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Ortiz Sanjuán JM, Argüello H, Cabrera-Rubio R, Crispie F, Cotter PD, Garrido JJ, Ekhlas D, Burgess CM, Manzanilla EG. Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs. Anim Microbiome 2024; 6:18. [PMID: 38627869 PMCID: PMC11022352 DOI: 10.1186/s42523-024-00306-7] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 03/31/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Post weaning diarrhoea (PWD) causes piglet morbidity and mortality at weaning and is a major driver for antimicrobial use worldwide. New regulations in the EU limit the use of in-feed antibiotics (Ab) and therapeutic zinc oxide (ZnO) to prevent PWD. New approaches to control PWD are needed, and understanding the role of the microbiota in this context is key. In this study, shotgun metagenome sequencing was used to describe the taxonomic and functional evolution of the faecal microbiota of the piglet during the first two weeks post weaning within three experimental groups, Ab, ZnO and no medication, on commercial farms using antimicrobials regularly in the post weaning period. RESULTS Diversity was affected by day post weaning (dpw), treatment used and diarrhoea but not by the farm. Microbiota composition evolved towards the dominance of groups of species such as Prevotella spp. at day 14dpw. ZnO inhibited E. coli overgrowth, promoted higher abundance of the family Bacteroidaceae and decreased Megasphaera spp. Animals treated with Ab exhibited inconsistent taxonomic changes across time points, with an overall increase of Limosilactobacillus reuteri and Megasphaera elsdenii. Samples from non-medicated pigs showed virulence-related functions at 7dpw, and specific ETEC-related virulence factors were detected in all samples presenting diarrhoea. Differential microbiota functions of pigs treated with ZnO were related to sulphur and DNA metabolism, as well as mechanisms of antimicrobial and heavy metal resistance, whereas Ab treated animals exhibited functions related to antimicrobial resistance and virulence. CONCLUSION Ab and particularly ZnO maintained a stable microbiota composition and functionality during the two weeks post weaning, by limiting E. coli overgrowth, and ultimately preventing microbiota dysbiosis. Future approaches to support piglet health should be able to reproduce this stable gut microbiota transition during the post weaning period, in order to maintain optimal gut physiological and productive conditions.
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Affiliation(s)
- Juan M Ortiz Sanjuán
- Pig Development Department, Teagasc Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland.
- Grupo de Genómica y Mejora Animal, Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain.
| | - Héctor Argüello
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, León, Spain
| | - Raúl Cabrera-Rubio
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Institute, University College Cork, Co. Cork, Ireland
| | - Fiona Crispie
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Institute, University College Cork, Co. Cork, Ireland
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Institute, University College Cork, Co. Cork, Ireland
- VistaMilk SFI Research Centre, Fermoy, Co. Cork, Ireland
| | - Juan J Garrido
- Grupo de Genómica y Mejora Animal, Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain
| | - Daniel Ekhlas
- Pig Development Department, Teagasc Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland
- Department of Food Safety, Teagasc Food Research Centre, Ashtown, Dublin, Ireland
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Catherine M Burgess
- Department of Food Safety, Teagasc Food Research Centre, Ashtown, Dublin, Ireland
| | - Edgar G Manzanilla
- Pig Development Department, Teagasc Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
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Ortiz Sanjuán JM, Manzanilla EG, Cabrera-Rubio R, Crispie F, Cotter PD, Garrido JJ, Ekhlas D, O’Neill L, Argüello H. Fine-tuning of post-weaning pig microbiome structure and functionality by in-feed zinc oxide and antibiotics use. Front Cell Infect Microbiol 2024; 14:1354449. [PMID: 38384302 PMCID: PMC10879578 DOI: 10.3389/fcimb.2024.1354449] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 01/22/2024] [Indexed: 02/23/2024] Open
Abstract
Introduction Post-weaning diarrhoea (PWD) is a multifactorial disease that affects piglets after weaning, contributing to productive and economic losses. Its control includes the use of in-feed prophylactic antibiotics and therapeutic zinc oxide (ZnO), treatments that, since 2022, are no longer permitted in the European Union due to spread of antimicrobial resistance genes and pollution of soil with heavy metals. A dysbiosis in the microbiota has been suggested as a potential risk factor of PWD onset. Understanding pig's microbiota development around weaning and its changes in response to ZnO and antibiotics is crucial to develop feasible alternatives to prophylactic and metaphylactic antimicrobial use. Methods This study used shotgun metagenomic sequencing to investigate the environmental and faecal microbiota on 10 farms using (Treated) or not using (ZnO-free) in-feed antibiotics and ZnO during the first 14 days post-weaning (dpw). Environmental samples from clean pens were collected at weaning day (0dpw), and faecal samples at 0, 7 and 14dpw. Diarrhoeic faecal samples were collected at 7dpw when available. Results The analysis of data revealed that the faecal microbiota composition and its functionality was impacted by the sampling time point (microbiota maturation after weaning) but not by the farm environment. Treatment with antibiotics and ZnO showed no effects on diversity indices while the analyses of microbiota taxonomic and functional profiles revealed increased abundance of taxa and metabolic functions associated with Phascolarctobacterium succinatutens or different species of Prevotella spp. on the Treated farms, and with Megasphaera elsdenii and Escherichia coli on the ZnO-free farms. The analysis of diarrhoea samples revealed that the treatment favoured the microbiota transition or maturation from 0dpw to 14dpw in Treated farms, resembling the composition of healthy animals, when compared to diarrhoea from ZnO-free farms, which were linked in composition to 0dpw samples. Discussion The results provide a comprehensive overview of the beneficial effects of ZnO and antibiotics in PWD in the microbiota transition after weaning, preventing the overgrowth of pathogens such as pathogenic E. coli and revealing the key aspects in microbiota maturation that antibiotics or ZnO alternatives should fulfil.
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Affiliation(s)
- Juan M. Ortiz Sanjuán
- Pig Development Department, Teagasc Grassland Research and Innovation Centre, Moorepark, Cork, Ireland
- Grupo de Genómica y Mejora Animal, Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain
| | - Edgar G. Manzanilla
- Pig Development Department, Teagasc Grassland Research and Innovation Centre, Moorepark, Cork, Ireland
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Raúl Cabrera-Rubio
- Teagasc Food Research Centre, Moorepark, Cork, Ireland
- APC Microbiome Institute Science Foundation Ireland (SFI) Research Centre, University College Cork, Cork, Ireland
| | - Fiona Crispie
- Teagasc Food Research Centre, Moorepark, Cork, Ireland
- APC Microbiome Institute Science Foundation Ireland (SFI) Research Centre, University College Cork, Cork, Ireland
| | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, Cork, Ireland
- APC Microbiome Institute Science Foundation Ireland (SFI) Research Centre, University College Cork, Cork, Ireland
- VistaMilk Science Foundation Ireland (SFI) Research Centre, Cork, Ireland
| | - Juan J. Garrido
- Grupo de Genómica y Mejora Animal, Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain
| | - Daniel Ekhlas
- Pig Development Department, Teagasc Grassland Research and Innovation Centre, Moorepark, Cork, Ireland
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Lorcan O’Neill
- Pig Development Department, Teagasc Grassland Research and Innovation Centre, Moorepark, Cork, Ireland
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Héctor Argüello
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, León, Spain
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Cabrera-Rubio R, Pickett-Nairne K, González-Solares S, Collado MC, Venter C. The Maternal Diet Index and Offspring Microbiota at 1 Month of Life: Insights from the Mediterranean Birth Cohort MAMI. Nutrients 2024; 16:314. [PMID: 38276552 PMCID: PMC10821217 DOI: 10.3390/nu16020314] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/11/2024] [Accepted: 01/15/2024] [Indexed: 01/27/2024] Open
Abstract
Background: Maternal diet during pregnancy may play a role in infant health outcomes via the maternal microbiota. We assessed the association of the maternal diet index for the Mediterranean area (MDI-med) with infant gut microbiota at 1 month of life. Methods: The MAMI study is a longitudinal birth cohort in the Mediterranean area. In this work, a cross-sectional study, including 120 mother-infant dyads with available maternal diet and infant microbiota at 1-month-old data, was undertaken. The MDI developed in the US (MDI-US) was adapted for the MAMI cohort (MDI-med). Stratification based on extreme values resulted (22 in the "lower" MDI-med group and 23 in the "upper" group from the mean). Relative microbial abundances and alpha (microbial richness and diversity indexes) and beta diversity (Bray-Curtis distance matrix) were compared between the groups. Results: Higher maternal daily vegetable intake and lower red meat intake were the characteristics of the "upper" MDI-med group. Significantly lower microbial diversity (Shannon and InvSimpson index (p = 0.01)), but no changes in richness (Chao1 index) nor in beta-diversity, using Bray-Curtis distance, were observed in the "upper" group, compared to the "lower" MDI-med group. A higher relative abundance of the Bifidobacterium genus (Actinomycetota phylum) was associated with maternal daily vegetable and yogurt intake. Conclusion: Reduced infant microbial diversity at 1 month of age was associated with "upper" MDI-med scores. Higher maternal intakes of vegetables and yogurt were associated with higher relative abundances of the Bifidobacterium genus in the infant gut. Further studies are needed to understand the link between pregnancy diet, infant microbiota, and health outcomes.
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Affiliation(s)
- Raúl Cabrera-Rubio
- Institute of Agrochemistry and Food Technology, National Research Council (IATA-CSIC), Agustin Escardino 7, 46980 Paterna, Spain;
| | - Kaci Pickett-Nairne
- Department of Pediatrics, University of Colorado School of Medicine, University of Colorado, Aurora, CO 80045, USA; (K.P.-N.); (C.V.)
| | - Sonia González-Solares
- Department of Functional Biology, University of Oviedo, 33006 Oviedo, Spain;
- Diet, Microbiota and Health Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Maria Carmen Collado
- Institute of Agrochemistry and Food Technology, National Research Council (IATA-CSIC), Agustin Escardino 7, 46980 Paterna, Spain;
| | - Carina Venter
- Department of Pediatrics, University of Colorado School of Medicine, University of Colorado, Aurora, CO 80045, USA; (K.P.-N.); (C.V.)
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Vázquez L, Cabrera-Rubio R, Tamames J, Mayo B, Flórez AB. Assessment of short-read shotgun sequencing and microbiome analysis of faecal samples to discriminate between equol producers and non-producers. Benef Microbes 2023:1-14. [PMID: 37078124 DOI: 10.3920/bm2022.0027] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
Abstract
Among the isoflavones and isoflavone-derived metabolites, equol, which in the human gut is synthesised from daidzein by minority bacterial populations, shows the strongest estrogenic and antioxidant activity. The beneficial effects on human health of isoflavone consumption might be partially or indeed totally attributable to this equol. Although some of the bacterial strains involved in its formation have been identified, the interplay between the composition and functionality of the gut microbiota and equol producer phenotype has hardly been studied. In this study, after shotgun metagenomic sequencing, different pipelines for the taxonomic and functional annotation of sequencing data were used in the search for similarities and differences in the faecal metagenome of equol-producing (n=3) and non-producing (n=2) women, with special focus on equol-producing taxa and their equol-associated genes. The taxonomic profiles of the samples differed significantly depending on the analytical method followed, although the microbial diversity detected by each tool was very similar at the phylum, genus and species levels. Equol-producing taxa were detected in both equol producers and non-producers, but no correlation between the abundance of equol-producing taxa and the equol producing/non-producing phenotype was found. Indeed, functional metagenomic analysis was unable to identify the genes involved in equol production, even in samples from equol producers. By aligning equol operons with the collected metagenomics data, a small number of reads mapping to equol-associated sequences were recognised in samples from both equol producers and equol non-producers, but only two reads mapping onto equol reductase-encoding genes in a sample from an equol producer. In conclusion, the taxonomic analysis of metagenomic data might not be suitable for detecting and quantifying equol-producing microbes in human faeces. Functional analysis of the data might provide an alternative. However, to detect the genetic makeup of the minority gut populations, more extensive sequencing than that achieved in the present study might be required.
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Affiliation(s)
- L Vázquez
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares s/n, 33300-Villaviciosa, Asturias, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Avenida de Roma s/n, 33011-Oviedo, Asturias, Spain
| | - R Cabrera-Rubio
- Alimentary Pharmabiotic Centre (APC), Microbiome Institute, University College Cork, Cork, Ireland
- Moorepark Teagasc Food Research Centre, Fermoy, Ireland
| | - J Tamames
- Departamento de Biología de Sistemas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Cantoblanco, Madrid, Spain
| | - B Mayo
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares s/n, 33300-Villaviciosa, Asturias, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Avenida de Roma s/n, 33011-Oviedo, Asturias, Spain
| | - A B Flórez
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares s/n, 33300-Villaviciosa, Asturias, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Avenida de Roma s/n, 33011-Oviedo, Asturias, Spain
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Ortiz Sanjuán JM, Manzanilla EG, Cabrera-Rubio R, Crispie F, Cotter PD, Garrido JJ, Argüello H. Using Shotgun Sequencing to Describe the Changes Induced by In-Feed Zinc Oxide and Apramycin in the Microbiomes of Pigs One Week Postweaning. Microbiol Spectr 2022; 10:e0159722. [PMID: 35950862 PMCID: PMC9431492 DOI: 10.1128/spectrum.01597-22] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 07/18/2022] [Indexed: 11/20/2022] Open
Abstract
Postweaning diarrhea (PWD) is a relevant problem associated with early weaning on pig farms. For decades, in-feed antibiotics and therapeutic zinc oxide (ZnO) have been widely used to prevent PWD in piglets. The European Union is banning both strategies in 2022 due to antimicrobial resistance and environmental contamination concerns, respectively. Understanding the effects of these products on the pig microbiome is crucial for correcting potential microbial disbalances that would prompt PWD. Using shotgun sequencing, three trials were carried out to explore the impact of in-feed apramycin and ZnO, combined with different farm hygiene protocols, on the fecal microbiomes of piglets 7 days postweaning. In trial 1, 28-day-old piglets were allocated to one of three groups: control diet (Ct), Ct + ZnO (Zn), and Ct + apramycin (Ab). In trials 2 and 3, piglets were allocated to the same treatments, but the trials also included different cleaning protocols, achieving different hygiene levels. In-feed treatments impacted the richness, diversity, and relative abundance of the piglets' microbiome more than hygiene. Pigs in the Ct group showed higher species richness than pigs in the Ab and Zn groups. A clustering analysis evidenced a link between Enterobacteriaceae in the Ct group; Lactobacillaceae and Veillonellaceae mainly in the Ct group; and Bacteroidaceae, Ruminococcaceae, Oscillospiraceae, Acidaminococcaceae, and Lactobacillaceae in the Ab and Zn groups. Functional data analysis revealed a higher abundance of virulence genes in the Ct group microbiomes and heavy metal and antimicrobial resistance-related functions in the Zn treatment group. The results demonstrate that alternatives to Ab and ZnO should balance the microbial abundance and stimulate the growth of commensals to outcompete potential pathogens. IMPORTANCE Weaning is a critical period for piglets, during which potentially harmful bacteria such as Escherichia coli can increase in abundance in the intestine, creating digestive problems and diarrhea. In-feed antibiotics, the most frequent administration route for antibiotics in livestock, and therapeutic doses of zinc oxide (ZnO) help to control diarrhea but prompt secondary problems such as antimicrobial resistance and soil pollution from heavy metals. Understanding how these strategies impact the gut microbiota is crucial for establishing health biomarkers and designing successful replacement strategies. Using shotgun sequencing, this study compares the microbiota of pigs after early weaning when treated with in-feed antibiotics, ZnO, or treatment-free diets to describe differences that could define the susceptibility to infections, providing the basis for future research on improving intestinal resilience through microbiota-based strategies.
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Affiliation(s)
- Juan M. Ortiz Sanjuán
- Pig Development Department, Teagasc Grassland Research and Innovation Centre, Moorepark, Fermoy, County Cork, Ireland
- Grupo de Genómica y Mejora Animal, Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain
| | - Edgar G. Manzanilla
- Pig Development Department, Teagasc Grassland Research and Innovation Centre, Moorepark, Fermoy, County Cork, Ireland
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Raúl Cabrera-Rubio
- Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, County Cork, Ireland
| | - Fiona Crispie
- Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, County Cork, Ireland
| | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, County Cork, Ireland
- VistaMilk SFI Research Centre, Fermoy, County Cork, Ireland
| | - Juan J. Garrido
- Grupo de Genómica y Mejora Animal, Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain
| | - Héctor Argüello
- Animal Health Department, Veterinary Faculty, Universidad de León, León, Spain
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6
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Argüello H, Rodríguez-Gómez IM, Sánchez-Carvajal JM, Pallares FJ, Díaz I, Cabrera-Rubio R, Crispie F, Cotter PD, Mateu E, Martín-Valls G, Carrasco L, Gómez-Laguna J. Porcine reproductive and respiratory syndrome virus impacts on gut microbiome in a strain virulence-dependent fashion. Microb Biotechnol 2021; 15:1007-1016. [PMID: 33656781 PMCID: PMC8913879 DOI: 10.1111/1751-7915.13757] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 12/23/2020] [Accepted: 01/05/2021] [Indexed: 12/24/2022] Open
Abstract
Porcine reproductive and respiratory syndrome (PRRS) is a viral disease defined by reproductive problems, respiratory distress and a negative impact on growth rate and general condition. Virulent PRRS virus (PRRSV) strains have emerged in the last years with evident knowledge gaps in their impact on the host immune response. Thus, the present study examines the impact of acute PRRS virus (PRRSV) infection, with two strains of different virulence, on selected immune parameters and on the gut microbiota composition of infected pigs using 16S rRNA compositional sequencing. Pigs were infected with a low virulent (PRRS_3249) or a virulent (Lena) PRRSV‐1 strain and euthanized at 1, 3, 6, 8 or 13 days post‐inoculation (dpi). Faeces were collected from each animal at the necropsy time‐point. Alpha and beta diversity analyses demonstrated that infection, particularly with the Lena strain, impacted the microbiome composition from 6 dpi onwards. Taxonomic differences revealed that infected pigs had higher abundance of Treponema and Methanobrevibacter (FDR < 0.05). Differences were more considerable for Lena‐ than for PRRS_3249‐infected pigs, showing the impact of strain virulence in the intestinal changes. Lena‐infected pigs had reduced abundancies of anaerobic commensals such as Roseburia, Anaerostipes, Butyricicoccus and Prevotella (P < 0.05). The depletion of these desirable commensals was significantly correlated to infection severity measured by viraemia, clinical signs, lung lesions and immune parameters (IL‐6, IFN‐γ and Hp serum levels). Altogether, the results from this study demonstrate the indirect impact of PRRSV infection on gut microbiome composition in a strain virulence‐dependent fashion and its association with selected immune markers.
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Affiliation(s)
- Héctor Argüello
- Infectious Diseases and Epidemiology Unit, Department of Animal Health, Faculty of Veterinary Medicine, University of León, León, Spain
| | - Irene Magdalena Rodríguez-Gómez
- Department of Anatomy and Comparative Pathology and Toxicology, Faculty of Veterinary Medicine, University of Córdoba, International Excellence Agrifood Campus 'ceiA3', Córdoba, Spain
| | - Jose María Sánchez-Carvajal
- Department of Anatomy and Comparative Pathology and Toxicology, Faculty of Veterinary Medicine, University of Córdoba, International Excellence Agrifood Campus 'ceiA3', Córdoba, Spain
| | - Francisco José Pallares
- Department of Anatomy and Comparative Pathology, Faculty of Veterinary Medicine, University of Murcia, Mare Nostrum Excellence Campus, Murcia, Spain
| | - Iván Díaz
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Bellaterra, Spain
| | - Raúl Cabrera-Rubio
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland.,APC Microbiome Ireland, Cork, Ireland
| | - Fiona Crispie
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland.,APC Microbiome Ireland, Cork, Ireland
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland.,APC Microbiome Ireland, Cork, Ireland.,Vistamilk, Fermoy, Co. Cork, Ireland
| | - Enric Mateu
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Bellaterra, Spain.,Department of Animal Health and Anatomy, Faculty of Veterinary Medicine, Autonomous University of Barcelona, Bellaterra, Spain
| | - Gerard Martín-Valls
- Department of Animal Health and Anatomy, Faculty of Veterinary Medicine, Autonomous University of Barcelona, Bellaterra, Spain
| | - Librado Carrasco
- Department of Anatomy and Comparative Pathology and Toxicology, Faculty of Veterinary Medicine, University of Córdoba, International Excellence Agrifood Campus 'ceiA3', Córdoba, Spain
| | - Jaime Gómez-Laguna
- Department of Anatomy and Comparative Pathology and Toxicology, Faculty of Veterinary Medicine, University of Córdoba, International Excellence Agrifood Campus 'ceiA3', Córdoba, Spain
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Mencía-Ares O, Cabrera-Rubio R, Cobo-Díaz JF, Álvarez-Ordóñez A, Gómez-García M, Puente H, Cotter PD, Crispie F, Carvajal A, Rubio P, Argüello H. Antimicrobial use and production system shape the fecal, environmental, and slurry resistomes of pig farms. Microbiome 2020; 8:164. [PMID: 33213522 PMCID: PMC7678069 DOI: 10.1186/s40168-020-00941-7] [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] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 10/17/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND The global threat of antimicrobial resistance (AMR) is a One Health problem impacted by antimicrobial use (AMU) for human and livestock applications. Extensive Iberian swine production is based on a more sustainable and eco-friendly management system, providing an excellent opportunity to evaluate how sustained differences in AMU impact the resistome, not only in the animals but also on the farm environment. Here, we evaluate the resistome footprint of an extensive pig farming system, maintained for decades, as compared to that of industrialized intensive pig farming by analyzing 105 fecal, environmental and slurry metagenomes from 38 farms. RESULTS Our results evidence a significantly higher abundance of antimicrobial resistance genes (ARGs) on intensive farms and a link between AMU and AMR to certain antimicrobial classes. We observed differences in the resistome across sample types, with a higher richness and dispersion of ARGs within environmental samples than on those from feces or slurry. Indeed, a deeper analysis revealed that differences among the three sample types were defined by taxa-ARGs associations. Interestingly, mobilome analyses revealed that the observed AMR differences between intensive and extensive farms could be linked to differences in the abundance of mobile genetic elements (MGEs). Thus, while there were no differences in the abundance of chromosomal-associated ARGs between intensive and extensive herds, a significantly higher abundance of integrons in the environment and plasmids, regardless of the sample type, was detected on intensive farms. CONCLUSIONS Overall, this study shows how AMU, production system, and sample type influence, mainly through MGEs, the profile and dispersion of ARGs in pig production. Video Abstract.
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Affiliation(s)
- Oscar Mencía-Ares
- Department of Animal Health, Faculty of Veterinary, Universidad de León, León, Spain
| | - Raúl Cabrera-Rubio
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Institute, University College Cork, Co. Cork, Ireland
| | - José Francisco Cobo-Díaz
- Department of Food Hygiene and Technology, Faculty of Veterinary, Universidad de León, León, Spain
- Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Avelino Álvarez-Ordóñez
- Department of Food Hygiene and Technology, Faculty of Veterinary, Universidad de León, León, Spain
- Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Manuel Gómez-García
- Department of Animal Health, Faculty of Veterinary, Universidad de León, León, Spain
| | - Héctor Puente
- Department of Animal Health, Faculty of Veterinary, Universidad de León, León, Spain
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Institute, University College Cork, Co. Cork, Ireland
- VistaMilk SFI Research Centre, Fermoy, Co. Cork, Ireland
| | - Fiona Crispie
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Institute, University College Cork, Co. Cork, Ireland
| | - Ana Carvajal
- Department of Animal Health, Faculty of Veterinary, Universidad de León, León, Spain.
| | - Pedro Rubio
- Department of Animal Health, Faculty of Veterinary, Universidad de León, León, Spain
| | - Héctor Argüello
- Department of Animal Health, Faculty of Veterinary, Universidad de León, León, Spain
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Macori G, Bellio A, Bianchi DM, Chiesa F, Gallina S, Romano A, Zuccon F, Cabrera-Rubio R, Cauquil A, Merda D, Auvray F, Decastelli L. Genome-Wide Profiling of Enterotoxigenic Staphylococcus aureus Strains Used for the Production of Naturally Contaminated Cheeses. Genes (Basel) 2019; 11:E33. [PMID: 31892220 PMCID: PMC7016664 DOI: 10.3390/genes11010033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 12/19/2019] [Accepted: 12/22/2019] [Indexed: 12/12/2022] Open
Abstract
Staphylococcus aureus is a major human pathogen and an important cause of livestock infections. More than 20 staphylococcal enterotoxins with emetic activity can be produced by specific strains responsible for staphylococcal food poisoning, one of the most common food-borne diseases. Whole genome sequencing provides a comprehensive view of the genome structure and gene content that have largely been applied in outbreak investigations and genomic comparisons. In this study, six enterotoxigenic S. aureus strains were characterised using a combination of molecular, phenotypical and computational methods. The genomes were analysed for the presence of virulence factors (VFs), where we identified 110 genes and classified them into five categories: adherence (n = 31), exoenzymes (n = 28), genes involved in host immune system evasion (n = 7); iron uptake regulatory system (n = 8); secretion machinery factors and toxins' genes (n = 36), and 39 genes coding for transcriptional regulators related to staphylococcal VFs. Each group of VFs revealed correlations among the six enterotoxigenic strains, and further analysis revealed their accessory genomic content, including mobile genetic elements. The plasmids pLUH02 and pSK67 were detected in the strain ProNaCC1 and ProNaCC7, respectively, carrying out the genes sed, ser, and selj. The genes carried out by prophages were detected in the strain ProNaCC2 (see), ProNaCC4, and ProNaCC7 (both positive for sea). The strain ProNaCC5 resulted positive for the genes seg, sei, sem, sen, seo grouped in an exotoxin gene cluster, and the strain ProNaCC6 resulted positive for seh, a transposon-associated gene. The six strains were used for the production of naturally contaminated cheeses which were tested with the European Screening Method for staphylococcal enterotoxins. The results obtained from the analysis of toxins produced in cheese, combined with the genomic features represent a portrait of the strains that can be used for the production of staphylococcal enterotoxin-positive cheese as reference material.
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Affiliation(s)
- Guerrino Macori
- National Reference Laboratory for Coagulase-Positive Staphylococci including Staphylococcus aureus, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via Bologna 148, 10154 Torino, Italy; (A.B.); (D.M.B.); (S.G.); (A.R.); (F.Z.); (L.D.)
| | - Alberto Bellio
- National Reference Laboratory for Coagulase-Positive Staphylococci including Staphylococcus aureus, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via Bologna 148, 10154 Torino, Italy; (A.B.); (D.M.B.); (S.G.); (A.R.); (F.Z.); (L.D.)
| | - Daniela Manila Bianchi
- National Reference Laboratory for Coagulase-Positive Staphylococci including Staphylococcus aureus, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via Bologna 148, 10154 Torino, Italy; (A.B.); (D.M.B.); (S.G.); (A.R.); (F.Z.); (L.D.)
| | - Francesco Chiesa
- Dipartimento di Scienze Veterinarie, Università di Torino, 10095 Grugliasco, Italy;
| | - Silvia Gallina
- National Reference Laboratory for Coagulase-Positive Staphylococci including Staphylococcus aureus, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via Bologna 148, 10154 Torino, Italy; (A.B.); (D.M.B.); (S.G.); (A.R.); (F.Z.); (L.D.)
| | - Angelo Romano
- National Reference Laboratory for Coagulase-Positive Staphylococci including Staphylococcus aureus, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via Bologna 148, 10154 Torino, Italy; (A.B.); (D.M.B.); (S.G.); (A.R.); (F.Z.); (L.D.)
| | - Fabio Zuccon
- National Reference Laboratory for Coagulase-Positive Staphylococci including Staphylococcus aureus, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via Bologna 148, 10154 Torino, Italy; (A.B.); (D.M.B.); (S.G.); (A.R.); (F.Z.); (L.D.)
| | - Raúl Cabrera-Rubio
- Teagasc Food Research Centre, Moorepark, Fermoy, P61 C996, Ireland-APC Microbiome Ireland, University College Cork, T12YT20 Cork, Ireland;
| | - Alexandra Cauquil
- European Laboratory for Coagulase-Positive Staphylococci including Staphylococcus aureus, Laboratory for Food Safety, ANSES, Université Paris-Est, F-94700 Maisons-Alfort, France; (A.C.); (D.M.); (F.A.)
| | - Déborah Merda
- European Laboratory for Coagulase-Positive Staphylococci including Staphylococcus aureus, Laboratory for Food Safety, ANSES, Université Paris-Est, F-94700 Maisons-Alfort, France; (A.C.); (D.M.); (F.A.)
| | - Fréderic Auvray
- European Laboratory for Coagulase-Positive Staphylococci including Staphylococcus aureus, Laboratory for Food Safety, ANSES, Université Paris-Est, F-94700 Maisons-Alfort, France; (A.C.); (D.M.); (F.A.)
| | - Lucia Decastelli
- National Reference Laboratory for Coagulase-Positive Staphylococci including Staphylococcus aureus, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via Bologna 148, 10154 Torino, Italy; (A.B.); (D.M.B.); (S.G.); (A.R.); (F.Z.); (L.D.)
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9
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Esteban-Torres M, Santamaría L, Cabrera-Rubio R, Plaza-Vinuesa L, Crispie F, de Las Rivas B, Cotter P, Muñoz R. A Diverse Range of Human Gut Bacteria Have the Potential To Metabolize the Dietary Component Gallic Acid. Appl Environ Microbiol 2018; 84:e01558-18. [PMID: 30054365 PMCID: PMC6146992 DOI: 10.1128/aem.01558-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 07/24/2018] [Indexed: 12/27/2022] Open
Abstract
The human gut microbiota contains a broad variety of bacteria that possess functional genes, with resultant metabolites that affect human physiology and therefore health. Dietary gallates are phenolic components that are present in many foods and beverages and are regarded as having health-promoting attributes. However, the potential for metabolism of these phenolic compounds by the human microbiota remains largely unknown. The emergence of high-throughput sequencing (HTS) technologies allows this issue to be addressed. In this study, HTS was used to assess the incidence of gallate-decarboxylating bacteria within the gut microbiota of healthy individuals for whom bacterial diversity was previously determined to be high. This process was facilitated by the design and application of degenerate PCR primers to amplify a region encoding the catalytic C subunit of gallate decarboxylase (LpdC) from total metagenomic DNA extracted from human fecal samples. HTS resulted in the generation of a total of 3,261,967 sequence reads and revealed that the primary gallate-decarboxylating microbial phyla in the intestinal microbiota were Firmicutes (74.6%), Proteobacteria (17.6%), and Actinobacteria (7.8%). These reads corresponded to 53 genera, i.e., 47% of the bacterial genera detected previously in these samples. Among these genera, Anaerostipes and Klebsiella accounted for the majority of reads (40%). The usefulness of the HTS-lpdC method was demonstrated by the production of pyrogallol from gallic acid, as expected for functional gallate decarboxylases, among representative strains belonging to species identified in the human gut microbiota by this method.IMPORTANCE Despite the increasing wealth of sequencing data, the health contributions of many bacteria found in the human gut microbiota have yet to be elucidated. This study applies a novel experimental approach to predict the ability of gut microbes to carry out a specific metabolic activity, i.e., gallate metabolism. The study showed that, while gallate-decarboxylating bacteria represented 47% of the bacterial genera detected previously in the same human fecal samples, no gallate decarboxylase homologs were identified from representatives of Bacteroidetes The presence of functional gallate decarboxylases was demonstrated in representative Proteobacteria and Firmicutes strains from the human microbiota, an observation that could be of considerable relevance to the in vivo production of pyrogallol, a physiologically important bioactive compound.
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Affiliation(s)
- María Esteban-Torres
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición (ICTAN-CSIC), Madrid, Spain
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Laura Santamaría
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición (ICTAN-CSIC), Madrid, Spain
| | | | - Laura Plaza-Vinuesa
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición (ICTAN-CSIC), Madrid, Spain
| | | | - Blanca de Las Rivas
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición (ICTAN-CSIC), Madrid, Spain
| | | | - Rosario Muñoz
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición (ICTAN-CSIC), Madrid, Spain
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10
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Collado MC, Engen PA, Bandín C, Cabrera-Rubio R, Voigt RM, Green SJ, Naqib A, Keshavarzian A, Scheer FAJL, Garaulet M. Timing of food intake impacts daily rhythms of human salivary microbiota: a randomized, crossover study. FASEB J 2018; 32:2060-2072. [PMID: 29233857 DOI: 10.1096/fj.201700697rr] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The composition of the diet (what we eat) has been widely related to the microbiota profile. However, whether the timing of food consumption (when we eat) influences microbiota in humans is unknown. A randomized, crossover study was performed in 10 healthy normal-weight young women to test the effect of the timing of food intake on the human microbiota in the saliva and fecal samples. More specifically, to determine whether eating late alters daily rhythms of human salivary microbiota, we interrogated salivary microbiota in samples obtained at 4 specific time points over 24 h, to achieve a better understanding of the relationship between food timing and metabolic alterations in humans. Results revealed significant diurnal rhythms in salivary diversity and bacterial relative abundance ( i.e., TM7 and Fusobacteria) across both early and late eating conditions. More importantly, meal timing affected diurnal rhythms in diversity of salivary microbiota toward an inverted rhythm between the eating conditions, and eating late increased the number of putative proinflammatory taxa, showing a diurnal rhythm in the saliva. In a randomized, crossover study, we showed for the first time the impact of the timing of food intake on human salivary microbiota. Eating the main meal late inverts the daily rhythm of salivary microbiota diversity which may have a deleterious effect on the metabolism of the host.-Collado, M. C., Engen, P. A., Bandín, C., Cabrera-Rubio, R., Voigt, R. M., Green, S. J., Naqib, A., Keshavarzian, A., Scheer, F. A. J. L., Garaulet, M. Timing of food intake impacts daily rhythms of human salivary microbiota: a randomized, crossover study.
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Affiliation(s)
- María Carmen Collado
- Department of Biotechnology, Institute of Agrochemistry and Food Technology-Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | - Phillip A Engen
- Division of Digestive Diseases and Nutrition, Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois, USA
| | - Cristina Bandín
- Department of Physiology, University of Murcia, Murcia Spain.,Murcian Institute of Biosanitary Research (IMIB)-Arrixaca, Murcia, Spain
| | - Raúl Cabrera-Rubio
- Department of Biotechnology, Institute of Agrochemistry and Food Technology-Spanish National Research Council (IATA-CSIC), Valencia, Spain.,Alimentary Pharmabiotic Centre (APC) Microbiome Institute, University College Cork, Cork, Ireland.,Moorepark Teagasc Food Research Centre, Fermoy, Ireland
| | - Robin M Voigt
- Division of Digestive Diseases and Nutrition, Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois, USA
| | - Stefan J Green
- DNA Services Facility, Research Resources Center, University of Illinois at Chicago, Chicago, Illinois, USA.,Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Ankur Naqib
- DNA Services Facility, Research Resources Center, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Ali Keshavarzian
- Division of Digestive Diseases and Nutrition, Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois, USA.,Department of Pharmacology, Rush University Medical Center, Chicago, Illinois, USA.,Department of Physiology, Rush University Medical Center, Chicago, Illinois, USA.,Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Frank A J L Scheer
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, Massachusetts, USA; and.,Division of Sleep Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Marta Garaulet
- Department of Physiology, University of Murcia, Murcia Spain.,Murcian Institute of Biosanitary Research (IMIB)-Arrixaca, Murcia, Spain
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11
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Mira-Pascual L, Cabrera-Rubio R, Ocon S, Costales P, Parra A, Suarez A, Moris F, Rodrigo L, Mira A, Collado MC. Microbial mucosal colonic shifts associated with the development of colorectal cancer reveal the presence of different bacterial and archaeal biomarkers. J Gastroenterol 2015; 50:167-79. [PMID: 24811328 DOI: 10.1007/s00535-014-0963-x] [Citation(s) in RCA: 174] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 04/11/2014] [Indexed: 02/04/2023]
Abstract
BACKGROUND Epidemiological studies demonstrate a link between gastrointestinal cancers and environmental factors such as diet. It has been suggested that environmental cancer risk is determined by the interaction between diet and microbes. Thus, the purpose of this study was to examine the hypothesis that microbiota composition during colorectal cancer (CRC) progression might differ depending on the stage of the disease. METHODS A total of 28 age-matched and sex-matched subjects, seven with CRC adenocarcinoma, 11 with tubular adenomas and ten healthy subjects with intact colon, were included into the study. Microbiomes from mucosal and fecal samples were analyzed with 16S ribosomal RNA gene pyrosequencing, together with quantitative PCR of specific bacteria and archaea. RESULTS The principal coordinates analysis clearly separated healthy tissue samples from polyps and tumors, supporting the presence of specific bacterial consortia that are associated with affected sites and that can serve as potential biomarkers of CRC progression. A higher presence of Fusobacterium nucleatum and Enterobacteriaceae was found by qPCR in samples from CRC compared to healthy controls. We observed a correlation between CRC process development and levels of Methanobacteriales (R = 0.537, P = 0.007) and Methanobrevibacterium (R = 0.574, P = 0.03) in fecal samples. CONCLUSION Differences in microbial and archaeal composition between mucosal samples from healthy and disease tissues were observed in tubular adenoma and adenocarcinoma. In addition, microbiota from mucosal samples represented the underlying dysbiosis, whereas fecal samples seem not to be appropriate to detect shifts in microbial composition. CRC risk is influenced by microbial composition, showing differences according to disease progression step and tumor severity.
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Affiliation(s)
- L Mira-Pascual
- Department of Biotechnology, Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Av. Agustin Escardino 7, 49860, Paterna, Valencia, Spain
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12
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Camelo-Castillo A, Benítez-Páez A, Belda-Ferre P, Cabrera-Rubio R, Mira A. Streptococcus dentisani sp. nov., a novel member of the mitis group. Int J Syst Evol Microbiol 2014. [DOI: 10.1099/ijs.0.062802-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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13
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Gomar-Vercher S, Cabrera-Rubio R, Mira A, Montiel-Company JM, Almerich-Silla JM. Relationship of children's salivary microbiota with their caries status: a pyrosequencing study. Clin Oral Investig 2014; 18:2087-94. [PMID: 24532386 DOI: 10.1007/s00784-014-1200-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 01/30/2014] [Indexed: 02/08/2023]
Abstract
PURPOSE Different dental caries status could be related with alterations in oral microbiota. Previous studies have collected saliva as a representative medium of the oral ecosystem. The purpose of this study was to assess the composition of oral microbiota and its relation to the presence of dental caries at different degrees of severity. MATERIALS AND METHODS One hundred ten saliva samples from 12-year-old children were taken and divided into six groups defined in strict accordance with their dental caries prevalence according to the International Caries Detection and Assessment System II criteria. These samples were studied by pyrosequencing PCR products of the 16S ribosomal RNA gene. RESULTS The results showed statistically significant intergroup differences at the class and genus taxonomic levels. Streptococcus is the most frequent genus in all groups; although it did not show intergroup statistical differences. In patients with cavities, Porphyromonas and Prevotella showed an increasing percentage compared to healthy individuals. Bacterial diversity diminished as the severity of the disease increased, so those patients with more advanced stages of caries presented less bacterial diversity than healthy subjects. CONCLUSION Although microbial composition tended to be different, the intragroup variation is large, as evidenced by the lack of clear intragroup clustering in principal component analyses. Thus, no clear differences were found, indicating that using bacterial composition as the sole source of biomarkers for dental caries may not be reliable in the unstimulated saliva samples used in the current study.
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Affiliation(s)
- S Gomar-Vercher
- Stomatology Department, University of Valencia, C/Gascó Oliag 1, 46010, Valencia, Spain
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14
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Camelo-Castillo A, Benítez-Páez A, Belda-Ferre P, Cabrera-Rubio R, Mira A. Streptococcus dentisani sp. nov., a novel member of the mitis group. Int J Syst Evol Microbiol 2014; 64:60-65. [DOI: 10.1099/ijs.0.054098-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Genomic, taxonomic and biochemical studies were performed on two strains of α-haemolytic streptococci that showed them to be clustered with major members of the
Streptococcus mitis
group. These Gram-stain-positive strains were isolated from tooth surfaces of caries-free humans and showed the classical spherical shape of streptococcal species growing in chains. Sequence analysis from concatenated 16S and 23S rRNA gene and sodA genes showed that these strains belonged to the mitis group, but both of them clustered into a new phylogenetic branch. The genomes of these two isolates were sequenced, and whole-genome average nucleotide identity (ANI) demonstrated that these strains significantly differed from any streptococcal species, showing ANI values under 91 % even when compared with the phylogenetically closest species such as
Streptococcus oralis
and
S. mitis
. Biochemically, the two isolates also showed distinct metabolic features relative to closely related species, like α-galactosidase activity. From the results of the present study, the name Streptococcus dentisani sp. nov. is proposed to accommodate these novel strains, which have been deposited in open collections at the Spanish type Culture Collection (CECT) and Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures (DSMZ), being respectively identified as Streptococcus dentisani Str. 7746 ( = CECT 8313 = DSM 27089) and Streptococcus dentisani Str. 7747T ( = CECT 8312T = DSM 27088T).
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Affiliation(s)
- Anny Camelo-Castillo
- Oral Microbiome Laboratory, Genomics & Health Department – Center for Advanced Research in Public Health (CSISP-FISABIO), Valencia, Spain
| | - Alfonso Benítez-Páez
- Oral Microbiome Laboratory, Genomics & Health Department – Center for Advanced Research in Public Health (CSISP-FISABIO), Valencia, Spain
| | - Pedro Belda-Ferre
- Oral Microbiome Laboratory, Genomics & Health Department – Center for Advanced Research in Public Health (CSISP-FISABIO), Valencia, Spain
| | - Raúl Cabrera-Rubio
- Oral Microbiome Laboratory, Genomics & Health Department – Center for Advanced Research in Public Health (CSISP-FISABIO), Valencia, Spain
| | - Alex Mira
- Oral Microbiome Laboratory, Genomics & Health Department – Center for Advanced Research in Public Health (CSISP-FISABIO), Valencia, Spain
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15
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Mirón L, Mira A, Rocha-Ramírez V, Belda-Ferre P, Cabrera-Rubio R, Folch-Mallol J, Cardénas-Vázquez R, DeLuna A, Hernández AL, Maya-Elizarrarás E, Schondube JE. Gut Bacterial Diversity of the House Sparrow (Passer domesticus) Inferred by 16S rRNA Sequence Analysis. ACTA ACUST UNITED AC 2014. [DOI: 10.4303/mg/235853] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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16
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Simón-Soro A, Belda-Ferre P, Cabrera-Rubio R, Alcaraz LD, Mira A. A tissue-dependent hypothesis of dental caries. Caries Res 2013; 47:591-600. [PMID: 24080530 DOI: 10.1159/000351663] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Accepted: 04/18/2013] [Indexed: 11/19/2022] Open
Abstract
Current understanding of dental caries considers this disease a demineralization of the tooth tissues due to the acid produced by sugar-fermenting microorganisms. Thus, caries is considered a diet- and pH-dependent process. We present here the first metagenomic analysis of the bacterial communities present at different stages of caries development, with the aim of determining whether the bacterial composition and biochemical profile are specific to the tissue affected. The data show that microbial composition at the initial, enamel-affecting stage of caries is significantly different from that found at subsequent stages, as well as from dental plaque of sound tooth surfaces. Although the relative proportion of Streptococcus mutans increased from 0.12% in dental plaque to 0.72% in enamel caries, Streptococcus mitis and Streptococcus sanguinis were the dominant streptococci in these lesions. The functional profile of caries-associated bacterial communities indicates that genes involved in acid stress tolerance and dietary sugar fermentation are overrepresented only at the initial stage (enamel caries), whereas other genes coding for osmotic stress tolerance as well as collagenases and other proteases enabling dentin degradation are significantly overrepresented in dentin cavities. The results support a scenario in which pH and diet are determinants of the disease during the degradation of enamel, but in dentin caries lesions not only acidogenic but also proteolytic bacteria are involved. We propose that caries disease is a process of varying etiology, in which acid-producing bacteria are the vehicle to penetrate enamel and allow dentin degrading microorganisms to expand the cavity.
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Affiliation(s)
- A Simón-Soro
- Department of Genomics and Health, Center for Advanced Research in Public Health, Valencia, Spain
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17
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Abstract
We aimed to determine the bacterial diversity of different oral micro-niches and to assess whether saliva and plaque samples are representative of oral microbial composition. We took minute samples from each surface of the individual teeth and gingival crevices of two healthy volunteers (112 samples per donor), as well as samples from the tongue dorsum and non-stimulated and stimulated saliva. DNA was extracted from 67 selected samples of each donor, and the 16S rRNA gene was amplified by PCR and pyrosequenced to obtain, on average, over 2,700 reads per sample, which were taxonomically assigned to obtain a geographic map of bacterial diversity at each tooth and sulcus location. Analysis of the data shows considerable differences in bacterial composition between teeth at different intra-oral locations and between surfaces of the same tooth. The most pronounced differences were observed in incisors and canines, where genera like Streptococcus were found at 40% to 70% on the vestibular surfaces but were almost absent on the lingual sides. Saliva samples, especially non-stimulated saliva, were not representative of supra-and subgingival plaque in the two individuals tested. We suggest that more precise sampling is required for the proper determination of oral microbial composition and to relate that diversity to epidemiological, clinical, and etiological parameters.
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Affiliation(s)
- A Simón-Soro
- Center for Advanced Research in Public Health (CSISP), Valencia, Spain
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18
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Delgado S, Cabrera-Rubio R, Mira A, Suárez A, Mayo B. Microbiological survey of the human gastric ecosystem using culturing and pyrosequencing methods. Microb Ecol 2013; 65:763-72. [PMID: 23397369 DOI: 10.1007/s00248-013-0192-5] [Citation(s) in RCA: 140] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Accepted: 01/21/2013] [Indexed: 05/09/2023]
Abstract
Stomach mucosa biopsies and gastric juices samples of 12 healthy persons were analysed by culturing in selective- and non-selective-rich media. Microbial DNA from four mucosal samples was also amplified by nested PCR using universal bacterial primers, and the 16S rDNA amplicons pyrosequenced. The total number of cultivable microorganisms recovered from the samples ranged from 10(2) to 10(4) cfu/g or ml. The isolates were identified at the species level by PCR amplification and sequencing of the 16S rDNA. Isolates belonged mainly to four genera; Propionibacterium, Lactobacillus, Streptococcus and Staphylococcus. A total of 15,622 high-quality 16S rDNA sequence reads were obtained by pyrosequencing from the four mucosal samples. Sequence analysis grouped the reads into 59 families and 69 genera, revealing wide bacterial diversity. Considerable differences in the composition of the gastric microbiota were observed among the subjects, although in all samples the most abundant operational taxonomic units belonged to Streptococcus, Propionibacterium and Lactobacillus. Comparison of the stomach microbiota with that present in other parts of the human gastrointestinal tract revealed distinctive microbial communities. This is the first study in which a combination of culture and culture-independent techniques has been used to explore the bacterial diversity of the human stomach.
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Affiliation(s)
- Susana Delgado
- Departamento de Microbiología y Bioquímica de Productos Lácteos, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Villaviciosa, Asturias, Spain.
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19
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Cabrera-Rubio R, Garcia-Núñez M, Setó L, Antó JM, Moya A, Monsó E, Mira A. Microbiome diversity in the bronchial tracts of patients with chronic obstructive pulmonary disease. J Clin Microbiol 2012; 50:3562-8. [PMID: 22915614 PMCID: PMC3486223 DOI: 10.1128/jcm.00767-12] [Citation(s) in RCA: 146] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Culture of bacteria from bronchial secretions in respiratory patients has low sensitivity and does not allow for complete assessment of microbial diversity across different bronchial compartments. In addition, a significant number of clinical studies are based on sputum samples, and it is not known to what extent they describe the real diversity of the mucosa. In order to identify previously unrecognized lower airway bacteria and to investigate the complexity and distribution of microbiota in patients with chronic obstructive pulmonary disease (COPD), we performed PCR amplification and pyrosequencing of the 16S rRNA gene in patients not showing signs or symptoms of infection. Four types of respiratory samples (sputum, bronchial aspirate, bronchoalveolar lavage, and bronchial mucosa) were taken from each individual, obtaining on average >1,000 16S rRNA sequences per sample. The total number of genera per patient was >100, showing a high diversity, with Streptococcus, Prevotella, Moraxella, Haemophilus, Acinetobacter, Fusobacterium, and Neisseria being the most commonly identified. Sputum samples showed significantly lower diversity than the other three sample types. Lower-bronchial-tree samples, i.e., bronchoalveolar lavage and bronchial mucosa, showed a very similar bacterial compositions in contrast to sputum and bronchial aspirate samples. Thus, sputum and bronchial aspirate samples are upper bronchial tree samples that are not representative of the lower bronchial mucosa flora, and bronchoalveolar lavage samples showed the results closest to those for the bronchial mucosa. Our data confirm that the bronchial tree is not sterile in COPD patients and support the existence a different microbiota in the upper and lower compartments.
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Affiliation(s)
- Raúl Cabrera-Rubio
- Department of Genomics and Health, Center for Public Health Research, Valencia, Spain
| | - Marian Garcia-Núñez
- CIBER de Enfermedades Respiratorias–CIBERes, Bunyola, Mallorca, Illes Balears, Spain
- Fundació Institut Universitari Parc Taulí, Sabadell, Spain
| | - Laia Setó
- CIBER de Enfermedades Respiratorias–CIBERes, Bunyola, Mallorca, Illes Balears, Spain
- Fundació Institut Universitari Parc Taulí, Sabadell, Spain
| | - Josep M. Antó
- Centre for Research in Environmental Epidemiology, Barcelona, Spain
- IMIM (Hospital del Mar Research Institute), Barcelona, Spain
- CIBER de Epidemiología y Salud Pública (CIBEResp), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Andrés Moya
- Department of Genomics and Health, Center for Public Health Research, Valencia, Spain
- CIBER de Epidemiología y Salud Pública (CIBEResp), Barcelona, Spain
| | - Eduard Monsó
- CIBER de Enfermedades Respiratorias–CIBERes, Bunyola, Mallorca, Illes Balears, Spain
- Fundació Institut Universitari Parc Taulí, Sabadell, Spain
- Pulmonary Department, Hospital Universitari Parc Taulí, Sabadell, Spain
- Departament de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Alex Mira
- Department of Genomics and Health, Center for Public Health Research, Valencia, Spain
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Alcaraz L, Belda-Ferre P, Cabrera-Rubio R, Romero H, Simon-Soro A, Pignatelli M, Mira A. Identifying a healthy oral microbiome through metagenomics. Clin Microbiol Infect 2012; 18 Suppl 4:54-7. [DOI: 10.1111/j.1469-0691.2012.03857.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Abstract
When a bacterial genome is compared to the metagenome of an environment it inhabits, most genes recruit at high sequence identity. In free-living bacteria (for instance marine bacteria compared against the ocean metagenome) certain genomic regions are totally absent in recruitment plots, representing therefore genes unique to individual bacterial isolates. We show that these Metagenomic Islands (MIs) are also visible in bacteria living in human hosts when their genomes are compared to sequences from the human microbiome, despite the compartmentalized structure of human-related environments such as the gut. From an applied point of view, MIs of human pathogens (e.g. those identified in enterohaemorragic Escherichia coli against the gut metagenome or in pathogenic Neisseria meningitidis against the oral metagenome) include virulence genes that appear to be absent in related strains or species present in the microbiome of healthy individuals. We propose that this strategy (i.e. recruitment analysis of pathogenic bacteria against the metagenome of healthy subjects) can be used to detect pathogenicity regions in species where the genes involved in virulence are poorly characterized. Using this approach, we detect well-known pathogenicity islands and identify new potential virulence genes in several human pathogens.
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Affiliation(s)
- Pedro Belda-Ferre
- Joint Unit of Research in Genomics and Health, Centre for Public Health Research-Cavanilles Institute for Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain
| | - Raúl Cabrera-Rubio
- Joint Unit of Research in Genomics and Health, Centre for Public Health Research-Cavanilles Institute for Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain
| | - Andrés Moya
- Joint Unit of Research in Genomics and Health, Centre for Public Health Research-Cavanilles Institute for Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain
- Centro de Investigación Biomédica en Red especializado en Epidemiología y Salud Pública, Madrid, Spain
| | - Alex Mira
- Joint Unit of Research in Genomics and Health, Centre for Public Health Research-Cavanilles Institute for Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain
- * E-mail:
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