospital Universitario La Paz, Instituto de Investigación Hospital Universitario La Paz (IdiPAZ), Valencia
| | - Andrés Moya
- Area of Genomics and Health, FISABIO-Salud Pública, Valencia
- Institute of Integrative Systems Biology, University of Valencia and CSIC, Valencia
- CIBER in Epidemiology and Public Health, Madrid
| | | | - María José Gosalbes
- Area of Genomics and Health, FISABIO-Salud Pública, Valencia
- CIBER in Epidemiology and Public Health, Madrid
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Medina DA, Li T, Thomson P, Artacho A, Pérez-Brocal V, Moya A. Cross-Regional View of Functional and Taxonomic Microbiota Composition in Obesity and Post-obesity Treatment Shows Country Specific Microbial Contribution. Front Microbiol 2019; 10:2346. [PMID: 31681211 PMCID: PMC6812679 DOI: 10.3389/fmicb.2019.02346] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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: 10/29/2018] [Accepted: 09/26/2019] [Indexed: 02/05/2023] Open
Abstract
Gut microbiota has been shown to have an important influence on host health. The microbial composition of the human gut microbiota is modulated by diet and other lifestyle habits and it has been reported that microbial diversity is altered in obese people. Obesity is a worldwide health problem that negatively impacts the quality of life. Currently, the widespread treatment for obesity is bariatric surgery. Interestingly, gut microbiota has been shown to be a relevant factor in effective weight loss after bariatric surgery. Since that the human gut microbiota of normal subjects differs between geographic regions, it is possible that rearrangements of the gut microbiota in dysbiosis context are also region-specific. To better understand how gut microbiota contribute to obesity, this study compared the composition of the human gut microbiota of obese and lean people from six different regions and showed that the microbiota compositions in the context of obesity were specific to each studied geographic location. Furthermore, we analyzed the functional patterns using shotgun DNA metagenomic sequencing and compared the results with other obesity-related metagenomic studies, we observed that microbial contribution to functional pathways were country-specific. Nevertheless, our study showed that although microbial composition of obese patients was country-specific, the overall metabolic functions appeared to be the same between countries, indicating that different microbiota components contribute to similar metabolic outcomes to yield functional redundancy. Furthermore, we studied the microbiota functional changes of obese patients after bariatric surgery, by shotgun metagenomics sequencing and observed that changes in functional pathways were specific to the type of obesity treatment. In all, our study provides new insights into the differences and similarities of obese gut microbiota in relation to geographic location and obesity treatments.
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Affiliation(s)
- Daniel A. Medina
- Laboratorio de Biotecnología Aplicada, Facultad de Medicina Veterinaria, Universidad San Sebastián, Puerto Montt, Chile
- *Correspondence: Daniel A. Medina,
| | - Tianlu Li
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Spain
| | - Pamela Thomson
- Departamento de Ingeniería Química y Bioprocesos, Escuela de Ingeniería, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alejandro Artacho
- Genomics and Health Area, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO)-Salud Pública, Valencia, Spain
| | - 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
| | - Andrés Moya
- Genomics and Health Area, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO)-Salud Pública, Valencia, Spain
- Integrative Systems Biology Institute, University of Valencia, CSIC, Valencia, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBEResp), Madrid, Spain
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Amaretti A, Gozzoli C, Simone M, Raimondi S, Righini L, Pérez-Brocal V, García-López R, Moya A, Rossi M. Profiling of Protein Degraders in Cultures of Human Gut Microbiota. Front Microbiol 2019; 10:2614. [PMID: 31803157 PMCID: PMC6874058 DOI: 10.3389/fmicb.2019.02614] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 10/28/2019] [Indexed: 02/05/2023] Open
Abstract
Unabsorbed proteins reach the colon and are fermented by the microbiota, yielding a variety of harmful metabolites. In the present study, a 16S rRNA gene survey identified the bacterial taxa flourishing in 11 batch fermentations with proteins and peptones as the sole fermentable substrates, inoculated with the feces of six healthy adults. Organic acids, ammonia, and indole resulting from protein breakdown and fermentation accumulated in all of the cultures. Analysis of differential abundances among time-points identified Enterobacteriaceae, Burkholderiaceae, and Desulfovibrionaceae (including Esherichia-Shigella, Sutterella, Parasutterella, and Bilophila) among the bacteria that especially in the cultures with low inoculation load. Lachnospiraceae and Ruminococcaceae also encompassed many taxa that significantly expanded, mainly in cultures inoculated with high inoculation load, and showed the strongest correlation with the production of ammonium, indole, and p-cresol. Anaerotruncus, Dorea, Oscillibacter, Eubacterium oxidoreducens, Lachnoclostridium, Paeniclostridium, and Rombutsia were among them. Other Firmicutes (e.g., Roseburia, Ruminococcus, Lachnospira, Dialister, Erysipelotrichaceae, and Streptococcaceae) and many Bacteroidetes (e.g., Barnesiellaceae, Prevotellaceae, and Rickenelliaceae) decreased. Sequences attributed to Bacteroides, unresolved at the level of species, presented opposite contributions, resulting in no significant changes in the genus. This study sheds light on the multitude of bacterial taxa putatively participating in protein catabolism in the colon. Protein fermentation was confirmed as unfavorable to health, due to both the production of toxic metabolites and the blooming of opportunistic pathogens and pro-inflammatory bacteria.
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Affiliation(s)
- Alberto Amaretti
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
- BIOGEST-SITEIA, University of Modena and Reggio Emilia, Modena, Italy
| | - Caterina Gozzoli
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Marta Simone
- 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
| | - Lucia Righini
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Vicente Pérez-Brocal
- Area of Genomics and Health, Foundation for the Promotion of Sanitary and Biomedical Research of Valencian Community (FISABIO-Public Health), Valencia, Spain
- CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Rodrigo García-López
- Area of Genomics and Health, Foundation for the Promotion of Sanitary and Biomedical Research of Valencian Community (FISABIO-Public Health), Valencia, Spain
- CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Andrés Moya
- Area of Genomics and Health, Foundation for the Promotion of Sanitary and Biomedical Research of Valencian Community (FISABIO-Public Health), Valencia, Spain
- CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Institute for Integrative Systems Biology (ISysBio), University of Valencia, Spanish National Research Council (CSIC-UVEG), Valencia, Spain
| | - Maddalena Rossi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
- BIOGEST-SITEIA, University of Modena and Reggio Emilia, Modena, Italy
- *Correspondence: Maddalena Rossi,
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Ibarra-Juarez LA, Desgarennes D, Vázquez-Rosas-Landa M, Villafan E, Alonso-Sánchez A, Ferrera-Rodríguez O, Moya A, Carrillo D, Cruz L, Carrión G, López-Buenfil A, García-Avila C, Ibarra-Laclette E, Lamelas A. Impact of Rearing Conditions on the Ambrosia Beetle's Microbiome. Life (Basel) 2018; 8:E63. [PMID: 30551580 PMCID: PMC6316638 DOI: 10.3390/life8040063] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [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: 10/23/2018] [Revised: 12/05/2018] [Accepted: 12/07/2018] [Indexed: 02/07/2023] Open
Abstract
Ambrosia beetles, along with termites and leafcutter ants, are the only fungus-farming lineages within the tree of life. Bacteria harbored by ambrosia beetles may play an essential role in the nutritional symbiotic interactions with their associated fungi; however, little is known about the impact of rearing conditions on the microbiota of ambrosia beetles. We have used culture-independent methods to explore the effect of rearing conditions on the microbiome associated with Xyleborus affinis, Xyleborus bispinatus, and Xyleborus volvulus, evaluating different media in laboratory-controlled conditions and comparing wild and laboratory conditions. Our results revealed that rearing conditions affected the fungal and bacterial microbiome structure and had a strong influence on bacterial metabolic capacities. We propose that the rearing conditions influence the ambrosia-associated fungal and bacterial communities. Furthermore, bacterial microbiome flexibility may help beetles adapt to different substrates.
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Affiliation(s)
- Luis Arturo Ibarra-Juarez
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A. C., Xalapa C.P. 91070, Mexico.
- Cátedras CONACyT. Instituto de Ecología, A. C., Carretera Antigua a Coatepec 351, Xalapa C.P. 91070, Mexico.
| | - Damaris Desgarennes
- Red de Biodiversidad y Sistemática, Instituto de Ecología A. C., Xalapa C.P. 91070, Mexico.
| | | | - Emanuel Villafan
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A. C., Xalapa C.P. 91070, Mexico.
| | | | | | - Andrés Moya
- Joint Unit of Research in Genomics and Health, Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO), 46010 Valencia, Spain.
- Institute for Integrative System Biology, University of Valencia-CSIC, 46010 Valencia, Spain.
| | - Daniel Carrillo
- Tropical Research and Education Center, University of Florida, Homestead, FL 33031, USA.
| | - Luisa Cruz
- Tropical Research and Education Center, University of Florida, Homestead, FL 33031, USA.
| | - Gloria Carrión
- Red de Biodiversidad y Sistemática, Instituto de Ecología A. C., Xalapa C.P. 91070, Mexico.
| | - Abel López-Buenfil
- Servicio Nacional de Sanidad, Inocuidad y Calidad Agroalimentaria, Unidad Integral de Diagnóstico, Servicios y Constatación, Tecámac, Estado de Mexico 55740, Mexico.
| | - Clemente García-Avila
- Servicio Nacional de Sanidad, Inocuidad y Calidad Agroalimentaria, Unidad Integral de Diagnóstico, Servicios y Constatación, Tecámac, Estado de Mexico 55740, Mexico.
| | - Enrique Ibarra-Laclette
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A. C., Xalapa C.P. 91070, Mexico.
| | - Araceli Lamelas
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A. C., Xalapa C.P. 91070, Mexico.
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Abstract
A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.
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Affiliation(s)
- Fernando J Ballesteros
- Observatori Astronòmic, Universitat de València, Parque Científico de la Universitat de València, Paterna, Spain.
| | - Vicent J Martinez
- Observatori Astronòmic, Universitat de València, Parque Científico de la Universitat de València, Paterna, Spain
| | - Bartolo Luque
- Departamento de Matemática Aplicada y Estadística, ETSI Aeronauticos, Universidad Politécnica de Madrid, Madrid, Spain
| | - Lucas Lacasa
- School of Mathematical Sciences, Queen Mary University of London, Mile End Road, London, E14NS, UK
| | - Enric Valor
- Departament de Física de la Terra i Termodinàmica, Universitat de València, Valencia, Spain
| | - Andrés Moya
- Instituto de Biología Integrativa de Sistemas, Universitat de València-CSIC, Parque Científico de la Universitat de València, Paterna, Spain
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37
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Affiliation(s)
- Andrés Moya
- Institute of Integrative Systems Biology, University of València, 46010 València, Spain, and Foundation for the Promotion of Health and Biomedical Research of València Region (FISABIO), 46020 València, Spain.
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Vázquez-Castellanos JF, Serrano-Villar S, Jiménez-Hernández N, Soto Del Rio MD, Gayo S, Rojo D, Ferrer M, Barbas C, Moreno S, Estrada V, Rattei T, Latorre A, Moya A, Gosalbes MJ. Interplay between gut microbiota metabolism and inflammation in HIV infection. ISME J 2018; 12:1964-1976. [PMID: 29789624 PMCID: PMC6052150 DOI: 10.1038/s41396-018-0151-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 04/12/2018] [Accepted: 04/28/2018] [Indexed: 02/07/2023]
Abstract
HIV infection causes a disruption of gut-associated lymphoid tissue, driving a shift in the composition of gut microbiota. A deeper understanding of the metabolic changes and how they affect the interplay with the host is needed. Here, we assessed functional modifications of HIV-associated microbiota by combining metagenomic and metatranscriptomic analyses. The transcriptionally active microbiota was well-adapted to the inflamed environment, overexpressing pathways related to resistance to oxidative stress. Furthermore, gut inflammation was maintained by the Gram-negative nature of the HIV-associated microbiota and underexpression of anti-inflammatory processes, such as short chain fatty acid biosynthesis or indole production. We performed co-occurrence and metabolic network analyses that showed relevance in the microbiota structure of both taxonomic and metabolic HIV-associated biomarkers. The Bayesian network revealed the most determinant pathways for maintaining the structure stability of the bacterial community. In addition, we identified the taxa's contribution to metabolic activities and their interactions with host health.
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Affiliation(s)
- Jorge F Vázquez-Castellanos
- Foundation for the Promotion of Sanitary and Biomedical Research of Valencian Community (FISABIO), Valencia, Spain
- CIBER en Epidemiología y Salud Pública (CIBEResp), Madrid, Spain
| | - Sergio Serrano-Villar
- Department of Infectious Diseases, University Hospital Ramón y Cajal and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
| | - Nuria Jiménez-Hernández
- Foundation for the Promotion of Sanitary and Biomedical Research of Valencian Community (FISABIO), Valencia, Spain
| | - María Dolores Soto Del Rio
- Department of Agricultural, Forest and Food Sciences, Università degli Studi di Torino, Turin, Piedmont, Italy
| | - Sara Gayo
- Foundation for the Promotion of Sanitary and Biomedical Research of Valencian Community (FISABIO), Valencia, Spain
| | - David Rojo
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Madrid, Spain
| | - Manuel Ferrer
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Madrid, Spain
- CSIC, Institute of Catalysis, Madrid, Spain
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, 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
| | - Tomas Rattei
- Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Amparo Latorre
- Foundation for the Promotion of Sanitary and Biomedical Research of Valencian Community (FISABIO), Valencia, Spain
- CIBER en Epidemiología y Salud Pública (CIBEResp), Madrid, Spain
- Integrative Systems Biology Institute (I2SysBio), University of Valencia and Spanish Research Council (CSIC), Valencia, Spain
| | - Andrés Moya
- Foundation for the Promotion of Sanitary and Biomedical Research of Valencian Community (FISABIO), Valencia, Spain.
- CIBER en Epidemiología y Salud Pública (CIBEResp), Madrid, Spain.
- Integrative Systems Biology Institute (I2SysBio), University of Valencia and Spanish Research Council (CSIC), Valencia, Spain.
| | - María José Gosalbes
- Foundation for the Promotion of Sanitary and Biomedical Research of Valencian Community (FISABIO), Valencia, Spain.
- CIBER en Epidemiología y Salud Pública (CIBEResp), Madrid, Spain.
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Garcia-Nuñez M, Gallego M, Monton C, Capilla S, Millares L, Pomares X, Espasa M, Ferrari R, Moya A, Monsó E, Perez-Brocal V. The respiratory virome in chronic obstructive pulmonary disease. Future Virol 2018. [DOI: 10.2217/fvl-2018-0027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Aim: To characterize the respiratory virome in moderate/severe chronic obstructive pulmonary disease (COPD) patients using metagenomics, with healthy subjects as the reference. Patients & Methods: Sputum COPD samples were collected during stability and exacerbations with negative usual-care microbiologic analysis. Results: Eukaryotic viruses from the Anelloviridae, Herpesviridae and Retroviridae families and phages from the Shiphoviridae family were commonly found in COPD, and the respiratory virome in stability and noninfectious exacerbations showed a substantial similarity. DNA viruses with the highest relative abundance in COPD are Anelloviridae. Conclusion: These results support a colonizing role for eukaryotic viruses in COPD and highlight the importance of analyzing both DNA and RNA viruses when focusing on the respiratory virome.
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Affiliation(s)
- Marian Garcia-Nuñez
- Department of Respiratory Medicine, Parc Taulí Hospital Universitari. Institut d'Investigació i Innovació Parc Taulí I3PT, Universitat Autonoma de Barcelona, Sabadell, Spain
- Centro de Investigación en Red de Enfermedades Respiratorias, CIBERES, Bunyola, Spain
- Fundació Insitut d'Investigació GermansTrias i Pujol, Badalona, Spain
| | - Miguel Gallego
- Department of Respiratory Medicine, Parc Taulí Hospital Universitari. Institut d'Investigació i Innovació Parc Taulí I3PT, Universitat Autonoma de Barcelona, Sabadell, Spain
- Centro de Investigación en Red de Enfermedades Respiratorias, CIBERES, Bunyola, Spain
| | - Concepción Monton
- Department of Respiratory Medicine, Parc Taulí Hospital Universitari. Institut d'Investigació i Innovació Parc Taulí I3PT, Universitat Autonoma de Barcelona, Sabadell, Spain
| | - Silvia Capilla
- Department of Microbiology, Parc Taulí Hospital Universitari. Institut d'Investigació i Innovació Parc Taulí I3PT, Universitat Autonoma de Barcelona, Sabadell, Spain
| | - Laura Millares
- Department of Respiratory Medicine, Parc Taulí Hospital Universitari. Institut d'Investigació i Innovació Parc Taulí I3PT, Universitat Autonoma de Barcelona, Sabadell, Spain
- Centro de Investigación en Red de Enfermedades Respiratorias, CIBERES, Bunyola, Spain
- Fundació Insitut d'Investigació GermansTrias i Pujol, Badalona, Spain
| | - Xavier Pomares
- Department of Respiratory Medicine, Parc Taulí Hospital Universitari. Institut d'Investigació i Innovació Parc Taulí I3PT, Universitat Autonoma de Barcelona, Sabadell, Spain
- Centro de Investigación en Red de Enfermedades Respiratorias, CIBERES, Bunyola, Spain
| | - Mateu Espasa
- Department of Microbiology, Parc Taulí Hospital Universitari. Institut d'Investigació i Innovació Parc Taulí I3PT, Universitat Autonoma de Barcelona, Sabadell, Spain
| | - Rafaella Ferrari
- 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
| | - 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
- Department of Genetics, Institut Cavanilles de Biodiversitat i Biologia Evolutiva, (ICBiBE) Universitat de València, València, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Eduard Monsó
- Department of Respiratory Medicine, Parc Taulí Hospital Universitari. Institut d'Investigació i Innovació Parc Taulí I3PT, Universitat Autonoma de Barcelona, Sabadell, Spain
- Centro de Investigación en Red de Enfermedades Respiratorias, CIBERES, Bunyola, Spain
| | - 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
- Department of Genetics, Institut Cavanilles de Biodiversitat i Biologia Evolutiva, (ICBiBE) Universitat de València, València, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
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Deusch S, Serrano-Villar S, Rojo D, Martínez-Martínez M, Bargiela R, Vázquez-Castellanos JF, Sainz T, Barbas C, Moya A, Moreno S, Gosalbes MJ, Estrada V, Seifert J, Ferrer M. Effects of HIV, antiretroviral therapy and prebiotics on the active fraction of the gut microbiota. AIDS 2018; 32:1229-1237. [PMID: 29683848 DOI: 10.1097/qad.0000000000001831] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [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: 02/07/2023]
Abstract
OBJECTIVE In a recent blinded randomized study, we found that in HIV-infected individuals a short supplementation with prebiotics (scGOS/lcFOS/glutamine) ameliorates dysbiosis of total gut bacteria, particularly among viremic untreated patients. Our study goal was to determine the fraction of the microbiota that becomes active during the intervention and that could provide additional functional information. DESIGN A total of six healthy individuals, and 16 HIV-infected patients comprising viremic untreated patients (n = 5) and antiretroviral therapy-treated patients that are further divided into immunological responders (n = 7) and immunological nonresponders (n = 4) completed the 6-week course of prebiotic treatment, including six patients receiving a placebo. METHODS Alpha and beta diversity of potentially active and total gut microbiota was evaluated using shotgun proteomics and 16S rRNA gene sequencing. RESULTS HIV infection decreased dormancy and increased alpha diversity of active bacteria in comparison with the healthy controls, whose richness was not further influenced by the prebiotic intervention. The effect of the prebiotics was most evident at the beta-diversity of active bacteria, particularly within viremic untreated patients. We found that the prebiotics did not only ameliorate dysbiosis of total bacteria in viremic untreated patients but also increased the abundance of active bacteria with strong immunomodulatory properties and amino acids metabolism, namely Bifidobacteriaceae, at similar levels to those in healthy individuals. This effect was attenuated in ART-treated individuals. CONCLUSION The effect of prebiotics was greater among ART-naive HIV-infected individuals than in ART-treated patients and healthy controls. This highlights the importance of therapies aimed at manipulating the microbiome in this group of patients.
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Affiliation(s)
- Simon Deusch
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Sergio Serrano-Villar
- Department of Infectious Diseases, Hospital Universitario Ramón y Cajal, Facultad de Medicina, Universidad de Alcalá (IRYCIS)
| | - David Rojo
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, CEU San Pablo University
| | | | - Rafael Bargiela
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Madrid
| | - 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 Instituto de Biología Integrativa de Sistemas (Universidad de Valencia y CSIC), Valencia
- CIBER en Epidemiología y Salud Pública (CIBERESP)
| | - Talía Sainz
- Department of Pediatrics, Tropical and Infectious Diseases Unit, Hospital La Paz and La Paz Research Institute (IdiPAZ)
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, CEU San Pablo University
| | - 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 Instituto de Biología Integrativa de Sistemas (Universidad de Valencia y CSIC), Valencia
- CIBER en Epidemiología y Salud Pública (CIBERESP)
| | - Santiago Moreno
- Department of Infectious Diseases, Hospital Universitario Ramón y Cajal, Facultad de Medicina, Universidad de Alcalá (IRYCIS)
| | - 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-Salud Pública) y el Instituto de Biología Integrativa de Sistemas (Universidad de Valencia y CSIC), Valencia
- CIBER en Epidemiología y Salud Pública (CIBERESP)
| | - Vicente Estrada
- HIV Unit, Department of Internal Medicine, University Hospital Clínico San Carlos, Madrid, Spain
| | - Jana Seifert
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Manuel Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Madrid
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Serena C, Ceperuelo-Mallafré V, Keiran N, Queipo-Ortuño MI, Bernal R, Gomez-Huelgas R, Urpi-Sarda M, Sabater M, Pérez-Brocal V, Andrés-Lacueva C, Moya A, Tinahones FJ, Fernández-Real JM, Vendrell J, Fernández-Veledo S. Elevated circulating levels of succinate in human obesity are linked to specific gut microbiota. ISME J 2018; 12:1642-1657. [PMID: 29434314 PMCID: PMC6018807 DOI: 10.1038/s41396-018-0068-2] [Citation(s) in RCA: 212] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 12/21/2017] [Accepted: 01/12/2018] [Indexed: 02/07/2023]
Abstract
Gut microbiota-related metabolites are potential clinical biomarkers for cardiovascular disease (CVD). Circulating succinate, a metabolite produced by both microbiota and the host, is increased in hypertension, ischemic heart disease, and type 2 diabetes. We aimed to analyze systemic levels of succinate in obesity, a major risk factor for CVD, and its relationship with gut microbiome. We explored the association of circulating succinate with specific metagenomic signatures in cross-sectional and prospective cohorts of Caucasian Spanish subjects. Obesity was associated with elevated levels of circulating succinate concomitant with impaired glucose metabolism. This increase was associated with specific changes in gut microbiota related to succinate metabolism: a higher relative abundance of succinate-producing Prevotellaceae (P) and Veillonellaceae (V), and a lower relative abundance of succinate-consuming Odoribacteraceae (O) and Clostridaceae (C) in obese individuals, with the (P + V/O + C) ratio being a main determinant of plasma succinate. Weight loss intervention decreased (P + V/O + C) ratio coincident with the reduction in circulating succinate. In the spontaneous evolution after good dietary advice, alterations in circulating succinate levels were linked to specific metagenomic signatures associated with carbohydrate metabolism and energy production with independence of body weight change. Our data support the importance of microbe-microbe interactions for the metabolite signature of gut microbiome and uncover succinate as a potential microbiota-derived metabolite related to CVD risk.
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Affiliation(s)
- Carolina Serena
- Unitat de Recerca, Hospital Universitari de Tarragona Joan XXIII, Institut d´Investigació Sanitària Pere Virgili, Tarragona, Spain
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain
| | - Victoria Ceperuelo-Mallafré
- Unitat de Recerca, Hospital Universitari de Tarragona Joan XXIII, Institut d´Investigació Sanitària Pere Virgili, Tarragona, Spain
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain
| | - Noelia Keiran
- Unitat de Recerca, Hospital Universitari de Tarragona Joan XXIII, Institut d´Investigació Sanitària Pere Virgili, Tarragona, Spain
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain
| | - Maria Isabel Queipo-Ortuño
- Unidad de Gestión Clínica de Endocrinología y Nutrición, Instituto de Investigación Biomédica de Málaga (IBIMA), Hospital Universitario de Málaga Virgen de la Victoria, Universidad de Málaga, 29010, Málaga, Spain
- CIBER de Obesidad y Nutrición (CIBERObN), Instituto de Salud Carlos III, Madrid, Spain
| | - Rosa Bernal
- CIBER de Obesidad y Nutrición (CIBERObN), Instituto de Salud Carlos III, Madrid, Spain
- Servicio de Medicina Interna, IBIMA, Hospital Regional Universitario de Málaga, 29010, Málaga, Spain
| | - Ricardo Gomez-Huelgas
- CIBER de Obesidad y Nutrición (CIBERObN), Instituto de Salud Carlos III, Madrid, Spain
- Servicio de Medicina Interna, IBIMA, Hospital Regional Universitario de Málaga, 29010, Málaga, Spain
| | - Mireia Urpi-Sarda
- Biomarkers and Nutrimetabolomics Laboratory, Nutrition, Food Science and Gastronomy Department, Faculty of Pharmacy and Food Science, University of Barcelona, Barcelona, 08028, Spain
- CIBER Fragilidad y Envejecimiento Saludable (CIBERFES), Instituto de Salud Carlos III, Madrid, 28028, Spain
| | - Mónica Sabater
- CIBER de Obesidad y Nutrición (CIBERObN), Instituto de Salud Carlos III, Madrid, Spain
- Department of Diabetes Endocrinology and Nutrition, Institut d'Investigació Biomèdica de Girona (IdIBGi), Girona, Spain
| | - Vicente Pérez-Brocal
- Genomics and Health Area, Foundation for the Promotion of Sanitary and Biomedical Research (FISABIO), València, Spain
- CIBER de Epidemiology y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Cristina Andrés-Lacueva
- Biomarkers and Nutrimetabolomics Laboratory, Nutrition, Food Science and Gastronomy Department, Faculty of Pharmacy and Food Science, University of Barcelona, Barcelona, 08028, Spain
- CIBER Fragilidad y Envejecimiento Saludable (CIBERFES), Instituto de Salud Carlos III, Madrid, 28028, Spain
| | - Andres Moya
- Genomics and Health Area, Foundation for the Promotion of Sanitary and Biomedical Research (FISABIO), València, Spain
- CIBER de Epidemiology y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
- Institute of Integrative Systems Biology, Universitat de València, València, Spain
| | - Francisco J Tinahones
- Unidad de Gestión Clínica de Endocrinología y Nutrición, Instituto de Investigación Biomédica de Málaga (IBIMA), Hospital Universitario de Málaga Virgen de la Victoria, Universidad de Málaga, 29010, Málaga, Spain
- CIBER de Obesidad y Nutrición (CIBERObN), Instituto de Salud Carlos III, Madrid, Spain
| | - Jose Manuel Fernández-Real
- CIBER de Obesidad y Nutrición (CIBERObN), Instituto de Salud Carlos III, Madrid, Spain
- Department of Diabetes Endocrinology and Nutrition, Institut d'Investigació Biomèdica de Girona (IdIBGi), Girona, Spain
| | - Joan Vendrell
- Unitat de Recerca, Hospital Universitari de Tarragona Joan XXIII, Institut d´Investigació Sanitària Pere Virgili, Tarragona, Spain.
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain.
- Universitat Rovira i Virgili, Tarragona, Spain.
| | - Sonia Fernández-Veledo
- Unitat de Recerca, Hospital Universitari de Tarragona Joan XXIII, Institut d´Investigació Sanitària Pere Virgili, Tarragona, Spain.
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain.
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Martínez-Cano DJ, Bor G, Moya A, Delaye L. Testing the Domino Theory of Gene Loss in Buchnera aphidicola: The Relevance of Epistatic Interactions. Life (Basel) 2018; 8:life8020017. [PMID: 29843462 PMCID: PMC6027505 DOI: 10.3390/life8020017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 05/06/2018] [Revised: 05/24/2018] [Accepted: 05/25/2018] [Indexed: 02/07/2023] Open
Abstract
The domino theory of gene loss states that when some particular gene loses its function and cripples a cellular function, selection will relax in all functionally related genes, which may allow for the non-functionalization and loss of these genes. Here we study the role of epistasis in determining the pattern of gene losses in a set of genes participating in cell envelope biogenesis in the endosymbiotic bacteria Buchnera aphidicola. We provide statistical evidence indicating pairs of genes in B. aphidicola showing correlated gene loss tend to have orthologs in Escherichia coli known to have alleviating epistasis. In contrast, pairs of genes in B. aphidicola not showing correlated gene loss tend to have orthologs in E. coli known to have aggravating epistasis. These results suggest that during the process of genome reduction in B. aphidicola by gene loss, positive or alleviating epistasis facilitates correlated gene losses while negative or aggravating epistasis impairs correlated gene losses. We interpret this as evidence that the reduced proteome of B. aphidicola contains less pathway redundancy and more compensatory interactions, mimicking the situation of E. coli when grown under environmental constrains.
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Affiliation(s)
- David J Martínez-Cano
- Departamento de Ingeniería Genética, CINVESTAV Irapuato, Km. 9.6 Libramiento Norte Carretera Irapuato-León, 36821 Irapuato, Guanajuato, Mexico.
| | - Gil Bor
- CIMAT, A.P. 402, Guanajuato 36000, Gto., Mexico.
| | - Andrés Moya
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO)-Salud Pública, Avenida de Catalunya 21, 46020 València, Spain.
- Institute for Integrative Systems Biology, Universitat de València, Calle Catedrático José Beltrán 2, 46980 Paterna, València, Spain.
| | - Luis Delaye
- Departamento de Ingeniería Genética, CINVESTAV Irapuato, Km. 9.6 Libramiento Norte Carretera Irapuato-León, 36821 Irapuato, Guanajuato, Mexico.
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Abstract
Antibiotic resistance is recognized as one of the major challenges in public health. The global spread of antibiotic resistance is the consequence of a constant flow of information across multi-hierarchical interactions, involving cellular (clones), subcellular (resistance genes located in plasmids, transposons, and integrons), and supracellular (clonal complexes, genetic exchange communities, and microbiotic ensembles) levels. In order to study such multilevel complexity, we propose to establish an experimental epidemiology model for the transmission of antibiotic resistance with the cockroach Blatella germanica. This paper reports the results of five types of preliminary experiments with B. germanica populations that allow us to conclude that this animal is an appropriate model for experimental epidemiology: (i) the composition, transmission, and acquisition of gut microbiota and endosymbionts; (ii) the effect of different diets on gut microbiota; (iii) the effect of antibiotics on host fitness; (iv) the evaluation of the presence of antibiotic resistance genes in natural- and lab-reared populations; and (v) the preparation of plasmids harboring specific antibiotic resistance genes. The basic idea is to have populations with higher and lower antibiotic exposure, simulating the hospital and the community, respectively, and with a certain migration rate of insects between populations. In parallel, we present a computational model based on P-membrane computing that will mimic the experimental system of antibiotic resistance transmission. The proposal serves as a proof of concept for the development of more-complex population dynamics of antibiotic resistance transmission that are of interest in public health, which can help us evaluate procedures and design appropriate interventions in epidemiology.
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Affiliation(s)
- Pablo Llop
- Foundation for the Promotion of Sanitary and Biomedical Research in the Valencian Region (FISABIO), València, Spain
| | - Amparo Latorre
- Foundation for the Promotion of Sanitary and Biomedical Research in the Valencian Region (FISABIO), València, Spain
- Integrative Systems Biology Institute, Universitat de València, València, Spain
- Network Research Center for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Andrés Moya
- Foundation for the Promotion of Sanitary and Biomedical Research in the Valencian Region (FISABIO), València, Spain
- Integrative Systems Biology Institute, Universitat de València, València, Spain
- Network Research Center for Epidemiology and Public Health (CIBERESP), Madrid, Spain
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Abstract
The origin and shape of metabolic scaling has been controversial since Kleiber found that basal metabolic rate of animals seemed to vary as a power law of their body mass with exponent 3/4, instead of 2/3, as a surface-to-volume argument predicts. The universality of exponent 3/4 -claimed in terms of the fractal properties of the nutrient network- has recently been challenged according to empirical evidence that observed a wealth of robust exponents deviating from 3/4. Here we present a conceptually simple thermodynamic framework, where the dependence of metabolic rate with body mass emerges from a trade-off between the energy dissipated as heat and the energy efficiently used by the organism to maintain its metabolism. This balance tunes the shape of an additive model from which different effective scalings can be recovered as particular cases, thereby reconciling previously inconsistent empirical evidence in mammals, birds, insects and even plants under a unified framework. This model is biologically motivated, fits remarkably well the data, and also explains additional features such as the relation between energy lost as heat and mass, the role and influence of different climatic environments or the difference found between endotherms and ectotherms.
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Affiliation(s)
- Fernando J Ballesteros
- Observatori Astronòmic, Universitat de València, Parque Científico de la Universitat de València, Paterna, Spain.
| | - Vicent J Martinez
- Observatori Astronòmic, Universitat de València, Parque Científico de la Universitat de València, Paterna, Spain
| | - Bartolo Luque
- Departamento de Matemática Aplicada y Estadística, ETSI Aeronauticos, Universidad Politécnica de Madrid, Madrid, Spain
| | - Lucas Lacasa
- School of Mathematical Sciences, Queen Mary University of London, Mile End Road, London, E14NS, UK
| | - Enric Valor
- Departament de Física de la Terra i Termodinàmica, Universitat de València, Valencia, Spain
| | - Andrés Moya
- Instituto de Biología Integrativa de Sistemas, Universitat de València-CSIC, Parque Científico de la Universitat de València, Paterna, Spain
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Gil R, Vargas-Chavez C, López-Madrigal S, Santos-García D, Latorre A, Moya A. Tremblaya phenacola PPER: an evolutionary beta-gammaproteobacterium collage. ISME J 2018; 12:124-135. [PMID: 28914880 PMCID: PMC5739004 DOI: 10.1038/ismej.2017.144] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 05/31/2017] [Accepted: 07/28/2017] [Indexed: 02/07/2023]
Abstract
Many insects rely on bacterial endosymbionts to obtain nutrients that are scarce in their highly specialized diets. The most surprising example corresponds to the endosymbiotic system found in mealybugs from subfamily Pseudococcinae in which two bacteria, the betaproteobacterium 'Candidatus Tremblaya princeps' and a gammaproteobacterium, maintain a nested endosymbiotic consortium. In the sister subfamily Phenacoccinae, however, a single beta-endosymbiont, 'Candidatus Tremblaya phenacola', has been described. In a previous study, we detected a trpB gene of gammaproteobacterial origin in 'Ca. Tremblaya phenacola' from two Phenacoccus species, apparently indicating an unusual case of horizontal gene transfer (HGT) in a bacterial endosymbiont. What we found by sequencing the genome of 'Ca. Tremblaya phenacola' PPER, single endosymbiont of Phenacoccus peruvianus, goes beyond a HGT phenomenon. It rather represents a genome fusion between a beta and a gammaproteobacterium, followed by massive rearrangements and loss of redundant genes, leading to an unprecedented evolutionary collage. Mediated by the presence of several repeated sequences, there are many possible genome arrangements, and different subgenomic sequences might coexist within the same population.
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Affiliation(s)
- Rosario Gil
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE), Universitat de València, Valencia, Spain
- Evolutionary Systems Biology of Symbionts Research Program, Institute for Integrative Systems Biology, Universitat de València/CSIC, Paterna (Valencia), Spain
- Institute for Integrative Systems Biology, Universitat de València/CSIC, C/Catedrático José Beltrán 2, 46980 Paterna (Valencia), Spain. E-mail:
| | - Carlos Vargas-Chavez
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE), Universitat de València, Valencia, Spain
- Evolutionary Systems Biology of Symbionts Research Program, Institute for Integrative Systems Biology, Universitat de València/CSIC, Paterna (Valencia), Spain
| | - Sergio López-Madrigal
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE), Universitat de València, Valencia, Spain
| | - Diego Santos-García
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE), Universitat de València, Valencia, Spain
| | - Amparo Latorre
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE), Universitat de València, Valencia, Spain
- Evolutionary Systems Biology of Symbionts Research Program, Institute for Integrative Systems Biology, Universitat de València/CSIC, Paterna (Valencia), Spain
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana, Valencia, Spain
| | - Andrés Moya
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE), Universitat de València, Valencia, Spain
- Evolutionary Systems Biology of Symbionts Research Program, Institute for Integrative Systems Biology, Universitat de València/CSIC, Paterna (Valencia), Spain
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana, Valencia, Spain
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Džunková M, Martinez-Martinez D, Gardlík R, Behuliak M, Janšáková K, Jiménez N, Vázquez-Castellanos JF, Martí JM, D’Auria G, Bandara HMHN, Latorre A, Celec P, Moya A. Oxidative stress in the oral cavity is driven by individual-specific bacterial communities. NPJ Biofilms Microbiomes 2018; 4:29. [PMID: 30510769 PMCID: PMC6258756 DOI: 10.1038/s41522-018-0072-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Accepted: 10/15/2018] [Indexed: 02/07/2023] Open
Abstract
The term "bacterial dysbiosis" is being used quite extensively in metagenomic studies, however, the identification of harmful bacteria often fails due to large overlap between the bacterial species found in healthy volunteers and patients. We hypothesized that the pathogenic oral bacteria are individual-specific and they correlate with oxidative stress markers in saliva which reflect the inflammatory processes in the oral cavity. Temporally direct and lagged correlations between the markers and bacterial taxa were computed individually for 26 volunteers who provided saliva samples during one month (21.2 ± 2.7 samples/volunteer, 551 samples in total). The volunteers' microbiomes differed significantly by their composition and also by their degree of microbiome temporal variability and oxidative stress markers fluctuation. The results showed that each of the marker-taxa pairs can have negative correlations in some volunteers while positive in others. Streptococcus mutans, which used to be associated with caries before the metagenomics era, had the most prominent correlations with the oxidative stress markers, however, these correlations were not confirmed in all volunteers. The importance of longitudinal samples collections in correlation studies was underlined by simulation of single sample collections in 1000 different combinations which produced contradictory results. In conclusion, the distinct intra-individual correlation patterns suggest that different bacterial consortia might be involved in the oxidative stress induction in each human subject. In the future, decreasing cost of DNA sequencing will allow to analyze multiple samples from each patient, which might help to explore potential diagnostic applications and understand pathogenesis of microbiome-associated oral diseases.
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Affiliation(s)
- Mária Džunková
- grid.484129.2Department of Genomics and Health, Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO-Public Health), Valencia, Spain
- CIBER in Epidemiology and Public Health (CIBEResp), Madrid, Spain
- 0000 0001 2173 938Xgrid.5338.dInstitute for Integrative Systems Biology (I2SysBio), The University of Valencia and The Spanish National Research Council (CSIC)-UVEG, Valencia, Spain
- 0000 0000 9320 7537grid.1003.2Australian Centre for Ecogenomics, The University of Queensland, St Lucia, QLD Australia
| | - Daniel Martinez-Martinez
- grid.484129.2Department of Genomics and Health, Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO-Public Health), Valencia, Spain
- CIBER in Epidemiology and Public Health (CIBEResp), Madrid, Spain
- 0000 0001 2173 938Xgrid.5338.dInstitute for Integrative Systems Biology (I2SysBio), The University of Valencia and The Spanish National Research Council (CSIC)-UVEG, Valencia, Spain
| | - Roman Gardlík
- 0000000109409708grid.7634.6Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, Bratislava, Slovakia
| | - Michal Behuliak
- 0000000109409708grid.7634.6Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, Bratislava, Slovakia
- 0000 0001 1015 3316grid.418095.1Institute of Physiology, Academy of Sciences of the Czech Republic, Praha, Czech Republic
| | - Katarína Janšáková
- 0000000109409708grid.7634.6Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, Bratislava, Slovakia
- 0000000109409708grid.7634.6Institute of Physiology, Faculty of Medicine, Comenius University, Bratislava, Slovakia
| | - Nuria Jiménez
- grid.484129.2Department of Genomics and Health, Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO-Public Health), Valencia, Spain
- CIBER in Epidemiology and Public Health (CIBEResp), Madrid, Spain
- 0000 0001 2173 938Xgrid.5338.dInstitute for Integrative Systems Biology (I2SysBio), The University of Valencia and The Spanish National Research Council (CSIC)-UVEG, Valencia, Spain
| | - Jorge F. Vázquez-Castellanos
- grid.484129.2Department of Genomics and Health, Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO-Public Health), Valencia, Spain
- CIBER in Epidemiology and Public Health (CIBEResp), Madrid, Spain
| | - Jose Manuel Martí
- 0000 0001 2173 938Xgrid.5338.dInstitute for Integrative Systems Biology (I2SysBio), The University of Valencia and The Spanish National Research Council (CSIC)-UVEG, Valencia, Spain
| | - Giuseppe D’Auria
- CIBER in Epidemiology and Public Health (CIBEResp), Madrid, Spain
- grid.484129.2Sequencing and Bioinformatics Service of the Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO-Public Health), Valencia, Spain
| | - H. M. H. N. Bandara
- 0000 0000 9320 7537grid.1003.2School of Dentistry, The University of Queensland, Herston, QLD Australia
| | - Amparo Latorre
- grid.484129.2Department of Genomics and Health, Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO-Public Health), Valencia, Spain
- CIBER in Epidemiology and Public Health (CIBEResp), Madrid, Spain
- 0000 0001 2173 938Xgrid.5338.dInstitute for Integrative Systems Biology (I2SysBio), The University of Valencia and The Spanish National Research Council (CSIC)-UVEG, Valencia, Spain
| | - Peter Celec
- 0000000109409708grid.7634.6Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, Bratislava, Slovakia
| | - Andrés Moya
- grid.484129.2Department of Genomics and Health, Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO-Public Health), Valencia, Spain
- CIBER in Epidemiology and Public Health (CIBEResp), Madrid, Spain
- 0000 0001 2173 938Xgrid.5338.dInstitute for Integrative Systems Biology (I2SysBio), The University of Valencia and The Spanish National Research Council (CSIC)-UVEG, Valencia, Spain
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Santos-Garcia D, Juravel K, Freilich S, Zchori-Fein E, Latorre A, Moya A, Morin S, Silva FJ. To B or Not to B: Comparative Genomics Suggests Arsenophonus as a Source of B Vitamins in Whiteflies. Front Microbiol 2018; 9:2254. [PMID: 30319574 PMCID: PMC6167482 DOI: 10.3389/fmicb.2018.02254] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [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: 05/23/2018] [Accepted: 09/04/2018] [Indexed: 02/05/2023] Open
Abstract
Insect lineages feeding on nutritionally restricted diets such as phloem sap, xylem sap, or blood, were able to diversify by acquiring bacterial species that complement lacking nutrients. These bacteria, considered obligate/primary endosymbionts, share a long evolutionary history with their hosts. In some cases, however, these endosymbionts are not able to fulfill all of their host's nutritional requirements, driving the acquisition of additional symbiotic species. Phloem-feeding members of the insect family Aleyrodidae (whiteflies) established an obligate relationship with Candidatus Portiera aleyrodidarum, which provides its hots with essential amino acids and carotenoids. In addition, many whitefly species harbor additional endosymbionts which may potentially further supplement their host's diet. To test this hypothesis, genomes of several endosymbionts of the whiteflies Aleurodicus dispersus, Aleurodicus floccissimus and Trialeurodes vaporariorum were analyzed. In addition to Portiera, all three species were found to harbor one Arsenophonus and one Wolbachia endosymbiont. A comparative analysis of Arsenophonus genomes revealed that although all three are capable of synthesizing B vitamins and cofactors, such as pyridoxal, riboflavin, or folate, their genomes and phylogenetic relationship vary greatly. Arsenophonus of A. floccissimus and T. vaporariorum belong to the same clade, and display characteristics of facultative endosymbionts, such as large genomes (3 Mb) with thousands of genes and pseudogenes, intermediate GC content, and mobile genetic elements. In contrast, Arsenophonus of A. dispersus belongs to a different lineage and displays the characteristics of a primary endosymbiont-a reduced genome (670 kb) with ~400 genes, 32% GC content, and no mobile genetic elements. However, the presence of 274 pseudogenes suggests that this symbiotic association is more recent than other reported primary endosymbionts of hemipterans. The gene repertoire of Arsenophonus of A. dispersus is completely integrated in the symbiotic consortia, and the biosynthesis of most vitamins occurs in shared pathways with its host. In addition, Wolbachia endosymbionts have also retained the ability to produce riboflavin, flavin adenine dinucleotide, and folate, and may make a nutritional contribution. Taken together, our results show that Arsenophonus hold a pivotal place in whitefly nutrition by their ability to produce B vitamins.
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Affiliation(s)
- Diego Santos-Garcia
- Department of Entomology, The Hebrew University of Jerusalem, Rehovot, Israel
- *Correspondence: Diego Santos-Garcia
| | - Ksenia Juravel
- Department of Entomology, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Shiri Freilich
- Institute of Plant Sciences, Newe-Ya'ar Research Center, Agricultural Research Organization, Ramat-Yishai, Israel
| | - Einat Zchori-Fein
- Department of Entomology, Newe-Ya'ar Research Center, Agricultural Research Organization, Volcani Center, Ramat-Yishai, Israel
| | - Amparo Latorre
- Institute for Integrative Systems Biology, Universitat de València-CSIC, València, Spain
- Unidad Mixta de Investigación en Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO) and Institute for Integrative Systems Biology, Universitat de València, València, Spain
| | - Andrés Moya
- Institute for Integrative Systems Biology, Universitat de València-CSIC, València, Spain
- Unidad Mixta de Investigación en Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO) and Institute for Integrative Systems Biology, Universitat de València, València, Spain
| | - Shai Morin
- Department of Entomology, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Francisco J. Silva
- Institute for Integrative Systems Biology, Universitat de València-CSIC, València, Spain
- Unidad Mixta de Investigación en Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO) and Institute for Integrative Systems Biology, Universitat de València, València, Spain
- Francisco J. Silva
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Pérez-Brocal V, Moya A. The analysis of the oral DNA virome reveals which viruses are widespread and rare among healthy young adults in Valencia (Spain). PLoS One 2018; 13:e0191867. [PMID: 29420668 PMCID: PMC5805259 DOI: 10.1371/journal.pone.0191867] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [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: 10/06/2017] [Accepted: 01/13/2018] [Indexed: 02/07/2023] Open
Abstract
We have analysed oral wash samples from 72 healthy young adults in Valencia (Spain) for a metagenomic analysis through the construction of shotgun libraries and high-throughput-sequencing. The oral viral communities have been taxonomically characterised as well as and the gene content from the latter. The majority of viruses are found in few individuals, with single occurrences being the most widespread ones, whereas universally distributed viruses, while present, are relatively rare, with bacteriophages from families Siphoviridae and Myoviridae, and Streptococcus phages, as well as the eukaryotic viral family Herpesviridae amongst the most widespread viruses. No significant differences were found between females and males for either viruses and bacteria in abundance and alpha and beta diversity. The virome show similarities with other oral viromes previously reported for healthy individuals, suggesting the existence of a universal core of oral viruses, at least in the Western society, regardless of the geographical location.
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Affiliation(s)
- Vicente Pérez-Brocal
- Genomics and Health, FISABIO-Public Health, Valencia, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- * E-mail:
| | - Andrés Moya
- Genomics and Health, FISABIO-Public Health, Valencia, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Integrative Systems Biology Institute (I2Sysbio) University of Valencia and Spanish Research Council (CSIC), Valencia, Spain
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Dinleyici EC, Martínez-Martínez D, Kara A, Karbuz A, Dalgic N, Metin O, Yazar AS, Guven S, Kurugol Z, Turel O, Kucukkoc M, Yasa O, Eren M, Ozen M, Martí JM, P. Garay C, Vandenplas Y, Moya A. Time Series Analysis of the Microbiota of Children Suffering From Acute Infectious Diarrhea and Their Recovery After Treatment. Front Microbiol 2018; 9:1230. [PMID: 29946306 PMCID: PMC6005867 DOI: 10.3389/fmicb.2018.01230] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [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: 02/25/2018] [Accepted: 05/22/2018] [Indexed: 02/05/2023] Open
Abstract
Gut microbiota is closely related to acute infectious diarrhea, one of the leading causes of mortality and morbidity in children worldwide. Understanding the dynamics of the recovery from this disease is of clinical interest. This work aims to correlate the dynamics of gut microbiota with the evolution of children who were suffering from acute infectious diarrhea caused by a rotavirus, and their recovery after the administration of a probiotic, Saccharomyces boulardii CNCM I-745. The experiment involved 10 children with acute infectious diarrhea caused by a rotavirus, and six healthy children, all aged between 3 and 4 years. The children who suffered the rotavirus infection received S. boulardii CNCM I-745 twice daily for the first 5 days of the experiment. Fecal samples were collected from each participant at 0, 3, 5, 10, and 30 days after probiotic administration. Microbial composition was characterized by 16S rRNA gene sequencing. Alpha and beta diversity were calculated, along with dynamical analysis based on Taylor's law to assess the temporal stability of the microbiota. All children infected with the rotavirus stopped having diarrhea at day 3 after the intervention. We observed low alpha diversities in the first 5 days (p-value < 0.05, Wilcoxon test), larger at 10 and 30 days after probiotic treatment. Canonical correspondence analysis (CCA) showed differences in the gut microbiota of healthy children and of those who suffered from acute diarrhea in the first days (p-value < 0.05, ADONIS test), but not in the last days of the experiment. Temporal variability was larger in children infected with the rotavirus than in healthy ones. In particular, Gammaproteobacteria class was found to be abundant in children with acute diarrhea. We identified the microbiota transition from a diseased state to a healthy one with time, whose characterization may lead to relevant clinical data. This work highlights the importance of using time series for the study of dysbiosis related to diarrhea.
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Affiliation(s)
- Ener C. Dinleyici
- Department of Pediatrics, Faculty of Medicine, Eskisehir Osmangazi University, Eskisehir, Turkey
| | | | - Ates Kara
- Pediatric Infectious Disease Unit, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Adem Karbuz
- Department of Pediatrics, Okmeydani Education and Research Hospital, Istanbul, Turkey
| | - Nazan Dalgic
- Division of Pediatric Infectious Diseases, Sisli Etfal Training and Research Hospital, Istanbul, Turkey
| | - Ozge Metin
- Division of Pediatric Infectious Diseases, Konya Training and Research Hospital, Konya, Turkey
| | - Ahmet S. Yazar
- Department of Pediatrics, Umraniye Education and Research Hospital, Istanbul, Turkey
| | - Sirin Guven
- Department of Pediatrics, Umraniye Education and Research Hospital, Istanbul, Turkey
| | - Zafer Kurugol
- Department of Pediatrics, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Ozden Turel
- Department of Pediatric Infectious Disease Unit, Faculty of Medicine, Bezmialem Vakif University, Istanbul, Turkey
| | - Mehmet Kucukkoc
- Department of Pediatric Infectious Disease Unit, Faculty of Medicine, Bezmialem Vakif University, Istanbul, Turkey
| | - Olcay Yasa
- Department of Pediatrics, Goztepe Training and Research Hospital, SB Istanbul Medeniyet University, Istanbul, Turkey
| | - Makbule Eren
- Department of Pediatrics, Faculty of Medicine, Eskisehir Osmangazi University, Eskisehir, Turkey
| | - Metehan Ozen
- Department of Pediatrics, Acibadem University Faculty of Medicine, Istanbul, Turkey
| | - Jose Manuel Martí
- Institute for Integrative Systems Biology, Catedrático José Beltrán, Valencia, Spain
| | - Carlos P. Garay
- Institute for Integrative Systems Biology, Catedrático José Beltrán, Valencia, Spain
| | - Yvan Vandenplas
- Department of Pediatrics, UZ Brussel, Vrije Universiteit Brussel, Brussels, Belgium
| | - Andrés Moya
- Institute for Integrative Systems Biology, Catedrático José Beltrán, Valencia, Spain
- Area de Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública), Valencia, Spain
- CIBER en Epidemiología y Salud Pública (CIBEResp), Madrid, Spain
- *Correspondence: Andrés Moya
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50
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Serrano-Villar S, Vázquez-Castellanos JF, Vallejo A, Latorre A, Sainz T, Ferrando-Martínez S, Rojo D, Martínez-Botas J, Del Romero J, Madrid N, Leal M, Mosele JI, Motilva MJ, Barbas C, Ferrer M, Moya A, Moreno S, Gosalbes MJ, Estrada V. The effects of prebiotics on microbial dysbiosis, butyrate production and immunity in HIV-infected subjects. Mucosal Immunol 2017; 10:1279-1293. [PMID: 28000678 DOI: 10.1038/mi.2016.122] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [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: 08/10/2016] [Accepted: 11/19/2016] [Indexed: 02/06/2023]
Abstract
Altered interactions between the gut mucosa and bacteria during HIV infection seem to contribute to chronic immune dysfunction. A deeper understanding of how nutritional interventions could ameliorate gut dysbiosis is needed. Forty-four subjects, including 12 HIV+ viremic untreated (VU) patients, 23 antiretroviral therapy-treated (ART+) virally suppressed patients (15 immunological responders and 8 non-responders) and 9 HIV- controls (HIV-), were blindly randomized to receive either prebiotics (scGOS/lcFOS/glutamine) or placebo (34/10) over 6 weeks in this pilot study. We assessed fecal microbiota composition using deep 16S rRNA gene sequencing and several immunological and genetic markers involved in HIV immunopathogenesis. The short dietary supplementation attenuated HIV-associated dysbiosis, which was most apparent in VU individuals but less so in ART+ subjects, whose gut microbiota was found more resilient. This compositional shift was not observed in the placebo arm. Significantly, declines in indirect markers of bacterial translocation and T-cell activation, improvement of thymic output, and changes in butyrate production were observed. Increases in the abundance of Faecalibacterium and Lachnospira strongly correlated with moderate but significant increases of butyrate production and amelioration of the inflammatory biomarkers soluble CD14 and high-sensitivity C-reactive protein, especially among VU. Hence, the bacterial butyrate synthesis pathway holds promise as a viable target for interventions.
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Affiliation(s)
- S Serrano-Villar
- Department of Infectious Diseases, Hospital Universitario Ramón y Cajal, Facultad de Medicina, Universidad de Alcalá (IRYCIS), Madrid, Spain
| | - J 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 Instituto Cavanilles de Biodiversidad y Biología Evolutiva (Universidad de Valencia), Valencia, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - A Vallejo
- Department of Infectious Diseases, Hospital Universitario Ramón y Cajal, Facultad de Medicina, Universidad de Alcalá (IRYCIS), Madrid, Spain
| | - A 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 Instituto Cavanilles de Biodiversidad y Biología Evolutiva (Universidad de Valencia), Valencia, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - T Sainz
- Department of Pediatric Infectious Diseases, University Hospital La Paz, and La Paz Research Institute, Madrid, Spain
| | - S Ferrando-Martínez
- Laboratory of Immunovirology, Biomedicine Institute of Seville (IBIS), Department of Infectious Diseases, University Hospital Virgen del Rocío, Sevilla, Spain
| | - D Rojo
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, CEU San Pablo University, Madrid, Spain
| | - J Martínez-Botas
- Department of Biochemistry, University Hospital Ramón y Cajal-IRYCIS, Madrid, Spain
- CIBER of Obesity and Nutrition Pathophysiology (CIBEROBN), Madrid, Spain
| | | | - N Madrid
- Department of Infectious Diseases, Hospital Universitario Ramón y Cajal, Facultad de Medicina, Universidad de Alcalá (IRYCIS), Madrid, Spain
| | - M Leal
- Laboratory of Immunovirology, Biomedicine Institute of Seville (IBIS), Department of Infectious Diseases, University Hospital Virgen del Rocío, Sevilla, Spain
| | - J I Mosele
- Food Technology Department, Agrotecnio Center, University of Lleida, Spain
| | - M J Motilva
- Food Technology Department, Agrotecnio Center, University of Lleida, Spain
| | - C Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, CEU San Pablo University, Madrid, Spain
| | - M Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - A 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 Instituto Cavanilles de Biodiversidad y Biología Evolutiva (Universidad de Valencia), Valencia, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - S Moreno
- Department of Infectious Diseases, Hospital Universitario Ramón y Cajal, Facultad de Medicina, Universidad de Alcalá (IRYCIS), Madrid, Spain
| | - M 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-Salud Pública) y el Instituto Cavanilles de Biodiversidad y Biología Evolutiva (Universidad de Valencia), Valencia, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - V Estrada
- HIV Unit, Department of Internal Medicine, University Hospital Clínico San Carlos, Madrid, Spain
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