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Marcos-Fernández R, Ruiz L, Blanco-Míguez A, Margolles A, Sánchez B. Precision modification of the human gut microbiota targeting surface-associated proteins. Sci Rep 2021; 11:1270. [PMID: 33446697 PMCID: PMC7809461 DOI: 10.1038/s41598-020-80187-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 12/14/2020] [Indexed: 01/29/2023] Open
Abstract
This work describes a new procedure that allows the targeted modification of the human gut microbiota by using antibodies raised against bacterial surface-associated proteins specific to the microorganism of interest. To this end, a polyclonal antibody recognising the surface-associated protein Surface Layer Protein A of Lactobacillus acidophilus DSM20079T was developed. By conjugating this antibody with fluorescent probes and magnetic particles, we were able to specifically identify this bacterium both in a synthetic, and in real gut microbiotas by means of a flow cytometry approach. Further, we demonstrated the applicability of this antibody to deplete complex human gut microbiotas from L. acidophilus in a single step. L. acidophilus was found to interact with other bacteria both in synthetic and in real microbiotas, as reflected by its concomitant depletion together with other species. Further optimization of the procedure including a trypsin step enabled to achieve the selective and complete isolation of this species. Depleting a single species from a gut microbiota, using antibodies recognizing specific cell surface elements of the target organism, will open up novel ways to tackle research on the specific immunomodulatory and metabolic contributions of a bacterium of interest in the context of a complex human gut microbiota, including the investigation into therapeutic applications by adding/depleting a key bacterium. This represents the first work in which an antibody/flow-cytometry based application enabled the targeted edition of human gut microbiotas, and represents the basis for the design of precision microbiome-based therapies.
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Affiliation(s)
- Raquel Marcos-Fernández
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300, Villaviciosa, Asturias, Spain
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain
| | - Lorena Ruiz
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300, Villaviciosa, Asturias, Spain
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain
| | - Aitor Blanco-Míguez
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300, Villaviciosa, Asturias, Spain
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain
| | - Abelardo Margolles
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300, Villaviciosa, Asturias, Spain.
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain.
| | - Borja Sánchez
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300, Villaviciosa, Asturias, Spain.
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain.
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Hidalgo-Cantabrana C, Moro-García MA, Blanco-Míguez A, Fdez-Riverola F, Oliván M, Royo LJ, Riestra S, Margolles A, Lourenço A, Alonso-Arias R, Sánchez B. The extracellular proteins of Lactobacillus acidophilus DSM 20079T display anti-inflammatory effect in both in piglets, healthy human donors and Crohn’s Disease patients. J Funct Foods 2020. [DOI: 10.1016/j.jff.2019.103660] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Cambeiro-Pérez N, Hidalgo-Cantabrana C, Moro-García MA, Alonso-Arias R, Simal-Gándara J, Sánchez B, Martínez-Carballo E. A Metabolomics Approach Reveals Immunomodulatory Effects of Proteinaceous Molecules Derived From Gut Bacteria Over Human Peripheral Blood Mononuclear Cells. Front Microbiol 2018; 9:2701. [PMID: 30524384 PMCID: PMC6262353 DOI: 10.3389/fmicb.2018.02701] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 10/23/2018] [Indexed: 01/24/2023] Open
Abstract
There are strong evidences that probiotics influence the immune status of the host, in a strain-specific manner, acting in the gastrointestinal tract. On the hypothesis that certain extracellular proteins and peptides from gut bacteria may mediate part of this immunomodulation and assuming they are able to diffuse through the mucus layer and interact with immune cells we have developed this work. Our study attempts to understand the immunomodulatory mechanisms of (i) Pext, the extracellular protein fraction of Lactobacillus acidophilus DSM20079T, (ii) HM14, a peptide encrypted in an extracellular glycoside hydrolase from Bifidobacterium longum NCIMB 8809 and (iii) Escherichia coli O111:B4 lipopolysaccharide (LPS), a well-known pro-inflammatory molecule, over human peripheral blood mononuclear cells (PBMCs). An untargeted LC-ESI-QTOF-MS metabolomics approach was applied to reveal intracellular changes in treated-PBMCs isolated from healthy donors. Differences in NADH arrest, NAD+ concentration reduction, as well as increases in palmitic acid and methanephrin were observed in HM14 and Pext treated-cells compared to those stimulated with LPS. This would support an anti-inflammatory molecular mechanism of action of such proteinaceous molecules. Moreover, this methodology has confirms the importance of metabolomics approaches to better understanding immune cell responses to gut bacterial-derived molecules.
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Affiliation(s)
- Noelia Cambeiro-Pérez
- Nutrition and Bromatology Group, Department of Analytical and Food Chemistry, Faculty of Food Science, University of Vigo, Ourense, Spain
| | - Claudio Hidalgo-Cantabrana
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas, Villaviciosa, Spain.,Department of Immunology, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Marco A Moro-García
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas, Villaviciosa, Spain.,Department of Immunology, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Rebeca Alonso-Arias
- Department of Immunology, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Jesús Simal-Gándara
- Nutrition and Bromatology Group, Department of Analytical and Food Chemistry, Faculty of Food Science, University of Vigo, Ourense, Spain
| | - Borja Sánchez
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas, Villaviciosa, Spain
| | - Elena Martínez-Carballo
- Nutrition and Bromatology Group, Department of Analytical and Food Chemistry, Faculty of Food Science, University of Vigo, Ourense, Spain
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Ruiz L, Hidalgo C, Blanco-Míguez A, Lourenço A, Sánchez B, Margolles A. Tackling probiotic and gut microbiota functionality through proteomics. J Proteomics 2016; 147:28-39. [DOI: 10.1016/j.jprot.2016.03.023] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 02/19/2016] [Accepted: 03/10/2016] [Indexed: 12/24/2022]
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The Isolation, Identification and Analyses of Lactobacillus Genus Bacteria with Probiotic Potential. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016. [PMID: 26566644 DOI: 10.1007/5584_2015_5008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
103 strains of lactic acid bacteria of Lactobacillus genus were isolated from natural sources and identified for genus and species level with API tests and 16S rRNA sequencing. However, only 27 strains from isolated cultures demonstrated a high stability to gastric stress and from that - only 15 strains were highly resistant to intestinal stress. Results indicated that only some isolated cultures of lactobacilli possessed potential probiotical properties and could serve as new probiotics for dairy industry with high resistance to gastro-intestinal stresses.
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Bifidogenic effect of grain larvae extract on serum lipid, glucose and intestinal microflora in rats. J Biosci 2015; 40:513-20. [DOI: 10.1007/s12038-015-9540-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Ten years of subproteome investigations in lactic acid bacteria: A key for food starter and probiotic typing. J Proteomics 2015; 127:332-9. [PMID: 25957532 DOI: 10.1016/j.jprot.2015.04.028] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 04/22/2015] [Accepted: 04/26/2015] [Indexed: 12/29/2022]
Abstract
The definition of safety and efficacy of food-employed bacteria as well as probiotic strains is a continuous, often unattended, challenge. Proteomic techniques such as 2DE, DIGE and LC/LC-MS/MS are suitable and powerful tools to reveal new aspects (positive and negative) of "known" and "unknown" strains that can be employed in food making and as nutraceutical supplements for human health. Unfortunately, these techniques are not used as extensively as it should be wise. The present report describes the most significant results obtained by our research group in 10years of study on subproteomes in bacteria, chiefly lactic acid bacteria. Production of desired and undesired metabolites, differences between strains belonging to same species but isolated from different ecological niches, the effect of cryoprotectants on survival to lyophilization as well as the adhesive capability of strains, were elucidated by analysis of cytosolic, membrane-enriched, surface and extracellular proteomes. The present review opens a window on a yet largely underexplored field and highlights the huge potential of subproteome investigations for more rational choice of microbial strains as food starters, probiotics and for production of nutraceuticals. These analyses will hopefully contribute to manufacturing safer and healthier food and food supplements in the near future. This article is part of a Special Issue entitled: HUPO 2014.
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